From 6cc2e3ed53708bc07da7932adc0326faac9c670f Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sat, 14 Oct 2023 21:09:25 +0200
Subject: [PATCH 001/501] first version of bot/test.sh script

---
 bot/test.sh | 224 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 224 insertions(+)
 create mode 100755 bot/test.sh

diff --git a/bot/test.sh b/bot/test.sh
new file mode 100755
index 0000000000..6d217caf92
--- /dev/null
+++ b/bot/test.sh
@@ -0,0 +1,224 @@
+#!/usr/bin/env bash
+#
+# script to run tests or the test suite for the whole EESSI software layer or
+# just what has been built in a job. Intended use is that it is called
+# at the end of a (batch) job running on a compute node.
+#
+# This script is part of the EESSI software layer, see
+# https://github.com/EESSI/software-layer.git
+#
+# author: Thomas Roeblitz (@trz42)
+#
+# license: GPLv2
+#
+
+# ASSUMPTIONs:
+# + assumption for the build step (as run through bot/build.sh which is provided
+#   in this repository too)
+#  - working directory has been prepared by the bot with a checkout of a
+#    pull request (OR by some other means)
+#  - the working directory contains a directory 'cfg' where the main config
+#    file 'job.cfg' has been deposited
+#  - the directory may contain any additional files referenced in job.cfg
+# + assumptions for the test step
+#  - temporary storage is still available
+#    example
+#    Using /localscratch/9640860/NESSI/eessi.x765Dd8mFh as tmp directory (to resume session add '--resume /localscratch/9640860/NESSI/eessi.x765Dd8mFh').
+#  - run test-suite.sh inside build container using tmp storage from build step
+#    plus possibly additional settings (repo, etc.)
+#  - needed setup steps may be similar to bot/inspect.sh (PR#317)
+
+# stop as soon as something fails
+set -e
+
+# source utils.sh and cfg_files.sh
+source scripts/utils.sh
+source scripts/cfg_files.sh
+
+# defaults
+export JOB_CFG_FILE="${JOB_CFG_FILE_OVERRIDE:=./cfg/job.cfg}"
+HOST_ARCH=$(uname -m)
+
+# check if ${JOB_CFG_FILE} exists
+if [[ ! -r "${JOB_CFG_FILE}" ]]; then
+    fatal_error "job config file (JOB_CFG_FILE=${JOB_CFG_FILE}) does not exist or not readable"
+fi
+echo "bot/test.sh: showing ${JOB_CFG_FILE} from software-layer side"
+cat ${JOB_CFG_FILE}
+
+echo "bot/test.sh: obtaining configuration settings from '${JOB_CFG_FILE}'"
+cfg_load ${JOB_CFG_FILE}
+
+# if http_proxy is defined in ${JOB_CFG_FILE} use it, if not use env var $http_proxy
+HTTP_PROXY=$(cfg_get_value "site_config" "http_proxy")
+HTTP_PROXY=${HTTP_PROXY:-${http_proxy}}
+echo "bot/test.sh: HTTP_PROXY='${HTTP_PROXY}'"
+
+# if https_proxy is defined in ${JOB_CFG_FILE} use it, if not use env var $https_proxy
+HTTPS_PROXY=$(cfg_get_value "site_config" "https_proxy")
+HTTPS_PROXY=${HTTPS_PROXY:-${https_proxy}}
+echo "bot/test.sh: HTTPS_PROXY='${HTTPS_PROXY}'"
+
+LOCAL_TMP=$(cfg_get_value "site_config" "local_tmp")
+echo "bot/test.sh: LOCAL_TMP='${LOCAL_TMP}'"
+# TODO should local_tmp be mandatory? --> then we check here and exit if it is not provided
+
+# check if path to copy build logs to is specified, so we can copy build logs for failing builds there
+BUILD_LOGS_DIR=$(cfg_get_value "site_config" "build_logs_dir")
+echo "bot/test.sh: BUILD_LOGS_DIR='${BUILD_LOGS_DIR}'"
+# if $BUILD_LOGS_DIR is set, add it to $SINGULARITY_BIND so the path is available in the build container
+if [[ ! -z ${BUILD_LOGS_DIR} ]]; then
+    mkdir -p ${BUILD_LOGS_DIR}
+    if [[ -z ${SINGULARITY_BIND} ]]; then
+        export SINGULARITY_BIND="${BUILD_LOGS_DIR}"
+    else
+        export SINGULARITY_BIND="${SINGULARITY_BIND},${BUILD_LOGS_DIR}"
+    fi
+fi
+
+# check if path to directory on shared filesystem is specified,
+# and use it as location for source tarballs used by EasyBuild if so
+SHARED_FS_PATH=$(cfg_get_value "site_config" "shared_fs_path")
+echo "bot/test.sh: SHARED_FS_PATH='${SHARED_FS_PATH}'"
+# if $SHARED_FS_PATH is set, add it to $SINGULARITY_BIND so the path is available in the build container
+if [[ ! -z ${SHARED_FS_PATH} ]]; then
+    mkdir -p ${SHARED_FS_PATH}
+    if [[ -z ${SINGULARITY_BIND} ]]; then
+        export SINGULARITY_BIND="${SHARED_FS_PATH}"
+    else
+        export SINGULARITY_BIND="${SINGULARITY_BIND},${SHARED_FS_PATH}"
+    fi
+fi
+
+SINGULARITY_CACHEDIR=$(cfg_get_value "site_config" "container_cachedir")
+echo "bot/test.sh: SINGULARITY_CACHEDIR='${SINGULARITY_CACHEDIR}'"
+if [[ ! -z ${SINGULARITY_CACHEDIR} ]]; then
+    # make sure that separate directories are used for different CPU families
+    SINGULARITY_CACHEDIR=${SINGULARITY_CACHEDIR}/${HOST_ARCH}
+    export SINGULARITY_CACHEDIR
+fi
+
+# try to determine tmp directory from build job
+RESUME_DIR=$(grep 'Using .* as tmp directory' slurm-${SLURM_JOBID}.out | head -1 | awk '{print $2}')
+
+if [[ -z ${RESUME_DIR} ]]; then
+  echo -n "setting \$STORAGE by replacing any var in '${LOCAL_TMP}' -> "
+  # replace any env variable in ${LOCAL_TMP} with its
+  #   current value (e.g., a value that is local to the job)
+  STORAGE=$(envsubst <<< ${LOCAL_TMP})
+  echo "'${STORAGE}'"
+
+  # make sure ${STORAGE} exists
+  mkdir -p ${STORAGE}
+
+  # make sure the base tmp storage is unique
+  JOB_STORAGE=$(mktemp --directory --tmpdir=${STORAGE} bot_job_tmp_XXX)
+  echo "bot/test.sh: created unique base tmp storage directory at ${JOB_STORAGE}"
+
+  RESUME_TGZ=${PWD}/previous_tmp/build_step/$(ls previous_tmp/build_step)
+  if [[ -z ${RESUME_TGZ} ]]; then
+    echo "bot/test.sh: no information about tmp directory and tarball of build step; --> giving up"
+    exit 2
+  fi
+fi
+
+# obtain list of modules to be loaded
+LOAD_MODULES=$(cfg_get_value "site_config" "load_modules")
+echo "bot/test.sh: LOAD_MODULES='${LOAD_MODULES}'"
+
+# singularity/apptainer settings: CONTAINER, HOME, TMPDIR, BIND
+CONTAINER=$(cfg_get_value "repository" "container")
+export SINGULARITY_HOME="${PWD}:/eessi_bot_job"
+export SINGULARITY_TMPDIR="${PWD}/singularity_tmpdir"
+mkdir -p ${SINGULARITY_TMPDIR}
+
+# load modules if LOAD_MODULES is not empty
+if [[ ! -z ${LOAD_MODULES} ]]; then
+    for mod in $(echo ${LOAD_MODULES} | tr ',' '\n')
+    do
+        echo "bot/test.sh: loading module '${mod}'"
+        module load ${mod}
+    done
+else
+    echo "bot/test.sh: no modules to be loaded"
+fi
+
+# determine repository to be used from entry .repository in ${JOB_CFG_FILE}
+REPOSITORY=$(cfg_get_value "repository" "repo_id")
+EESSI_REPOS_CFG_DIR_OVERRIDE=$(cfg_get_value "repository" "repos_cfg_dir")
+export EESSI_REPOS_CFG_DIR_OVERRIDE=${EESSI_REPOS_CFG_DIR_OVERRIDE:-${PWD}/cfg}
+echo "bot/test.sh: EESSI_REPOS_CFG_DIR_OVERRIDE='${EESSI_REPOS_CFG_DIR_OVERRIDE}'"
+
+# determine pilot version to be used from .repository.repo_version in ${JOB_CFG_FILE}
+# here, just set & export EESSI_PILOT_VERSION_OVERRIDE
+# next script (eessi_container.sh) makes use of it via sourcing init scripts
+# (e.g., init/eessi_defaults or init/minimal_eessi_env)
+export EESSI_PILOT_VERSION_OVERRIDE=$(cfg_get_value "repository" "repo_version")
+echo "bot/test.sh: EESSI_PILOT_VERSION_OVERRIDE='${EESSI_PILOT_VERSION_OVERRIDE}'"
+
+# determine CVMFS repo to be used from .repository.repo_name in ${JOB_CFG_FILE}
+# here, just set EESSI_CVMFS_REPO_OVERRIDE, a bit further down
+# "source init/eessi_defaults" via sourcing init/minimal_eessi_env
+export EESSI_CVMFS_REPO_OVERRIDE=$(cfg_get_value "repository" "repo_name")
+echo "bot/test.sh: EESSI_CVMFS_REPO_OVERRIDE='${EESSI_CVMFS_REPO_OVERRIDE}'"
+
+# determine architecture to be used from entry .architecture in ${JOB_CFG_FILE}
+# fallbacks:
+#  - ${CPU_TARGET} handed over from bot
+#  - left empty to let downstream script(s) determine subdir to be used
+EESSI_SOFTWARE_SUBDIR_OVERRIDE=$(cfg_get_value "architecture" "software_subdir")
+EESSI_SOFTWARE_SUBDIR_OVERRIDE=${EESSI_SOFTWARE_SUBDIR_OVERRIDE:-${CPU_TARGET}}
+export EESSI_SOFTWARE_SUBDIR_OVERRIDE
+echo "bot/test.sh: EESSI_SOFTWARE_SUBDIR_OVERRIDE='${EESSI_SOFTWARE_SUBDIR_OVERRIDE}'"
+
+# get EESSI_OS_TYPE from .architecture.os_type in ${JOB_CFG_FILE} (default: linux)
+EESSI_OS_TYPE=$(cfg_get_value "architecture" "os_type")
+export EESSI_OS_TYPE=${EESSI_OS_TYPE:-linux}
+echo "bot/test.sh: EESSI_OS_TYPE='${EESSI_OS_TYPE}'"
+
+# prepare arguments to eessi_container.sh common to build and tarball steps
+declare -a COMMON_ARGS=()
+COMMON_ARGS+=("--verbose")
+COMMON_ARGS+=("--access" "rw")
+COMMON_ARGS+=("--mode" "run")
+[[ ! -z ${CONTAINER} ]] && COMMON_ARGS+=("--container" "${CONTAINER}")
+[[ ! -z ${HTTP_PROXY} ]] && COMMON_ARGS+=("--http-proxy" "${HTTP_PROXY}")
+[[ ! -z ${HTTPS_PROXY} ]] && COMMON_ARGS+=("--https-proxy" "${HTTPS_PROXY}")
+[[ ! -z ${REPOSITORY} ]] && COMMON_ARGS+=("--repository" "${REPOSITORY}")
+
+# make sure to use the same parent dir for storing tarballs of tmp
+PREVIOUS_TMP_DIR=${PWD}/previous_tmp
+
+# prepare directory to store tarball of tmp for build step
+TARBALL_TMP_TEST_STEP_DIR=${PREVIOUS_TMP_DIR}/test_step
+mkdir -p ${TARBALL_TMP_TEST_STEP_DIR}
+
+# prepare arguments to eessi_container.sh specific to test step
+declare -a TEST_STEP_ARGS=()
+TEST_STEP_ARGS+=("--save" "${TARBALL_TMP_TEST_STEP_DIR}")
+
+if [[ -z ${RESUME_DIR} ]]; then
+  TEST_STEP_ARGS+=("--storage" "${STORAGE}")
+  TEST_STEP_ARGS+=("--resume" "${RESUME_TGZ}")
+else
+  TEST_STEP_ARGS+=("--resume" "${RESUME_DIR}")
+fi
+
+# prepare arguments to test_suite.sh (specific to test step)
+declare -a TEST_SUITE_ARGS=()
+# if [[ ${EESSI_SOFTWARE_SUBDIR_OVERRIDE} =~ .*/generic$ ]]; then
+#     TEST_SUITE_ARGS+=("--generic")
+# fi
+# [[ ! -z ${BUILD_LOGS_DIR} ]] && TEST_SUITE_ARGS+=("--build-logs-dir" "${BUILD_LOGS_DIR}")
+# [[ ! -z ${SHARED_FS_PATH} ]] && TEST_SUITE_ARGS+=("--shared-fs-path" "${SHARED_FS_PATH}")
+
+# create tmp file for output of build step
+test_outerr=$(mktemp test.outerr.XXXX)
+
+echo "Executing command to build software:"
+echo "./eessi_container.sh ${COMMON_ARGS[@]} ${TEST_STEP_ARGS[@]}"
+echo "                     -- ./test_suite.sh \"${TEST_SUITE_ARGS[@]}\" \"$@\" 2>&1 | tee -a ${test_outerr}"
+./eessi_container.sh "${COMMON_ARGS[@]}" "${TEST_STEP_ARGS[@]}" \
+                     -- ./test_suite.sh "${TEST_SUITE_ARGS[@]}" "$@" 2>&1 | tee -a ${test_outerr}
+
+exit 0

From 9a32dc629b34e4bbc91fda349198611a6a96a082 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sun, 15 Oct 2023 20:29:14 +0200
Subject: [PATCH 002/501] scripts to run tests after a build job has finished

---
 run_tests.sh  |   4 ++
 test_suite.sh | 184 ++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 188 insertions(+)
 create mode 100644 run_tests.sh
 create mode 100644 test_suite.sh

diff --git a/run_tests.sh b/run_tests.sh
new file mode 100644
index 0000000000..ccbc751f22
--- /dev/null
+++ b/run_tests.sh
@@ -0,0 +1,4 @@
+#!/bin/bash
+base_dir=$(dirname $(realpath $0))
+source ${base_dir}/init/eessi_defaults
+./run_in_compat_layer_env.sh ./test_suite.sh "$@"
diff --git a/test_suite.sh b/test_suite.sh
new file mode 100644
index 0000000000..fcaaa339d2
--- /dev/null
+++ b/test_suite.sh
@@ -0,0 +1,184 @@
+#!/bin/bash
+#
+# Run sanity check for all requested modules (and built dependencies)?
+# get ec from diff
+# set up EasyBuild
+# run `eb --sanity-only ec`
+
+display_help() {
+  echo "usage: $0 [OPTIONS]"
+  echo "  -g | --generic         -  instructs script to test for generic architecture target"
+  echo "  -h | --help            -  display this usage information"
+  echo "  -x | --http-proxy URL  -  provides URL for the environment variable http_proxy"
+  echo "  -y | --https-proxy URL -  provides URL for the environment variable https_proxy"
+}
+
+POSITIONAL_ARGS=()
+
+while [[ $# -gt 0 ]]; do
+  case $1 in
+    -g|--generic)
+      EASYBUILD_OPTARCH="GENERIC"
+      shift
+      ;;
+    -h|--help)
+      display_help  # Call your function
+      # no shifting needed here, we're done.
+      exit 0
+      ;;
+    -x|--http-proxy)
+      export http_proxy="$2"
+      shift 2
+      ;;
+    -y|--https-proxy)
+      export https_proxy="$2"
+      shift 2
+      ;;
+    --build-logs-dir)
+      export build_logs_dir="${2}"
+      shift 2
+      ;;
+    --shared-fs-path)
+      export shared_fs_path="${2}"
+      shift 2
+      ;;
+    -*|--*)
+      echo "Error: Unknown option: $1" >&2
+      exit 1
+      ;;
+    *)  # No more options
+      POSITIONAL_ARGS+=("$1") # save positional arg
+      shift
+      ;;
+  esac
+done
+
+set -- "${POSITIONAL_ARGS[@]}"
+
+TOPDIR=$(dirname $(realpath $0))
+
+source $TOPDIR/scripts/utils.sh
+
+# honor $TMPDIR if it is already defined, use /tmp otherwise
+if [ -z $TMPDIR ]; then
+    export WORKDIR=/tmp/$USER
+else
+    export WORKDIR=$TMPDIR/$USER
+fi
+
+TMPDIR=$(mktemp -d)
+
+echo ">> Setting up environment..."
+
+source $TOPDIR/init/minimal_eessi_env
+
+if [ -d $EESSI_CVMFS_REPO ]; then
+    echo_green "$EESSI_CVMFS_REPO available, OK!"
+else
+    fatal_error "$EESSI_CVMFS_REPO is not available!"
+fi
+
+# make sure we're in Prefix environment by checking $SHELL
+if [[ ${SHELL} = ${EPREFIX}/bin/bash ]]; then
+    echo_green ">> It looks like we're in a Gentoo Prefix environment, good!"
+else
+    fatal_error "Not running in Gentoo Prefix environment, run '${EPREFIX}/startprefix' first!"
+fi
+
+# avoid that pyc files for EasyBuild are stored in EasyBuild installation directory
+export PYTHONPYCACHEPREFIX=$TMPDIR/pycache
+
+DETECTION_PARAMETERS=''
+GENERIC=0
+EB='eb'
+if [[ "$EASYBUILD_OPTARCH" == "GENERIC" ]]; then
+    echo_yellow ">> GENERIC build/test requested, taking appropriate measures!"
+    DETECTION_PARAMETERS="$DETECTION_PARAMETERS --generic"
+    GENERIC=1
+    EB='eb --optarch=GENERIC'
+fi
+
+echo ">> Determining software subdirectory to use for current build/test host..."
+if [ -z $EESSI_SOFTWARE_SUBDIR_OVERRIDE ]; then
+  export EESSI_SOFTWARE_SUBDIR_OVERRIDE=$(python3 $TOPDIR/eessi_software_subdir.py $DETECTION_PARAMETERS)
+  echo ">> Determined \$EESSI_SOFTWARE_SUBDIR_OVERRIDE via 'eessi_software_subdir.py $DETECTION_PARAMETERS' script"
+else
+  echo ">> Picking up pre-defined \$EESSI_SOFTWARE_SUBDIR_OVERRIDE: ${EESSI_SOFTWARE_SUBDIR_OVERRIDE}"
+fi
+
+# Set all the EESSI environment variables (respecting $EESSI_SOFTWARE_SUBDIR_OVERRIDE)
+# $EESSI_SILENT - don't print any messages
+# $EESSI_BASIC_ENV - give a basic set of environment variables
+EESSI_SILENT=1 EESSI_BASIC_ENV=1 source $TOPDIR/init/eessi_environment_variables
+
+if [[ -z ${EESSI_SOFTWARE_SUBDIR} ]]; then
+    fatal_error "Failed to determine software subdirectory?!"
+elif [[ "${EESSI_SOFTWARE_SUBDIR}" != "${EESSI_SOFTWARE_SUBDIR_OVERRIDE}" ]]; then
+    fatal_error "Values for EESSI_SOFTWARE_SUBDIR_OVERRIDE (${EESSI_SOFTWARE_SUBDIR_OVERRIDE}) and EESSI_SOFTWARE_SUBDIR (${EESSI_SOFTWARE_SUBDIR}) differ!"
+else
+    echo_green ">> Using ${EESSI_SOFTWARE_SUBDIR} as software subdirectory!"
+fi
+
+echo ">> Initializing Lmod..."
+source $EPREFIX/usr/share/Lmod/init/bash
+ml_version_out=$TMPDIR/ml.out
+ml --version &> $ml_version_out
+if [[ $? -eq 0 ]]; then
+    echo_green ">> Found Lmod ${LMOD_VERSION}"
+else
+    fatal_error "Failed to initialize Lmod?! (see output in ${ml_version_out}"
+fi
+
+echo ">> Configuring EasyBuild..."
+source $TOPDIR/configure_easybuild
+
+echo ">> Setting up \$MODULEPATH..."
+# make sure no modules are loaded
+module --force purge
+# ignore current $MODULEPATH entirely
+module unuse $MODULEPATH
+module use $EASYBUILD_INSTALLPATH/modules/all
+if [[ -z ${MODULEPATH} ]]; then
+    fatal_error "Failed to set up \$MODULEPATH?!"
+else
+    echo_green ">> MODULEPATH set up: ${MODULEPATH}"
+fi
+
+# assume there's only one diff file that corresponds to the PR patch file
+pr_diff=$(ls [0-9]*.diff | head -1)
+
+# "split" the file by prefixing each line belonging to the same file with the
+# same number
+split_file=$(awk '/^\+\+\+/{n++}{print n, "  ", $0 }' ${pr_diff})
+
+# determine which easystack files may have changed
+changed_es_files=$(echo "${split_file}" | grep '^[0-9 ]*+++ ./eessi.*.yml$' | egrep -v 'known-issues|missing')
+
+# process all changed easystackfiles
+for es_file_num in $(echo "${changed_es_files}" | cut -f1 -d' ')
+do
+    # determine added lines that do not contain a yaml comment only
+    added_lines=$(echo "${split_file}" | grep "${es_file_num}    + " | sed -e "s/^"${es_file_num}"    + //" | grep -v "^[ ]*#")
+    # determine easyconfigs
+    easyconfigs=$(echo "${added_lines}" | cut -f3 -d' ')
+    # get easystack file name
+    easystack_file=$(echo "${changed_es_files}" | grep "^${es_file_num}" | sed -e "s/^"${es_file_num}"    ... .\///")
+    echo -e "Processing easystack file ${easystack_file}...\n\n"
+
+    # determine version of EasyBuild module to load based on EasyBuild version included in name of easystack file
+    eb_version=$(echo ${easystack_file} | sed 's/.*eb-\([0-9.]*\).*/\1/g')
+
+    # load EasyBuild module
+    module load EasyBuild/${eb_version}
+
+    echo_green "All set, let's run sanity checks for installed packages..."
+
+    for easyconfig in ${easyconfigs};
+    do
+        echo "Running sanity check for '${easyconfig}'..."
+        eb --sanity-check-only ${easyconfig}
+    done
+done
+
+echo ">> Cleaning up ${TMPDIR}..."
+rm -r ${TMPDIR}

From 17cfd02779833bd5f2df96655f3dc19bb5f880e8 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sun, 15 Oct 2023 20:30:44 +0200
Subject: [PATCH 003/501] small adjustments to test script

---
 bot/test.sh | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/bot/test.sh b/bot/test.sh
index 6d217caf92..89c1a6a8bf 100755
--- a/bot/test.sh
+++ b/bot/test.sh
@@ -206,9 +206,9 @@ fi
 
 # prepare arguments to test_suite.sh (specific to test step)
 declare -a TEST_SUITE_ARGS=()
-# if [[ ${EESSI_SOFTWARE_SUBDIR_OVERRIDE} =~ .*/generic$ ]]; then
-#     TEST_SUITE_ARGS+=("--generic")
-# fi
+if [[ ${EESSI_SOFTWARE_SUBDIR_OVERRIDE} =~ .*/generic$ ]]; then
+    TEST_SUITE_ARGS+=("--generic")
+fi
 # [[ ! -z ${BUILD_LOGS_DIR} ]] && TEST_SUITE_ARGS+=("--build-logs-dir" "${BUILD_LOGS_DIR}")
 # [[ ! -z ${SHARED_FS_PATH} ]] && TEST_SUITE_ARGS+=("--shared-fs-path" "${SHARED_FS_PATH}")
 
@@ -217,8 +217,8 @@ test_outerr=$(mktemp test.outerr.XXXX)
 
 echo "Executing command to build software:"
 echo "./eessi_container.sh ${COMMON_ARGS[@]} ${TEST_STEP_ARGS[@]}"
-echo "                     -- ./test_suite.sh \"${TEST_SUITE_ARGS[@]}\" \"$@\" 2>&1 | tee -a ${test_outerr}"
+echo "                     -- ./run_tests.sh \"${TEST_SUITE_ARGS[@]}\" \"$@\" 2>&1 | tee -a ${test_outerr}"
 ./eessi_container.sh "${COMMON_ARGS[@]}" "${TEST_STEP_ARGS[@]}" \
-                     -- ./test_suite.sh "${TEST_SUITE_ARGS[@]}" "$@" 2>&1 | tee -a ${test_outerr}
+                     -- ./run_tests.sh "${TEST_SUITE_ARGS[@]}" "$@" 2>&1 | tee -a ${test_outerr}
 
 exit 0

From 9166400aa2c1d18c431ea7f409e1357a0823d73b Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 20 Oct 2023 21:58:43 +0200
Subject: [PATCH 004/501] Easyconfig that can extend EESSI

---
 EESSI-2023.06-extend.eb | 85 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 85 insertions(+)
 create mode 100644 EESSI-2023.06-extend.eb

diff --git a/EESSI-2023.06-extend.eb b/EESSI-2023.06-extend.eb
new file mode 100644
index 0000000000..e4fafb860c
--- /dev/null
+++ b/EESSI-2023.06-extend.eb
@@ -0,0 +1,85 @@
+easyblock = 'Binary'
+
+name = 'EESSI'
+version = '2023.06'
+versionsuffix = '-extend'
+
+homepage = 'https://eessi.github.io/docs/'
+
+description = """
+ The goal of the European Environment for Scientific Software Installations
+ (EESSI, pronounced as "easy") is to build a common stack of scientific
+ software installations for HPC systems and beyond, including laptops,
+ personal workstations and cloud infrastructure.
+
+ This module allows you to extend EESSI using the same configuration for
+ EasyBuild as EESSI itself uses. It installs the modules in a special location
+ that is configurable in the CVMFS configuration (so can be on a shared
+ filesystem), and automatically found when using the default EESSI environment. 
+"""
+
+toolchain = SYSTEM
+
+source_urls = None
+sources = ['eb_hooks.py']
+checksums = ['8ae609f99b6953beae89aa1945913686c86c156509dbc55e2b6b8017b13fcf66']
+
+# Don't extend the PATH
+prepend_to_path = None
+
+# All the dependencies we filter in EESSI
+local_deps_to_filter = "Autoconf,Automake,Autotools,binutils,bzip2,DBus,flex,gettext,gperf,help2man,intltool,libreadline,libtool,Lua,M4,makeinfo,ncurses,util-linux,XZ,zlib"
+local_arch_specific_deps_to_filter = {'aarch64': ',yasm', 'x86_64': ''}
+local_deps_to_filter += local_arch_specific_deps_to_filter[ARCH]
+
+modextravars = {
+    'EASYBUILD_FILTER_DEPS': local_deps_to_filter,
+    'EASYBUILD_IGNORE_OSDEPS': '1',
+    'EASYBUILD_DEBUG': '1',
+    'EASYBUILD_TRACE': '1',
+    'EASYBUILD_ZIP_LOGS': 'bzip2',
+    'EASYBUILD_RPATH': '1',
+    'EASYBUILD_FILTER_ENV_VARS': 'LD_LIBRARY_PATH',
+    'EASYBUILD_READ_ONLY_INSTALLDIR': '1',
+    'EASYBUILD_MODULE_EXTENSIONS': '1',
+    'EASYBUILD_EXPERIMENTAL': '1',
+    'EASYBUILD_HOOKS': '%(installdir)s/eb_hooks.py',
+}
+
+# Need a few other variables, but they are more dynamic
+# EASYBUILD_SYSROOT=${EPREFIX}
+# EASYBUILD_PREFIX=${WORKDIR}/easybuild
+# EASYBUILD_INSTALLPATH=${EESSI_PREFIX}/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR}
+# EASYBUILD_SOURCEPATH=${WORKDIR}/easybuild/sources:${EESSI_SOURCEPATH}
+modluafooter = """
+if (mode() == "load") then
+  -- Use a working directory for temporary build files
+  if (os.getenv("WORKING_DIR") == nil) then
+    LmodMessage("-- Using /tmp as a temporary working directory for installations, you can override this by setting the environment variable WORKING_DIR and reloading the module (e.g., /dev/shm is a common option)")
+  end
+end
+working_dir = os.getenv("WORKING_DIR") or "/tmp"
+-- Gather the EPREFIX to use as a sysroot
+sysroot = os.getenv("EPREFIX")
+-- Use an installation prefix that we _should_ have write access to
+easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), 'versions', 'host_injections')
+if (mode() == "load") then
+  LmodMessage("-- To create installations for EESSI, you _must_ have write permissions to " .. easybuild_installpath)
+  -- Advise them to reuse sources
+  if (os.getenv("EASYBUILD_SOURCEPATH") == nil) then
+    LmodMessage("-- You may wish to configure a sources directory for EasyBuild (for example, via setting the environment variable EASYBUILD_SOURCEPATH) to allow you to reuse existing sources for packages.")
+  end
+end
+-- Set the relevant environment variables for EasyBuild
+setenv ("EASYBUILD_SYSROOT", sysroot)
+setenv ("EASYBUILD_PREFIX", pathJoin(working_dir, "easybuild"))
+setenv ("EASYBUILD_INSTALLPATH", easybuild_installpath)
+always_load("EasyBuild")
+"""
+
+sanity_check_paths = {
+    'files': ['eb_hooks.py'],
+    'dirs': ['']
+}
+
+moduleclass = 'devel'

From f1a0e71a4b1f01c3b9937a302f50dc87b252c99f Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 20 Oct 2023 22:00:21 +0200
Subject: [PATCH 005/501] Add extension of EESSI to MODULEPATH

---
 init/Magic_Castle/bash           | 2 +-
 init/bash                        | 2 ++
 init/eessi_environment_variables | 2 ++
 3 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/init/Magic_Castle/bash b/init/Magic_Castle/bash
index 85e4d54241..219c6d3a85 100644
--- a/init/Magic_Castle/bash
+++ b/init/Magic_Castle/bash
@@ -10,7 +10,7 @@ source $(dirname "$BASH_SOURCE")/../eessi_environment_variables
 
 # Provide a clean MODULEPATH
 export MODULEPATH_ROOT=$EESSI_MODULEPATH
-export MODULEPATH=$EESSI_MODULEPATH
+export MODULEPATH=$EESSI_EXTEND_MODULEPATH:$EESSI_MODULEPATH
 
 # Extensions are too many, let's not print them by default (requires Lmod 8.4.12)
 export LMOD_AVAIL_EXTENSIONS=no
diff --git a/init/bash b/init/bash
index ea605db0b5..bf8ada4fd2 100644
--- a/init/bash
+++ b/init/bash
@@ -26,6 +26,8 @@ if [ $? -eq 0 ]; then
     # prepend location of modules for EESSI software stack to $MODULEPATH
     echo "Prepending $EESSI_MODULEPATH to \$MODULEPATH..." >> $output
     module use $EESSI_MODULEPATH
+    echo "Prepending $EESSI_EXTEND_MODULEPATH to \$MODULEPATH..." >> $output
+    module use $EESSI_EXTEND_MODULEPATH
 
     #echo >> $output
     #echo "*** Known problems in the ${EESSI_PILOT_VERSION} pilot software stack ***" >> $output
diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index 10ac1926f4..7b4f82bbd3 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -60,6 +60,8 @@ if [ -d $EESSI_PREFIX ]; then
           if [ -d $EESSI_MODULEPATH ]; then
             export EESSI_MODULEPATH=$EESSI_MODULEPATH
             echo "Using ${EESSI_MODULEPATH} as the directory to be added to MODULEPATH." >> $output
+            export EESSI_EXTEND_MODULEPATH=${EESSI_MODULEPATH/versions/host_injections}
+            echo "Using ${EESSI_EXTEND_MODULEPATH} as the extension directory to be added to MODULEPATH." >> $output
           else
             error "EESSI module path at $EESSI_MODULEPATH not found!"
             false

From 98f20cdd9dd83c481065f30ab6657367d06b869b Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Tue, 7 Nov 2023 13:14:24 +0100
Subject: [PATCH 006/501] Allow for both site and user extensions to EESSI

---
 ...nd.eb => EESSI-extend-2023.06-easybuild.eb | 30 ++++++++++++-------
 init/Magic_Castle/bash                        |  2 +-
 init/bash                                     |  6 ++--
 init/eessi_environment_variables              |  6 ++--
 4 files changed, 29 insertions(+), 15 deletions(-)
 rename EESSI-2023.06-extend.eb => EESSI-extend-2023.06-easybuild.eb (69%)

diff --git a/EESSI-2023.06-extend.eb b/EESSI-extend-2023.06-easybuild.eb
similarity index 69%
rename from EESSI-2023.06-extend.eb
rename to EESSI-extend-2023.06-easybuild.eb
index e4fafb860c..fd9f897326 100644
--- a/EESSI-2023.06-extend.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -1,8 +1,9 @@
 easyblock = 'Binary'
 
-name = 'EESSI'
+name = 'EESSI-extend'
 version = '2023.06'
-versionsuffix = '-extend'
+# May have different ways to extend EESSI in future (manually, other tools,...)
+versionsuffix = '-easybuild'
 
 homepage = 'https://eessi.github.io/docs/'
 
@@ -13,9 +14,10 @@ description = """
  personal workstations and cloud infrastructure.
 
  This module allows you to extend EESSI using the same configuration for
- EasyBuild as EESSI itself uses. It installs the modules in a special location
- that is configurable in the CVMFS configuration (so can be on a shared
- filesystem), and automatically found when using the default EESSI environment. 
+ EasyBuild as EESSI itself uses. The default installation is the users
+ home directory, but this can be overridden for a site installation (by setting
+ EESSI_SITE_INSTALL) or for a direct installation under CVMFS (by setting
+ EESSI_CVMFS_INSTALL). 
 """
 
 toolchain = SYSTEM
@@ -55,14 +57,20 @@ modluafooter = """
 if (mode() == "load") then
   -- Use a working directory for temporary build files
   if (os.getenv("WORKING_DIR") == nil) then
-    LmodMessage("-- Using /tmp as a temporary working directory for installations, you can override this by setting the environment variable WORKING_DIR and reloading the module (e.g., /dev/shm is a common option)")
+    LmodMessage("-- Using /tmp/$USER as a temporary working directory for installations, you can override this by setting the environment variable WORKING_DIR and reloading the module (e.g., /dev/shm is a common option)")
   end
 end
-working_dir = os.getenv("WORKING_DIR") or "/tmp"
+working_dir = os.getenv("WORKING_DIR") or pathJoin("/tmp", os.getenv("USER"))
 -- Gather the EPREFIX to use as a sysroot
-sysroot = os.getenv("EPREFIX")
+sysroot = os.getenv("EESSI_EPREFIX")
 -- Use an installation prefix that we _should_ have write access to
-easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), 'versions', 'host_injections')
+if (os.getenv("EESSI_CVMFS_INSTALL") ~= nil) then
+  easybuild_installpath = os.getenv("EESSI_SOFTWARE_PATH")
+elseif (os.getenv("EESSI_SITE_INSTALL") ~= nil) then 
+  easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), 'versions', 'host_injections')
+else
+  easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), os.getenv("EESSI_CVMFS_REPO"), pathJoin(os.getenv("HOME"), "eessi"))
+end
 if (mode() == "load") then
   LmodMessage("-- To create installations for EESSI, you _must_ have write permissions to " .. easybuild_installpath)
   -- Advise them to reuse sources
@@ -74,7 +82,9 @@ end
 setenv ("EASYBUILD_SYSROOT", sysroot)
 setenv ("EASYBUILD_PREFIX", pathJoin(working_dir, "easybuild"))
 setenv ("EASYBUILD_INSTALLPATH", easybuild_installpath)
-always_load("EasyBuild")
+if not ( isloaded("EasyBuild") ) then
+    load("EasyBuild")
+end
 """
 
 sanity_check_paths = {
diff --git a/init/Magic_Castle/bash b/init/Magic_Castle/bash
index 219c6d3a85..0ee9d612f3 100644
--- a/init/Magic_Castle/bash
+++ b/init/Magic_Castle/bash
@@ -10,7 +10,7 @@ source $(dirname "$BASH_SOURCE")/../eessi_environment_variables
 
 # Provide a clean MODULEPATH
 export MODULEPATH_ROOT=$EESSI_MODULEPATH
-export MODULEPATH=$EESSI_EXTEND_MODULEPATH:$EESSI_MODULEPATH
+export MODULEPATH=$EESSI_USER_MODULEPATH:$EESSI_SITE_MODULEPATH:$EESSI_MODULEPATH
 
 # Extensions are too many, let's not print them by default (requires Lmod 8.4.12)
 export LMOD_AVAIL_EXTENSIONS=no
diff --git a/init/bash b/init/bash
index bf8ada4fd2..76c1e9154a 100644
--- a/init/bash
+++ b/init/bash
@@ -26,8 +26,10 @@ if [ $? -eq 0 ]; then
     # prepend location of modules for EESSI software stack to $MODULEPATH
     echo "Prepending $EESSI_MODULEPATH to \$MODULEPATH..." >> $output
     module use $EESSI_MODULEPATH
-    echo "Prepending $EESSI_EXTEND_MODULEPATH to \$MODULEPATH..." >> $output
-    module use $EESSI_EXTEND_MODULEPATH
+    echo "Prepending site path $EESSI_SITE_MODULEPATH to \$MODULEPATH..." >> $output
+    module use $EESSI_SITE_MODULEPATH
+    echo "Prepending user path $EESSI_SITE_MODULEPATH to \$MODULEPATH..." >> $output
+    module use $EESSI_USER_MODULEPATH
 
     #echo >> $output
     #echo "*** Known problems in the ${EESSI_PILOT_VERSION} pilot software stack ***" >> $output
diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index 7b4f82bbd3..656fbc6637 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -60,8 +60,10 @@ if [ -d $EESSI_PREFIX ]; then
           if [ -d $EESSI_MODULEPATH ]; then
             export EESSI_MODULEPATH=$EESSI_MODULEPATH
             echo "Using ${EESSI_MODULEPATH} as the directory to be added to MODULEPATH." >> $output
-            export EESSI_EXTEND_MODULEPATH=${EESSI_MODULEPATH/versions/host_injections}
-            echo "Using ${EESSI_EXTEND_MODULEPATH} as the extension directory to be added to MODULEPATH." >> $output
+            export EESSI_SITE_MODULEPATH=${EESSI_MODULEPATH/versions/host_injections}
+            echo "Using ${EESSI_SITE_MODULEPATH} as the site extension directory to be added to MODULEPATH." >> $output
+            export EESSI_USER_MODULEPATH=${EESSI_MODULEPATH/${EESSI_CVMFS_REPO}/${HOME}\/eessi}
+            echo "Using ${EESSI_USER_MODULEPATH} as the user extension directory to be added to MODULEPATH." >> $output
           else
             error "EESSI module path at $EESSI_MODULEPATH not found!"
             false

From 60cb5dc90187b8b8506933a74cc51e07b67cfe0a Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Tue, 7 Nov 2023 13:15:20 +0100
Subject: [PATCH 007/501] Update EESSI-extend-2023.06-easybuild.eb

---
 EESSI-extend-2023.06-easybuild.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index fd9f897326..ce55f619fb 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -30,7 +30,7 @@ checksums = ['8ae609f99b6953beae89aa1945913686c86c156509dbc55e2b6b8017b13fcf66']
 prepend_to_path = None
 
 # All the dependencies we filter in EESSI
-local_deps_to_filter = "Autoconf,Automake,Autotools,binutils,bzip2,DBus,flex,gettext,gperf,help2man,intltool,libreadline,libtool,Lua,M4,makeinfo,ncurses,util-linux,XZ,zlib"
+local_deps_to_filter = "Autoconf,Automake,Autotools,binutils,bzip2,DBus,flex,gettext,gperf,help2man,intltool,libreadline,libtool,M4,makeinfo,ncurses,util-linux,XZ,zlib"
 local_arch_specific_deps_to_filter = {'aarch64': ',yasm', 'x86_64': ''}
 local_deps_to_filter += local_arch_specific_deps_to_filter[ARCH]
 

From 8fe3892e8bb41a8054bd8cfeea34e96888235db3 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Tue, 7 Nov 2023 13:48:53 +0100
Subject: [PATCH 008/501] Escape hyphen for gsub

---
 EESSI-extend-2023.06-easybuild.eb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index ce55f619fb..8993c63cc3 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -69,7 +69,8 @@ if (os.getenv("EESSI_CVMFS_INSTALL") ~= nil) then
 elseif (os.getenv("EESSI_SITE_INSTALL") ~= nil) then 
   easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), 'versions', 'host_injections')
 else
-  easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), os.getenv("EESSI_CVMFS_REPO"), pathJoin(os.getenv("HOME"), "eessi"))
+  -- Would have liked to use os.getenv("EESSI_CVMFS_REPO") here but the hypen needs to be escaped
+  easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), "/cvmfs/pilot.eessi%-hpc.org", pathJoin(os.getenv("HOME"), "eessi"))
 end
 if (mode() == "load") then
   LmodMessage("-- To create installations for EESSI, you _must_ have write permissions to " .. easybuild_installpath)

From ab2c260e4d9b9a1b70b7246b10977437ad0fcd15 Mon Sep 17 00:00:00 2001
From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com>
Date: Wed, 29 Nov 2023 10:38:57 +0100
Subject: [PATCH 009/501] {2023.06}[foss/2023a] OpenFOAM v10

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
index e685785f16..b67e894825 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
@@ -12,3 +12,4 @@ easyconfigs:
       options:
         from-pr: 19270
   - SciPy-bundle-2023.07-gfbf-2023a.eb
+  - OpenFOAM-10-foss-2023a.eb

From 3439e8b07981dff466b9efb1af4215bedb603351 Mon Sep 17 00:00:00 2001
From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com>
Date: Fri, 1 Dec 2023 12:06:39 +0100
Subject: [PATCH 010/501] Include gnuplot fix from PR
 easybuilders/easyconfigs#19261

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
index 4a302c409b..514ed0b86e 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
@@ -22,4 +22,7 @@ easyconfigs:
       options:
         from-pr: 19339
   - Qt5-5.15.10-GCCcore-12.3.0.eb
+  - gnuplot-5.4.8-GCCcore-12.3.0.eb: 
+      options:
+        from-pr: 19261
   - OpenFOAM-10-foss-2023a.eb

From 10751d25858239fe78465a5e523fc0077ac4b487 Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Fri, 15 Dec 2023 15:15:14 +0100
Subject: [PATCH 011/501] Add pre test hook to skip netCDF tests

---
 eb_hooks.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/eb_hooks.py b/eb_hooks.py
index 6fe92c7f7b..2081bfedab 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -366,6 +366,18 @@ def pre_test_hook_ignore_failing_tests_SciPybundle(self, *args, **kwargs):
     if self.name == 'SciPy-bundle' and self.version in ['2021.10', '2023.07'] and cpu_target == CPU_TARGET_NEOVERSE_V1:
         self.cfg['testopts'] = "|| echo ignoring failing tests" 
 
+def pre_test_hook_ignore_failing_tests_netCDF(self, *args, **kwargs):
+    """
+    Pre-test hook for SciPy-bundle: skip failing tests for selected netCDF versions on neoverse_v1
+    cfr. https://github.com/EESSI/software-layer/issues/325
+    The following tests are problematic:
+        163 - nc_test4_run_par_test (Timeout)
+        190 - h5_test_run_par_tests (Timeout)
+    A few other tests are skipped in the easyconfig and patches for similar issues, see above issue for details.
+    """
+    cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
+    if self.name == 'netCDF' and self.version == '4.9.2' and cpu_target == CPU_TARGET_NEOVERSE_V1:
+        self.cfg['testopts'] = "|| echo ignoring failing tests" 
 
 def pre_single_extension_hook(ext, *args, **kwargs):
     """Main pre-configure hook: trigger custom functions based on software name."""

From 94206acbcc02da084ba4d5d85219d9ae92f885ac Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Fri, 15 Dec 2023 15:16:05 +0100
Subject: [PATCH 012/501] Add correct issue reference in hook

---
 eb_hooks.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index 2081bfedab..3074eb8ee3 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -369,7 +369,7 @@ def pre_test_hook_ignore_failing_tests_SciPybundle(self, *args, **kwargs):
 def pre_test_hook_ignore_failing_tests_netCDF(self, *args, **kwargs):
     """
     Pre-test hook for SciPy-bundle: skip failing tests for selected netCDF versions on neoverse_v1
-    cfr. https://github.com/EESSI/software-layer/issues/325
+    cfr. https://github.com/EESSI/software-layer/issues/425
     The following tests are problematic:
         163 - nc_test4_run_par_test (Timeout)
         190 - h5_test_run_par_tests (Timeout)

From db150f4838c47d25e7a683ae239c44b25dd88a6d Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Fri, 15 Dec 2023 16:34:42 +0100
Subject: [PATCH 013/501] Fix hook

---
 eb_hooks.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/eb_hooks.py b/eb_hooks.py
index 3074eb8ee3..bf5da0cc64 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -430,6 +430,7 @@ def pre_single_extension_isoband(ext, *args, **kwargs):
     'ESPResSo': pre_test_hook_ignore_failing_tests_ESPResSo,
     'FFTW.MPI': pre_test_hook_ignore_failing_tests_FFTWMPI,
     'SciPy-bundle': pre_test_hook_ignore_failing_tests_SciPybundle,
+    'netCDF': pre_test_hook_ignore_failing_tests_netCDF,
 }
 
 PRE_SINGLE_EXTENSION_HOOKS = {

From 363f42c9bdaa905c0c094f69479b62520ae3a1e0 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sun, 17 Dec 2023 10:53:00 +0100
Subject: [PATCH 014/501] {2023.06}[foss/2023a] R-bundle-CRAN 2023.12

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
index a9323d3df6..f6d01ee828 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
@@ -32,3 +32,6 @@ easyconfigs:
   - R-4.3.2-gfbf-2023a.eb:
       options:
         from-pr: 19185
+  - R-bundle-CRAN-2023.12-foss-2023a.eb:
+      options:
+        from-pr: 19170

From 69fe0569451b708ce13ba506854d44f383b213f2 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sun, 17 Dec 2023 18:12:04 +0100
Subject: [PATCH 015/501] fix for LERC sanity check RPATH failure

---
 .../2023.06/eessi-2023.06-eb-4.8.2-2023a.yml                 | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
index f6d01ee828..7371ee2176 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
@@ -32,6 +32,11 @@ easyconfigs:
   - R-4.3.2-gfbf-2023a.eb:
       options:
         from-pr: 19185
+  - LERC-4.0.0-GCCcore-12.3.0.eb:
+      # avoid RPATH-related sanity check errors by compiling LERC's test binary in postinstallcmds;
+      # see https://github.com/easybuilders/easybuild-easyconfigs/pull/19386
+      options:
+        from-pr: 19386
   - R-bundle-CRAN-2023.12-foss-2023a.eb:
       options:
         from-pr: 19170

From 34b7e850bd8ece75a0d01fae5ddc62412701f945 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Mon, 18 Dec 2023 11:36:14 +0100
Subject: [PATCH 016/501] use patch for MPFR

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
index 7371ee2176..c5fb6a0425 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
@@ -32,6 +32,9 @@ easyconfigs:
   - R-4.3.2-gfbf-2023a.eb:
       options:
         from-pr: 19185
+  - MPFR-4.2.0-GCCcore-12.3.0.eb:
+      options:
+        from-pr: 19438
   - LERC-4.0.0-GCCcore-12.3.0.eb:
       # avoid RPATH-related sanity check errors by compiling LERC's test binary in postinstallcmds;
       # see https://github.com/easybuilders/easybuild-easyconfigs/pull/19386

From 98b51a90fa62e65ab9d87b096246b4744e8b96ab Mon Sep 17 00:00:00 2001
From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com>
Date: Wed, 3 Jan 2024 19:16:34 +0100
Subject: [PATCH 017/501] Use only half the cores to build OpenFOAM

---
 eb_hooks.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index 8e29d2c103..edff46221a 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -79,7 +79,7 @@ def post_ready_hook(self, *args, **kwargs):
     # 'parallel' easyconfig parameter is set via EasyBlock.set_parallel in ready step based on available cores.
     # here we reduce parallellism to only use half of that for selected software,
     # to avoid failing builds/tests due to out-of-memory problems
-    if self.name in ['TensorFlow']:
+    if self.name in ['TensorFlow'] or self.name in ['OpenFOAM']:
         parallel = self.cfg['parallel']
         if parallel > 1:
             self.cfg['parallel'] = parallel // 2

From 9c0ca0d408304ece1cdeed0aeabb42b9403bfd94 Mon Sep 17 00:00:00 2001
From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com>
Date: Mon, 8 Jan 2024 11:31:46 +0100
Subject: [PATCH 018/501] Revert to using all cores in OpenFOAM tests

Reducing in half did not solve issue with hanging/crashing in sanity checks
---
 eb_hooks.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index 3b52b54e9e..00aee51816 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -80,7 +80,7 @@ def post_ready_hook(self, *args, **kwargs):
     # 'parallel' easyconfig parameter is set via EasyBlock.set_parallel in ready step based on available cores.
     # here we reduce parallellism to only use half of that for selected software,
     # to avoid failing builds/tests due to out-of-memory problems
-    if self.name in ['TensorFlow'] or self.name in ['OpenFOAM']:
+    if self.name in ['TensorFlow']:
         parallel = self.cfg['parallel']
         if parallel > 1:
             self.cfg['parallel'] = parallel // 2

From fdf0d9a1ee712f2d46eaeaaf6614eb15846441d7 Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Wed, 10 Jan 2024 17:18:22 +0100
Subject: [PATCH 019/501] add zen4 / AMD Genoa

---
 init/arch_specs/eessi_arch_x86.spec           |  7 ++---
 .../x86_64/amd/zen4/Azure-Alma8-9V33X.cpuinfo | 27 +++++++++++++++++++
 .../x86_64/amd/zen4/Azure-Alma8-9V33X.output  |  1 +
 .../x86_64/amd/zen4/Shinx-RHEL8-9654.cpuinfo  | 27 +++++++++++++++++++
 .../x86_64/amd/zen4/Shinx-RHEL8-9654.output   |  1 +
 5 files changed, 60 insertions(+), 3 deletions(-)
 create mode 100644 tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.cpuinfo
 create mode 100644 tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.output
 create mode 100644 tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.cpuinfo
 create mode 100644 tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.output

diff --git a/init/arch_specs/eessi_arch_x86.spec b/init/arch_specs/eessi_arch_x86.spec
index 8d01cb0c03..bfbc5b4be1 100755
--- a/init/arch_specs/eessi_arch_x86.spec
+++ b/init/arch_specs/eessi_arch_x86.spec
@@ -1,6 +1,7 @@
 # x86_64 CPU architecture specifications
 # Software path in EESSI 	| Vendor ID 	| List of defining CPU features
-"x86_64/intel/haswell"		"GenuineIntel"	"avx2 fma" 		# Intel Haswell, Broadwell
+"x86_64/intel/haswell"		"GenuineIntel"	"avx2 fma" 						# Intel Haswell, Broadwell
 "x86_64/intel/skylake_avx512"	"GenuineIntel"	"avx2 fma avx512f avx512bw avx512cd avx512dq avx512vl"	# Intel Skylake, Cascade Lake
-"x86_64/amd/zen2"		"AuthenticAMD"	"avx2 fma"		# AMD Rome
-"x86_64/amd/zen3"		"AuthenticAMD"	"avx2 fma vaes"		# AMD Milan, Milan-X
+"x86_64/amd/zen2"		"AuthenticAMD"	"avx2 fma"						# AMD Rome
+"x86_64/amd/zen3"		"AuthenticAMD"	"avx2 fma vaes"						# AMD Milan, Milan-X
+"x86_64/amd/zen4"		"AuthenticAMD"	"avx2 fma vaes avx512f avx512ifma"			# AMD Genoa, Genoa-X
diff --git a/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.cpuinfo b/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.cpuinfo
new file mode 100644
index 0000000000..4a97da862c
--- /dev/null
+++ b/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.cpuinfo
@@ -0,0 +1,27 @@
+processor       : 0
+vendor_id       : AuthenticAMD
+cpu family      : 25
+model           : 17
+model name      : AMD EPYC 9V33X 96-Core Processor
+stepping        : 1
+microcode       : 0xffffffff
+cpu MHz         : 3705.853
+cache size      : 1024 KB
+physical id     : 0
+siblings        : 88
+core id         : 0
+cpu cores       : 88
+apicid          : 0
+initial apicid  : 0
+fpu             : yes
+fpu_exception   : yes
+cpuid level     : 13
+wp              : yes
+flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl tsc_reliable nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand hypervisor lahf_lm cmp_legacy svm cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw topoext perfctr_core invpcid_single vmmcall fsgsbase bmi1 avx2 smep bmi2 erms invpcid avx512f avx512dq rdseed adx smap avx512ifma clflushopt clwb avx512cd sha_ni avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves avx512_bf16 clzero xsaveerptr arat npt nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold v_vmsave_vmload avx512vbmi umip avx512_vbmi2 gfni vaes vpclmulqdq avx512_vnni avx512_bitalg avx512_vpopcntdq rdpid fsrm
+bugs            : sysret_ss_attrs null_seg spectre_v1 spectre_v2 spec_store_bypass
+bogomips        : 5100.08
+TLB size        : 3584 4K pages
+clflush size    : 64
+cache_alignment : 64
+address sizes   : 48 bits physical, 48 bits virtual
+power management:
diff --git a/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.output b/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.output
new file mode 100644
index 0000000000..950740a78c
--- /dev/null
+++ b/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.output
@@ -0,0 +1 @@
+x86_64/amd/zen4
diff --git a/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.cpuinfo b/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.cpuinfo
new file mode 100644
index 0000000000..f28381d7a2
--- /dev/null
+++ b/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.cpuinfo
@@ -0,0 +1,27 @@
+processor	: 0
+vendor_id	: AuthenticAMD
+cpu family	: 25
+model		: 17
+model name	: AMD EPYC 9654 96-Core Processor
+stepping	: 1
+microcode	: 0xa10113e
+cpu MHz		: 3699.993
+cache size	: 1024 KB
+physical id	: 0
+siblings	: 96
+core id		: 0
+cpu cores	: 96
+apicid		: 0
+initial apicid	: 0
+fpu		: yes
+fpu_exception	: yes
+cpuid level	: 16
+wp		: yes
+flags		: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb cat_l3 cdp_l3 invpcid_single hw_pstate ssbd mba perfmon_v2 ibrs ibpb stibp vmmcall fsgsbase bmi1 avx2 smep bmi2 erms invpcid cqm rdt_a avx512f avx512dq rdseed adx avx512ifma clflushopt clwb avx512cd sha_ni avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local avx512_bf16 clzero irperf xsaveerptr wbnoinvd amd_ppin cppc arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif v_spec_ctrl avx512vbmi umip pku ospke avx512_vbmi2 gfni vaes vpclmulqdq avx512_vnni avx512_bitalg avx512_vpopcntdq la57 rdpid overflow_recov succor smca fsrm flush_l1d
+bugs		: sysret_ss_attrs spectre_v1 spectre_v2 spec_store_bypass
+bogomips	: 4799.99
+TLB size	: 3584 4K pages
+clflush size	: 64
+cache_alignment	: 64
+address sizes	: 52 bits physical, 57 bits virtual
+power management: ts ttp tm hwpstate cpb eff_freq_ro [13] [14]
diff --git a/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.output b/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.output
new file mode 100644
index 0000000000..950740a78c
--- /dev/null
+++ b/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.output
@@ -0,0 +1 @@
+x86_64/amd/zen4

From 1ee221bdbfe0ae6015ca3765a8e23b0760a2323f Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Wed, 10 Jan 2024 17:24:21 +0100
Subject: [PATCH 020/501] add all.output tests

---
 tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.all.output | 1 +
 tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.all.output  | 1 +
 2 files changed, 2 insertions(+)
 create mode 100644 tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.all.output
 create mode 100644 tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.all.output

diff --git a/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.all.output b/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.all.output
new file mode 100644
index 0000000000..e1bbd79e4a
--- /dev/null
+++ b/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.all.output
@@ -0,0 +1 @@
+x86_64/amd/zen4:x86_64/amd/zen3:x86_64/amd/zen2:x86_64/generic
diff --git a/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.all.output b/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.all.output
new file mode 100644
index 0000000000..e1bbd79e4a
--- /dev/null
+++ b/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.all.output
@@ -0,0 +1 @@
+x86_64/amd/zen4:x86_64/amd/zen3:x86_64/amd/zen2:x86_64/generic

From 680e7b91836c33caeb1c2c493f0589d4b5a73219 Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Wed, 10 Jan 2024 17:28:59 +0100
Subject: [PATCH 021/501] adding zen4 checks

---
 .github/workflows/tests_archdetect.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/tests_archdetect.yml b/.github/workflows/tests_archdetect.yml
index 37338693c5..d1407637e0 100644
--- a/.github/workflows/tests_archdetect.yml
+++ b/.github/workflows/tests_archdetect.yml
@@ -13,6 +13,8 @@ jobs:
           - x86_64/intel/skylake_avx512/archspec-linux-6132
           - x86_64/amd/zen2/Azure-CentOS7-7V12
           - x86_64/amd/zen3/Azure-CentOS7-7V73X
+          - x86_64/amd/zen4/Azure-Alma8-9V33X
+          - x86_64/amd/zen4/Shinx-RHEL8-9654
           - ppc64le/power9le/unknown-power9le
           - aarch64/neoverse_n1/Azure-Ubuntu20-Altra
           - aarch64/neoverse_n1/AWS-awslinux-graviton2

From 7070c047ebf57918dd0ae19c11ade011e99cefff Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Wed, 10 Jan 2024 18:00:17 +0100
Subject: [PATCH 022/501] commenting out power to prevent conflict

---
 .github/workflows/tests_archdetect.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests_archdetect.yml b/.github/workflows/tests_archdetect.yml
index d1407637e0..45e8dd2e60 100644
--- a/.github/workflows/tests_archdetect.yml
+++ b/.github/workflows/tests_archdetect.yml
@@ -15,10 +15,10 @@ jobs:
           - x86_64/amd/zen3/Azure-CentOS7-7V73X
           - x86_64/amd/zen4/Azure-Alma8-9V33X
           - x86_64/amd/zen4/Shinx-RHEL8-9654
-          - ppc64le/power9le/unknown-power9le
           - aarch64/neoverse_n1/Azure-Ubuntu20-Altra
           - aarch64/neoverse_n1/AWS-awslinux-graviton2
           - aarch64/neoverse_v1/AWS-awslinux-graviton3
+          # - ppc64le/power9le/unknown-power9le
       fail-fast: false
     steps:
     - name: checkout

From ad70b6b0857f6e3508a73c4675795de30f6b40eb Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Wed, 10 Jan 2024 19:27:14 +0100
Subject: [PATCH 023/501] commenting out power9 to prevent conflict

---
 .github/workflows/tests_archdetect.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/tests_archdetect.yml b/.github/workflows/tests_archdetect.yml
index 45e8dd2e60..68d25250ca 100644
--- a/.github/workflows/tests_archdetect.yml
+++ b/.github/workflows/tests_archdetect.yml
@@ -18,6 +18,8 @@ jobs:
           - aarch64/neoverse_n1/Azure-Ubuntu20-Altra
           - aarch64/neoverse_n1/AWS-awslinux-graviton2
           - aarch64/neoverse_v1/AWS-awslinux-graviton3
+          # commented out since these targets are currently not supported in software.eessi.io repo
+          # (and some tests assume that the corresponding subdirectory in software layer is there)
           # - ppc64le/power9le/unknown-power9le
       fail-fast: false
     steps:

From fd3103e1f75157edffcf16023ef4fb6431c6b5eb Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Wed, 10 Jan 2024 20:15:18 +0100
Subject: [PATCH 024/501] move to software.eessi.io

---
 .github/workflows/test_eessi.yml                  | 14 +++++++-------
 .github/workflows/test_eessi_container_script.yml | 12 ++++++------
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/test_eessi.yml b/.github/workflows/test_eessi.yml
index 04195dd619..7c96b091d2 100644
--- a/.github/workflows/test_eessi.yml
+++ b/.github/workflows/test_eessi.yml
@@ -10,7 +10,7 @@ jobs:
       fail-fast: false
       matrix:
         EESSI_VERSION:
-        - 2021.12
+        - 2023.06
         EESSI_SOFTWARE_SUBDIR:
         - aarch64/generic
         - aarch64/graviton2
@@ -24,19 +24,19 @@ jobs:
         - name: Check out software-layer repository
           uses: actions/checkout@93ea575cb5d8a053eaa0ac8fa3b40d7e05a33cc8 # v3.1.0
 
-        - name: Mount EESSI CernVM-FS pilot repository
+        - name: Mount EESSI CernVM-FS software repository
           uses: cvmfs-contrib/github-action-cvmfs@d4641d0d591c9a5c3be23835ced2fb648b44c04b # v3.1
           with:
               cvmfs_config_package: https://github.com/EESSI/filesystem-layer/releases/download/latest/cvmfs-config-eessi_latest_all.deb
               cvmfs_http_proxy: DIRECT
-              cvmfs_repositories: pilot.eessi-hpc.org
+              cvmfs_repositories: software.eessi.io
 
         - name: Test check_missing_installations.sh script
           run: |
-              source /cvmfs/pilot.eessi-hpc.org/versions/${{matrix.EESSI_VERSION}}/init/bash
+              source /cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}/init/bash
               module load EasyBuild
               eb --version
-              export EESSI_PREFIX=/cvmfs/pilot.eessi-hpc.org/versions/${{matrix.EESSI_VERSION}}
+              export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}
               export EESSI_OS_TYPE=linux
               export EESSI_SOFTWARE_SUBDIR=${{matrix.EESSI_SOFTWARE_SUBDIR}}
               env | grep ^EESSI | sort
@@ -45,10 +45,10 @@ jobs:
 
         - name: Test check_missing_installations.sh with missing package (GCC/8.3.0)
           run: |
-              source /cvmfs/pilot.eessi-hpc.org/versions/${{matrix.EESSI_VERSION}}/init/bash
+              source /cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}/init/bash
               module load EasyBuild
               eb --version
-              export EESSI_PREFIX=/cvmfs/pilot.eessi-hpc.org/versions/${{matrix.EESSI_VERSION}}
+              export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}
               export EESSI_OS_TYPE=linux
               export EESSI_SOFTWARE_SUBDIR=${{matrix.EESSI_SOFTWARE_SUBDIR}}
               env | grep ^EESSI | sort
diff --git a/.github/workflows/test_eessi_container_script.yml b/.github/workflows/test_eessi_container_script.yml
index 929fb22cec..590aa4225b 100644
--- a/.github/workflows/test_eessi_container_script.yml
+++ b/.github/workflows/test_eessi_container_script.yml
@@ -90,15 +90,15 @@ jobs:
               elif [[ ${{matrix.SCRIPT_TEST}} == 'readwrite' ]]; then
                 outfile=out_readwrite.txt
                 fn="test_${RANDOM}.txt"
-                echo "touch /cvmfs/pilot.eessi-hpc.org/${fn}" > test_script.sh
+                echo "touch /cvmfs/software.eessi.io/${fn}" > test_script.sh
                 chmod u+x test_script.sh
                 export SINGULARITY_BIND="$PWD:/test"
                 ./eessi_container.sh --verbose --access rw --mode run /test/test_script.sh > ${outfile}
 
                 tmpdir=$(grep "\-\-resume" ${outfile} | sed "s/.*--resume \([^']*\).*/\1/g")
                 # note: must use '--access rw' again here, since touched file is in overlay upper dir
-                ./eessi_container.sh --verbose --resume ${tmpdir} --access rw --mode shell <<< "ls -l /cvmfs/pilot.eessi-hpc.org/${fn}" > ${outfile}
-                grep "/cvmfs/pilot.eessi-hpc.org/${fn}$" $outfile
+                ./eessi_container.sh --verbose --resume ${tmpdir} --access rw --mode shell <<< "ls -l /cvmfs/software.eessi.io/${fn}" > ${outfile}
+                grep "/cvmfs/software.eessi.io/${fn}$" $outfile
 
               # test use of --resume
               elif [[ ${{matrix.SCRIPT_TEST}} == 'resume' ]]; then
@@ -120,12 +120,12 @@ jobs:
               elif [[ ${{matrix.SCRIPT_TEST}} == 'save' ]]; then
                 outfile=out_save.txt
                 fn="test_${RANDOM}.txt"
-                test_cmd="touch /cvmfs/pilot.eessi-hpc.org/${fn}"
+                test_cmd="touch /cvmfs/software.eessi.io/${fn}"
                 ./eessi_container.sh --verbose --mode shell --access rw --save test-save.tar <<< "${test_cmd}" 2>&1 | tee ${outfile}
                 rm -f ${outfile}
 
-                ./eessi_container.sh --verbose --mode shell --access rw --resume test-save.tar <<< "ls -l /cvmfs/pilot.eessi-hpc.org/${fn}" > ${outfile}
-                grep "/cvmfs/pilot.eessi-hpc.org/${fn}$" $outfile
+                ./eessi_container.sh --verbose --mode shell --access rw --resume test-save.tar <<< "ls -l /cvmfs/software.eessi.io/${fn}" > ${outfile}
+                grep "/cvmfs/software.eessi.io/${fn}$" $outfile
 
                 tar tfv test-save.tar | grep "overlay-upper/${fn}"
 

From a13bce84ca477c9d866ad722993252aad924d5fd Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Wed, 10 Jan 2024 20:20:48 +0100
Subject: [PATCH 025/501] move from pilot to software

---
 .github/workflows/tests_readme.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests_readme.yml b/.github/workflows/tests_readme.yml
index 5c6d0318d4..034dae3780 100644
--- a/.github/workflows/tests_readme.yml
+++ b/.github/workflows/tests_readme.yml
@@ -24,7 +24,7 @@ jobs:
         - name: verify if README.md is consistent with EESSI_PILOT_VERSION from init/eessi_defaults
           run: |
             source init/eessi_defaults
-            grep "${EESSI_PILOT_VERSION}" README.md
+            grep "${EESSI_VERSION}" README.md
 
         - name: verify if README.md is consistent with EESSI_CVMFS_REPO from init/eessi_defaults
           run: |

From 473a5b52b960881f2b4371978279976b9a8bccae Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Thu, 11 Jan 2024 03:51:20 +0100
Subject: [PATCH 026/501] move EESSI action to v3

---
 .github/workflows/tests_archdetect.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/tests_archdetect.yml b/.github/workflows/tests_archdetect.yml
index 68d25250ca..f09567d125 100644
--- a/.github/workflows/tests_archdetect.yml
+++ b/.github/workflows/tests_archdetect.yml
@@ -26,7 +26,8 @@ jobs:
     - name: checkout
       uses: actions/checkout@93ea575cb5d8a053eaa0ac8fa3b40d7e05a33cc8 # v3.1.0
     - name: Enable EESSI
-      uses: eessi/github-action-eessi@58b50fd2eead2162c2b9ac258d4fb60cc9f30503 # v2.0.13
+      #uses: eessi/github-action-eessi@58b50fd2eead2162c2b9ac258d4fb60cc9f30503 # v2.0.13
+      uses: eessi/github-action-eessi@v3
     - name: test eessi_archdetect.sh
       run: |
           export EESSI_MACHINE_TYPE=${{matrix.proc_cpuinfo}}

From 807d78471ad4104d0ff3f590dbc697d6cd2a3968 Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Mon, 15 Jan 2024 11:27:42 +0100
Subject: [PATCH 027/501] fix upstream merge

---
 .github/workflows/test_eessi.yml | 72 --------------------------------
 1 file changed, 72 deletions(-)
 delete mode 100644 .github/workflows/test_eessi.yml

diff --git a/.github/workflows/test_eessi.yml b/.github/workflows/test_eessi.yml
deleted file mode 100644
index 7c96b091d2..0000000000
--- a/.github/workflows/test_eessi.yml
+++ /dev/null
@@ -1,72 +0,0 @@
-# documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
-name: Tests relying on having EESSI pilot repo mounted
-on: [push, pull_request, workflow_dispatch]
-permissions:
-  contents: read # to fetch code (actions/checkout)
-jobs:
-  eessi_pilot_repo:
-    runs-on: ubuntu-20.04
-    strategy:
-      fail-fast: false
-      matrix:
-        EESSI_VERSION:
-        - 2023.06
-        EESSI_SOFTWARE_SUBDIR:
-        - aarch64/generic
-        - aarch64/graviton2
-        - aarch64/graviton3
-        - x86_64/amd/zen2
-        - x86_64/amd/zen3
-        - x86_64/intel/haswell
-        - x86_64/intel/skylake_avx512
-        - x86_64/generic
-    steps:
-        - name: Check out software-layer repository
-          uses: actions/checkout@93ea575cb5d8a053eaa0ac8fa3b40d7e05a33cc8 # v3.1.0
-
-        - name: Mount EESSI CernVM-FS software repository
-          uses: cvmfs-contrib/github-action-cvmfs@d4641d0d591c9a5c3be23835ced2fb648b44c04b # v3.1
-          with:
-              cvmfs_config_package: https://github.com/EESSI/filesystem-layer/releases/download/latest/cvmfs-config-eessi_latest_all.deb
-              cvmfs_http_proxy: DIRECT
-              cvmfs_repositories: software.eessi.io
-
-        - name: Test check_missing_installations.sh script
-          run: |
-              source /cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}/init/bash
-              module load EasyBuild
-              eb --version
-              export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}
-              export EESSI_OS_TYPE=linux
-              export EESSI_SOFTWARE_SUBDIR=${{matrix.EESSI_SOFTWARE_SUBDIR}}
-              env | grep ^EESSI | sort
-              echo "just run check_missing_installations.sh (should use eessi-${{matrix.EESSI_VERSION}}.yml)"
-              ./check_missing_installations.sh
-
-        - name: Test check_missing_installations.sh with missing package (GCC/8.3.0)
-          run: |
-              source /cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}/init/bash
-              module load EasyBuild
-              eb --version
-              export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}
-              export EESSI_OS_TYPE=linux
-              export EESSI_SOFTWARE_SUBDIR=${{matrix.EESSI_SOFTWARE_SUBDIR}}
-              env | grep ^EESSI | sort
-              echo "modify eessi-${{matrix.EESSI_VERSION}}.yml by adding a missing package (GCC/8.3.0)"
-              echo "  GCC:" >> eessi-${{matrix.EESSI_VERSION}}.yml
-              echo "    toolchains:" >> eessi-${{matrix.EESSI_VERSION}}.yml
-              echo "      SYSTEM:" >> eessi-${{matrix.EESSI_VERSION}}.yml
-              echo "        versions: '8.3.0'" >> eessi-${{matrix.EESSI_VERSION}}.yml
-              tail -n 4 eessi-${{matrix.EESSI_VERSION}}.yml
-              # note, check_missing_installations.sh exits 1 if a package was
-              # missing, which is intepreted as false (exit code based, not
-              # boolean logic), hence when the script exits 0 if no package was
-              # missing it is interpreted as true, thus the test did not capture
-              # the missing package
-              if ./check_missing_installations.sh; then
-                echo "did NOT capture missing package; test FAILED"
-                exit 1
-              else
-                echo "captured missing package; test PASSED"
-                exit 0
-              fi

From 41f6dea98fa5a4b14b590ba42dffec9eacfaf8a5 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Mon, 15 Jan 2024 10:39:09 +0000
Subject: [PATCH 028/501] {2023.06}[foss/2022b] R v4.2.2

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml  | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
new file mode 100644
index 0000000000..f8af4b5b45
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
@@ -0,0 +1,2 @@
+easyconfigs:
+  - R-4.2.2-foss-2022b.eb

From 5955adcf75954b2fd66680af051f5feb7c9a1fc9 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Thu, 25 Jan 2024 20:56:54 +0000
Subject: [PATCH 029/501] {2023.06}[GCCcore/13.2.0] Qt5 v5.15.11

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 4dd31dbd5d..0d1863f5f3 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -8,3 +8,6 @@ easyconfigs:
   - matplotlib-3.8.2-gfbf-2023b.eb:
       options:
         from-pr: 19552
+  - Qt5-5.15.11-GCCcore-13.2.0.eb:
+      options:
+        from-pr: 19320

From 0f3646ef0eec6a89aa1a8a5479c8040264af5af3 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Mon, 5 Feb 2024 17:28:18 +0100
Subject: [PATCH 030/501] Second attempt at having the bot run the test suite,
 now based on Thomas' PR 366

---
 bot/check-test.sh | 66 ++++++++++++++++++++++++++++++++++
 run_tests.sh      | 10 +++++-
 test_suite.sh     | 92 +++++++++++++++++++++++++++++------------------
 3 files changed, 132 insertions(+), 36 deletions(-)
 create mode 100644 bot/check-test.sh

diff --git a/bot/check-test.sh b/bot/check-test.sh
new file mode 100644
index 0000000000..9fc783aa99
--- /dev/null
+++ b/bot/check-test.sh
@@ -0,0 +1,66 @@
+#!/bin/bash
+#
+# Dummy script that only creates test result file for the bot, without actually checking anything
+#
+# This script is part of the EESSI software layer, see
+# https://github.com/EESSI/software-layer.git
+#
+# author: Kenneth Hoste (HPC-UGent)
+#
+# license: GPLv2
+#
+job_dir=${PWD}
+job_out="slurm-${SLURM_JOB_ID}.out"
+job_test_result_file="_bot_job${SLURM_JOB_ID}.test"
+
+# ReFrame prints e.g.
+#[----------] start processing checks
+#[ RUN      ] GROMACS_EESSI %benchmark_info=HECBioSim/Crambin %nb_impl=cpu %scale=2_nodes %module_name=GROMACS/2021.3-foss-2021a /d597cff4 @snellius:rome+default
+#[ RUN      ] GROMACS_EESSI %benchmark_info=HECBioSim/Crambin %nb_impl=cpu %scale=2_nodes %module_name=GROMACS/2021.3-foss-2021a /d597cff4 @snellius:genoa+default
+#[ RUN      ] GROMACS_EESSI %benchmark_info=HECBioSim/Crambin %nb_impl=cpu %scale=1_cpn_2_nodes %module_name=GROMACS/2021.3-foss-2021a /f4194106 @snellius:genoa+default
+#[     FAIL ] (1/3) GROMACS_EESSI %benchmark_info=HECBioSim/Crambin %nb_impl=cpu %scale=2_nodes %module_name=GROMACS/2021.3-foss-2021a /d597cff4 @snellius:genoa+default
+#==> test failed during 'sanity': test staged in '/scratch-shared/casparl/reframe_output/staging/snellius/genoa/default/GROMACS_EESSI_d597cff4'
+#[       OK ] (2/3) GROMACS_EESSI %benchmark_info=HECBioSim/Crambin %nb_impl=cpu %scale=2_nodes %module_name=GROMACS/2021.3-foss-2021a /d597cff4 @snellius:rome+default
+#P: perf: 8.441 ns/day (r:0, l:None, u:None)
+#[     FAIL ] (3/3) GROMACS_EESSI %benchmark_info=HECBioSim/Crambin %nb_impl=cpu %scale=1_cpn_2_nodes %module_name=GROMACS/2021.3-foss-2021a /f4194106 @snellius:genoa+default
+#==> test failed during 'sanity': test staged in '/scratch-shared/casparl/reframe_output/staging/snellius/genoa/default/GROMACS_EESSI_f4194106'
+#[----------] all spawned checks have finished
+#[  FAILED  ] Ran 3/3 test case(s) from 2 check(s) (2 failure(s), 0 skipped, 0 aborted)
+
+# We will grep for the last and final line, since this reflects the overall result
+# Specifically, we grep for FAILED, since this is also what we print if a step in the test script itself fails
+FAILED=-1
+if [[ ${SLURM} -eq 1 ]]; then
+  GP_failed='\[\s*FAILED\s*\]'
+  grep_out=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_failed}")
+  [[ $? -eq 0 ]] && FAILED=1 || FAILED=0
+  # have to be careful to not add searched for pattern into slurm out file
+  [[ ${VERBOSE} -ne 0 ]] && echo ">> searching for '"${GP_failed}"'"
+  [[ ${VERBOSE} -ne 0 ]] && echo "${grep_out}"
+fi
+
+
+# Here, we grep for 'ERROR:', which is printed if a fatal_error is encountered when executing the test step
+# I.e. this is an error in execution of the run_tests.sh itself, NOT in running the actual tests
+ERROR=-1
+if [[ ${SLURM} -eq 1 ]]; then
+  GP_error='ERROR: '
+  grep_out=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_error}")
+  [[ $? -eq 0 ]] && ERROR=1 || ERROR=0
+  # have to be careful to not add searched for pattern into slurm out file
+  [[ ${VERBOSE} -ne 0 ]] && echo ">> searching for '"${GP_error}"'"
+  [[ ${VERBOSE} -ne 0 ]] && echo "${grep_out}"
+fi
+
+echo "[TEST]" > ${job_test_result_file}
+if [[ ${ERROR} -eq 1 ]]; then
+    echo "comment_description = Failure to execute test step" >> ${job_test_result_file}
+    echo "status = FAILURE" >> ${job_test_result_file}
+elif [[ ${FAILED} -eq 1 ]]; then
+    echo "comment_description = EESSI test suite produced failures" >> ${job_test_result_file}
+else
+    echo "comment_description = Test step run succesfully" >> ${job_test_result_file}
+    echo "status = SUCCESS" >> ${job_test_result_file}
+fi
+
+exit 0
diff --git a/run_tests.sh b/run_tests.sh
index ccbc751f22..69672f18f3 100644
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -1,4 +1,12 @@
 #!/bin/bash
 base_dir=$(dirname $(realpath $0))
 source ${base_dir}/init/eessi_defaults
-./run_in_compat_layer_env.sh ./test_suite.sh "$@"
+
+# Note: for these tests, we _don't_ run in the compat layer env
+# These tests should mimic what users do, and they are typically not in a prefix environment
+
+# Run eb --sanity-check-only on changed easyconfigs
+# TODO: in the future we may implement this as a light first check.
+
+# Run the test suite
+./test_suite.sh "$@"
diff --git a/test_suite.sh b/test_suite.sh
index fcaaa339d2..36262a6cbf 100644
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -144,41 +144,63 @@ else
     echo_green ">> MODULEPATH set up: ${MODULEPATH}"
 fi
 
-# assume there's only one diff file that corresponds to the PR patch file
-pr_diff=$(ls [0-9]*.diff | head -1)
-
-# "split" the file by prefixing each line belonging to the same file with the
-# same number
-split_file=$(awk '/^\+\+\+/{n++}{print n, "  ", $0 }' ${pr_diff})
-
-# determine which easystack files may have changed
-changed_es_files=$(echo "${split_file}" | grep '^[0-9 ]*+++ ./eessi.*.yml$' | egrep -v 'known-issues|missing')
-
-# process all changed easystackfiles
-for es_file_num in $(echo "${changed_es_files}" | cut -f1 -d' ')
-do
-    # determine added lines that do not contain a yaml comment only
-    added_lines=$(echo "${split_file}" | grep "${es_file_num}    + " | sed -e "s/^"${es_file_num}"    + //" | grep -v "^[ ]*#")
-    # determine easyconfigs
-    easyconfigs=$(echo "${added_lines}" | cut -f3 -d' ')
-    # get easystack file name
-    easystack_file=$(echo "${changed_es_files}" | grep "^${es_file_num}" | sed -e "s/^"${es_file_num}"    ... .\///")
-    echo -e "Processing easystack file ${easystack_file}...\n\n"
-
-    # determine version of EasyBuild module to load based on EasyBuild version included in name of easystack file
-    eb_version=$(echo ${easystack_file} | sed 's/.*eb-\([0-9.]*\).*/\1/g')
-
-    # load EasyBuild module
-    module load EasyBuild/${eb_version}
-
-    echo_green "All set, let's run sanity checks for installed packages..."
-
-    for easyconfig in ${easyconfigs};
-    do
-        echo "Running sanity check for '${easyconfig}'..."
-        eb --sanity-check-only ${easyconfig}
-    done
-done
+# TODO: this should not be hardcoded. Ideally, we put some logic in place to discover the newest version
+# of the ReFrame module available in the current environment
+module load ReFrame/4.3.3
+if [[ $? -eq 0 ]]; then
+    echo_green ">> Loaded ReFrame/4.3.3"
+else
+    fatal_error "Failed to load the ReFrame module"
+fi
+
+# Check ReFrame came with the hpctestlib and we can import it
+python3 -c 'import hpctestlib.sciapps.gromacs'
+if [[ $? -eq 0 ]]; then
+    echo_green "Succesfully found and imported hpctestlib.sciapps.gromas"
+else
+    fatal_error "Failed to load hpctestlib"
+fi
+
+# Clone the EESSI test suite
+git clone https://github.com/EESSI/test-suite EESSI-test-suite
+export TESTSUITEPREFIX=$PWD/EESSI-test-suite
+export PYTHONPATH=$TESTSUITEPREFIX:$PYTHONPATH
+
+# Check that we can import from the testsuite
+python3 -c 'import eessi.testsuite'
+if [[ $? -eq 0 ]]; then
+    echo_green "Succesfully found and imported eessi.testsuite"
+else
+    fatal_error "FAILED to import from eessi.testsuite in Python"
+fi
+
+# Configure ReFrame
+export RFM_CONFIG_FILES=$TESTSUITEPREFIX/config/github_actions.py
+export RFM_CHECK_SEARCH_PATH=$TESTSUITEPREFIX/eessi/testsuite/tests
+export RFM_CHECK_SEARCH_RECURSIVE=1
+export RFM_PREFIX=$PWD/reframe_runs
+
+# Check we can run reframe
+reframe --version
+if [[ $? -eq 0 ]]; then
+    echo_green "Succesfully ran reframe --version"
+else
+    fatal_error "Failed to run ReFrame --version"
+fi
+
+# List the tests we want to run
+export REFRAME_ARGS='--tag CI --tag 1_nodes'
+reframe "${REFRAME_ARGS}" --list
+if [[ $? -eq 0 ]]; then
+    echo_green "Succesfully listed ReFrame tests with command: reframe ${REFRAME_ARGS} --list"
+else
+    fatal_error "Failed to list ReFrame tests with command: reframe ${REFRAME_ARGS} --list"
+fi
+
+# Run all tests
+reframe "${REFRAME_ARGS}" --run
 
 echo ">> Cleaning up ${TMPDIR}..."
 rm -r ${TMPDIR}
+
+exit 0

From 34fca15420fb37eeb136da55542b44b0a474a63d Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Mon, 5 Feb 2024 17:35:29 +0100
Subject: [PATCH 031/501] Make a very simple change to an easystack file so we
 are able to trigger the bot build and test procedures and see if this PR
 actually works

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 82190071ab..4c73b5887a 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -15,3 +15,4 @@ easyconfigs:
       options:
         from-pr: 19573
   - scikit-learn-1.3.1-gfbf-2023a.eb
+  - patchelf-0.18.0-GCCcore-12.3.0.eb

From 3faae9de814b96cd07896bd4042ae7b5b4b50f63 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 10:00:25 +0100
Subject: [PATCH 032/501] Make scripts executable

---
 bot/check-test.sh | 0
 run_tests.sh      | 0
 test_suite.sh     | 0
 3 files changed, 0 insertions(+), 0 deletions(-)
 mode change 100644 => 100755 bot/check-test.sh
 mode change 100644 => 100755 run_tests.sh
 mode change 100644 => 100755 test_suite.sh

diff --git a/bot/check-test.sh b/bot/check-test.sh
old mode 100644
new mode 100755
diff --git a/run_tests.sh b/run_tests.sh
old mode 100644
new mode 100755
diff --git a/test_suite.sh b/test_suite.sh
old mode 100644
new mode 100755

From 081e2b195b1dd948ae86d4f8e1634d368db3b467 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 10:30:25 +0100
Subject: [PATCH 033/501] Check for existence of SLURM output first

---
 bot/check-test.sh | 20 ++++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index 9fc783aa99..9308a87e8e 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -13,6 +13,17 @@ job_dir=${PWD}
 job_out="slurm-${SLURM_JOB_ID}.out"
 job_test_result_file="_bot_job${SLURM_JOB_ID}.test"
 
+# Check that job output file is found
+[[ ${VERBOSE} -ne 0 ]] && echo ">> searching for job output file(s) matching '"${job_out}"'"
+if  [[ -f ${job_out} ]]; then
+    SLURM=1
+    [[ ${VERBOSE} -ne 0 ]] && echo "   found slurm output file '"${job_out}"'"
+else
+    SLURM=0
+    [[ ${VERBOSE} -ne 0 ]] && echo "   Slurm output file '"${job_out}"' NOT found"
+fi
+
+
 # ReFrame prints e.g.
 #[----------] start processing checks
 #[ RUN      ] GROMACS_EESSI %benchmark_info=HECBioSim/Crambin %nb_impl=cpu %scale=2_nodes %module_name=GROMACS/2021.3-foss-2021a /d597cff4 @snellius:rome+default
@@ -39,7 +50,6 @@ if [[ ${SLURM} -eq 1 ]]; then
   [[ ${VERBOSE} -ne 0 ]] && echo "${grep_out}"
 fi
 
-
 # Here, we grep for 'ERROR:', which is printed if a fatal_error is encountered when executing the test step
 # I.e. this is an error in execution of the run_tests.sh itself, NOT in running the actual tests
 ERROR=-1
@@ -53,11 +63,13 @@ if [[ ${SLURM} -eq 1 ]]; then
 fi
 
 echo "[TEST]" > ${job_test_result_file}
-if [[ ${ERROR} -eq 1 ]]; then
-    echo "comment_description = Failure to execute test step" >> ${job_test_result_file}
+if [[ ${SLURM} -eq 0 ]]; then
+    echo "comment_description = FAILED (job output file not found)" >> ${job_test_result_file}
+elif [[ ${ERROR} -eq 1 ]]; then
+    echo "comment_description = FAILED (test step failed to execute)" >> ${job_test_result_file}
     echo "status = FAILURE" >> ${job_test_result_file}
 elif [[ ${FAILED} -eq 1 ]]; then
-    echo "comment_description = EESSI test suite produced failures" >> ${job_test_result_file}
+    echo "comment_description = FAILED (EESSI test suite produced failures)" >> ${job_test_result_file}
 else
     echo "comment_description = Test step run succesfully" >> ${job_test_result_file}
     echo "status = SUCCESS" >> ${job_test_result_file}

From 9b6fa731d6ac55e3e57538eda01c9c47d73300b1 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 10:43:20 +0100
Subject: [PATCH 034/501] Clarify return messages from the bot

---
 bot/check-test.sh |  8 ++++----
 test_suite.sh     | 20 --------------------
 2 files changed, 4 insertions(+), 24 deletions(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index 9308a87e8e..05c7589640 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -64,14 +64,14 @@ fi
 
 echo "[TEST]" > ${job_test_result_file}
 if [[ ${SLURM} -eq 0 ]]; then
-    echo "comment_description = FAILED (job output file not found)" >> ${job_test_result_file}
+    echo "comment_description = :cry: FAILED (job output file not found, cannot check test results)" >> ${job_test_result_file}
 elif [[ ${ERROR} -eq 1 ]]; then
-    echo "comment_description = FAILED (test step failed to execute)" >> ${job_test_result_file}
+    echo "comment_description = :cry: FAILED (EESSI test suite was not run, test step itself failed to execute)" >> ${job_test_result_file}
     echo "status = FAILURE" >> ${job_test_result_file}
 elif [[ ${FAILED} -eq 1 ]]; then
-    echo "comment_description = FAILED (EESSI test suite produced failures)" >> ${job_test_result_file}
+    echo "comment_description = :cry: FAILED (EESSI test suite produced failures)" >> ${job_test_result_file}
 else
-    echo "comment_description = Test step run succesfully" >> ${job_test_result_file}
+    echo "comment_description = :grin: SUCCESS" >> ${job_test_result_file}
     echo "status = SUCCESS" >> ${job_test_result_file}
 fi
 
diff --git a/test_suite.sh b/test_suite.sh
index 36262a6cbf..7995f8aa3a 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -78,26 +78,9 @@ else
     fatal_error "$EESSI_CVMFS_REPO is not available!"
 fi
 
-# make sure we're in Prefix environment by checking $SHELL
-if [[ ${SHELL} = ${EPREFIX}/bin/bash ]]; then
-    echo_green ">> It looks like we're in a Gentoo Prefix environment, good!"
-else
-    fatal_error "Not running in Gentoo Prefix environment, run '${EPREFIX}/startprefix' first!"
-fi
-
 # avoid that pyc files for EasyBuild are stored in EasyBuild installation directory
 export PYTHONPYCACHEPREFIX=$TMPDIR/pycache
 
-DETECTION_PARAMETERS=''
-GENERIC=0
-EB='eb'
-if [[ "$EASYBUILD_OPTARCH" == "GENERIC" ]]; then
-    echo_yellow ">> GENERIC build/test requested, taking appropriate measures!"
-    DETECTION_PARAMETERS="$DETECTION_PARAMETERS --generic"
-    GENERIC=1
-    EB='eb --optarch=GENERIC'
-fi
-
 echo ">> Determining software subdirectory to use for current build/test host..."
 if [ -z $EESSI_SOFTWARE_SUBDIR_OVERRIDE ]; then
   export EESSI_SOFTWARE_SUBDIR_OVERRIDE=$(python3 $TOPDIR/eessi_software_subdir.py $DETECTION_PARAMETERS)
@@ -129,9 +112,6 @@ else
     fatal_error "Failed to initialize Lmod?! (see output in ${ml_version_out}"
 fi
 
-echo ">> Configuring EasyBuild..."
-source $TOPDIR/configure_easybuild
-
 echo ">> Setting up \$MODULEPATH..."
 # make sure no modules are loaded
 module --force purge

From cb48b36e590f1d36d7a8d08df22eb538b716c70b Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 11:32:15 +0100
Subject: [PATCH 035/501] Use EESSI_SOFTWARE_PATH instead of
 EASYBUILD_INSTALLPATH to set the modulepath. It should be the same, and we no
 longer configure EasyBuild, since we don't use it when running the test suite

---
 test_suite.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test_suite.sh b/test_suite.sh
index 7995f8aa3a..1464a3a5d4 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -117,7 +117,7 @@ echo ">> Setting up \$MODULEPATH..."
 module --force purge
 # ignore current $MODULEPATH entirely
 module unuse $MODULEPATH
-module use $EASYBUILD_INSTALLPATH/modules/all
+module use ${EESSI_SOFTWARE_PATH}/modules/all
 if [[ -z ${MODULEPATH} ]]; then
     fatal_error "Failed to set up \$MODULEPATH?!"
 else

From d1a0219486fe4a4c1ad94039b4b74b41ebf7da1f Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 12:02:12 +0100
Subject: [PATCH 036/501] Do git clone in a seperate script, so that that can
 be run in the prefix layer

---
 clone_eessi_test_suite.sh | 1 +
 run_tests.sh              | 3 ++-
 test_suite.sh             | 9 +++++++--
 3 files changed, 10 insertions(+), 3 deletions(-)
 create mode 100755 clone_eessi_test_suite.sh

diff --git a/clone_eessi_test_suite.sh b/clone_eessi_test_suite.sh
new file mode 100755
index 0000000000..f7684c8cfd
--- /dev/null
+++ b/clone_eessi_test_suite.sh
@@ -0,0 +1 @@
+git clone https://github.com/EESSI/test-suite EESSI-test-suite
diff --git a/run_tests.sh b/run_tests.sh
index 69672f18f3..90185fea17 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -9,4 +9,5 @@ source ${base_dir}/init/eessi_defaults
 # TODO: in the future we may implement this as a light first check.
 
 # Run the test suite
-./test_suite.sh "$@"
+./run_in_compat_layer_env.sh clone_eessi_test_suite.sh
+./test_suite.sh
diff --git a/test_suite.sh b/test_suite.sh
index 1464a3a5d4..6177f0a253 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -141,9 +141,14 @@ else
     fatal_error "Failed to load hpctestlib"
 fi
 
-# Clone the EESSI test suite
-git clone https://github.com/EESSI/test-suite EESSI-test-suite
+# Cloning should already be done by clone_eessi_test_suite.sh, which runs in compat layer to have 'git' available
+# git clone https://github.com/EESSI/test-suite EESSI-test-suite
 export TESTSUITEPREFIX=$PWD/EESSI-test-suite
+if [ -d $TESTSUITEPREFIX ]; then
+    echo_green "Clone of the test suite $TESTSUITEPREFIX available, OK!"
+else
+    fatal_error "Clone of the test suite $TESTSUITEPREFIX is not available!"
+fi
 export PYTHONPATH=$TESTSUITEPREFIX:$PYTHONPATH
 
 # Check that we can import from the testsuite

From 86d5d3d47d076fbdf0a61c57ca83fee8a1c87123 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 12:06:09 +0100
Subject: [PATCH 037/501] Should use the one from current dir

---
 run_tests.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/run_tests.sh b/run_tests.sh
index 90185fea17..bcca1ee417 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -9,5 +9,5 @@ source ${base_dir}/init/eessi_defaults
 # TODO: in the future we may implement this as a light first check.
 
 # Run the test suite
-./run_in_compat_layer_env.sh clone_eessi_test_suite.sh
+./run_in_compat_layer_env.sh ./clone_eessi_test_suite.sh
 ./test_suite.sh

From 7861aec18c0081c8ff24e7ed46d34f9ea52c2dae Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 12:10:56 +0100
Subject: [PATCH 038/501] Remove quotes, see if that helps

---
 test_suite.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test_suite.sh b/test_suite.sh
index 6177f0a253..1ac82a5e66 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -175,7 +175,7 @@ fi
 
 # List the tests we want to run
 export REFRAME_ARGS='--tag CI --tag 1_nodes'
-reframe "${REFRAME_ARGS}" --list
+reframe ${REFRAME_ARGS} --list
 if [[ $? -eq 0 ]]; then
     echo_green "Succesfully listed ReFrame tests with command: reframe ${REFRAME_ARGS} --list"
 else

From a7b5ee13c841e940ab136ee2d014b4426a23baa7 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 12:52:41 +0100
Subject: [PATCH 039/501] Apparently, we need to remove curly braces too

---
 test_suite.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test_suite.sh b/test_suite.sh
index 1ac82a5e66..46c3493f41 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -175,7 +175,7 @@ fi
 
 # List the tests we want to run
 export REFRAME_ARGS='--tag CI --tag 1_nodes'
-reframe ${REFRAME_ARGS} --list
+reframe $REFRAME_ARGS --list
 if [[ $? -eq 0 ]]; then
     echo_green "Succesfully listed ReFrame tests with command: reframe ${REFRAME_ARGS} --list"
 else

From f50e463e9d0d0f5d91b161805279b6a8a764b990 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 13:03:31 +0100
Subject: [PATCH 040/501] Make sure this actually gets reported as failure, as
 the ReFrame runtime fails to run the test suite (it is not an indication of
 tests failing themselves).

---
 test_suite.sh | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/test_suite.sh b/test_suite.sh
index 46c3493f41..8a69bdee8d 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -175,7 +175,7 @@ fi
 
 # List the tests we want to run
 export REFRAME_ARGS='--tag CI --tag 1_nodes'
-reframe $REFRAME_ARGS --list
+reframe ${REFRAME_ARGS} --list
 if [[ $? -eq 0 ]]; then
     echo_green "Succesfully listed ReFrame tests with command: reframe ${REFRAME_ARGS} --list"
 else
@@ -184,6 +184,12 @@ fi
 
 # Run all tests
 reframe "${REFRAME_ARGS}" --run
+if [[ $? -eq 0 ]]; then
+    echo_green "ReFrame runtime ran succesfully with command: reframe ${REFRAME_ARGS} --run."
+else
+    fatal_error "ReFrame runtime failed to run with command: reframe ${REFRAME_ARGS} --run."
+fi
+
 
 echo ">> Cleaning up ${TMPDIR}..."
 rm -r ${TMPDIR}

From f67df9bc1319053901aa506668533cbb8b99716f Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 13:04:49 +0100
Subject: [PATCH 041/501] Fix the actual issue: make sure that two arguments
 are interpreted seperately by not quoting them

---
 test_suite.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test_suite.sh b/test_suite.sh
index 8a69bdee8d..633333890c 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -183,7 +183,7 @@ else
 fi
 
 # Run all tests
-reframe "${REFRAME_ARGS}" --run
+reframe ${REFRAME_ARGS} --run
 if [[ $? -eq 0 ]]; then
     echo_green "ReFrame runtime ran succesfully with command: reframe ${REFRAME_ARGS} --run."
 else

From 3394851c5347a045431d7826f579ad5f35f01edf Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 13:32:27 +0100
Subject: [PATCH 042/501] See if we can make check-test formatting more fancy

---
 bot/check-test.sh | 84 +++++++++++++++++++++++++++++++++++++++++++----
 1 file changed, 78 insertions(+), 6 deletions(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index 05c7589640..3fa7c1d694 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -64,15 +64,87 @@ fi
 
 echo "[TEST]" > ${job_test_result_file}
 if [[ ${SLURM} -eq 0 ]]; then
-    echo "comment_description = :cry: FAILED (job output file not found, cannot check test results)" >> ${job_test_result_file}
+    summary=":cry: FAILURE"
+    summary_details="(job output file not found, cannot check test results)"# >> ${job_test_result_file}
+    status="FAILURE"
 elif [[ ${ERROR} -eq 1 ]]; then
-    echo "comment_description = :cry: FAILED (EESSI test suite was not run, test step itself failed to execute)" >> ${job_test_result_file}
-    echo "status = FAILURE" >> ${job_test_result_file}
+    summary=":cry: FAILURE"
+    summary_details="(EESSI test suite was not run, test step itself failed to execute)"# >> ${job_test_result_file}
+    status="FAILURE"
+#    echo "status = FAILURE" >> ${job_test_result_file}
 elif [[ ${FAILED} -eq 1 ]]; then
-    echo "comment_description = :cry: FAILED (EESSI test suite produced failures)" >> ${job_test_result_file}
+    summary=":cry: FAILURE"
+    summary_details="(EESSI test suite produced failures)"# >> ${job_test_result_file}
+    status="FAILURE"
 else
-    echo "comment_description = :grin: SUCCESS" >> ${job_test_result_file}
-    echo "status = SUCCESS" >> ${job_test_result_file}
+    summary=":grin: SUCCESS"# >> ${job_test_result_file}
+    summary_details=""
+    status="SUCCESS"
+#    echo "status = SUCCESS" >> ${job_test_result_file}
 fi
 
+function add_detail() {
+    actual=${1}
+    expected=${2}
+    success_msg="${3}"
+    failure_msg="${4}"
+    if [[ ${actual} -eq ${expected} ]]; then
+        success "${success_msg}"
+    else
+        failure "${failure_msg}"
+    fi
+}
+
+echo "[TEST]" > ${job_result_file}
+echo -n "comment_description = " >> ${job_result_file}
+
+# Use template for writing PR comment with details
+# construct and write complete PR comment details: implements third alternative
+comment_template="<details>__SUMMARY_FMT__<dl>__DETAILS_FMT____ARTEFACTS_FMT__</dl></details>"
+comment_summary_fmt="<summary>__SUMMARY__ _(click triangle for details)_</summary>"
+comment_details_fmt="<dt>_Details_</dt><dd>__DETAILS_LIST__</dd>"
+comment_success_item_fmt=":white_check_mark: __ITEM__"
+comment_failure_item_fmt=":x: __ITEM__"
+comment_artefacts_fmt="<dt>_Artefacts_</dt><dd>__ARTEFACTS_LIST__</dd>"
+comment_artefact_details_fmt="<details>__ARTEFACT_SUMMARY____ARTEFACT_DETAILS__</details>"
+
+comment_summary="${comment_summary_fmt/__SUMMARY__/${summary}}"
+
+# first construct comment_details_list, abbreviated CoDeList
+# then use it to set comment_details
+CoDeList=""
+
+success_msg="job output file <code>${job_out}</code>"
+failure_msg="no job output file <code>${job_out}</code>"
+CoDeList=${CoDeList}$(add_detail ${SLURM} 1 "${success_msg}" "${failure_msg}")
+
+success_msg="no message matching <code>${GP_error}</code>"
+failure_msg="found message matching <code>${GP_error}</code>"
+CoDeList=${CoDeList}$(add_detail ${ERROR} 0 "${success_msg}" "${failure_msg}")
+
+success_msg="no message matching <code>${GP_failed}</code>"
+failure_msg="found message matching <code>${GP_failed}</code>"
+CoDeList=${CoDeList}$(add_detail ${FAILED} 0 "${success_msg}" "${failure_msg}")
+
+# Should not be needed for testing, I think? Maybe for loading ReFrame module...
+# success_msg="no message matching <code>${GP_req_missing}</code>"
+# failure_msg="found message matching <code>${GP_req_missing}</code>"
+# CoDeList=${CoDeList}$(add_detail ${MISSING} 0 "${success_msg}" "${failure_msg}")
+# 
+# success_msg="found message(s) matching <code>${GP_no_missing}</code>"
+# failure_msg="no message matching <code>${GP_no_missing}</code>"
+# CoDeList=${CoDeList}$(add_detail ${NO_MISSING} 1 "${success_msg}" "${failure_msg}")
+# 
+# success_msg="found message matching <code>${GP_tgz_created}</code>"
+# failure_msg="no message matching <code>${GP_tgz_created}</code>"
+# CoDeList=${CoDeList}$(add_detail ${TGZ} 1 "${success_msg}" "${failure_msg}")
+
+comment_details="${comment_details_fmt/__DETAILS_LIST__/${CoDeList}}"
+
+comment_description=${comment_template/__SUMMARY_FMT__/${comment_summary}}
+comment_description=${comment_description/__DETAILS_FMT__/${comment_details}}
+
+# Actually writing the comment description to the result file
+echo "${comment_description}" >> ${job_result_file}
+
 exit 0

From 8e5682a47a589a2e251852ed674b71f16980ffc7 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 14:51:46 +0100
Subject: [PATCH 043/501] Replace the env var for the result file

---
 bot/check-test.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index 3fa7c1d694..89d3d6a3c6 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -95,8 +95,8 @@ function add_detail() {
     fi
 }
 
-echo "[TEST]" > ${job_result_file}
-echo -n "comment_description = " >> ${job_result_file}
+echo "[TEST]" > ${job_test_result_file}
+echo -n "comment_description = " >> ${job_test_result_file}
 
 # Use template for writing PR comment with details
 # construct and write complete PR comment details: implements third alternative
@@ -145,6 +145,6 @@ comment_description=${comment_template/__SUMMARY_FMT__/${comment_summary}}
 comment_description=${comment_description/__DETAILS_FMT__/${comment_details}}
 
 # Actually writing the comment description to the result file
-echo "${comment_description}" >> ${job_result_file}
+echo "${comment_description}" >> ${job_test_result_file}
 
 exit 0

From 6cf0cf959844081b004595bd3a6c21329ccf256d Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 14:53:21 +0100
Subject: [PATCH 044/501] Add missing functions

---
 bot/check-test.sh | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index 89d3d6a3c6..87c79b3b30 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -83,6 +83,24 @@ else
 #    echo "status = SUCCESS" >> ${job_test_result_file}
 fi
 
+function print_br_item() {
+    format="${1}"
+    item="${2}"
+    echo -n "${format//__ITEM__/${item}}<br/>"
+}
+
+function success() {
+    format="${comment_success_item_fmt}"
+    item="$1"
+    print_br_item "${format}" "${item}"
+}
+
+function failure() {
+    format="${comment_failure_item_fmt}"
+    item="$1"
+    print_br_item "${format}" "${item}"
+}
+
 function add_detail() {
     actual=${1}
     expected=${2}

From 7fe24e13cdef3f703b51930423a2296e3dc07d59 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 15:14:50 +0100
Subject: [PATCH 045/501] Remove artefacts from reporting

---
 bot/check-test.sh | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index 87c79b3b30..da06cd630b 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -118,13 +118,11 @@ echo -n "comment_description = " >> ${job_test_result_file}
 
 # Use template for writing PR comment with details
 # construct and write complete PR comment details: implements third alternative
-comment_template="<details>__SUMMARY_FMT__<dl>__DETAILS_FMT____ARTEFACTS_FMT__</dl></details>"
+comment_template="<details>__SUMMARY_FMT__<dl>__DETAILS_FMT__</dl></details>"
 comment_summary_fmt="<summary>__SUMMARY__ _(click triangle for details)_</summary>"
 comment_details_fmt="<dt>_Details_</dt><dd>__DETAILS_LIST__</dd>"
 comment_success_item_fmt=":white_check_mark: __ITEM__"
 comment_failure_item_fmt=":x: __ITEM__"
-comment_artefacts_fmt="<dt>_Artefacts_</dt><dd>__ARTEFACTS_LIST__</dd>"
-comment_artefact_details_fmt="<details>__ARTEFACT_SUMMARY____ARTEFACT_DETAILS__</details>"
 
 comment_summary="${comment_summary_fmt/__SUMMARY__/${summary}}"
 

From afc309a168048e54b625ec857a5d09a14ca1d585 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 15:25:33 +0100
Subject: [PATCH 046/501] Add a reason for the failure

---
 bot/check-test.sh | 42 ++++++++++++++++++++++--------------------
 1 file changed, 22 insertions(+), 20 deletions(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index da06cd630b..38e86efccd 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -65,24 +65,37 @@ fi
 echo "[TEST]" > ${job_test_result_file}
 if [[ ${SLURM} -eq 0 ]]; then
     summary=":cry: FAILURE"
-    summary_details="(job output file not found, cannot check test results)"# >> ${job_test_result_file}
+    summary_details="Reason: job output file not found, cannot check test results."
     status="FAILURE"
 elif [[ ${ERROR} -eq 1 ]]; then
     summary=":cry: FAILURE"
-    summary_details="(EESSI test suite was not run, test step itself failed to execute)"# >> ${job_test_result_file}
+    summary_details="Reason: EESSI test suite was not run, test step itself failed to execute."
     status="FAILURE"
-#    echo "status = FAILURE" >> ${job_test_result_file}
 elif [[ ${FAILED} -eq 1 ]]; then
     summary=":cry: FAILURE"
-    summary_details="(EESSI test suite produced failures)"# >> ${job_test_result_file}
+    summary_details="Reason: EESSI test suite produced failures."
     status="FAILURE"
 else
-    summary=":grin: SUCCESS"# >> ${job_test_result_file}
+    summary=":grin: SUCCESS"
     summary_details=""
     status="SUCCESS"
-#    echo "status = SUCCESS" >> ${job_test_result_file}
 fi
 
+
+echo "[TEST]" > ${job_test_result_file}
+echo -n "comment_description = " >> ${job_test_result_file}
+
+# Use template for writing PR comment with details
+# construct and write complete PR comment details: implements third alternative
+comment_template="<details>__SUMMARY_FMT__<dl>__DETAILS_FMT__</dl></details>"
+comment_summary_fmt="<summary>__SUMMARY__ _(click triangle for details)_</summary>"
+comment_details_fmt="<dt>_Details_</dt><dd>__DETAILS_LIST__</dd>"
+comment_success_item_fmt=":white_check_mark: __ITEM__"
+comment_failure_item_fmt=":x: __ITEM__"
+
+comment_summary="${comment_summary_fmt/__SUMMARY__/${summary}}"
+
+# Declare functions
 function print_br_item() {
     format="${1}"
     item="${2}"
@@ -113,22 +126,11 @@ function add_detail() {
     fi
 }
 
-echo "[TEST]" > ${job_test_result_file}
-echo -n "comment_description = " >> ${job_test_result_file}
-
-# Use template for writing PR comment with details
-# construct and write complete PR comment details: implements third alternative
-comment_template="<details>__SUMMARY_FMT__<dl>__DETAILS_FMT__</dl></details>"
-comment_summary_fmt="<summary>__SUMMARY__ _(click triangle for details)_</summary>"
-comment_details_fmt="<dt>_Details_</dt><dd>__DETAILS_LIST__</dd>"
-comment_success_item_fmt=":white_check_mark: __ITEM__"
-comment_failure_item_fmt=":x: __ITEM__"
-
-comment_summary="${comment_summary_fmt/__SUMMARY__/${summary}}"
-
 # first construct comment_details_list, abbreviated CoDeList
 # then use it to set comment_details
-CoDeList=""
+
+# Initialize with summary_details, which elaborates on the reason for failure
+CoDeList=$(print_br_item "__ITEM__" "${summary_details}"
 
 success_msg="job output file <code>${job_out}</code>"
 failure_msg="no job output file <code>${job_out}</code>"

From b84e48755dfb582a5a4bae3480e8865df179331e Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 15:32:07 +0100
Subject: [PATCH 047/501] Fixed missing bracket

---
 bot/check-test.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index 38e86efccd..e340907bb3 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -130,7 +130,7 @@ function add_detail() {
 # then use it to set comment_details
 
 # Initialize with summary_details, which elaborates on the reason for failure
-CoDeList=$(print_br_item "__ITEM__" "${summary_details}"
+CoDeList=$(print_br_item "__ITEM__" "${summary_details}")
 
 success_msg="job output file <code>${job_out}</code>"
 failure_msg="no job output file <code>${job_out}</code>"

From ef7bc0142f0ff518e82121371403c4da9bc0444d Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 15:48:44 +0100
Subject: [PATCH 048/501] Add reporting of the ReFrame result

---
 bot/check-test.sh | 22 ++++++++++++++++++----
 1 file changed, 18 insertions(+), 4 deletions(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index e340907bb3..78c153e5dc 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -43,11 +43,11 @@ fi
 FAILED=-1
 if [[ ${SLURM} -eq 1 ]]; then
   GP_failed='\[\s*FAILED\s*\]'
-  grep_out=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_failed}")
+  grep_reframe_result=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_failed}")
   [[ $? -eq 0 ]] && FAILED=1 || FAILED=0
   # have to be careful to not add searched for pattern into slurm out file
   [[ ${VERBOSE} -ne 0 ]] && echo ">> searching for '"${GP_failed}"'"
-  [[ ${VERBOSE} -ne 0 ]] && echo "${grep_out}"
+  [[ ${VERBOSE} -ne 0 ]] && echo "${grep_reframe_result}"
 fi
 
 # Here, we grep for 'ERROR:', which is printed if a fatal_error is encountered when executing the test step
@@ -62,6 +62,15 @@ if [[ ${SLURM} -eq 1 ]]; then
   [[ ${VERBOSE} -ne 0 ]] && echo "${grep_out}"
 fi
 
+# Grep for the success pattern, so we can report the amount of tests run
+if [[ ${SLURM} -eq 1 ]]; then
+  GP_success='\[\s*PASSED\s*\]'
+  grep_reframe_result=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_success}")
+  # have to be careful to not add searched for pattern into slurm out file
+  [[ ${VERBOSE} -ne 0 ]] && echo ">> searching for '"${GP_success}"'"
+  [[ ${VERBOSE} -ne 0 ]] && echo "${grep_reframe_result}"
+fi
+
 echo "[TEST]" > ${job_test_result_file}
 if [[ ${SLURM} -eq 0 ]]; then
     summary=":cry: FAILURE"
@@ -132,6 +141,11 @@ function add_detail() {
 # Initialize with summary_details, which elaborates on the reason for failure
 CoDeList=$(print_br_item "__ITEM__" "${summary_details}")
 
+# Add final ReFrame line as line
+if [[ ! -z ${grep_reframe_result} ]]; then
+    CoDeList=${CoDeList}$(print_br_item "__ITEM__" "${grep_reframe_result}"
+fi
+
 success_msg="job output file <code>${job_out}</code>"
 failure_msg="no job output file <code>${job_out}</code>"
 CoDeList=${CoDeList}$(add_detail ${SLURM} 1 "${success_msg}" "${failure_msg}")
@@ -140,8 +154,8 @@ success_msg="no message matching <code>${GP_error}</code>"
 failure_msg="found message matching <code>${GP_error}</code>"
 CoDeList=${CoDeList}$(add_detail ${ERROR} 0 "${success_msg}" "${failure_msg}")
 
-success_msg="no message matching <code>${GP_failed}</code>"
-failure_msg="found message matching <code>${GP_failed}</code>"
+success_msg="no message matching <code>""${GP_failed}""</code>"
+failure_msg="found message matching <code>""${GP_failed}""</code>"
 CoDeList=${CoDeList}$(add_detail ${FAILED} 0 "${success_msg}" "${failure_msg}")
 
 # Should not be needed for testing, I think? Maybe for loading ReFrame module...

From 867681a2ed7413b8ecdbf646d05a20d7d2553adc Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 16:01:40 +0100
Subject: [PATCH 049/501] Add missing bracket. Again

---
 bot/check-test.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index 78c153e5dc..7ff5f8a3ea 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -143,7 +143,7 @@ CoDeList=$(print_br_item "__ITEM__" "${summary_details}")
 
 # Add final ReFrame line as line
 if [[ ! -z ${grep_reframe_result} ]]; then
-    CoDeList=${CoDeList}$(print_br_item "__ITEM__" "${grep_reframe_result}"
+    CoDeList=${CoDeList}$(print_br_item "__ITEM__" "${grep_reframe_result}")
 fi
 
 success_msg="job output file <code>${job_out}</code>"

From 47e30cac825362f85138e1d6cb3fe8ba02f13c6e Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 16:17:25 +0100
Subject: [PATCH 050/501] Add some echo for debugging

---
 bot/check-test.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index 7ff5f8a3ea..1a2d8b5d5d 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -171,6 +171,9 @@ CoDeList=${CoDeList}$(add_detail ${FAILED} 0 "${success_msg}" "${failure_msg}")
 # failure_msg="no message matching <code>${GP_tgz_created}</code>"
 # CoDeList=${CoDeList}$(add_detail ${TGZ} 1 "${success_msg}" "${failure_msg}")
 
+echo "Finale CoDeList is:"
+echo ${CoDeList}
+
 comment_details="${comment_details_fmt/__DETAILS_LIST__/${CoDeList}}"
 
 comment_description=${comment_template/__SUMMARY_FMT__/${comment_summary}}

From 1bdadf884e8f18ec911f8961a894125a6c5cccce Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 16:24:34 +0100
Subject: [PATCH 051/501] more debugging output

---
 bot/check-test.sh | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index 1a2d8b5d5d..841b8ed01b 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -137,14 +137,20 @@ function add_detail() {
 
 # first construct comment_details_list, abbreviated CoDeList
 # then use it to set comment_details
+CoDeList=""
 
 # Initialize with summary_details, which elaborates on the reason for failure
-CoDeList=$(print_br_item "__ITEM__" "${summary_details}")
+if [[ ! -z ${summary_details} ]]; then
+    CoDeList=${CoDeList}$(print_br_item "__ITEM__" "${summary_details}")
+fi
 
 # Add final ReFrame line as line
 if [[ ! -z ${grep_reframe_result} ]]; then
     CoDeList=${CoDeList}$(print_br_item "__ITEM__" "${grep_reframe_result}")
 fi
+echo "CoDeList up here is"
+echo ${CoDeList}
+
 
 success_msg="job output file <code>${job_out}</code>"
 failure_msg="no job output file <code>${job_out}</code>"

From 5152f5e47380c462c234566f5fc3c29922694ef1 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 16:54:02 +0100
Subject: [PATCH 052/501] Lets try some nicer formatting with headers etc. See
 if this actually prints something.

---
 bot/check-test.sh | 62 ++++++++++++++++++++++++++++++++---------------
 1 file changed, 42 insertions(+), 20 deletions(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index 841b8ed01b..8f8eb66f5e 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -74,19 +74,19 @@ fi
 echo "[TEST]" > ${job_test_result_file}
 if [[ ${SLURM} -eq 0 ]]; then
     summary=":cry: FAILURE"
-    summary_details="Reason: job output file not found, cannot check test results."
+    reason="Reason: job output file not found, cannot check test results."
     status="FAILURE"
 elif [[ ${ERROR} -eq 1 ]]; then
     summary=":cry: FAILURE"
-    summary_details="Reason: EESSI test suite was not run, test step itself failed to execute."
+    reason="Reason: EESSI test suite was not run, test step itself failed to execute."
     status="FAILURE"
 elif [[ ${FAILED} -eq 1 ]]; then
     summary=":cry: FAILURE"
-    summary_details="Reason: EESSI test suite produced failures."
+    reason="Reason: EESSI test suite produced failures."
     status="FAILURE"
 else
     summary=":grin: SUCCESS"
-    summary_details=""
+    reason=""
     status="SUCCESS"
 fi
 
@@ -96,13 +96,36 @@ echo -n "comment_description = " >> ${job_test_result_file}
 
 # Use template for writing PR comment with details
 # construct and write complete PR comment details: implements third alternative
-comment_template="<details>__SUMMARY_FMT__<dl>__DETAILS_FMT__</dl></details>"
-comment_summary_fmt="<summary>__SUMMARY__ _(click triangle for details)_</summary>"
-comment_details_fmt="<dt>_Details_</dt><dd>__DETAILS_LIST__</dd>"
+comment_template="<details>__SUMMARY_FMT__<dl>__REASON_FMT____REFRAME_FMT____DETAILS_FMT__</dl></details>"
 comment_success_item_fmt=":white_check_mark: __ITEM__"
 comment_failure_item_fmt=":x: __ITEM__"
 
+# Initialize comment_description
+comment_description=${comment_template}
+
+# Now, start replacing template items one by one
+comment_summary_fmt="<summary>__SUMMARY__ _(click triangle for details)_</summary>"
 comment_summary="${comment_summary_fmt/__SUMMARY__/${summary}}"
+comment_description=${comment_description/__SUMMARY_FMT__/${comment_summary}}
+
+
+# Omit this if there is no reason (e.g. because it was succesful)
+if [[ -z ${reason} ]]; then
+    comment_reason_fmt="<dt>_Reason_</dt><dd>__REASONS__</dd>"
+    reason_details="${comment_reason_fmt/__REASONS__/${reason}}"
+    comment_description=${comment_description/__REASON_FMT__/${reason_details}}
+else
+    comment_description=${comment_description/__REASON_FMT__/""}
+fi
+
+# Omit this if there is no reframe summary (i.e. the workflow didn't run succesfully)
+if [[ -z ${grep_reframe_result} ]]; then
+    comment_reframe_fmt="<dt>_ReFrame Summary_</dt><dd>__REFRAME_SUMMARY__</dd>"
+    reframe_summary=${comment_reframe_ftm/__REFRAME_SUMMARY__/${grep_reframe_result}}
+    comment_description=${comment_description/__REFRAME_FMT__/${reframe_summary}}
+else
+    comment_description=${comment_description/__REFRAME_FMT__/""}
+fi
 
 # Declare functions
 function print_br_item() {
@@ -139,17 +162,17 @@ function add_detail() {
 # then use it to set comment_details
 CoDeList=""
 
-# Initialize with summary_details, which elaborates on the reason for failure
-if [[ ! -z ${summary_details} ]]; then
-    CoDeList=${CoDeList}$(print_br_item "__ITEM__" "${summary_details}")
-fi
-
-# Add final ReFrame line as line
-if [[ ! -z ${grep_reframe_result} ]]; then
-    CoDeList=${CoDeList}$(print_br_item "__ITEM__" "${grep_reframe_result}")
-fi
-echo "CoDeList up here is"
-echo ${CoDeList}
+# # Initialize with summary_details, which elaborates on the reason for failure
+# if [[ ! -z ${summary_details} ]]; then
+#     CoDeList=${CoDeList}$(print_br_item "__ITEM__" "${summary_details}")
+# fi
+# 
+# # Add final ReFrame line as line
+# if [[ ! -z ${grep_reframe_result} ]]; then
+#     CoDeList=${CoDeList}$(print_br_item "__ITEM__" "${grep_reframe_result}")
+# fi
+# echo "CoDeList up here is"
+# echo ${CoDeList}
 
 
 success_msg="job output file <code>${job_out}</code>"
@@ -180,9 +203,8 @@ CoDeList=${CoDeList}$(add_detail ${FAILED} 0 "${success_msg}" "${failure_msg}")
 echo "Finale CoDeList is:"
 echo ${CoDeList}
 
+comment_details_fmt="<dt>_Details_</dt><dd>__DETAILS_LIST__</dd>"
 comment_details="${comment_details_fmt/__DETAILS_LIST__/${CoDeList}}"
-
-comment_description=${comment_template/__SUMMARY_FMT__/${comment_summary}}
 comment_description=${comment_description/__DETAILS_FMT__/${comment_details}}
 
 # Actually writing the comment description to the result file

From ea38c66114af601071e1edc626cf9952219a7a18 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 17:07:28 +0100
Subject: [PATCH 053/501] Inverse check, it was incorrect

---
 bot/check-test.sh | 21 ++++-----------------
 1 file changed, 4 insertions(+), 17 deletions(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index 8f8eb66f5e..01769bbac3 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -109,8 +109,8 @@ comment_summary="${comment_summary_fmt/__SUMMARY__/${summary}}"
 comment_description=${comment_description/__SUMMARY_FMT__/${comment_summary}}
 
 
-# Omit this if there is no reason (e.g. because it was succesful)
-if [[ -z ${reason} ]]; then
+# Only add if there is a reason (e.g. no reason for successful runs)
+if [[ ! -z ${reason} ]]; then
     comment_reason_fmt="<dt>_Reason_</dt><dd>__REASONS__</dd>"
     reason_details="${comment_reason_fmt/__REASONS__/${reason}}"
     comment_description=${comment_description/__REASON_FMT__/${reason_details}}
@@ -118,8 +118,8 @@ else
     comment_description=${comment_description/__REASON_FMT__/""}
 fi
 
-# Omit this if there is no reframe summary (i.e. the workflow didn't run succesfully)
-if [[ -z ${grep_reframe_result} ]]; then
+# Only add if there is a reframe summary (e.g. no reframe summary if reframe wasn't launched succesfully)
+if [[ ! -z ${grep_reframe_result} ]]; then
     comment_reframe_fmt="<dt>_ReFrame Summary_</dt><dd>__REFRAME_SUMMARY__</dd>"
     reframe_summary=${comment_reframe_ftm/__REFRAME_SUMMARY__/${grep_reframe_result}}
     comment_description=${comment_description/__REFRAME_FMT__/${reframe_summary}}
@@ -162,19 +162,6 @@ function add_detail() {
 # then use it to set comment_details
 CoDeList=""
 
-# # Initialize with summary_details, which elaborates on the reason for failure
-# if [[ ! -z ${summary_details} ]]; then
-#     CoDeList=${CoDeList}$(print_br_item "__ITEM__" "${summary_details}")
-# fi
-# 
-# # Add final ReFrame line as line
-# if [[ ! -z ${grep_reframe_result} ]]; then
-#     CoDeList=${CoDeList}$(print_br_item "__ITEM__" "${grep_reframe_result}")
-# fi
-# echo "CoDeList up here is"
-# echo ${CoDeList}
-
-
 success_msg="job output file <code>${job_out}</code>"
 failure_msg="no job output file <code>${job_out}</code>"
 CoDeList=${CoDeList}$(add_detail ${SLURM} 1 "${success_msg}" "${failure_msg}")

From 8edb6fffb401f0e74e0b975b5585d3f9257f88f8 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 17:11:41 +0100
Subject: [PATCH 054/501] Remove debugging output

---
 bot/check-test.sh | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index 01769bbac3..7a663f35d1 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -187,9 +187,6 @@ CoDeList=${CoDeList}$(add_detail ${FAILED} 0 "${success_msg}" "${failure_msg}")
 # failure_msg="no message matching <code>${GP_tgz_created}</code>"
 # CoDeList=${CoDeList}$(add_detail ${TGZ} 1 "${success_msg}" "${failure_msg}")
 
-echo "Finale CoDeList is:"
-echo ${CoDeList}
-
 comment_details_fmt="<dt>_Details_</dt><dd>__DETAILS_LIST__</dd>"
 comment_details="${comment_details_fmt/__DETAILS_LIST__/${CoDeList}}"
 comment_description=${comment_description/__DETAILS_FMT__/${comment_details}}

From 26bd2cb04af381af580805b094f69c096ea40410 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 17:33:12 +0100
Subject: [PATCH 055/501] Correct the regex pattern to account for the fact
 that the slurm output file contains special characters in that pattern that
 are NOT whitespace

---
 bot/check-test.sh | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index 7a663f35d1..aebd56d333 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -42,7 +42,7 @@ fi
 # Specifically, we grep for FAILED, since this is also what we print if a step in the test script itself fails
 FAILED=-1
 if [[ ${SLURM} -eq 1 ]]; then
-  GP_failed='\[\s*FAILED\s*\]'
+  GP_failed='\[.*FAILED.*\].*Ran .* test case'
   grep_reframe_result=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_failed}")
   [[ $? -eq 0 ]] && FAILED=1 || FAILED=0
   # have to be careful to not add searched for pattern into slurm out file
@@ -64,7 +64,7 @@ fi
 
 # Grep for the success pattern, so we can report the amount of tests run
 if [[ ${SLURM} -eq 1 ]]; then
-  GP_success='\[\s*PASSED\s*\]'
+  GP_success='\[.*PASSED.*\].*Ran .* test case'
   grep_reframe_result=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_success}")
   # have to be careful to not add searched for pattern into slurm out file
   [[ ${VERBOSE} -ne 0 ]] && echo ">> searching for '"${GP_success}"'"
@@ -119,6 +119,8 @@ else
 fi
 
 # Only add if there is a reframe summary (e.g. no reframe summary if reframe wasn't launched succesfully)
+echo "ReFrame result:"
+echo "${grep_reframe_result}"
 if [[ ! -z ${grep_reframe_result} ]]; then
     comment_reframe_fmt="<dt>_ReFrame Summary_</dt><dd>__REFRAME_SUMMARY__</dd>"
     reframe_summary=${comment_reframe_ftm/__REFRAME_SUMMARY__/${grep_reframe_result}}

From 416b72d3cb18d6150e0ef8760cd5b66867e29496 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 17:45:30 +0100
Subject: [PATCH 056/501] Corrected typo

---
 bot/check-test.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index aebd56d333..702add848d 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -123,7 +123,7 @@ echo "ReFrame result:"
 echo "${grep_reframe_result}"
 if [[ ! -z ${grep_reframe_result} ]]; then
     comment_reframe_fmt="<dt>_ReFrame Summary_</dt><dd>__REFRAME_SUMMARY__</dd>"
-    reframe_summary=${comment_reframe_ftm/__REFRAME_SUMMARY__/${grep_reframe_result}}
+    reframe_summary=${comment_reframe_fmt/__REFRAME_SUMMARY__/${grep_reframe_result}}
     comment_description=${comment_description/__REFRAME_FMT__/${reframe_summary}}
 else
     comment_description=${comment_description/__REFRAME_FMT__/""}

From 19900937361e16259dce714c9e4acda4b09e0a7b Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 17:51:27 +0100
Subject: [PATCH 057/501] Trigger failure in the workflow on purpose, to show
 what that looks like

---
 test_suite.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test_suite.sh b/test_suite.sh
index 633333890c..4439821d56 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -166,7 +166,7 @@ export RFM_CHECK_SEARCH_RECURSIVE=1
 export RFM_PREFIX=$PWD/reframe_runs
 
 # Check we can run reframe
-reframe --version
+reframe --version BLABLABLA
 if [[ $? -eq 0 ]]; then
     echo_green "Succesfully ran reframe --version"
 else
@@ -174,7 +174,7 @@ else
 fi
 
 # List the tests we want to run
-export REFRAME_ARGS='--tag CI --tag 1_nodes'
+export REFRAME_ARGS='--tag CI --tag 1_node'
 reframe ${REFRAME_ARGS} --list
 if [[ $? -eq 0 ]]; then
     echo_green "Succesfully listed ReFrame tests with command: reframe ${REFRAME_ARGS} --list"

From 4b9885612fa13d2d1f45522ca1aa04ec333863b8 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 6 Feb 2024 18:11:30 +0100
Subject: [PATCH 058/501] Change order of checking error codes. If the ReFrame
 tests ran and we find that pattern, that should take priority. Other errors
 might have come from errors in the build phase...

---
 bot/check-test.sh | 24 +++++++++++++++++-------
 1 file changed, 17 insertions(+), 7 deletions(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index 702add848d..7b7ada98e7 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -62,10 +62,12 @@ if [[ ${SLURM} -eq 1 ]]; then
   [[ ${VERBOSE} -ne 0 ]] && echo "${grep_out}"
 fi
 
+SUCCESS=-1
 # Grep for the success pattern, so we can report the amount of tests run
 if [[ ${SLURM} -eq 1 ]]; then
   GP_success='\[.*PASSED.*\].*Ran .* test case'
   grep_reframe_result=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_success}")
+  [[ $? -eq 0 ]] && SUCCESS=1 || SUCCESS=0
   # have to be careful to not add searched for pattern into slurm out file
   [[ ${VERBOSE} -ne 0 ]] && echo ">> searching for '"${GP_success}"'"
   [[ ${VERBOSE} -ne 0 ]] && echo "${grep_reframe_result}"
@@ -74,19 +76,27 @@ fi
 echo "[TEST]" > ${job_test_result_file}
 if [[ ${SLURM} -eq 0 ]]; then
     summary=":cry: FAILURE"
-    reason="Reason: job output file not found, cannot check test results."
+    reason="Job output file not found, cannot check test results."
     status="FAILURE"
-elif [[ ${ERROR} -eq 1 ]]; then
+# Should come before general errors: if SUCCESS==1, it indicates the test suite ran succesfully
+# regardless of other things that might have gone wrong
+elif [[ ${SUCCESS} -eq 1 ]]; then
+    summary=":grin: SUCCESS"
+    reason=""
+    status="SUCCESS"
+# Should come before general errors: if FAILED==1, it indicates the test suite ran
+# otherwise the pattern wouldn't have been there
+elif [[ ${FAILED} -eq 1 ]]; then
     summary=":cry: FAILURE"
-    reason="Reason: EESSI test suite was not run, test step itself failed to execute."
+    reason="EESSI test suite produced failures."
     status="FAILURE"
-elif [[ ${FAILED} -eq 1 ]]; then
+elif [[ ${ERROR} -eq 1 ]]; then
     summary=":cry: FAILURE"
-    reason="Reason: EESSI test suite produced failures."
+    reason="EESSI test suite was not run, test step itself failed to execute."
     status="FAILURE"
 else
-    summary=":grin: SUCCESS"
-    reason=""
+    summary=":grin: FAILURE"
+    reason="Failed for unknown reason"
     status="SUCCESS"
 fi
 

From 0f261420106862049091494d6a640a6c46de5dd8 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Wed, 7 Feb 2024 12:11:25 +0100
Subject: [PATCH 059/501] Make sure we don't overwrite the grepped result from
 failures

---
 bot/check-test.sh | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index 7b7ada98e7..8af45d26a6 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -43,11 +43,11 @@ fi
 FAILED=-1
 if [[ ${SLURM} -eq 1 ]]; then
   GP_failed='\[.*FAILED.*\].*Ran .* test case'
-  grep_reframe_result=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_failed}")
+  grep_reframe_failed=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_failed}")
   [[ $? -eq 0 ]] && FAILED=1 || FAILED=0
   # have to be careful to not add searched for pattern into slurm out file
   [[ ${VERBOSE} -ne 0 ]] && echo ">> searching for '"${GP_failed}"'"
-  [[ ${VERBOSE} -ne 0 ]] && echo "${grep_reframe_result}"
+  [[ ${VERBOSE} -ne 0 ]] && echo "${grep_reframe_failed}"
 fi
 
 # Here, we grep for 'ERROR:', which is printed if a fatal_error is encountered when executing the test step
@@ -66,11 +66,17 @@ SUCCESS=-1
 # Grep for the success pattern, so we can report the amount of tests run
 if [[ ${SLURM} -eq 1 ]]; then
   GP_success='\[.*PASSED.*\].*Ran .* test case'
-  grep_reframe_result=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_success}")
+  grep_reframe_success=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_success}")
   [[ $? -eq 0 ]] && SUCCESS=1 || SUCCESS=0
   # have to be careful to not add searched for pattern into slurm out file
   [[ ${VERBOSE} -ne 0 ]] && echo ">> searching for '"${GP_success}"'"
-  [[ ${VERBOSE} -ne 0 ]] && echo "${grep_reframe_result}"
+  [[ ${VERBOSE} -ne 0 ]] && echo "${grep_reframe_success}"
+fi
+
+if [[ ! -z ${grep_reframe_failed} ]]; then
+    grep_reframe_results=${grep_reframe_failed}
+else
+    grep_reframe_results=${grep_reframe_success}
 fi
 
 echo "[TEST]" > ${job_test_result_file}

From 94e0bb5e3b886192508d95485b221b3ec7a6ff5e Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Wed, 7 Feb 2024 13:09:31 +0100
Subject: [PATCH 060/501] Fix plural/singular typo

---
 bot/check-test.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index 8af45d26a6..39901f0691 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -74,9 +74,9 @@ if [[ ${SLURM} -eq 1 ]]; then
 fi
 
 if [[ ! -z ${grep_reframe_failed} ]]; then
-    grep_reframe_results=${grep_reframe_failed}
+    grep_reframe_result=${grep_reframe_failed}
 else
-    grep_reframe_results=${grep_reframe_success}
+    grep_reframe_result=${grep_reframe_success}
 fi
 
 echo "[TEST]" > ${job_test_result_file}

From 9e7ac1c7c4f2f64250ef504810d057e0cb3e5225 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Wed, 7 Feb 2024 13:25:45 +0100
Subject: [PATCH 061/501] Be a bit more expressive about what we are doing

---
 test_suite.sh | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/test_suite.sh b/test_suite.sh
index 4439821d56..1610d87738 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -165,8 +165,11 @@ export RFM_CHECK_SEARCH_PATH=$TESTSUITEPREFIX/eessi/testsuite/tests
 export RFM_CHECK_SEARCH_RECURSIVE=1
 export RFM_PREFIX=$PWD/reframe_runs
 
+echo "Configured reframe with the following environment variables:"
+env | grep "RFM_"
+
 # Check we can run reframe
-reframe --version BLABLABLA
+reframe --version
 if [[ $? -eq 0 ]]; then
     echo_green "Succesfully ran reframe --version"
 else
@@ -175,6 +178,7 @@ fi
 
 # List the tests we want to run
 export REFRAME_ARGS='--tag CI --tag 1_node'
+echo "Listing tests: reframe ${REFRAME_ARGS} --list"
 reframe ${REFRAME_ARGS} --list
 if [[ $? -eq 0 ]]; then
     echo_green "Succesfully listed ReFrame tests with command: reframe ${REFRAME_ARGS} --list"
@@ -183,6 +187,7 @@ else
 fi
 
 # Run all tests
+echo "Running tests: reframe ${REFRAME_ARGS} --run"
 reframe ${REFRAME_ARGS} --run
 if [[ $? -eq 0 ]]; then
     echo_green "ReFrame runtime ran succesfully with command: reframe ${REFRAME_ARGS} --run."
@@ -190,7 +195,6 @@ else
     fatal_error "ReFrame runtime failed to run with command: reframe ${REFRAME_ARGS} --run."
 fi
 
-
 echo ">> Cleaning up ${TMPDIR}..."
 rm -r ${TMPDIR}
 

From 3a52bde23e5de6cfe4d5da170060c07d8dfc0009 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Wed, 7 Feb 2024 14:28:08 +0100
Subject: [PATCH 062/501] Change to dedicated config file for testing by the
 bot in the build job

---
 test_suite.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test_suite.sh b/test_suite.sh
index 1610d87738..d6699878f9 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -160,7 +160,7 @@ else
 fi
 
 # Configure ReFrame
-export RFM_CONFIG_FILES=$TESTSUITEPREFIX/config/github_actions.py
+export RFM_CONFIG_FILES=$TESTSUITEPREFIX/config/software_layer_bot.py
 export RFM_CHECK_SEARCH_PATH=$TESTSUITEPREFIX/eessi/testsuite/tests
 export RFM_CHECK_SEARCH_RECURSIVE=1
 export RFM_PREFIX=$PWD/reframe_runs

From 159e384bdef117265e09a0a420cce3fa6d8842c8 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Wed, 7 Feb 2024 14:47:54 +0100
Subject: [PATCH 063/501] Make it verbose, see if we can see why autodetect
 fails

---
 test_suite.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test_suite.sh b/test_suite.sh
index d6699878f9..a8e1b2d97a 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -177,7 +177,7 @@ else
 fi
 
 # List the tests we want to run
-export REFRAME_ARGS='--tag CI --tag 1_node'
+export REFRAME_ARGS='--tag CI --tag 1_node -vvv'
 echo "Listing tests: reframe ${REFRAME_ARGS} --list"
 reframe ${REFRAME_ARGS} --list
 if [[ $? -eq 0 ]]; then

From b92044e5f913ce0a6c7082c0ebfb4e238d47f95d Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Wed, 7 Feb 2024 16:23:53 +0100
Subject: [PATCH 064/501] Add ReFrame config template. Not that four template
 variables need to be replaced for this to be a valid ReFrame config file

---
 reframe_config_bot.py | 58 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 reframe_config_bot.py

diff --git a/reframe_config_bot.py b/reframe_config_bot.py
new file mode 100644
index 0000000000..65ccf9f43e
--- /dev/null
+++ b/reframe_config_bot.py
@@ -0,0 +1,58 @@
+# WARNING: this file is intended as template and the __X__ template variables need to be replaced
+# before it can act as a configuration file
+# Once replaced, this is a config file for running tests after the build phase, by the bot
+
+from eessi.testsuite.common_config import common_logging_config
+from eessi.testsuite.constants import *  # noqa: F403
+
+
+site_configuration = {
+    'systems': [
+        {
+            'name': 'Testing in bot Build jobs for EESSI software Layer',
+            'descr': 'Software-layer bot',
+            'hostnames': ['.*'],
+            'modules_system': 'lmod',
+            'partitions': [
+                {
+                    'name': 'default',
+                    'scheduler': 'local',
+                    'launcher': 'mpirun',
+                    'environs': ['default'],
+                    'features': [FEATURES[CPU]],
+                    'processor': {
+                        'num_cpus': __NUM_CPUS__,
+                        'num_sockets': __NUM_SOCKETS__,
+                        'num_cpus_per_core': __NUM_CPUS_PER_CORE__,
+                        'num_cpus_per_socket': __NUM_CPUS_PER_SOCKET__,
+                    }
+                    'resources': [
+                        {
+                            'name': 'memory',
+                            'options': ['--mem={size}'],
+                        }
+                    ],
+                    'max_jobs': 1
+                    }
+                ]
+            }
+        ],
+    'environments': [
+        {
+            'name': 'default',
+            'cc': 'cc',
+            'cxx': '',
+            'ftn': ''
+            }
+        ],
+    'general': [
+        {
+            'purge_environment': True,
+            'resolve_module_conflicts': False,  # avoid loading the module before submitting the job
+            # Enable automatic detection of CPU architecture
+            # See https://reframe-hpc.readthedocs.io/en/stable/configure.html#auto-detecting-processor-information
+            'remote_detect': True,
+        }
+    ],
+    'logging': common_logging_config(),
+}

From 02b0e3115dfc81387554f0cb9fe2c292e60098ab Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Wed, 7 Feb 2024 16:30:18 +0100
Subject: [PATCH 065/501] Use template config file and make replacements based
 on lscpu

---
 test_suite.sh | 31 +++++++++++++++++++++++++++++--
 1 file changed, 29 insertions(+), 2 deletions(-)

diff --git a/test_suite.sh b/test_suite.sh
index a8e1b2d97a..f5cc7fabfd 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -156,11 +156,11 @@ python3 -c 'import eessi.testsuite'
 if [[ $? -eq 0 ]]; then
     echo_green "Succesfully found and imported eessi.testsuite"
 else
-    fatal_error "FAILED to import from eessi.testsuite in Python"
+    fatal_error "Failed to import from eessi.testsuite in Python"
 fi
 
 # Configure ReFrame
-export RFM_CONFIG_FILES=$TESTSUITEPREFIX/config/software_layer_bot.py
+export RFM_CONFIG_FILES=$TOPDIR/reframe_config_bot.py
 export RFM_CHECK_SEARCH_PATH=$TESTSUITEPREFIX/eessi/testsuite/tests
 export RFM_CHECK_SEARCH_RECURSIVE=1
 export RFM_PREFIX=$PWD/reframe_runs
@@ -168,6 +168,33 @@ export RFM_PREFIX=$PWD/reframe_runs
 echo "Configured reframe with the following environment variables:"
 env | grep "RFM_"
 
+# Inject correct CPU properties into the ReFrame config file
+cpuinfo=$(lscpu)
+if [[ "${cpuinfo}" =~ CPU\(s\):[^0-9]*([0-9]+) ]]; then
+    cpu_count=${BASH_REMATCH[1]}
+else
+    fatal_error "Failed to get the number of CPUs for the current test hardware with lscpu."
+fi
+if [[ "${text}" =~ Socket\(s\):[^0-9]*([0-9]+) ]]; then
+    socket_count=${BASH_REMATCH[1]}
+else
+    fatal_error "Failed to get the number of sockets for the current test hardware with lscpu."
+fi
+if [[ "${text}" =~ (Thread\(s\) per core:[^0-9]*([0-9]+)) ]]; then
+    threads_per_core=${BASH_REMATCH[2]}
+else
+    fatal_error "Failed to get the number of threads per core for the current test hardware with lscpu."
+fi
+if [[ "${text}" =~ (Core\(s\) per socket:[^0-9]*([0-9]+)) ]]; then
+    cores_per_socket=${BASH_REMATCH[2]}
+else
+    fatal_error "Failed to get the number of cores per socket for the current test hardware with lscpu."
+fi
+sed -i "s/__NUM_CPUS__/${cpu_count}/g" $RFM_CONFIG_FILES
+sed -i "s/__NUM_SOCKETS__/${socket_count}/g" $RFM_CONFIG_FILES
+sed -i "s/__NUM_CPUS_PER_CORE__/${threads_per_core}/g" $RFM_CONFIG_FILES
+sed -i "s/__NUM_CPUS_PER_SOCKETS__/${cores_per_socket}/g" $RFM_CONFIG_FILES
+
 # Check we can run reframe
 reframe --version
 if [[ $? -eq 0 ]]; then

From 58c4cfa772454405c456503c29a6fc8d59956910 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Wed, 7 Feb 2024 16:39:46 +0100
Subject: [PATCH 066/501] Fix incorrect variable name

---
 test_suite.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test_suite.sh b/test_suite.sh
index f5cc7fabfd..7ba5282327 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -175,17 +175,17 @@ if [[ "${cpuinfo}" =~ CPU\(s\):[^0-9]*([0-9]+) ]]; then
 else
     fatal_error "Failed to get the number of CPUs for the current test hardware with lscpu."
 fi
-if [[ "${text}" =~ Socket\(s\):[^0-9]*([0-9]+) ]]; then
+if [[ "${cpuinfo}" =~ Socket\(s\):[^0-9]*([0-9]+) ]]; then
     socket_count=${BASH_REMATCH[1]}
 else
     fatal_error "Failed to get the number of sockets for the current test hardware with lscpu."
 fi
-if [[ "${text}" =~ (Thread\(s\) per core:[^0-9]*([0-9]+)) ]]; then
+if [[ "${cpuinfo}" =~ (Thread\(s\) per core:[^0-9]*([0-9]+)) ]]; then
     threads_per_core=${BASH_REMATCH[2]}
 else
     fatal_error "Failed to get the number of threads per core for the current test hardware with lscpu."
 fi
-if [[ "${text}" =~ (Core\(s\) per socket:[^0-9]*([0-9]+)) ]]; then
+if [[ "${cpuinfo}" =~ (Core\(s\) per socket:[^0-9]*([0-9]+)) ]]; then
     cores_per_socket=${BASH_REMATCH[2]}
 else
     fatal_error "Failed to get the number of cores per socket for the current test hardware with lscpu."

From 2fc121e86399b7c7c3cab6092b609a91a88db43f Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Wed, 7 Feb 2024 16:57:48 +0100
Subject: [PATCH 067/501] Missing comma

---
 reframe_config_bot.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/reframe_config_bot.py b/reframe_config_bot.py
index 65ccf9f43e..bbe8a7e2df 100644
--- a/reframe_config_bot.py
+++ b/reframe_config_bot.py
@@ -25,7 +25,7 @@
                         'num_sockets': __NUM_SOCKETS__,
                         'num_cpus_per_core': __NUM_CPUS_PER_CORE__,
                         'num_cpus_per_socket': __NUM_CPUS_PER_SOCKET__,
-                    }
+                    },
                     'resources': [
                         {
                             'name': 'memory',

From db08f4f39a618450c70f1d52f43c46f244011545 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Wed, 7 Feb 2024 21:30:43 +0100
Subject: [PATCH 068/501] Corrected typo

---
 test_suite.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test_suite.sh b/test_suite.sh
index 7ba5282327..9bd95c6749 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -193,7 +193,7 @@ fi
 sed -i "s/__NUM_CPUS__/${cpu_count}/g" $RFM_CONFIG_FILES
 sed -i "s/__NUM_SOCKETS__/${socket_count}/g" $RFM_CONFIG_FILES
 sed -i "s/__NUM_CPUS_PER_CORE__/${threads_per_core}/g" $RFM_CONFIG_FILES
-sed -i "s/__NUM_CPUS_PER_SOCKETS__/${cores_per_socket}/g" $RFM_CONFIG_FILES
+sed -i "s/__NUM_CPUS_PER_SOCKET__/${cores_per_socket}/g" $RFM_CONFIG_FILES
 
 # Check we can run reframe
 reframe --version

From 6b3a6ccc985314e5c66c8097e8eb26e1c1fb3546 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Wed, 7 Feb 2024 21:47:43 +0100
Subject: [PATCH 069/501] Remove verbose flags

---
 test_suite.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test_suite.sh b/test_suite.sh
index 9bd95c6749..99643c42b8 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -204,7 +204,7 @@ else
 fi
 
 # List the tests we want to run
-export REFRAME_ARGS='--tag CI --tag 1_node -vvv'
+export REFRAME_ARGS='--tag CI --tag 1_node'
 echo "Listing tests: reframe ${REFRAME_ARGS} --list"
 reframe ${REFRAME_ARGS} --list
 if [[ $? -eq 0 ]]; then

From a70b4f132e36f078cb3b4f0d802f96a877699050 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Wed, 7 Feb 2024 21:55:16 +0100
Subject: [PATCH 070/501] Pick name without spaces, to avoid issues with
 directories

---
 reframe_config_bot.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/reframe_config_bot.py b/reframe_config_bot.py
index bbe8a7e2df..ad66a72041 100644
--- a/reframe_config_bot.py
+++ b/reframe_config_bot.py
@@ -9,7 +9,7 @@
 site_configuration = {
     'systems': [
         {
-            'name': 'Testing in bot Build jobs for EESSI software Layer',
+            'name': 'BotBuildTests',
             'descr': 'Software-layer bot',
             'hostnames': ['.*'],
             'modules_system': 'lmod',

From ce24e6d6de196ca191371b186b449b7a9d4aa5c9 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Thu, 8 Feb 2024 17:50:39 +0100
Subject: [PATCH 071/501] Pick more meaningful name for SLURM variable, namely
 SLURM_OUTPUT_FOUND

---
 bot/check-build.sh | 22 +++++++++++-----------
 bot/check-test.sh  | 18 +++++++++---------
 2 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/bot/check-build.sh b/bot/check-build.sh
index ec1ca56bba..42dca46a08 100755
--- a/bot/check-build.sh
+++ b/bot/check-build.sh
@@ -95,18 +95,18 @@ job_dir=${PWD}
 
 [[ ${VERBOSE} -ne 0 ]] && echo ">> analysing job in directory ${job_dir}"
 
-job_out="slurm-${SLURM_JOB_ID}.out"
+job_out="slurm-${SLURM_OUTPUT_FOUND_JOB_ID}.out"
 [[ ${VERBOSE} -ne 0 ]] && echo ">> searching for job output file(s) matching '"${job_out}"'"
 if  [[ -f ${job_out} ]]; then
-    SLURM=1
+    SLURM_OUTPUT_FOUND=1
     [[ ${VERBOSE} -ne 0 ]] && echo "   found slurm output file '"${job_out}"'"
 else
-    SLURM=0
+    SLURM_OUTPUT_FOUND=0
     [[ ${VERBOSE} -ne 0 ]] && echo "   Slurm output file '"${job_out}"' NOT found"
 fi
 
 ERROR=-1
-if [[ ${SLURM} -eq 1 ]]; then
+if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]]; then
   GP_error='ERROR: '
   grep_out=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_error}")
   [[ $? -eq 0 ]] && ERROR=1 || ERROR=0
@@ -116,7 +116,7 @@ if [[ ${SLURM} -eq 1 ]]; then
 fi
 
 FAILED=-1
-if [[ ${SLURM} -eq 1 ]]; then
+if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]]; then
   GP_failed='FAILED: '
   grep_out=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_failed}")
   [[ $? -eq 0 ]] && FAILED=1 || FAILED=0
@@ -126,7 +126,7 @@ if [[ ${SLURM} -eq 1 ]]; then
 fi
 
 MISSING=-1
-if [[ ${SLURM} -eq 1 ]]; then
+if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]]; then
   GP_req_missing=' required modules missing:'
   grep_out=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_req_missing}")
   [[ $? -eq 0 ]] && MISSING=1 || MISSING=0
@@ -136,7 +136,7 @@ if [[ ${SLURM} -eq 1 ]]; then
 fi
 
 NO_MISSING=-1
-if [[ ${SLURM} -eq 1 ]]; then
+if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]]; then
   GP_no_missing='No missing installations'
   grep_out=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_no_missing}")
   [[ $? -eq 0 ]] && NO_MISSING=1 || NO_MISSING=0
@@ -147,7 +147,7 @@ fi
 
 TGZ=-1
 TARBALL=
-if [[ ${SLURM} -eq 1 ]]; then
+if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]]; then
   GP_tgz_created="\.tar\.gz created!"
   grep_out=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_tgz_created}" | sort -u)
   if [[ $? -eq 0 ]]; then
@@ -169,9 +169,9 @@ fi
 [[ ${VERBOSE} -ne 0 ]] && echo "  NO_MISSING.: $([[ $NO_MISSING -eq 1 ]] && echo 'yes' || echo 'no') (yes)"
 [[ ${VERBOSE} -ne 0 ]] && echo "  TGZ_CREATED: $([[ $TGZ -eq 1 ]] && echo 'yes' || echo 'no') (yes)"
 
-job_result_file=_bot_job${SLURM_JOB_ID}.result
+job_result_file=_bot_job${SLURM_OUTPUT_FOUND_JOB_ID}.result
 
-if [[ ${SLURM} -eq 1 ]] && \
+if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]] && \
    [[ ${ERROR} -eq 0 ]] && \
    [[ ${FAILED} -eq 0 ]] && \
    [[ ${MISSING} -eq 0 ]] && \
@@ -340,7 +340,7 @@ CoDeList=""
 
 success_msg="job output file <code>${job_out}</code>"
 failure_msg="no job output file <code>${job_out}</code>"
-CoDeList=${CoDeList}$(add_detail ${SLURM} 1 "${success_msg}" "${failure_msg}")
+CoDeList=${CoDeList}$(add_detail ${SLURM_OUTPUT_FOUND} 1 "${success_msg}" "${failure_msg}")
 
 success_msg="no message matching <code>${GP_error}</code>"
 failure_msg="found message matching <code>${GP_error}</code>"
diff --git a/bot/check-test.sh b/bot/check-test.sh
index 39901f0691..549afd2f65 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -10,16 +10,16 @@
 # license: GPLv2
 #
 job_dir=${PWD}
-job_out="slurm-${SLURM_JOB_ID}.out"
-job_test_result_file="_bot_job${SLURM_JOB_ID}.test"
+job_out="slurm-${SLURM_OUTPUT_FOUND_JOB_ID}.out"
+job_test_result_file="_bot_job${SLURM_OUTPUT_FOUND_JOB_ID}.test"
 
 # Check that job output file is found
 [[ ${VERBOSE} -ne 0 ]] && echo ">> searching for job output file(s) matching '"${job_out}"'"
 if  [[ -f ${job_out} ]]; then
-    SLURM=1
+    SLURM_OUTPUT_FOUND=1
     [[ ${VERBOSE} -ne 0 ]] && echo "   found slurm output file '"${job_out}"'"
 else
-    SLURM=0
+    SLURM_OUTPUT_FOUND=0
     [[ ${VERBOSE} -ne 0 ]] && echo "   Slurm output file '"${job_out}"' NOT found"
 fi
 
@@ -41,7 +41,7 @@ fi
 # We will grep for the last and final line, since this reflects the overall result
 # Specifically, we grep for FAILED, since this is also what we print if a step in the test script itself fails
 FAILED=-1
-if [[ ${SLURM} -eq 1 ]]; then
+if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]]; then
   GP_failed='\[.*FAILED.*\].*Ran .* test case'
   grep_reframe_failed=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_failed}")
   [[ $? -eq 0 ]] && FAILED=1 || FAILED=0
@@ -53,7 +53,7 @@ fi
 # Here, we grep for 'ERROR:', which is printed if a fatal_error is encountered when executing the test step
 # I.e. this is an error in execution of the run_tests.sh itself, NOT in running the actual tests
 ERROR=-1
-if [[ ${SLURM} -eq 1 ]]; then
+if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]]; then
   GP_error='ERROR: '
   grep_out=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_error}")
   [[ $? -eq 0 ]] && ERROR=1 || ERROR=0
@@ -64,7 +64,7 @@ fi
 
 SUCCESS=-1
 # Grep for the success pattern, so we can report the amount of tests run
-if [[ ${SLURM} -eq 1 ]]; then
+if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]]; then
   GP_success='\[.*PASSED.*\].*Ran .* test case'
   grep_reframe_success=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_success}")
   [[ $? -eq 0 ]] && SUCCESS=1 || SUCCESS=0
@@ -80,7 +80,7 @@ else
 fi
 
 echo "[TEST]" > ${job_test_result_file}
-if [[ ${SLURM} -eq 0 ]]; then
+if [[ ${SLURM_OUTPUT_FOUND} -eq 0 ]]; then
     summary=":cry: FAILURE"
     reason="Job output file not found, cannot check test results."
     status="FAILURE"
@@ -182,7 +182,7 @@ CoDeList=""
 
 success_msg="job output file <code>${job_out}</code>"
 failure_msg="no job output file <code>${job_out}</code>"
-CoDeList=${CoDeList}$(add_detail ${SLURM} 1 "${success_msg}" "${failure_msg}")
+CoDeList=${CoDeList}$(add_detail ${SLURM_OUTPUT_FOUND} 1 "${success_msg}" "${failure_msg}")
 
 success_msg="no message matching <code>${GP_error}</code>"
 failure_msg="found message matching <code>${GP_error}</code>"

From 9881c2ad5f93c617c075e8df81d770033ec2a121 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Thu, 8 Feb 2024 17:51:36 +0100
Subject: [PATCH 072/501] Correct erroneous status

---
 bot/check-test.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index 549afd2f65..9724f45832 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -103,7 +103,7 @@ elif [[ ${ERROR} -eq 1 ]]; then
 else
     summary=":grin: FAILURE"
     reason="Failed for unknown reason"
-    status="SUCCESS"
+    status="FAILURE"
 fi
 
 

From 1446055cb5cd4306d61809c67b5dcda4ce930c8b Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Thu, 8 Feb 2024 17:53:09 +0100
Subject: [PATCH 073/501] Rename CoDeList variable to comment_details_list

---
 bot/check-build.sh | 18 +++++++++---------
 bot/check-test.sh  | 18 +++++++++---------
 2 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/bot/check-build.sh b/bot/check-build.sh
index 42dca46a08..584d4ff828 100755
--- a/bot/check-build.sh
+++ b/bot/check-build.sh
@@ -334,35 +334,35 @@ echo -n "comment_description = " >> ${job_result_file}
 
 comment_summary="${comment_summary_fmt/__SUMMARY__/${summary}}"
 
-# first construct comment_details_list, abbreviated CoDeList
+# first construct comment_details_list, abbreviated comment_details_list
 # then use it to set comment_details
-CoDeList=""
+comment_details_list=""
 
 success_msg="job output file <code>${job_out}</code>"
 failure_msg="no job output file <code>${job_out}</code>"
-CoDeList=${CoDeList}$(add_detail ${SLURM_OUTPUT_FOUND} 1 "${success_msg}" "${failure_msg}")
+comment_details_list=${comment_details_list}$(add_detail ${SLURM_OUTPUT_FOUND} 1 "${success_msg}" "${failure_msg}")
 
 success_msg="no message matching <code>${GP_error}</code>"
 failure_msg="found message matching <code>${GP_error}</code>"
-CoDeList=${CoDeList}$(add_detail ${ERROR} 0 "${success_msg}" "${failure_msg}")
+comment_details_list=${comment_details_list}$(add_detail ${ERROR} 0 "${success_msg}" "${failure_msg}")
 
 success_msg="no message matching <code>${GP_failed}</code>"
 failure_msg="found message matching <code>${GP_failed}</code>"
-CoDeList=${CoDeList}$(add_detail ${FAILED} 0 "${success_msg}" "${failure_msg}")
+comment_details_list=${comment_details_list}$(add_detail ${FAILED} 0 "${success_msg}" "${failure_msg}")
 
 success_msg="no message matching <code>${GP_req_missing}</code>"
 failure_msg="found message matching <code>${GP_req_missing}</code>"
-CoDeList=${CoDeList}$(add_detail ${MISSING} 0 "${success_msg}" "${failure_msg}")
+comment_details_list=${comment_details_list}$(add_detail ${MISSING} 0 "${success_msg}" "${failure_msg}")
 
 success_msg="found message(s) matching <code>${GP_no_missing}</code>"
 failure_msg="no message matching <code>${GP_no_missing}</code>"
-CoDeList=${CoDeList}$(add_detail ${NO_MISSING} 1 "${success_msg}" "${failure_msg}")
+comment_details_list=${comment_details_list}$(add_detail ${NO_MISSING} 1 "${success_msg}" "${failure_msg}")
 
 success_msg="found message matching <code>${GP_tgz_created}</code>"
 failure_msg="no message matching <code>${GP_tgz_created}</code>"
-CoDeList=${CoDeList}$(add_detail ${TGZ} 1 "${success_msg}" "${failure_msg}")
+comment_details_list=${comment_details_list}$(add_detail ${TGZ} 1 "${success_msg}" "${failure_msg}")
 
-comment_details="${comment_details_fmt/__DETAILS_LIST__/${CoDeList}}"
+comment_details="${comment_details_fmt/__DETAILS_LIST__/${comment_details_list}}"
 
 
 # first construct comment_artefacts_list, abbreviated CoArList
diff --git a/bot/check-test.sh b/bot/check-test.sh
index 9724f45832..fe1fcfe85d 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -176,37 +176,37 @@ function add_detail() {
     fi
 }
 
-# first construct comment_details_list, abbreviated CoDeList
+# first construct comment_details_list, abbreviated comment_details_list
 # then use it to set comment_details
-CoDeList=""
+comment_details_list=""
 
 success_msg="job output file <code>${job_out}</code>"
 failure_msg="no job output file <code>${job_out}</code>"
-CoDeList=${CoDeList}$(add_detail ${SLURM_OUTPUT_FOUND} 1 "${success_msg}" "${failure_msg}")
+comment_details_list=${comment_details_list}$(add_detail ${SLURM_OUTPUT_FOUND} 1 "${success_msg}" "${failure_msg}")
 
 success_msg="no message matching <code>${GP_error}</code>"
 failure_msg="found message matching <code>${GP_error}</code>"
-CoDeList=${CoDeList}$(add_detail ${ERROR} 0 "${success_msg}" "${failure_msg}")
+comment_details_list=${comment_details_list}$(add_detail ${ERROR} 0 "${success_msg}" "${failure_msg}")
 
 success_msg="no message matching <code>""${GP_failed}""</code>"
 failure_msg="found message matching <code>""${GP_failed}""</code>"
-CoDeList=${CoDeList}$(add_detail ${FAILED} 0 "${success_msg}" "${failure_msg}")
+comment_details_list=${comment_details_list}$(add_detail ${FAILED} 0 "${success_msg}" "${failure_msg}")
 
 # Should not be needed for testing, I think? Maybe for loading ReFrame module...
 # success_msg="no message matching <code>${GP_req_missing}</code>"
 # failure_msg="found message matching <code>${GP_req_missing}</code>"
-# CoDeList=${CoDeList}$(add_detail ${MISSING} 0 "${success_msg}" "${failure_msg}")
+# comment_details_list=${comment_details_list}$(add_detail ${MISSING} 0 "${success_msg}" "${failure_msg}")
 # 
 # success_msg="found message(s) matching <code>${GP_no_missing}</code>"
 # failure_msg="no message matching <code>${GP_no_missing}</code>"
-# CoDeList=${CoDeList}$(add_detail ${NO_MISSING} 1 "${success_msg}" "${failure_msg}")
+# comment_details_list=${comment_details_list}$(add_detail ${NO_MISSING} 1 "${success_msg}" "${failure_msg}")
 # 
 # success_msg="found message matching <code>${GP_tgz_created}</code>"
 # failure_msg="no message matching <code>${GP_tgz_created}</code>"
-# CoDeList=${CoDeList}$(add_detail ${TGZ} 1 "${success_msg}" "${failure_msg}")
+# comment_details_list=${comment_details_list}$(add_detail ${TGZ} 1 "${success_msg}" "${failure_msg}")
 
 comment_details_fmt="<dt>_Details_</dt><dd>__DETAILS_LIST__</dd>"
-comment_details="${comment_details_fmt/__DETAILS_LIST__/${CoDeList}}"
+comment_details="${comment_details_fmt/__DETAILS_LIST__/${comment_details_list}}"
 comment_description=${comment_description/__DETAILS_FMT__/${comment_details}}
 
 # Actually writing the comment description to the result file

From f80c0eb42f891c686cd1818ccbfc353e8bb29f05 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Thu, 8 Feb 2024 17:54:00 +0100
Subject: [PATCH 074/501] Remove commented section, it is not relevant

---
 bot/check-test.sh | 13 -------------
 1 file changed, 13 deletions(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index fe1fcfe85d..9e7a524607 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -192,19 +192,6 @@ success_msg="no message matching <code>""${GP_failed}""</code>"
 failure_msg="found message matching <code>""${GP_failed}""</code>"
 comment_details_list=${comment_details_list}$(add_detail ${FAILED} 0 "${success_msg}" "${failure_msg}")
 
-# Should not be needed for testing, I think? Maybe for loading ReFrame module...
-# success_msg="no message matching <code>${GP_req_missing}</code>"
-# failure_msg="found message matching <code>${GP_req_missing}</code>"
-# comment_details_list=${comment_details_list}$(add_detail ${MISSING} 0 "${success_msg}" "${failure_msg}")
-# 
-# success_msg="found message(s) matching <code>${GP_no_missing}</code>"
-# failure_msg="no message matching <code>${GP_no_missing}</code>"
-# comment_details_list=${comment_details_list}$(add_detail ${NO_MISSING} 1 "${success_msg}" "${failure_msg}")
-# 
-# success_msg="found message matching <code>${GP_tgz_created}</code>"
-# failure_msg="no message matching <code>${GP_tgz_created}</code>"
-# comment_details_list=${comment_details_list}$(add_detail ${TGZ} 1 "${success_msg}" "${failure_msg}")
-
 comment_details_fmt="<dt>_Details_</dt><dd>__DETAILS_LIST__</dd>"
 comment_details="${comment_details_fmt/__DETAILS_LIST__/${comment_details_list}}"
 comment_description=${comment_description/__DETAILS_FMT__/${comment_details}}

From ff5baace136c589becaf42adab32b4a0eed7afc6 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com>
Date: Thu, 8 Feb 2024 17:57:36 +0100
Subject: [PATCH 075/501] Update run_tests.sh

Avoid a one-line script (if possible)

Co-authored-by: Kenneth Hoste <kenneth.hoste@ugent.be>
---
 run_tests.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/run_tests.sh b/run_tests.sh
index bcca1ee417..5e9fcb543d 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -9,5 +9,5 @@ source ${base_dir}/init/eessi_defaults
 # TODO: in the future we may implement this as a light first check.
 
 # Run the test suite
-./run_in_compat_layer_env.sh ./clone_eessi_test_suite.sh
+./run_in_compat_layer_env.sh "git clone https://github.com/EESSI/test-suite EESSI-test-suite"
 ./test_suite.sh

From 4adae1838edd1146d1a4a8c4322bffeb5e49db64 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Thu, 8 Feb 2024 18:42:47 +0100
Subject: [PATCH 076/501] Fix mistake in replacing SLURM with
 SLURM_OUTPUT_FOUND

---
 bot/check-build.sh | 4 ++--
 bot/check-test.sh  | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/bot/check-build.sh b/bot/check-build.sh
index 584d4ff828..1b46652049 100755
--- a/bot/check-build.sh
+++ b/bot/check-build.sh
@@ -95,7 +95,7 @@ job_dir=${PWD}
 
 [[ ${VERBOSE} -ne 0 ]] && echo ">> analysing job in directory ${job_dir}"
 
-job_out="slurm-${SLURM_OUTPUT_FOUND_JOB_ID}.out"
+job_out="slurm-${SLURM_JOB_ID}.out"
 [[ ${VERBOSE} -ne 0 ]] && echo ">> searching for job output file(s) matching '"${job_out}"'"
 if  [[ -f ${job_out} ]]; then
     SLURM_OUTPUT_FOUND=1
@@ -169,7 +169,7 @@ fi
 [[ ${VERBOSE} -ne 0 ]] && echo "  NO_MISSING.: $([[ $NO_MISSING -eq 1 ]] && echo 'yes' || echo 'no') (yes)"
 [[ ${VERBOSE} -ne 0 ]] && echo "  TGZ_CREATED: $([[ $TGZ -eq 1 ]] && echo 'yes' || echo 'no') (yes)"
 
-job_result_file=_bot_job${SLURM_OUTPUT_FOUND_JOB_ID}.result
+job_result_file=_bot_job${SLURM_JOB_ID}.result
 
 if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]] && \
    [[ ${ERROR} -eq 0 ]] && \
diff --git a/bot/check-test.sh b/bot/check-test.sh
index 9e7a524607..faf6e440fa 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -10,8 +10,8 @@
 # license: GPLv2
 #
 job_dir=${PWD}
-job_out="slurm-${SLURM_OUTPUT_FOUND_JOB_ID}.out"
-job_test_result_file="_bot_job${SLURM_OUTPUT_FOUND_JOB_ID}.test"
+job_out="slurm-${SLURM_JOB_ID}.out"
+job_test_result_file="_bot_job${SLURM__JOB_ID}.test"
 
 # Check that job output file is found
 [[ ${VERBOSE} -ne 0 ]] && echo ">> searching for job output file(s) matching '"${job_out}"'"

From 9e6955f53e70d3848ca2199756150993c36212ec Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Thu, 8 Feb 2024 18:52:44 +0100
Subject: [PATCH 077/501] Change name of the template for the ReFrame config
 file to make clear it is a template. Then, alter the sed commands so that
 they output to a new file: the actual config file

---
 reframe_config_bot.py => reframe_config_bot.py.tmpl | 0
 test_suite.sh                                       | 9 +++++----
 2 files changed, 5 insertions(+), 4 deletions(-)
 rename reframe_config_bot.py => reframe_config_bot.py.tmpl (100%)

diff --git a/reframe_config_bot.py b/reframe_config_bot.py.tmpl
similarity index 100%
rename from reframe_config_bot.py
rename to reframe_config_bot.py.tmpl
diff --git a/test_suite.sh b/test_suite.sh
index 99643c42b8..b3884c3b81 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -161,6 +161,7 @@ fi
 
 # Configure ReFrame
 export RFM_CONFIG_FILES=$TOPDIR/reframe_config_bot.py
+export RFM_CONFIG_FILE_TEMPLATE=$TOPDIR/reframe_config_bot.py.tmpl
 export RFM_CHECK_SEARCH_PATH=$TESTSUITEPREFIX/eessi/testsuite/tests
 export RFM_CHECK_SEARCH_RECURSIVE=1
 export RFM_PREFIX=$PWD/reframe_runs
@@ -190,10 +191,10 @@ if [[ "${cpuinfo}" =~ (Core\(s\) per socket:[^0-9]*([0-9]+)) ]]; then
 else
     fatal_error "Failed to get the number of cores per socket for the current test hardware with lscpu."
 fi
-sed -i "s/__NUM_CPUS__/${cpu_count}/g" $RFM_CONFIG_FILES
-sed -i "s/__NUM_SOCKETS__/${socket_count}/g" $RFM_CONFIG_FILES
-sed -i "s/__NUM_CPUS_PER_CORE__/${threads_per_core}/g" $RFM_CONFIG_FILES
-sed -i "s/__NUM_CPUS_PER_SOCKET__/${cores_per_socket}/g" $RFM_CONFIG_FILES
+sed "s/__NUM_CPUS__/${cpu_count}/g" $RFM_CONFIG_FILE_TEMPLATE > $RFM_CONFIG_FILES
+sed "s/__NUM_SOCKETS__/${socket_count}/g" $RFM_CONFIG_FILE_TEMPLATE > $RFM_CONFIG_FILES
+sed "s/__NUM_CPUS_PER_CORE__/${threads_per_core}/g" $RFM_CONFIG_FILE_TEMPLATE > $RFM_CONFIG_FILES
+sed "s/__NUM_CPUS_PER_SOCKET__/${cores_per_socket}/g" $RFM_CONFIG_FILE_TEMPLATE > $RFM_CONFIG_FILES
 
 # Check we can run reframe
 reframe --version

From 08a7fd8eaa64dce298624e1d4f6054d2938a7fcc Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Thu, 8 Feb 2024 18:55:20 +0100
Subject: [PATCH 078/501] Fix typo in variable

---
 bot/check-test.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index faf6e440fa..ef52206346 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -11,7 +11,7 @@
 #
 job_dir=${PWD}
 job_out="slurm-${SLURM_JOB_ID}.out"
-job_test_result_file="_bot_job${SLURM__JOB_ID}.test"
+job_test_result_file="_bot_job${SLURM_JOB_ID}.test"
 
 # Check that job output file is found
 [[ ${VERBOSE} -ne 0 ]] && echo ">> searching for job output file(s) matching '"${job_out}"'"

From 8b5bde5413553c03f58ce788ef03e78ae87f343b Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Thu, 8 Feb 2024 18:56:07 +0100
Subject: [PATCH 079/501] No longer needed

---
 clone_eessi_test_suite.sh | 1 -
 1 file changed, 1 deletion(-)
 delete mode 100755 clone_eessi_test_suite.sh

diff --git a/clone_eessi_test_suite.sh b/clone_eessi_test_suite.sh
deleted file mode 100755
index f7684c8cfd..0000000000
--- a/clone_eessi_test_suite.sh
+++ /dev/null
@@ -1 +0,0 @@
-git clone https://github.com/EESSI/test-suite EESSI-test-suite

From 5d383eb8bc4c729cfa85d1aeae9ea10d82000c5c Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Thu, 8 Feb 2024 19:03:29 +0100
Subject: [PATCH 080/501] Added header, rephrased some comments

---
 run_tests.sh | 23 +++++++++++++++++------
 1 file changed, 17 insertions(+), 6 deletions(-)

diff --git a/run_tests.sh b/run_tests.sh
index 5e9fcb543d..0c51a14807 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -1,13 +1,24 @@
 #!/bin/bash
+#
+# This script gets invoked by the bot/test.sh script to run within the EESSI container
+# Thus, this script defines all of the steps that should run for the tests.
+# Note that, unless we have good reason, we don't run test steps in the prefix environment:
+# users also typically don't run in the prefix environment, and we want to check if the
+# software works well in that specific setup.
+#
+# This script is part of the EESSI software layer, see
+# https://github.com/EESSI/software-layer.git
+#
+# author: Caspar van Leeuwe (@casparvl)
+#
+# license: GPLv2
+#
+
 base_dir=$(dirname $(realpath $0))
 source ${base_dir}/init/eessi_defaults
 
-# Note: for these tests, we _don't_ run in the compat layer env
-# These tests should mimic what users do, and they are typically not in a prefix environment
-
-# Run eb --sanity-check-only on changed easyconfigs
-# TODO: in the future we may implement this as a light first check.
+# Git clone has to be run in compat layer, to make the git command available
+./run_in_compat_layer_env.sh "git clone https://github.com/EESSI/test-suite EESSI-test-suite"
 
 # Run the test suite
-./run_in_compat_layer_env.sh "git clone https://github.com/EESSI/test-suite EESSI-test-suite"
 ./test_suite.sh

From cdf79712184e89a31afaaff3880fc7cf0387b2e5 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Thu, 8 Feb 2024 19:13:11 +0100
Subject: [PATCH 081/501] Fix headers

---
 run_tests.sh  |  2 +-
 test_suite.sh | 13 +++++++++----
 2 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/run_tests.sh b/run_tests.sh
index 0c51a14807..de7fd8c2e1 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -9,7 +9,7 @@
 # This script is part of the EESSI software layer, see
 # https://github.com/EESSI/software-layer.git
 #
-# author: Caspar van Leeuwe (@casparvl)
+# author: Caspar van Leeuwen (@casparvl)
 #
 # license: GPLv2
 #
diff --git a/test_suite.sh b/test_suite.sh
index b3884c3b81..ffe8955f1e 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -1,9 +1,14 @@
 #!/bin/bash
 #
-# Run sanity check for all requested modules (and built dependencies)?
-# get ec from diff
-# set up EasyBuild
-# run `eb --sanity-only ec`
+# This script creates a ReFrame config file from a template, in which CPU properties get replaced
+# based on where this script is run (typically: a build node). Then, it runs the EESSI test suite.
+#
+# This script is part of the EESSI software layer, see
+# https://github.com/EESSI/software-layer.git
+#
+# author: Caspar van Leeuwen (@casparvl)
+#
+# license: GPLv2
 
 display_help() {
   echo "usage: $0 [OPTIONS]"

From 79a9ad320aec47ac368ed96f72e0f59a0cfbe9f5 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Thu, 8 Feb 2024 19:16:10 +0100
Subject: [PATCH 082/501] Load default ReFrame version

---
 test_suite.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/test_suite.sh b/test_suite.sh
index ffe8955f1e..1f6d8ae44d 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -129,11 +129,11 @@ else
     echo_green ">> MODULEPATH set up: ${MODULEPATH}"
 fi
 
-# TODO: this should not be hardcoded. Ideally, we put some logic in place to discover the newest version
-# of the ReFrame module available in the current environment
-module load ReFrame/4.3.3
+# Load the ReFrame module
+# Currently, we load the default version. Maybe we should somehow make this configurable in the future?
+module load ReFrame
 if [[ $? -eq 0 ]]; then
-    echo_green ">> Loaded ReFrame/4.3.3"
+    echo_green ">> Loaded ReFrame module"
 else
     fatal_error "Failed to load the ReFrame module"
 fi

From 2f280e4304b520de295fdb408218e3125b153853 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Thu, 8 Feb 2024 19:21:24 +0100
Subject: [PATCH 083/501] Point to docs for ReFrame config

---
 test_suite.sh | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/test_suite.sh b/test_suite.sh
index 1f6d8ae44d..d2403b91d8 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -130,7 +130,7 @@ else
 fi
 
 # Load the ReFrame module
-# Currently, we load the default version. Maybe we should somehow make this configurable in the future?
+ Currently, we load the default version. Maybe we should somehow make this configurable in the future?
 module load ReFrame
 if [[ $? -eq 0 ]]; then
     echo_green ">> Loaded ReFrame module"
@@ -139,15 +139,16 @@ else
 fi
 
 # Check ReFrame came with the hpctestlib and we can import it
-python3 -c 'import hpctestlib.sciapps.gromacs'
+reframe_import="hpctestlib.sciapps.gromacs"
+python3 -c "import ${reframe_import}"
 if [[ $? -eq 0 ]]; then
-    echo_green "Succesfully found and imported hpctestlib.sciapps.gromas"
+    echo_green "Succesfully found and imported ${reframe_import}"
 else
-    fatal_error "Failed to load hpctestlib"
+    fatal_error "Failed to import ${reframe_import}"
 fi
 
-# Cloning should already be done by clone_eessi_test_suite.sh, which runs in compat layer to have 'git' available
-# git clone https://github.com/EESSI/test-suite EESSI-test-suite
+# Cloning should already be done in run_tests.sh before test_suite.sh is invoked
+# Check if that succeeded
 export TESTSUITEPREFIX=$PWD/EESSI-test-suite
 if [ -d $TESTSUITEPREFIX ]; then
     echo_green "Clone of the test suite $TESTSUITEPREFIX available, OK!"
@@ -157,14 +158,15 @@ fi
 export PYTHONPATH=$TESTSUITEPREFIX:$PYTHONPATH
 
 # Check that we can import from the testsuite
-python3 -c 'import eessi.testsuite'
+testsuite_import="eessi.testsuite"
+python3 -c "import ${testsuite_import}"
 if [[ $? -eq 0 ]]; then
-    echo_green "Succesfully found and imported eessi.testsuite"
+    echo_green "Succesfully found and imported ${testsuite_import}"
 else
-    fatal_error "Failed to import from eessi.testsuite in Python"
+    fatal_error "Failed to import ${testsuite_import}"
 fi
 
-# Configure ReFrame
+# Configure ReFrame, see https://www.eessi.io/docs/test-suite/installation-configuration
 export RFM_CONFIG_FILES=$TOPDIR/reframe_config_bot.py
 export RFM_CONFIG_FILE_TEMPLATE=$TOPDIR/reframe_config_bot.py.tmpl
 export RFM_CHECK_SEARCH_PATH=$TESTSUITEPREFIX/eessi/testsuite/tests

From e5d60b9c6bd2b3a39a32454a9ee6707320693c11 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Thu, 8 Feb 2024 19:26:17 +0100
Subject: [PATCH 084/501] Fix silly mistake: I was overwriting the ReFrame
 config file with every sed call

---
 test_suite.sh | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/test_suite.sh b/test_suite.sh
index d2403b91d8..755102e6bc 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -198,17 +198,18 @@ if [[ "${cpuinfo}" =~ (Core\(s\) per socket:[^0-9]*([0-9]+)) ]]; then
 else
     fatal_error "Failed to get the number of cores per socket for the current test hardware with lscpu."
 fi
-sed "s/__NUM_CPUS__/${cpu_count}/g" $RFM_CONFIG_FILE_TEMPLATE > $RFM_CONFIG_FILES
-sed "s/__NUM_SOCKETS__/${socket_count}/g" $RFM_CONFIG_FILE_TEMPLATE > $RFM_CONFIG_FILES
-sed "s/__NUM_CPUS_PER_CORE__/${threads_per_core}/g" $RFM_CONFIG_FILE_TEMPLATE > $RFM_CONFIG_FILES
-sed "s/__NUM_CPUS_PER_SOCKET__/${cores_per_socket}/g" $RFM_CONFIG_FILE_TEMPLATE > $RFM_CONFIG_FILES
+cp ${RFM_CONFIG_FILE_TEMPLATE} ${RFM_CONFIG_FILES}
+sed -i "s/__NUM_CPUS__/${cpu_count}/g" $RFM_CONFIG_FILES
+sed -i "s/__NUM_SOCKETS__/${socket_count}/g" $RFM_CONFIG_FILES
+sed -i "s/__NUM_CPUS_PER_CORE__/${threads_per_core}/g" $RFM_CONFIG_FILES
+sed -i "s/__NUM_CPUS_PER_SOCKET__/${cores_per_socket}/g" $RFM_CONFIG_FILES
 
 # Check we can run reframe
 reframe --version
 if [[ $? -eq 0 ]]; then
-    echo_green "Succesfully ran reframe --version"
+    echo_green "Succesfully ran 'reframe --version'"
 else
-    fatal_error "Failed to run ReFrame --version"
+    fatal_error "Failed to run 'reframe --version'"
 fi
 
 # List the tests we want to run
@@ -224,7 +225,8 @@ fi
 # Run all tests
 echo "Running tests: reframe ${REFRAME_ARGS} --run"
 reframe ${REFRAME_ARGS} --run
-if [[ $? -eq 0 ]]; then
+reframe_exit_code=$?
+if [[ ${reframe_exit_code} -eq 0 ]]; then
     echo_green "ReFrame runtime ran succesfully with command: reframe ${REFRAME_ARGS} --run."
 else
     fatal_error "ReFrame runtime failed to run with command: reframe ${REFRAME_ARGS} --run."
@@ -233,4 +235,4 @@ fi
 echo ">> Cleaning up ${TMPDIR}..."
 rm -r ${TMPDIR}
 
-exit 0
+exit ${reframe_exit_code}

From b5c60ccfc483602eb6cebb9e1f580c9d99cd964b Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Thu, 8 Feb 2024 19:28:32 +0100
Subject: [PATCH 085/501] See if @boegel is correct and if we don't actually
 need ANY software change to have the bot run...

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml   | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 4c73b5887a..82190071ab 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -15,4 +15,3 @@ easyconfigs:
       options:
         from-pr: 19573
   - scikit-learn-1.3.1-gfbf-2023a.eb
-  - patchelf-0.18.0-GCCcore-12.3.0.eb

From 7fc04d830d372abbebcf9ec3701e38d7b3fec4b8 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sun, 11 Feb 2024 21:46:02 +0100
Subject: [PATCH 086/501] {2023.06}[foss/2022b] ImageMagick v7.1.0-53

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
index 9e92c79062..b8fddd02bb 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
@@ -1,3 +1,4 @@
 easyconfigs:
   - SciPy-bundle-2023.02-gfbf-2022b.eb
   - GDAL-3.6.2-foss-2022b.eb
+  - ImageMagick-7.1.0-53-GCCcore-12.2.0.eb

From 69d6d2e227c6f2ceb0ad39068d6fe4a99d7fd24e Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Wed, 14 Feb 2024 14:55:14 +0100
Subject: [PATCH 087/501] Add escape character to star, so that the regex
 pattern prints correctly on GitHub in the report

---
 bot/check-test.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index ef52206346..bc5ba84101 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -188,6 +188,8 @@ success_msg="no message matching <code>${GP_error}</code>"
 failure_msg="found message matching <code>${GP_error}</code>"
 comment_details_list=${comment_details_list}$(add_detail ${ERROR} 0 "${success_msg}" "${failure_msg}")
 
+# Add an escape character to every *, for it to be printed correctly in the comment on GitHub
+GP_failed="${GP_failed//\*/\\*}"
 success_msg="no message matching <code>""${GP_failed}""</code>"
 failure_msg="found message matching <code>""${GP_failed}""</code>"
 comment_details_list=${comment_details_list}$(add_detail ${FAILED} 0 "${success_msg}" "${failure_msg}")

From 8491f9f090f5a55441904cd1d3b4c7ba5dacab4f Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Thu, 15 Feb 2024 11:58:49 +0100
Subject: [PATCH 088/501] Always use LMOD_RC file, and make sure loading CUDA
 apps always works when building

---
 eessi_container.sh               |  6 ++++++
 init/eessi_environment_variables | 16 +++++++++-------
 2 files changed, 15 insertions(+), 7 deletions(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index d6e9558202..143cbcc6c8 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -457,6 +457,12 @@ if [[ ${SETUP_NVIDIA} -eq 1 ]]; then
         mkdir -p ${EESSI_USR_LOCAL_CUDA}
         BIND_PATHS="${BIND_PATHS},${EESSI_VAR_LOG}:/var/log,${EESSI_USR_LOCAL_CUDA}:/usr/local/cuda"
         [[ ${VERBOSE} -eq 1 ]] && echo "BIND_PATHS=${BIND_PATHS}"
+        if [[ "${NVIDIA_MODE}" == "install" ]] ; then
+            # We need to "trick" our LMOD_RC file to allow us to load CUDA modules even without a CUDA driver
+            # (this works because we build within a container and the LMOD_RC recognises that)
+            touch ${EESSI_TMPDIR}/libcuda.so
+            export SINGULARITY_CONTAINLIBS="${EESSI_TMPDIR}/libcuda.so"
+        fi
     fi
 fi
 
diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index af5222e7b9..e042e8575a 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -50,6 +50,15 @@ if [ -d $EESSI_PREFIX ]; then
 
         show_msg "Using ${EESSI_SOFTWARE_SUBDIR} as software subdirectory."
         export EESSI_SOFTWARE_PATH=$EESSI_PREFIX/software/$EESSI_OS_TYPE/$EESSI_SOFTWARE_SUBDIR
+
+        # Configure our LMOD_RC file
+        export LMOD_RC="$EESSI_SOFTWARE_PATH/.lmod/lmodrc.lua"
+        if [ -f $LMOD_RC ]; then
+          show_msg "Found Lmod configuration file at $LMOD_RC"
+        else
+          error "Lmod configuration file not found at $LMOD_RC"
+        fi
+
         if [ ! -z $EESSI_BASIC_ENV ]; then
           show_msg "Only setting up basic environment, so we're done"
         elif [ -d $EESSI_SOFTWARE_PATH ]; then
@@ -76,13 +85,6 @@ if [ -d $EESSI_PREFIX ]; then
             false
           fi
 
-          export LMOD_RC="$EESSI_SOFTWARE_PATH/.lmod/lmodrc.lua"
-          if [ -f $LMOD_RC ]; then
-            show_msg "Found Lmod configuration file at $LMOD_RC"
-          else
-            error "Lmod configuration file not found at $LMOD_RC"
-          fi
-
         else
           error "EESSI software layer at $EESSI_SOFTWARE_PATH not found!"
         fi

From 2dd048e96cef85b203b76a9ca330c5c72813dbbc Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Thu, 15 Feb 2024 15:44:15 +0100
Subject: [PATCH 089/501] Add the list(SCALES.keys()) feature (though
 technically we could limit to singlenode already here...). Also, make sure
 color is not used for printing the ReFrame results, to avoid color-characters
 making it into the slurm output file

---
 reframe_config_bot.py.tmpl | 4 +++-
 test_suite.sh              | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/reframe_config_bot.py.tmpl b/reframe_config_bot.py.tmpl
index ad66a72041..b2f7916e79 100644
--- a/reframe_config_bot.py.tmpl
+++ b/reframe_config_bot.py.tmpl
@@ -19,7 +19,9 @@ site_configuration = {
                     'scheduler': 'local',
                     'launcher': 'mpirun',
                     'environs': ['default'],
-                    'features': [FEATURES[CPU]],
+                    'features': [
+                        FEATURES[CPU]
+                    ] + list(SCALES.keys()),
                     'processor': {
                         'num_cpus': __NUM_CPUS__,
                         'num_sockets': __NUM_SOCKETS__,
diff --git a/test_suite.sh b/test_suite.sh
index 755102e6bc..f8c46ef764 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -213,7 +213,7 @@ else
 fi
 
 # List the tests we want to run
-export REFRAME_ARGS='--tag CI --tag 1_node'
+export REFRAME_ARGS='--tag CI --tag 1_node --nocolor'
 echo "Listing tests: reframe ${REFRAME_ARGS} --list"
 reframe ${REFRAME_ARGS} --list
 if [[ $? -eq 0 ]]; then

From 0492b9e6d836ef75126ca5e8f613c7ad7487dc2b Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Thu, 15 Feb 2024 15:45:25 +0100
Subject: [PATCH 090/501] Try the original regex patterns, capturing spaces
 more specifically, now that we got rid of color characters

---
 bot/check-test.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index bc5ba84101..4b5f7575e5 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -42,7 +42,7 @@ fi
 # Specifically, we grep for FAILED, since this is also what we print if a step in the test script itself fails
 FAILED=-1
 if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]]; then
-  GP_failed='\[.*FAILED.*\].*Ran .* test case'
+  GP_failed='\[\s*FAILED\s*\].*Ran .* test case'
   grep_reframe_failed=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_failed}")
   [[ $? -eq 0 ]] && FAILED=1 || FAILED=0
   # have to be careful to not add searched for pattern into slurm out file
@@ -65,7 +65,7 @@ fi
 SUCCESS=-1
 # Grep for the success pattern, so we can report the amount of tests run
 if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]]; then
-  GP_success='\[.*PASSED.*\].*Ran .* test case'
+  GP_success='\[\s*PASSED\s*\].*Ran .* test case'
   grep_reframe_success=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_success}")
   [[ $? -eq 0 ]] && SUCCESS=1 || SUCCESS=0
   # have to be careful to not add searched for pattern into slurm out file

From ec61759dc7b8a2a39613aff55f6ae74a55dd2620 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Mon, 19 Feb 2024 12:11:54 +0100
Subject: [PATCH 091/501] Remove manual setup of MODULEPATH etc, and source the
 regular EESSI init script to do this

---
 test_suite.sh | 68 +++++++++++----------------------------------------
 1 file changed, 14 insertions(+), 54 deletions(-)

diff --git a/test_suite.sh b/test_suite.sh
index f8c46ef764..8a98fd59a8 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -74,63 +74,14 @@ fi
 TMPDIR=$(mktemp -d)
 
 echo ">> Setting up environment..."
-
-source $TOPDIR/init/minimal_eessi_env
-
-if [ -d $EESSI_CVMFS_REPO ]; then
-    echo_green "$EESSI_CVMFS_REPO available, OK!"
-else
-    fatal_error "$EESSI_CVMFS_REPO is not available!"
-fi
-
-# avoid that pyc files for EasyBuild are stored in EasyBuild installation directory
-export PYTHONPYCACHEPREFIX=$TMPDIR/pycache
-
-echo ">> Determining software subdirectory to use for current build/test host..."
-if [ -z $EESSI_SOFTWARE_SUBDIR_OVERRIDE ]; then
-  export EESSI_SOFTWARE_SUBDIR_OVERRIDE=$(python3 $TOPDIR/eessi_software_subdir.py $DETECTION_PARAMETERS)
-  echo ">> Determined \$EESSI_SOFTWARE_SUBDIR_OVERRIDE via 'eessi_software_subdir.py $DETECTION_PARAMETERS' script"
-else
-  echo ">> Picking up pre-defined \$EESSI_SOFTWARE_SUBDIR_OVERRIDE: ${EESSI_SOFTWARE_SUBDIR_OVERRIDE}"
-fi
-
-# Set all the EESSI environment variables (respecting $EESSI_SOFTWARE_SUBDIR_OVERRIDE)
-# $EESSI_SILENT - don't print any messages
-# $EESSI_BASIC_ENV - give a basic set of environment variables
-EESSI_SILENT=1 EESSI_BASIC_ENV=1 source $TOPDIR/init/eessi_environment_variables
-
-if [[ -z ${EESSI_SOFTWARE_SUBDIR} ]]; then
-    fatal_error "Failed to determine software subdirectory?!"
-elif [[ "${EESSI_SOFTWARE_SUBDIR}" != "${EESSI_SOFTWARE_SUBDIR_OVERRIDE}" ]]; then
-    fatal_error "Values for EESSI_SOFTWARE_SUBDIR_OVERRIDE (${EESSI_SOFTWARE_SUBDIR_OVERRIDE}) and EESSI_SOFTWARE_SUBDIR (${EESSI_SOFTWARE_SUBDIR}) differ!"
-else
-    echo_green ">> Using ${EESSI_SOFTWARE_SUBDIR} as software subdirectory!"
-fi
-
-echo ">> Initializing Lmod..."
-source $EPREFIX/usr/share/Lmod/init/bash
-ml_version_out=$TMPDIR/ml.out
-ml --version &> $ml_version_out
-if [[ $? -eq 0 ]]; then
-    echo_green ">> Found Lmod ${LMOD_VERSION}"
-else
-    fatal_error "Failed to initialize Lmod?! (see output in ${ml_version_out}"
-fi
-
-echo ">> Setting up \$MODULEPATH..."
-# make sure no modules are loaded
 module --force purge
-# ignore current $MODULEPATH entirely
-module unuse $MODULEPATH
-module use ${EESSI_SOFTWARE_PATH}/modules/all
-if [[ -z ${MODULEPATH} ]]; then
-    fatal_error "Failed to set up \$MODULEPATH?!"
-else
-    echo_green ">> MODULEPATH set up: ${MODULEPATH}"
-fi
+# Make sure defaults are set for EESSI_CVMFS_REPO and EESSI_VERSION, before initializing EESSI
+source $TOPDIR/init/eessi_defaults
+# Initialize EESSI
+source ${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/init/bash
 
 # Load the ReFrame module
- Currently, we load the default version. Maybe we should somehow make this configurable in the future?
+# Currently, we load the default version. Maybe we should somehow make this configurable in the future?
 module load ReFrame
 if [[ $? -eq 0 ]]; then
     echo_green ">> Loaded ReFrame module"
@@ -138,6 +89,15 @@ else
     fatal_error "Failed to load the ReFrame module"
 fi
 
+# Check that a system python3 is available
+python3_found=$(which python3)
+if [ -z ${python3_found} ]; then
+    fatal_error "No system python3 found"
+else
+    echo_green "System python3 found:"
+    python3 -V
+fi
+
 # Check ReFrame came with the hpctestlib and we can import it
 reframe_import="hpctestlib.sciapps.gromacs"
 python3 -c "import ${reframe_import}"

From f3f9721dac3f590768cb9dcb6fbcf26535f049d8 Mon Sep 17 00:00:00 2001
From: Tim Kok <tim.kok@surf.nl>
Date: Tue, 20 Feb 2024 15:12:53 +0100
Subject: [PATCH 092/501] {2023.06}[foss/2023b] WSClean 3.4 + DP3 6.0

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml  | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 4dd31dbd5d..fea9107dc0 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -8,3 +8,33 @@ easyconfigs:
   - matplotlib-3.8.2-gfbf-2023b.eb:
       options:
         from-pr: 19552
+  - AOFlagger-3.4.0-foss-2023b.eb:
+      options:
+        from-pr: 19840
+        # Exclude Lua from `filter-deps` as the compat layer version is too old for the software
+        filter-deps:
+          - Autoconf
+          - Automake
+          - Autotools
+          - binutils
+          - bzip2
+          - DBus
+          - flex
+          - gettext
+          - gperf
+          - help2man
+          - intltool
+          - libreadline
+          - libtool
+          - ncurses
+          - M4
+          - makeinfo
+          - util-linux
+          - XZ
+          - zlib
+  - DP3-6.0-foss-2023b.eb:
+      options:
+        from-pr: 19840
+  - WSClean-3.4-foss-2023b.eb:
+      options:
+        from-pr: 19840

From 9bae7f590a6bfe34e48fe20bc0be066ee407fb25 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 20 Feb 2024 15:26:18 +0100
Subject: [PATCH 093/501] add OpenMPI from PR 19940 (and rebuild: True)

---
 .../2023.06/eessi-2023.06-eb-4.8.2-2023a.yml         | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
index 75dc86c31a..70fb5bfbe0 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
@@ -22,10 +22,6 @@ easyconfigs:
       options:
         from-pr: 19339
   - Qt5-5.15.10-GCCcore-12.3.0.eb
-  - gnuplot-5.4.8-GCCcore-12.3.0.eb: 
-      options:
-        from-pr: 19261
-  - OpenFOAM-10-foss-2023a.eb
   - OSU-Micro-Benchmarks-7.1-1-gompi-2023a.eb
   - LHAPDF-6.5.4-GCC-12.3.0.eb:
       options:
@@ -56,3 +52,11 @@ easyconfigs:
   - BWA-0.7.17-20220923-GCCcore-12.3.0.eb:
       options: 
         from-pr: 19820 
+  - gnuplot-5.4.8-GCCcore-12.3.0.eb: 
+      options:
+        from-pr: 19261
+  - OpenMPI-4.1.5-GCC-12.3.0.eb:
+      options:
+      from-pr: 19940
+      rebuild: True
+  - OpenFOAM-10-foss-2023a.eb

From d3c1f654371126a5187d3a9e07b6def690f8725d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 20 Feb 2024 15:41:24 +0100
Subject: [PATCH 094/501] fix indentation

---
 .../2023.06/eessi-2023.06-eb-4.8.2-2023a.yml                  | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
index 70fb5bfbe0..b971c5adad 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
@@ -57,6 +57,6 @@ easyconfigs:
         from-pr: 19261
   - OpenMPI-4.1.5-GCC-12.3.0.eb:
       options:
-      from-pr: 19940
-      rebuild: True
+        from-pr: 19940
+        rebuild: True
   - OpenFOAM-10-foss-2023a.eb

From f8cd2aa673187d6c1b346d53658932368118bd2a Mon Sep 17 00:00:00 2001
From: Tim Kok <tim.kok@surf.nl>
Date: Tue, 20 Feb 2024 15:41:51 +0100
Subject: [PATCH 095/501] Remove AOFlagger (Lua is no longer part of
 filter-deps)

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml  | 24 -------------------
 1 file changed, 24 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index fea9107dc0..bf7e34932b 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -8,30 +8,6 @@ easyconfigs:
   - matplotlib-3.8.2-gfbf-2023b.eb:
       options:
         from-pr: 19552
-  - AOFlagger-3.4.0-foss-2023b.eb:
-      options:
-        from-pr: 19840
-        # Exclude Lua from `filter-deps` as the compat layer version is too old for the software
-        filter-deps:
-          - Autoconf
-          - Automake
-          - Autotools
-          - binutils
-          - bzip2
-          - DBus
-          - flex
-          - gettext
-          - gperf
-          - help2man
-          - intltool
-          - libreadline
-          - libtool
-          - ncurses
-          - M4
-          - makeinfo
-          - util-linux
-          - XZ
-          - zlib
   - DP3-6.0-foss-2023b.eb:
       options:
         from-pr: 19840

From eafbb6b757320ee003d678989c05bba6eb28ce2f Mon Sep 17 00:00:00 2001
From: Tim Kok <tim.kok@surf.nl>
Date: Tue, 20 Feb 2024 17:29:55 +0100
Subject: [PATCH 096/501] Include easyblocks from pr 3088 to fix Python path

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml   | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index bf7e34932b..e8496f371a 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -8,9 +8,27 @@ easyconfigs:
   - matplotlib-3.8.2-gfbf-2023b.eb:
       options:
         from-pr: 19552
+  - AOFlagger-3.4.0-foss-2023b.eb:
+      options:
+        from:pr: 19840
+        include-easyblocks-from-pr: 3088
+  - casacore-3.5.0-foss-2023b.eb:
+      options:
+        from:pr: 19840
+        include-easyblocks-from-pr: 3088
   - DP3-6.0-foss-2023b.eb:
       options:
         from-pr: 19840
+        include-easyblocks-from-pr: 3088
+  - IDG-1.2.0-foss-2023b.eb:
+      options:
+        from-pr: 19840
+        include-easyblocks-from-pr: 3088
+  - EveryBeam-0.5.2-foss-2023b.eb:
+      options:
+        from-pr: 19840
+        include-easyblocks-from-pr: 3088
   - WSClean-3.4-foss-2023b.eb:
       options:
         from-pr: 19840
+        include-easyblocks-from-pr: 3088

From df089de7c137ecb3232eca5f4266ca7d7cf577ed Mon Sep 17 00:00:00 2001
From: Tim Kok <tim.kok@surf.nl>
Date: Tue, 20 Feb 2024 17:42:44 +0100
Subject: [PATCH 097/501] Fix typo

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml                  | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index e8496f371a..c874d7753f 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -10,11 +10,11 @@ easyconfigs:
         from-pr: 19552
   - AOFlagger-3.4.0-foss-2023b.eb:
       options:
-        from:pr: 19840
+        from-pr: 19840
         include-easyblocks-from-pr: 3088
   - casacore-3.5.0-foss-2023b.eb:
       options:
-        from:pr: 19840
+        from-pr: 19840
         include-easyblocks-from-pr: 3088
   - DP3-6.0-foss-2023b.eb:
       options:

From 2ec41e17b8e6701323e2a1a2070bc7b82c417980 Mon Sep 17 00:00:00 2001
From: Tim Kok <tim.kok@surf.nl>
Date: Wed, 21 Feb 2024 07:49:52 +0100
Subject: [PATCH 098/501] List dependencies first

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml                | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index c874d7753f..d89bf6b1b0 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -16,15 +16,15 @@ easyconfigs:
       options:
         from-pr: 19840
         include-easyblocks-from-pr: 3088
-  - DP3-6.0-foss-2023b.eb:
+  - IDG-1.2.e0-foss-2023b.eb:
       options:
         from-pr: 19840
         include-easyblocks-from-pr: 3088
-  - IDG-1.2.0-foss-2023b.eb:
+  - EveryBeam-0.5.2-foss-2023b.eb:
       options:
         from-pr: 19840
         include-easyblocks-from-pr: 3088
-  - EveryBeam-0.5.2-foss-2023b.eb:
+  - DP3-6.0-foss-2023b.eb:
       options:
         from-pr: 19840
         include-easyblocks-from-pr: 3088

From d0ba0b724fb8ac8a4516d40731023e31fb190b02 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 21 Feb 2024 09:42:52 +0100
Subject: [PATCH 099/501] fix typo in IDG version

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index d89bf6b1b0..33acff2e23 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -16,7 +16,7 @@ easyconfigs:
       options:
         from-pr: 19840
         include-easyblocks-from-pr: 3088
-  - IDG-1.2.e0-foss-2023b.eb:
+  - IDG-1.2.0-foss-2023b.eb:
       options:
         from-pr: 19840
         include-easyblocks-from-pr: 3088

From 5d797a93f21bf7e898898af0e15bc063849c0bd8 Mon Sep 17 00:00:00 2001
From: Tim Kok <tim.kok@surf.nl>
Date: Wed, 21 Feb 2024 11:24:06 +0100
Subject: [PATCH 100/501] Include Armadillo-12.8.0-foss-2023b.eb

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml                  | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 33acff2e23..7d5ce34a83 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -12,6 +12,10 @@ easyconfigs:
       options:
         from-pr: 19840
         include-easyblocks-from-pr: 3088
+  - Armadillo-12.8.0-foss-2023b.eb:
+      options:
+        from-pr: 19840
+        include-easyblocks-from-pr: 3088
   - casacore-3.5.0-foss-2023b.eb:
       options:
         from-pr: 19840

From a55826ddc0f4175e6fb94b7eb355a263d7a4b759 Mon Sep 17 00:00:00 2001
From: Tim Kok <tim.kok@surf.nl>
Date: Wed, 21 Feb 2024 11:24:41 +0100
Subject: [PATCH 101/501] Revert "Include Armadillo-12.8.0-foss-2023b.eb"

This reverts commit b72730eecd5265829b58e8b09c7476d460bb011a.
---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml                  | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 7d5ce34a83..33acff2e23 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -12,10 +12,6 @@ easyconfigs:
       options:
         from-pr: 19840
         include-easyblocks-from-pr: 3088
-  - Armadillo-12.8.0-foss-2023b.eb:
-      options:
-        from-pr: 19840
-        include-easyblocks-from-pr: 3088
   - casacore-3.5.0-foss-2023b.eb:
       options:
         from-pr: 19840

From f63a4d83c0f307f7a7928f8deaab28f09f3ecf21 Mon Sep 17 00:00:00 2001
From: Tim Kok <tim.kok@surf.nl>
Date: Wed, 21 Feb 2024 11:24:06 +0100
Subject: [PATCH 102/501] Include Armadillo-12.8.0-foss-2023b.eb

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml                  | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 33acff2e23..7d5ce34a83 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -12,6 +12,10 @@ easyconfigs:
       options:
         from-pr: 19840
         include-easyblocks-from-pr: 3088
+  - Armadillo-12.8.0-foss-2023b.eb:
+      options:
+        from-pr: 19840
+        include-easyblocks-from-pr: 3088
   - casacore-3.5.0-foss-2023b.eb:
       options:
         from-pr: 19840

From 7a0acebeb3826ba3bbb6172da344d906c60f2a1c Mon Sep 17 00:00:00 2001
From: Tim Kok <tim.kok@surf.nl>
Date: Wed, 21 Feb 2024 15:35:54 +0100
Subject: [PATCH 103/501] Include arpack-ng-3.9.0-foss-2023b.eb

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml                  | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 7d5ce34a83..07c2af56a7 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -12,6 +12,10 @@ easyconfigs:
       options:
         from-pr: 19840
         include-easyblocks-from-pr: 3088
+  - arpack-ng-3.9.0-foss-2023b.eb:
+      options:
+        from-pr: 19840
+        include-easyblocks-from-pr: 3088
   - Armadillo-12.8.0-foss-2023b.eb:
       options:
         from-pr: 19840

From 5c546ea8bff9692f4f6fbd68c0951bc29ff78f05 Mon Sep 17 00:00:00 2001
From: Tim Kok <tim.kok@surf.nl>
Date: Thu, 22 Feb 2024 18:05:46 +0100
Subject: [PATCH 104/501] Disable 'vectorize' toolchain option for casacore
 3.5.0 on aarch64/neoverse_v1 with eb_hook

---
 eb_hooks.py | 29 ++++++++++++++++++++++++++---
 1 file changed, 26 insertions(+), 3 deletions(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index d29a837339..42f67278a8 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -21,7 +21,7 @@
 
 
 CPU_TARGET_NEOVERSE_V1 = 'aarch64/neoverse_v1'
-CPU_TARGET_AARCH64_GENERIC = 'aarch64/generic' 
+CPU_TARGET_AARCH64_GENERIC = 'aarch64/generic'
 
 EESSI_RPATH_OVERRIDE_ATTR = 'orig_rpath_override_dirs'
 
@@ -159,6 +159,28 @@ def post_prepare_hook(self, *args, **kwargs):
     if self.name in POST_PREPARE_HOOKS:
         POST_PREPARE_HOOKS[self.name](self, *args, **kwargs)
 
+def parse_hook_casacore_disable_vectorize(ec, eprefix):
+    """
+    Disable 'vectorize' toolchain option for casacore 3.5.0 on aarch64/neoverse_v1
+    Compiling casacore 3.5.0 with GCC 13.2.0 (foss-2023) gives an error when building for aarch64/neoverse_v1.
+    See also, https://github.com/EESSI/software-layer/pull/479
+    """
+    if ec.name == 'casacore':
+        tcname, tcversion = ec['toolchain']['name'], ec['toolchain']['version']
+        if (
+            LooseVersion(ec.version) == LooseVersion('3.5.0') and
+            tcname == 'foss' and tcversion == '2023b'
+        ):
+            if get_cpu_architecture() == CPU_TARGET_NEOVERSE_V1:
+                ec['toolchainopts']['vectorize'] = False
+                print_msg("Changed toochainopts for %s: %s", ec.name, ec['toolchainopts'])
+            else:
+                print_msg("Not changing option vectorize for %s on non-AARCH64", ec.name)
+        else:
+            print_msg("Not changing option vectorize for %s %s %s", ec.name, ec.version, ec.toolchain)
+
+    else:
+        raise EasyBuildError("casacore-specific hook triggered for non-casacore easyconfig?!")
 
 def parse_hook_cgal_toolchainopts_precise(ec, eprefix):
     """Enable 'precise' rather than 'strict' toolchain option for CGAL on POWER."""
@@ -327,7 +349,7 @@ def pre_configure_hook_wrf_aarch64(self, *args, **kwargs):
             if LooseVersion(self.version) <= LooseVersion('3.9.0'):
                     self.cfg.update('preconfigopts', "sed -i 's/%s/%s/g' arch/configure_new.defaults && " % (pattern, repl))
                     print_msg("Using custom preconfigopts for %s: %s", self.name, self.cfg['preconfigopts'])
-                    
+
             if LooseVersion('4.0.0') <= LooseVersion(self.version) <= LooseVersion('4.2.1'):
                     self.cfg.update('preconfigopts', "sed -i 's/%s/%s/g' arch/configure.defaults && " % (pattern, repl))
                     print_msg("Using custom preconfigopts for %s: %s", self.name, self.cfg['preconfigopts'])
@@ -414,7 +436,7 @@ def pre_test_hook_ignore_failing_tests_netCDF(self, *args, **kwargs):
     """
     cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
     if self.name == 'netCDF' and self.version == '4.9.2' and cpu_target == CPU_TARGET_NEOVERSE_V1:
-        self.cfg['testopts'] = "|| echo ignoring failing tests" 
+        self.cfg['testopts'] = "|| echo ignoring failing tests"
 
 def pre_test_hook_increase_max_failed_tests_arm_PyTorch(self, *args, **kwargs):
     """
@@ -579,6 +601,7 @@ def inject_gpu_property(ec):
 
 
 PARSE_HOOKS = {
+    'casacore': parse_hook_casacore_disable_vectorize,
     'CGAL': parse_hook_cgal_toolchainopts_precise,
     'fontconfig': parse_hook_fontconfig_add_fonts,
     'OpenBLAS': parse_hook_openblas_relax_lapack_tests_num_errors,

From 5b822a3e2292e80077956b0a3f7c9e453a1d25cd Mon Sep 17 00:00:00 2001
From: Tim Kok <tim.kok@surf.nl>
Date: Thu, 22 Feb 2024 18:09:02 +0100
Subject: [PATCH 105/501] Remove empty line

---
 eb_hooks.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index 42f67278a8..2cc9f63ad4 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -178,7 +178,6 @@ def parse_hook_casacore_disable_vectorize(ec, eprefix):
                 print_msg("Not changing option vectorize for %s on non-AARCH64", ec.name)
         else:
             print_msg("Not changing option vectorize for %s %s %s", ec.name, ec.version, ec.toolchain)
-
     else:
         raise EasyBuildError("casacore-specific hook triggered for non-casacore easyconfig?!")
 

From 889243779f41ee43c68079c2bd98133857d75e98 Mon Sep 17 00:00:00 2001
From: Tim Kok <tim.kok@surf.nl>
Date: Thu, 22 Feb 2024 18:11:03 +0100
Subject: [PATCH 106/501] Cleanup code

---
 eb_hooks.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index 2cc9f63ad4..448d6fe62c 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -159,10 +159,11 @@ def post_prepare_hook(self, *args, **kwargs):
     if self.name in POST_PREPARE_HOOKS:
         POST_PREPARE_HOOKS[self.name](self, *args, **kwargs)
 
+
 def parse_hook_casacore_disable_vectorize(ec, eprefix):
     """
     Disable 'vectorize' toolchain option for casacore 3.5.0 on aarch64/neoverse_v1
-    Compiling casacore 3.5.0 with GCC 13.2.0 (foss-2023) gives an error when building for aarch64/neoverse_v1.
+    Compiling casacore 3.5.0 with GCC 13.2.0 (foss-2023b) gives an error when building for aarch64/neoverse_v1.
     See also, https://github.com/EESSI/software-layer/pull/479
     """
     if ec.name == 'casacore':
@@ -181,6 +182,7 @@ def parse_hook_casacore_disable_vectorize(ec, eprefix):
     else:
         raise EasyBuildError("casacore-specific hook triggered for non-casacore easyconfig?!")
 
+
 def parse_hook_cgal_toolchainopts_precise(ec, eprefix):
     """Enable 'precise' rather than 'strict' toolchain option for CGAL on POWER."""
     if ec.name == 'CGAL':

From 4e5f2db05384b43af4ebbe4bca3b787660b21875 Mon Sep 17 00:00:00 2001
From: t1mk1k <96469032+t1mk1k@users.noreply.github.com>
Date: Fri, 23 Feb 2024 15:26:14 +0100
Subject: [PATCH 107/501] Retrieve cpu_target from EESSI env vars
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 eb_hooks.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index 448d6fe62c..747ca5f601 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -172,7 +172,8 @@ def parse_hook_casacore_disable_vectorize(ec, eprefix):
             LooseVersion(ec.version) == LooseVersion('3.5.0') and
             tcname == 'foss' and tcversion == '2023b'
         ):
-            if get_cpu_architecture() == CPU_TARGET_NEOVERSE_V1:
+            cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
+            if cpu_target == CPU_TARGET_NEOVERSE_V1:
                 ec['toolchainopts']['vectorize'] = False
                 print_msg("Changed toochainopts for %s: %s", ec.name, ec['toolchainopts'])
             else:

From 354407375cc65087c5850f162077b7fa22f785f2 Mon Sep 17 00:00:00 2001
From: Tim Kok <tim.kok@surf.nl>
Date: Fri, 23 Feb 2024 15:30:27 +0100
Subject: [PATCH 108/501] Specify print message for skipping non-neoverse_v1

---
 eb_hooks.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index 747ca5f601..15813ec354 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -177,7 +177,7 @@ def parse_hook_casacore_disable_vectorize(ec, eprefix):
                 ec['toolchainopts']['vectorize'] = False
                 print_msg("Changed toochainopts for %s: %s", ec.name, ec['toolchainopts'])
             else:
-                print_msg("Not changing option vectorize for %s on non-AARCH64", ec.name)
+                print_msg("Not changing option vectorize for %s on non-neoverse_v1", ec.name)
         else:
             print_msg("Not changing option vectorize for %s %s %s", ec.name, ec.version, ec.toolchain)
     else:

From 0aea4b44691d237d9359e0a35991b3874b2a092b Mon Sep 17 00:00:00 2001
From: Tim Kok <tim.kok@surf.nl>
Date: Mon, 26 Feb 2024 19:33:34 +0100
Subject: [PATCH 109/501] Create toolchainopts dict if it does not exist

---
 eb_hooks.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/eb_hooks.py b/eb_hooks.py
index 15813ec354..d93ee37067 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -174,6 +174,8 @@ def parse_hook_casacore_disable_vectorize(ec, eprefix):
         ):
             cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
             if cpu_target == CPU_TARGET_NEOVERSE_V1:
+                if not hasattr(ec, 'toolchainopts'):
+                    ec['toolchainopts'] = {}
                 ec['toolchainopts']['vectorize'] = False
                 print_msg("Changed toochainopts for %s: %s", ec.name, ec['toolchainopts'])
             else:

From 07296d3589587cf1090e574513185ad6e50b3d69 Mon Sep 17 00:00:00 2001
From: Tim Kok <tim.kok@surf.nl>
Date: Tue, 27 Feb 2024 11:17:33 +0100
Subject: [PATCH 110/501] Enable lax vector conversion for DP3

---
 eb_hooks.py | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/eb_hooks.py b/eb_hooks.py
index d93ee37067..1478f1a508 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -186,6 +186,32 @@ def parse_hook_casacore_disable_vectorize(ec, eprefix):
         raise EasyBuildError("casacore-specific hook triggered for non-casacore easyconfig?!")
 
 
+def parse_hook_dp3_enable_relaxed_vector_conversions(ec, eprefix):
+    """
+    Enable lax vector conversion for DP3 on aarch64/neoverse_v1
+    Compiling DP3 6.0 with GCC 13.2.0 (foss-2023b) gives a conversion error when building for aarch64/neoverse_v1.
+    See also, https://github.com/EESSI/software-layer/pull/479
+    """
+    if ec.name == 'DP3':
+        tcname, tcversion = ec['toolchain']['name'], ec['toolchain']['version']
+        if (
+            LooseVersion(ec.version) == LooseVersion('6.0') and
+            tcname == 'foss' and tcversion == '2023b'
+        ):
+            cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
+            if cpu_target == CPU_TARGET_NEOVERSE_V1:
+                if not hasattr(ec, 'configopts'):
+                    ec['configopts'] = ""
+                ec['configopts'] += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -flax-vector-conversions" '
+                print_msg("Changed configopts for %s: %s", ec.name, ec['configopts'])
+            else:
+                print_msg("Not changing configopts for %s on non-neoverse_v1", ec.name)
+        else:
+            print_msg("Not changing configopts for %s %s %s", ec.name, ec.version, ec.toolchain)
+    else:
+        raise EasyBuildError("DP3-specific hook triggered for non-DP3 easyconfig?!")
+
+
 def parse_hook_cgal_toolchainopts_precise(ec, eprefix):
     """Enable 'precise' rather than 'strict' toolchain option for CGAL on POWER."""
     if ec.name == 'CGAL':
@@ -607,6 +633,7 @@ def inject_gpu_property(ec):
 PARSE_HOOKS = {
     'casacore': parse_hook_casacore_disable_vectorize,
     'CGAL': parse_hook_cgal_toolchainopts_precise,
+    'DP3': parse_hook_dp3_enable_relaxed_vector_conversions,
     'fontconfig': parse_hook_fontconfig_add_fonts,
     'OpenBLAS': parse_hook_openblas_relax_lapack_tests_num_errors,
     'pybind11': parse_hook_pybind11_replace_catch2,

From 78ba8d8e304ec0ae4c82721e3e5fae7e25402f91 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Fri, 1 Mar 2024 12:53:07 +0100
Subject: [PATCH 111/501] Adding OSU microbenchmarks with GPU support for
 2023a, and one without GPU support for 2023b

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml  | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 0a0a625c35..0d8e71e86c 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -34,3 +34,5 @@ easyconfigs:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/19996
         from-pr: 19996
   - dask-2023.9.2-foss-2023a.eb
+  - OSU-Micro-Benchmarks-7.2-gompi-2023a-CUDA-12.1.1.eb
+  - OSU-Micro-Benchmarks-7.2-gompi-2023b.eb

From e666e2c4058a38b251697730a1551ba0ca34601a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 1 Mar 2024 13:42:12 +0100
Subject: [PATCH 112/501] launch with --fakeroot for build jobs triggered by
 bot

---
 eessi_container.sh | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/eessi_container.sh b/eessi_container.sh
index d6e9558202..55ce409e2b 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -585,6 +585,11 @@ if [[ "${ACCESS}" == "ro" ]]; then
 fi
 
 if [[ "${ACCESS}" == "rw" ]]; then
+  if [[ ! -z ${JOB_CFG_FILE} ]]; then
+    # always launch build jobs triggered by the job with --fakeroot,
+    # we drop back to a regular user in the build script
+    ADDITIONAL_CONTAINER_OPTIONS+=("--fakeroot")
+  fi
   mkdir -p ${EESSI_TMPDIR}/overlay-upper
   mkdir -p ${EESSI_TMPDIR}/overlay-work
 

From 34bc1c25bb0cdc926d05bcc0354069658bf73592 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 1 Mar 2024 13:42:36 +0100
Subject: [PATCH 113/501] remove existing dirs for rebuilds

---
 EESSI-install-software.sh | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 69de9d1997..2803880547 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -222,6 +222,23 @@ else
         echo_green "All set, let's start installing some software with EasyBuild v${eb_version} in ${EASYBUILD_INSTALLPATH}..."
     
         if [ -f ${easystack_file} ]; then
+            if [ $(basename $(dirname ${easystack_file} = 'rebuilds' ]; then
+              echo_green "Software rebuild(s) requested, so determining which existing installation have to be removed..."
+              # we need to remove existing installation directories first,
+              # so let's figure out which modules have to be rebuilt by doing a dry-run and grepping "someapp/someversion" for the relevant lines (with [R])
+              #  * [R] $CFGS/s/someapp/someapp-someversion.eb (module: someapp/someversion)
+              rebuild_apps=$(${EB} --dry-run-short --rebuild --easystack ${easystack_file} | grep "^ \* \[R\]" | grep -o "module: .*[^)]" | awk '{print $2}')
+              for app in ${rebuild_apps}; do
+                app_dir=${EASYBUILD_INSTALLPATH}/software/${app}
+                app_module=${EASYBUILD_INSTALLPATH}/modules/all/${app}.lua
+                echo_yellow "Removing ${appdir} and {app_module}..."
+                rm -rf ${appdir}
+                rm -rf ${app_module}
+              done
+            fi
+            # drop back to a regular user
+            su - eessi
+
             echo_green "Feeding easystack file ${easystack_file} to EasyBuild..."
     
             ${EB} --easystack ${TOPDIR}/${easystack_file} --robot

From 46e753208352710344e9c3f6ebb859c9e3975168 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 1 Mar 2024 13:46:55 +0100
Subject: [PATCH 114/501] rebuild all OpenMPI 4.1.x versions

---
 .../20240301-OpenMPI-4.1.x-fix-smcuda-eb-4.9.0.yml     | 10 ++++++++++
 1 file changed, 10 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/rebuilds/20240301-OpenMPI-4.1.x-fix-smcuda-eb-4.9.0.yml

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240301-OpenMPI-4.1.x-fix-smcuda-eb-4.9.0.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240301-OpenMPI-4.1.x-fix-smcuda-eb-4.9.0.yml
new file mode 100644
index 0000000000..7a6d3c63a3
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240301-OpenMPI-4.1.x-fix-smcuda-eb-4.9.0.yml
@@ -0,0 +1,10 @@
+easyconfigs:
+  - OpenMPI-4.1.4-GCC-12.2.0.eb:
+      options:
+        from-pr: 19940
+  - OpenMPI-4.1.5-GCC-12.3.0:
+      options:
+        from-pr: 19940
+  - OpenMPI-4.1.6-GCC-13.2.0:
+      options:
+        from-pr: 19940

From 21959d651c35c0cf70b68c239deed30f55bb95d2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 1 Mar 2024 13:58:22 +0100
Subject: [PATCH 115/501] add some comments/links

---
 .../rebuilds/20240301-OpenMPI-4.1.x-fix-smcuda-eb-4.9.0.yml  | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240301-OpenMPI-4.1.x-fix-smcuda-eb-4.9.0.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240301-OpenMPI-4.1.x-fix-smcuda-eb-4.9.0.yml
index 7a6d3c63a3..042d0a214c 100644
--- a/easystacks/software.eessi.io/2023.06/rebuilds/20240301-OpenMPI-4.1.x-fix-smcuda-eb-4.9.0.yml
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240301-OpenMPI-4.1.x-fix-smcuda-eb-4.9.0.yml
@@ -1,3 +1,8 @@
+# 2024-03-01
+# Rebuild all OpenMPI 4.1.x versions due to an issue with smcuda:
+# https://github.com/open-mpi/ompi/issues/12270
+# https://github.com/open-mpi/ompi/pull/12344
+# https://github.com/easybuilders/easybuild-easyconfigs/pull/19940
 easyconfigs:
   - OpenMPI-4.1.4-GCC-12.2.0.eb:
       options:

From 7054a587884b2cd56a44bf871d0cd052633a6e1f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 1 Mar 2024 13:59:35 +0100
Subject: [PATCH 116/501] fix syntax, add missing parentheses

---
 EESSI-install-software.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 2803880547..2e3641a3ae 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -222,7 +222,7 @@ else
         echo_green "All set, let's start installing some software with EasyBuild v${eb_version} in ${EASYBUILD_INSTALLPATH}..."
     
         if [ -f ${easystack_file} ]; then
-            if [ $(basename $(dirname ${easystack_file} = 'rebuilds' ]; then
+            if [ $(basename $(dirname ${easystack_file})) = 'rebuilds' ]; then
               echo_green "Software rebuild(s) requested, so determining which existing installation have to be removed..."
               # we need to remove existing installation directories first,
               # so let's figure out which modules have to be rebuilt by doing a dry-run and grepping "someapp/someversion" for the relevant lines (with [R])

From 1fd1609ec960e3b713e940076241f118677a3181 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Fri, 1 Mar 2024 14:00:03 +0100
Subject: [PATCH 117/501] 'which' is not working in the container, command -v
 is

---
 test_suite.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test_suite.sh b/test_suite.sh
index 8a98fd59a8..e9168184bc 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -90,7 +90,7 @@ else
 fi
 
 # Check that a system python3 is available
-python3_found=$(which python3)
+python3_found=$(command -v python3)
 if [ -z ${python3_found} ]; then
     fatal_error "No system python3 found"
 else

From 7b78861fe6ab49547adbcf22df8c044039fbcc3c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 1 Mar 2024 14:01:30 +0100
Subject: [PATCH 118/501] remove spaces from blank lines

---
 EESSI-install-software.sh | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 2e3641a3ae..25069689cc 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -208,19 +208,19 @@ if [ -z ${changed_easystacks} ]; then
     echo "No missing installations, party time!"  # Ensure the bot report success, as there was nothing to be build here
 else
     for easystack_file in ${changed_easystacks}; do
-    
+
         echo -e "Processing easystack file ${easystack_file}...\n\n"
-    
+
         # determine version of EasyBuild module to load based on EasyBuild version included in name of easystack file
         eb_version=$(echo ${easystack_file} | sed 's/.*eb-\([0-9.]*\).*/\1/g')
-    
+
         # load EasyBuild module (will be installed if it's not available yet)
         source ${TOPDIR}/load_easybuild_module.sh ${eb_version}
-    
+
         ${EB} --show-config
-    
+
         echo_green "All set, let's start installing some software with EasyBuild v${eb_version} in ${EASYBUILD_INSTALLPATH}..."
-    
+
         if [ -f ${easystack_file} ]; then
             if [ $(basename $(dirname ${easystack_file})) = 'rebuilds' ]; then
               echo_green "Software rebuild(s) requested, so determining which existing installation have to be removed..."
@@ -240,10 +240,10 @@ else
             su - eessi
 
             echo_green "Feeding easystack file ${easystack_file} to EasyBuild..."
-    
+
             ${EB} --easystack ${TOPDIR}/${easystack_file} --robot
             ec=$?
-    
+
             # copy EasyBuild log file if EasyBuild exited with an error
             if [ ${ec} -ne 0 ]; then
                 eb_last_log=$(unset EB_VERBOSE; eb --last-log)
@@ -253,12 +253,12 @@ else
                 # copy to build logs dir (with context added)
                 copy_build_log "${eb_last_log}" "${build_logs_dir}"
             fi
-    
+
             $TOPDIR/check_missing_installations.sh ${TOPDIR}/${easystack_file}
         else
             fatal_error "Easystack file ${easystack_file} not found!"
         fi
-    
+
     done
 fi
 

From 87e5ff09fbd8720d4cad0bf60647d970cbea0c87 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 1 Mar 2024 14:03:49 +0100
Subject: [PATCH 119/501] rename file to be able to find EB version

---
 ...b-4.9.0.yml => 20240301-eb-4.9.0-OpenMPI-4.1.x-fix-smcuda.yml} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename easystacks/software.eessi.io/2023.06/rebuilds/{20240301-OpenMPI-4.1.x-fix-smcuda-eb-4.9.0.yml => 20240301-eb-4.9.0-OpenMPI-4.1.x-fix-smcuda.yml} (100%)

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240301-OpenMPI-4.1.x-fix-smcuda-eb-4.9.0.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240301-eb-4.9.0-OpenMPI-4.1.x-fix-smcuda.yml
similarity index 100%
rename from easystacks/software.eessi.io/2023.06/rebuilds/20240301-OpenMPI-4.1.x-fix-smcuda-eb-4.9.0.yml
rename to easystacks/software.eessi.io/2023.06/rebuilds/20240301-eb-4.9.0-OpenMPI-4.1.x-fix-smcuda.yml

From d07879f4c28a798e84d4e22e30e874ce766c6deb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 1 Mar 2024 14:06:48 +0100
Subject: [PATCH 120/501] clarify comment about fakeroot

---
 eessi_container.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index 55ce409e2b..bedb269cfd 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -586,7 +586,8 @@ fi
 
 if [[ "${ACCESS}" == "rw" ]]; then
   if [[ ! -z ${JOB_CFG_FILE} ]]; then
-    # always launch build jobs triggered by the job with --fakeroot,
+    # always launch build jobs triggered by the job with --fakeroot in order to be able to remove existing installations, see:
+    # https://github.com/EESSI/software-layer/issues/312
     # we drop back to a regular user in the build script
     ADDITIONAL_CONTAINER_OPTIONS+=("--fakeroot")
   fi

From 135c3c890f00ca282af5dff53fa8f48c302c7247 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 1 Mar 2024 14:08:27 +0100
Subject: [PATCH 121/501] add --allow-use-as-root-and-accept-consequences

---
 EESSI-install-software.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 25069689cc..85cdcbcbbf 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -227,7 +227,7 @@ else
               # we need to remove existing installation directories first,
               # so let's figure out which modules have to be rebuilt by doing a dry-run and grepping "someapp/someversion" for the relevant lines (with [R])
               #  * [R] $CFGS/s/someapp/someapp-someversion.eb (module: someapp/someversion)
-              rebuild_apps=$(${EB} --dry-run-short --rebuild --easystack ${easystack_file} | grep "^ \* \[R\]" | grep -o "module: .*[^)]" | awk '{print $2}')
+              rebuild_apps=$(${EB} --allow-use-as-root-and-accept-consequences --dry-run-short --rebuild --easystack ${easystack_file} | grep "^ \* \[R\]" | grep -o "module: .*[^)]" | awk '{print $2}')
               for app in ${rebuild_apps}; do
                 app_dir=${EASYBUILD_INSTALLPATH}/software/${app}
                 app_module=${EASYBUILD_INSTALLPATH}/modules/all/${app}.lua

From f1831b44d53ecd525717c2c0b1049c0c4da1bca7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 1 Mar 2024 14:14:21 +0100
Subject: [PATCH 122/501] add missing $

---
 EESSI-install-software.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 85cdcbcbbf..4b87a8f0cd 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -231,7 +231,7 @@ else
               for app in ${rebuild_apps}; do
                 app_dir=${EASYBUILD_INSTALLPATH}/software/${app}
                 app_module=${EASYBUILD_INSTALLPATH}/modules/all/${app}.lua
-                echo_yellow "Removing ${appdir} and {app_module}..."
+                echo_yellow "Removing ${appdir} and ${app_module}..."
                 rm -rf ${appdir}
                 rm -rf ${app_module}
               done

From 68212a41298d9a90e95214ccbd971b6d9e2a626a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 1 Mar 2024 14:14:51 +0100
Subject: [PATCH 123/501] fix app_dir variable

---
 EESSI-install-software.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 4b87a8f0cd..6b5aeb39bc 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -231,7 +231,7 @@ else
               for app in ${rebuild_apps}; do
                 app_dir=${EASYBUILD_INSTALLPATH}/software/${app}
                 app_module=${EASYBUILD_INSTALLPATH}/modules/all/${app}.lua
-                echo_yellow "Removing ${appdir} and ${app_module}..."
+                echo_yellow "Removing ${app_dir} and ${app_module}..."
                 rm -rf ${appdir}
                 rm -rf ${app_module}
               done

From 6bcd0e3a8e35613979ed7e45b4ca546c7a46759f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 1 Mar 2024 14:28:15 +0100
Subject: [PATCH 124/501] split loop, first remove everything that needs to be
 removed, then drop back to regular user and do installations

---
 EESSI-install-software.sh | 43 +++++++++++++++++++++++----------------
 1 file changed, 26 insertions(+), 17 deletions(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 6b5aeb39bc..b7350f9fde 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -207,6 +207,32 @@ changed_easystacks=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z
 if [ -z ${changed_easystacks} ]; then
     echo "No missing installations, party time!"  # Ensure the bot report success, as there was nothing to be build here
 else
+    changed_easystacks_rebuilds=$(grep "/rebuilds/" <<< ${changed_easystacks})
+    for easystack_file in ${changed_easystacks_rebuilds}; do
+        # determine version of EasyBuild module to load based on EasyBuild version included in name of easystack file
+        eb_version=$(echo ${easystack_file} | sed 's/.*eb-\([0-9.]*\).*/\1/g')
+
+        # load EasyBuild module (will be installed if it's not available yet)
+        source ${TOPDIR}/load_easybuild_module.sh ${eb_version}
+
+        if [ -f ${easystack_file} ]; then
+            echo_green "Software rebuild(s) requested in ${easystack_file}, so determining which existing installation have to be removed..."
+            # we need to remove existing installation directories first,
+            # so let's figure out which modules have to be rebuilt by doing a dry-run and grepping "someapp/someversion" for the relevant lines (with [R])
+            #  * [R] $CFGS/s/someapp/someapp-someversion.eb (module: someapp/someversion)
+            rebuild_apps=$(${EB} --allow-use-as-root-and-accept-consequences --dry-run-short --rebuild --easystack ${easystack_file} | grep "^ \* \[R\]" | grep -o "module: .*[^)]" | awk '{print $2}')
+            for app in ${rebuild_apps}; do
+                app_dir=${EASYBUILD_INSTALLPATH}/software/${app}
+                app_module=${EASYBUILD_INSTALLPATH}/modules/all/${app}.lua
+                echo_yellow "Removing ${app_dir} and ${app_module}..."
+                rm -rf ${appdir}
+                rm -rf ${app_module}
+            done
+    done
+
+    # drop back to a regular user
+    su - eessi
+
     for easystack_file in ${changed_easystacks}; do
 
         echo -e "Processing easystack file ${easystack_file}...\n\n"
@@ -222,23 +248,6 @@ else
         echo_green "All set, let's start installing some software with EasyBuild v${eb_version} in ${EASYBUILD_INSTALLPATH}..."
 
         if [ -f ${easystack_file} ]; then
-            if [ $(basename $(dirname ${easystack_file})) = 'rebuilds' ]; then
-              echo_green "Software rebuild(s) requested, so determining which existing installation have to be removed..."
-              # we need to remove existing installation directories first,
-              # so let's figure out which modules have to be rebuilt by doing a dry-run and grepping "someapp/someversion" for the relevant lines (with [R])
-              #  * [R] $CFGS/s/someapp/someapp-someversion.eb (module: someapp/someversion)
-              rebuild_apps=$(${EB} --allow-use-as-root-and-accept-consequences --dry-run-short --rebuild --easystack ${easystack_file} | grep "^ \* \[R\]" | grep -o "module: .*[^)]" | awk '{print $2}')
-              for app in ${rebuild_apps}; do
-                app_dir=${EASYBUILD_INSTALLPATH}/software/${app}
-                app_module=${EASYBUILD_INSTALLPATH}/modules/all/${app}.lua
-                echo_yellow "Removing ${app_dir} and ${app_module}..."
-                rm -rf ${appdir}
-                rm -rf ${app_module}
-              done
-            fi
-            # drop back to a regular user
-            su - eessi
-
             echo_green "Feeding easystack file ${easystack_file} to EasyBuild..."
 
             ${EB} --easystack ${TOPDIR}/${easystack_file} --robot

From c81c0dec1709cd683c571bd50537999da1bdd8ca Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 1 Mar 2024 14:31:28 +0100
Subject: [PATCH 125/501] add missing else and fi

---
 EESSI-install-software.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index b7350f9fde..62cc1a3df2 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -228,6 +228,9 @@ else
                 rm -rf ${appdir}
                 rm -rf ${app_module}
             done
+        else
+            fatal_error "Easystack file ${easystack_file} not found!"
+        fi
     done
 
     # drop back to a regular user

From f99458395e44b9b063ad6f785e21a1f16edc16ac Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 1 Mar 2024 14:40:54 +0100
Subject: [PATCH 126/501] su without hypen

---
 EESSI-install-software.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 62cc1a3df2..01ca19336c 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -234,7 +234,7 @@ else
     done
 
     # drop back to a regular user
-    su - eessi
+    su eessi
 
     for easystack_file in ${changed_easystacks}; do
 

From 21e3735712a7679f385a20fa767d60a261854568 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 1 Mar 2024 15:28:28 +0100
Subject: [PATCH 127/501] rerun the script with a regular user after removing
 installations

---
 EESSI-install-software.sh | 63 ++++++++++++++++++++++-----------------
 1 file changed, 35 insertions(+), 28 deletions(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 01ca19336c..1e517bc243 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -187,6 +187,41 @@ fi
 # assume there's only one diff file that corresponds to the PR patch file
 pr_diff=$(ls [0-9]*.diff | head -1)
 
+# if this script is run as root, use PR patch file to determine if software needs to be removed first
+if [ $UID -eq 0 ]; then
+    changed_easystacks_rebuilds=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | egrep -v 'known-issues|missing') | grep "/rebuilds/
+    if [ -z ${changed_easystacks} ]; then
+        echo "No software needs to be removed."
+    else
+        for easystack_file in ${changed_easystacks_rebuilds}; do
+            # determine version of EasyBuild module to load based on EasyBuild version included in name of easystack file
+            eb_version=$(echo ${easystack_file} | sed 's/.*eb-\([0-9.]*\).*/\1/g')
+
+            # load EasyBuild module (will be installed if it's not available yet)
+            source ${TOPDIR}/load_easybuild_module.sh ${eb_version}
+
+            if [ -f ${easystack_file} ]; then
+                echo_green "Software rebuild(s) requested in ${easystack_file}, so determining which existing installation have to be removed..."
+                # we need to remove existing installation directories first,
+                # so let's figure out which modules have to be rebuilt by doing a dry-run and grepping "someapp/someversion" for the relevant lines (with [R])
+                #  * [R] $CFGS/s/someapp/someapp-someversion.eb (module: someapp/someversion)
+                rebuild_apps=$(${EB} --allow-use-as-root-and-accept-consequences --dry-run-short --rebuild --easystack ${easystack_file} | grep "^ \* \[R\]" | grep -o "module: .*[^)]" | awk '{print $2}')
+                for app in ${rebuild_apps}; do
+                    app_dir=${EASYBUILD_INSTALLPATH}/software/${app}
+                    app_module=${EASYBUILD_INSTALLPATH}/modules/all/${app}.lua
+                    echo_yellow "Removing ${app_dir} and ${app_module}..."
+                    rm -rf ${appdir}
+                    rm -rf ${app_module}
+                done
+            else
+                fatal_error "Easystack file ${easystack_file} not found!"
+            fi
+        done
+    fi
+    # now rerun the script with a regular user account to do the software installations
+    exec su eessi $( readlink -f "$0" ) -- "$@"
+fi
+
 # install any additional required scripts
 # order is important: these are needed to install a full CUDA SDK in host_injections
 # for now, this just reinstalls all scripts. Note the most elegant, but works
@@ -207,34 +242,6 @@ changed_easystacks=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z
 if [ -z ${changed_easystacks} ]; then
     echo "No missing installations, party time!"  # Ensure the bot report success, as there was nothing to be build here
 else
-    changed_easystacks_rebuilds=$(grep "/rebuilds/" <<< ${changed_easystacks})
-    for easystack_file in ${changed_easystacks_rebuilds}; do
-        # determine version of EasyBuild module to load based on EasyBuild version included in name of easystack file
-        eb_version=$(echo ${easystack_file} | sed 's/.*eb-\([0-9.]*\).*/\1/g')
-
-        # load EasyBuild module (will be installed if it's not available yet)
-        source ${TOPDIR}/load_easybuild_module.sh ${eb_version}
-
-        if [ -f ${easystack_file} ]; then
-            echo_green "Software rebuild(s) requested in ${easystack_file}, so determining which existing installation have to be removed..."
-            # we need to remove existing installation directories first,
-            # so let's figure out which modules have to be rebuilt by doing a dry-run and grepping "someapp/someversion" for the relevant lines (with [R])
-            #  * [R] $CFGS/s/someapp/someapp-someversion.eb (module: someapp/someversion)
-            rebuild_apps=$(${EB} --allow-use-as-root-and-accept-consequences --dry-run-short --rebuild --easystack ${easystack_file} | grep "^ \* \[R\]" | grep -o "module: .*[^)]" | awk '{print $2}')
-            for app in ${rebuild_apps}; do
-                app_dir=${EASYBUILD_INSTALLPATH}/software/${app}
-                app_module=${EASYBUILD_INSTALLPATH}/modules/all/${app}.lua
-                echo_yellow "Removing ${app_dir} and ${app_module}..."
-                rm -rf ${appdir}
-                rm -rf ${app_module}
-            done
-        else
-            fatal_error "Easystack file ${easystack_file} not found!"
-        fi
-    done
-
-    # drop back to a regular user
-    su eessi
 
     for easystack_file in ${changed_easystacks}; do
 

From 4f436b346bbba403fb8c23c939423ba12b8e1f54 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 1 Mar 2024 15:38:24 +0100
Subject: [PATCH 128/501] fix typo and add missing quote

---
 EESSI-install-software.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 1e517bc243..28bfb8534c 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -189,8 +189,8 @@ pr_diff=$(ls [0-9]*.diff | head -1)
 
 # if this script is run as root, use PR patch file to determine if software needs to be removed first
 if [ $UID -eq 0 ]; then
-    changed_easystacks_rebuilds=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | egrep -v 'known-issues|missing') | grep "/rebuilds/
-    if [ -z ${changed_easystacks} ]; then
+    changed_easystacks_rebuilds=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | egrep -v 'known-issues|missing') | grep "/rebuilds/"
+    if [ -z ${changed_easystacks_rebuilds} ]; then
         echo "No software needs to be removed."
     else
         for easystack_file in ${changed_easystacks_rebuilds}; do

From 0676fdab6d576d0af0b2f107bbd6f92e6cbde146 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 1 Mar 2024 15:44:04 +0100
Subject: [PATCH 129/501] fix syntax

---
 EESSI-install-software.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 28bfb8534c..0f1856891e 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -189,7 +189,7 @@ pr_diff=$(ls [0-9]*.diff | head -1)
 
 # if this script is run as root, use PR patch file to determine if software needs to be removed first
 if [ $UID -eq 0 ]; then
-    changed_easystacks_rebuilds=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | egrep -v 'known-issues|missing') | grep "/rebuilds/"
+    changed_easystacks_rebuilds=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | egrep -v 'known-issues|missing' | grep "/rebuilds/")
     if [ -z ${changed_easystacks_rebuilds} ]; then
         echo "No software needs to be removed."
     else

From 95d6aaa983c9a59e42ff28a6feab75f493dc2e7b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 1 Mar 2024 15:44:23 +0100
Subject: [PATCH 130/501] fix typo in app_dir variable

---
 EESSI-install-software.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 0f1856891e..7f44403c73 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -210,7 +210,7 @@ if [ $UID -eq 0 ]; then
                     app_dir=${EASYBUILD_INSTALLPATH}/software/${app}
                     app_module=${EASYBUILD_INSTALLPATH}/modules/all/${app}.lua
                     echo_yellow "Removing ${app_dir} and ${app_module}..."
-                    rm -rf ${appdir}
+                    rm -rf ${app_dir}
                     rm -rf ${app_module}
                 done
             else

From 314178937a1876eff79300fc0b562031ffc410a8 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Fri, 1 Mar 2024 15:58:01 +0100
Subject: [PATCH 131/501] Workaround for 'PSM3 can't open nic unit' error

---
 test_suite.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/test_suite.sh b/test_suite.sh
index e9168184bc..e3bab04aec 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -164,6 +164,9 @@ sed -i "s/__NUM_SOCKETS__/${socket_count}/g" $RFM_CONFIG_FILES
 sed -i "s/__NUM_CPUS_PER_CORE__/${threads_per_core}/g" $RFM_CONFIG_FILES
 sed -i "s/__NUM_CPUS_PER_SOCKET__/${cores_per_socket}/g" $RFM_CONFIG_FILES
 
+# Workaround for https://github.com/EESSI/software-layer/pull/467#issuecomment-1973341966
+export PSM3_DEVICES='self,shm'  # this is enough, since we only run single node for now
+
 # Check we can run reframe
 reframe --version
 if [[ $? -eq 0 ]]; then

From e52afc192fc900db8476cb4763a5655228ef9d0d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 1 Mar 2024 16:17:49 +0100
Subject: [PATCH 132/501] run removal step without Prefix

---
 EESSI-install-software.sh | 3 ++-
 install_software_layer.sh | 4 ++++
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 7f44403c73..097d0992e5 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -219,7 +219,8 @@ if [ $UID -eq 0 ]; then
         done
     fi
     # now rerun the script with a regular user account to do the software installations
-    exec su eessi $( readlink -f "$0" ) -- "$@"
+    #exec su eessi $( readlink -f "$0" ) -- "$@"
+    exit
 fi
 
 # install any additional required scripts
diff --git a/install_software_layer.sh b/install_software_layer.sh
index 82ca70b73f..85f856e86a 100755
--- a/install_software_layer.sh
+++ b/install_software_layer.sh
@@ -1,4 +1,8 @@
 #!/bin/bash
 base_dir=$(dirname $(realpath $0))
 source ${base_dir}/init/eessi_defaults
+if [ $UID -eq 0 ]; then
+    ./EESSI-install-software.sh "$@"
+    exec runuser -u eessi $( readlink -f "$0" ) -- "$@"
+fi
 ./run_in_compat_layer_env.sh ./EESSI-install-software.sh "$@"

From be4c59280fdf7de49adcc8029970987201f1b551 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 1 Mar 2024 16:36:38 +0100
Subject: [PATCH 133/501] move removal part to its own script, at least for now

---
 EESSI-install-software.sh |  36 --------
 EESSI-remove-software.sh  | 189 ++++++++++++++++++++++++++++++++++++++
 install_software_layer.sh |   2 +-
 3 files changed, 190 insertions(+), 37 deletions(-)
 create mode 100755 EESSI-remove-software.sh

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 097d0992e5..ab91d2c6de 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -187,42 +187,6 @@ fi
 # assume there's only one diff file that corresponds to the PR patch file
 pr_diff=$(ls [0-9]*.diff | head -1)
 
-# if this script is run as root, use PR patch file to determine if software needs to be removed first
-if [ $UID -eq 0 ]; then
-    changed_easystacks_rebuilds=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | egrep -v 'known-issues|missing' | grep "/rebuilds/")
-    if [ -z ${changed_easystacks_rebuilds} ]; then
-        echo "No software needs to be removed."
-    else
-        for easystack_file in ${changed_easystacks_rebuilds}; do
-            # determine version of EasyBuild module to load based on EasyBuild version included in name of easystack file
-            eb_version=$(echo ${easystack_file} | sed 's/.*eb-\([0-9.]*\).*/\1/g')
-
-            # load EasyBuild module (will be installed if it's not available yet)
-            source ${TOPDIR}/load_easybuild_module.sh ${eb_version}
-
-            if [ -f ${easystack_file} ]; then
-                echo_green "Software rebuild(s) requested in ${easystack_file}, so determining which existing installation have to be removed..."
-                # we need to remove existing installation directories first,
-                # so let's figure out which modules have to be rebuilt by doing a dry-run and grepping "someapp/someversion" for the relevant lines (with [R])
-                #  * [R] $CFGS/s/someapp/someapp-someversion.eb (module: someapp/someversion)
-                rebuild_apps=$(${EB} --allow-use-as-root-and-accept-consequences --dry-run-short --rebuild --easystack ${easystack_file} | grep "^ \* \[R\]" | grep -o "module: .*[^)]" | awk '{print $2}')
-                for app in ${rebuild_apps}; do
-                    app_dir=${EASYBUILD_INSTALLPATH}/software/${app}
-                    app_module=${EASYBUILD_INSTALLPATH}/modules/all/${app}.lua
-                    echo_yellow "Removing ${app_dir} and ${app_module}..."
-                    rm -rf ${app_dir}
-                    rm -rf ${app_module}
-                done
-            else
-                fatal_error "Easystack file ${easystack_file} not found!"
-            fi
-        done
-    fi
-    # now rerun the script with a regular user account to do the software installations
-    #exec su eessi $( readlink -f "$0" ) -- "$@"
-    exit
-fi
-
 # install any additional required scripts
 # order is important: these are needed to install a full CUDA SDK in host_injections
 # for now, this just reinstalls all scripts. Note the most elegant, but works
diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
new file mode 100755
index 0000000000..89e5be977e
--- /dev/null
+++ b/EESSI-remove-software.sh
@@ -0,0 +1,189 @@
+#!/bin/bash
+#
+# Script to install EESSI software stack (version set through init/eessi_defaults)
+
+# see example parsing of command line arguments at
+#   https://wiki.bash-hackers.org/scripting/posparams#using_a_while_loop
+#   https://stackoverflow.com/questions/192249/how-do-i-parse-command-line-arguments-in-bash
+
+display_help() {
+  echo "usage: $0 [OPTIONS]"
+  echo "  --build-logs-dir       -  location to copy EasyBuild logs to for failed builds"
+  echo "  -g | --generic         -  instructs script to build for generic architecture target"
+  echo "  -h | --help            -  display this usage information"
+  echo "  -x | --http-proxy URL  -  provides URL for the environment variable http_proxy"
+  echo "  -y | --https-proxy URL -  provides URL for the environment variable https_proxy"
+  echo "  --shared-fs-path       -  path to directory on shared filesystem that can be used"
+}
+
+POSITIONAL_ARGS=()
+
+while [[ $# -gt 0 ]]; do
+  case $1 in
+    -g|--generic)
+      EASYBUILD_OPTARCH="GENERIC"
+      shift
+      ;;
+    -h|--help)
+      display_help  # Call your function
+      # no shifting needed here, we're done.
+      exit 0
+      ;;
+    -x|--http-proxy)
+      export http_proxy="$2"
+      shift 2
+      ;;
+    -y|--https-proxy)
+      export https_proxy="$2"
+      shift 2
+      ;;
+    --build-logs-dir)
+      export build_logs_dir="${2}"
+      shift 2
+      ;;
+    --shared-fs-path)
+      export shared_fs_path="${2}"
+      shift 2
+      ;;
+    -*|--*)
+      echo "Error: Unknown option: $1" >&2
+      exit 1
+      ;;
+    *)  # No more options
+      POSITIONAL_ARGS+=("$1") # save positional arg
+      shift
+      ;;
+  esac
+done
+
+set -- "${POSITIONAL_ARGS[@]}"
+
+TOPDIR=$(dirname $(realpath $0))
+
+source $TOPDIR/scripts/utils.sh
+
+# honor $TMPDIR if it is already defined, use /tmp otherwise
+if [ -z $TMPDIR ]; then
+    export WORKDIR=/tmp/$USER
+else
+    export WORKDIR=$TMPDIR/$USER
+fi
+
+TMPDIR=$(mktemp -d)
+
+echo ">> Setting up environment..."
+
+source $TOPDIR/init/minimal_eessi_env
+
+if [ -d $EESSI_CVMFS_REPO ]; then
+    echo_green "$EESSI_CVMFS_REPO available, OK!"
+else
+    fatal_error "$EESSI_CVMFS_REPO is not available!"
+fi
+
+# avoid that pyc files for EasyBuild are stored in EasyBuild installation directory
+export PYTHONPYCACHEPREFIX=$TMPDIR/pycache
+
+DETECTION_PARAMETERS=''
+GENERIC=0
+EB='eb'
+if [[ "$EASYBUILD_OPTARCH" == "GENERIC" ]]; then
+    echo_yellow ">> GENERIC build requested, taking appropriate measures!"
+    DETECTION_PARAMETERS="$DETECTION_PARAMETERS --generic"
+    GENERIC=1
+    EB='eb --optarch=GENERIC'
+fi
+
+echo ">> Determining software subdirectory to use for current build host..."
+if [ -z $EESSI_SOFTWARE_SUBDIR_OVERRIDE ]; then
+  export EESSI_SOFTWARE_SUBDIR_OVERRIDE=$(python3 $TOPDIR/eessi_software_subdir.py $DETECTION_PARAMETERS)
+  echo ">> Determined \$EESSI_SOFTWARE_SUBDIR_OVERRIDE via 'eessi_software_subdir.py $DETECTION_PARAMETERS' script"
+else
+  echo ">> Picking up pre-defined \$EESSI_SOFTWARE_SUBDIR_OVERRIDE: ${EESSI_SOFTWARE_SUBDIR_OVERRIDE}"
+fi
+
+# Set all the EESSI environment variables (respecting $EESSI_SOFTWARE_SUBDIR_OVERRIDE)
+# $EESSI_SILENT - don't print any messages
+# $EESSI_BASIC_ENV - give a basic set of environment variables
+EESSI_SILENT=1 EESSI_BASIC_ENV=1 source $TOPDIR/init/eessi_environment_variables
+
+if [[ -z ${EESSI_SOFTWARE_SUBDIR} ]]; then
+    fatal_error "Failed to determine software subdirectory?!"
+elif [[ "${EESSI_SOFTWARE_SUBDIR}" != "${EESSI_SOFTWARE_SUBDIR_OVERRIDE}" ]]; then
+    fatal_error "Values for EESSI_SOFTWARE_SUBDIR_OVERRIDE (${EESSI_SOFTWARE_SUBDIR_OVERRIDE}) and EESSI_SOFTWARE_SUBDIR (${EESSI_SOFTWARE_SUBDIR}) differ!"
+else
+    echo_green ">> Using ${EESSI_SOFTWARE_SUBDIR} as software subdirectory!"
+fi
+
+echo ">> Initializing Lmod..."
+source $EPREFIX/usr/share/Lmod/init/bash
+ml_version_out=$TMPDIR/ml.out
+ml --version &> $ml_version_out
+if [[ $? -eq 0 ]]; then
+    echo_green ">> Found Lmod ${LMOD_VERSION}"
+else
+    fatal_error "Failed to initialize Lmod?! (see output in ${ml_version_out}"
+fi
+
+echo ">> Configuring EasyBuild..."
+source $TOPDIR/configure_easybuild
+
+if [ ! -z "${shared_fs_path}" ]; then
+    shared_eb_sourcepath=${shared_fs_path}/easybuild/sources
+    echo ">> Using ${shared_eb_sourcepath} as shared EasyBuild source path"
+    export EASYBUILD_SOURCEPATH=${shared_eb_sourcepath}:${EASYBUILD_SOURCEPATH}
+fi
+
+echo ">> Setting up \$MODULEPATH..."
+# make sure no modules are loaded
+module --force purge
+# ignore current $MODULEPATH entirely
+module unuse $MODULEPATH
+module use $EASYBUILD_INSTALLPATH/modules/all
+if [[ -z ${MODULEPATH} ]]; then
+    fatal_error "Failed to set up \$MODULEPATH?!"
+else
+    echo_green ">> MODULEPATH set up: ${MODULEPATH}"
+fi
+
+# assume there's only one diff file that corresponds to the PR patch file
+pr_diff=$(ls [0-9]*.diff | head -1)
+
+# if this script is run as root, use PR patch file to determine if software needs to be removed first
+if [ $UID -eq 0 ]; then
+    changed_easystacks_rebuilds=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | egrep -v 'known-issues|missing' | grep "/rebuilds/")
+    if [ -z ${changed_easystacks_rebuilds} ]; then
+        echo "No software needs to be removed."
+    else
+        for easystack_file in ${changed_easystacks_rebuilds}; do
+            # determine version of EasyBuild module to load based on EasyBuild version included in name of easystack file
+            eb_version=$(echo ${easystack_file} | sed 's/.*eb-\([0-9.]*\).*/\1/g')
+
+            # load EasyBuild module (will be installed if it's not available yet)
+            source ${TOPDIR}/load_easybuild_module.sh ${eb_version}
+
+            if [ -f ${easystack_file} ]; then
+                echo_green "Software rebuild(s) requested in ${easystack_file}, so determining which existing installation have to be removed..."
+                # we need to remove existing installation directories first,
+                # so let's figure out which modules have to be rebuilt by doing a dry-run and grepping "someapp/someversion" for the relevant lines (with [R])
+                #  * [R] $CFGS/s/someapp/someapp-someversion.eb (module: someapp/someversion)
+                rebuild_apps=$(${EB} --allow-use-as-root-and-accept-consequences --dry-run-short --rebuild --easystack ${easystack_file} | grep "^ \* \[R\]" | grep -o "module: .*[^)]" | awk '{print $2}')
+                for app in ${rebuild_apps}; do
+                    app_dir=${EASYBUILD_INSTALLPATH}/software/${app}
+                    app_module=${EASYBUILD_INSTALLPATH}/modules/all/${app}.lua
+                    echo_yellow "Removing ${app_dir} and ${app_module}..."
+                    rm -rf ${app_dir}
+                    rm -rf ${app_module}
+                done
+            else
+                fatal_error "Easystack file ${easystack_file} not found!"
+            fi
+        done
+    fi
+    # now rerun the script with a regular user account to do the software installations
+    #exec su eessi $( readlink -f "$0" ) -- "$@"
+    exit
+fi
+
+echo ">> Cleaning up ${TMPDIR}..."
+rm -r ${TMPDIR}
diff --git a/install_software_layer.sh b/install_software_layer.sh
index 85f856e86a..249140a503 100755
--- a/install_software_layer.sh
+++ b/install_software_layer.sh
@@ -2,7 +2,7 @@
 base_dir=$(dirname $(realpath $0))
 source ${base_dir}/init/eessi_defaults
 if [ $UID -eq 0 ]; then
-    ./EESSI-install-software.sh "$@"
+    ./EESSI-remove-software.sh "$@"
     exec runuser -u eessi $( readlink -f "$0" ) -- "$@"
 fi
 ./run_in_compat_layer_env.sh ./EESSI-install-software.sh "$@"

From efbeb561740f8ef5c066e1b064c16f45087c668f Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Mon, 4 Mar 2024 16:59:00 +0100
Subject: [PATCH 134/501] Use LMOD_CONFIG_DIR instead of LMOD_RC to allow user
 overrides of what we specify in our RC file, see search order on
 https://lmod.readthedocs.io/en/latest/145_properties.html?highlight=lmod_rc#the-properties-file-lmodrc-lua
 . Also, prefix our hooks with eessi_ to avoid unintentional clashes in
 namespace between site lmod configuration and eessi lmod configuration

---
 create_lmodrc.py                 | 8 ++++----
 init/eessi_environment_variables | 4 ++--
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/create_lmodrc.py b/create_lmodrc.py
index bc69dd4396..ff34906c0b 100755
--- a/create_lmodrc.py
+++ b/create_lmodrc.py
@@ -29,7 +29,7 @@
     return content
 end
 
-local function cuda_enabled_load_hook(t)
+local function eessi_cuda_enabled_load_hook(t)
     local frameStk  = require("FrameStk"):singleton()
     local mt        = frameStk:mt()
     local simpleName = string.match(t.modFullName, "(.-)/")
@@ -94,7 +94,7 @@
     end
 end
 
-local function openmpi_load_hook(t)
+local function eessi_openmpi_load_hook(t)
     -- disable smcuda BTL when loading OpenMPI module for aarch64/neoverse_v1,
     -- to work around hang/crash due to bug in OpenMPI;
     -- see https://gitlab.com/eessi/support/-/issues/41
@@ -114,8 +114,8 @@
     end
 end
 
-hook.register("load", cuda_enabled_load_hook)
-hook.register("load", openmpi_load_hook)
+hook.register("load", eessi_cuda_enabled_load_hook)
+hook.register("load", eessi_openmpi_load_hook)
 """
 
 def error(msg):
diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index af5222e7b9..d3a209630e 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -76,8 +76,8 @@ if [ -d $EESSI_PREFIX ]; then
             false
           fi
 
-          export LMOD_RC="$EESSI_SOFTWARE_PATH/.lmod/lmodrc.lua"
-          if [ -f $LMOD_RC ]; then
+          export LMOD_CONFIG_DIR="$EESSI_SOFTWARE_PATH/.lmod"
+          if [ -f $LMOD_CONFIG_DIR/lmodrc.lua ]; then
             show_msg "Found Lmod configuration file at $LMOD_RC"
           else
             error "Lmod configuration file not found at $LMOD_RC"

From 590cabd7c068a9986f0eba33792005a7b9ce883a Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 5 Mar 2024 10:42:27 +0100
Subject: [PATCH 135/501] Combine functions into a single function, before
 registering this as a hook. Lmod only permits the registration of a single
 function, trying to register a second function will just overwrite the first,
 as can be seen from
 https://github.com/TACC/Lmod/blob/a97d68193a6f32ebca4b4bd70dac0f6ac8fddefe/src/Hook.lua#L87

---
 create_lmodrc.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/create_lmodrc.py b/create_lmodrc.py
index ff34906c0b..621c8e271a 100755
--- a/create_lmodrc.py
+++ b/create_lmodrc.py
@@ -114,8 +114,15 @@
     end
 end
 
-hook.register("load", eessi_cuda_enabled_load_hook)
-hook.register("load", eessi_openmpi_load_hook)
+-- Combine both functions into a single one, as we can only register one function as load hook in lmod
+-- Also: make it non-local, so it can be imported and extended by other lmodrc files if needed
+function eessi_load_hook(t)
+    eessi_cuda_enabled_load_hook(t)
+    eessi_openmpi_load_hook(t)
+end
+
+
+hook.register("load", eessi_load_hook)
 """
 
 def error(msg):

From 340b8332ffb858ba43613f38bd4ac23d260cc31e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 5 Mar 2024 14:55:32 +0100
Subject: [PATCH 136/501] remove su, add error message

---
 EESSI-remove-software.sh | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index 89e5be977e..e55efe823e 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -180,10 +180,10 @@ if [ $UID -eq 0 ]; then
             fi
         done
     fi
-    # now rerun the script with a regular user account to do the software installations
-    #exec su eessi $( readlink -f "$0" ) -- "$@"
-    exit
+else
+    fatal_error "This script can only be run by root!"
 fi
 
-echo ">> Cleaning up ${TMPDIR}..."
-rm -r ${TMPDIR}
+
+#echo ">> Cleaning up ${TMPDIR}..."
+#rm -r ${TMPDIR}

From 88d21d9487272abbe951477be8727165d1c01795 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 5 Mar 2024 15:13:27 +0100
Subject: [PATCH 137/501] first run the EESSI-remove-software.sh script in a
 separate container session

---
 eessi_container.sh | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index bedb269cfd..09cec8964f 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -585,12 +585,12 @@ if [[ "${ACCESS}" == "ro" ]]; then
 fi
 
 if [[ "${ACCESS}" == "rw" ]]; then
-  if [[ ! -z ${JOB_CFG_FILE} ]]; then
+  #if [[ ! -z ${JOB_CFG_FILE} ]]; then
     # always launch build jobs triggered by the job with --fakeroot in order to be able to remove existing installations, see:
     # https://github.com/EESSI/software-layer/issues/312
     # we drop back to a regular user in the build script
-    ADDITIONAL_CONTAINER_OPTIONS+=("--fakeroot")
-  fi
+    #ADDITIONAL_CONTAINER_OPTIONS+=("--fakeroot")
+  #fi
   mkdir -p ${EESSI_TMPDIR}/overlay-upper
   mkdir -p ${EESSI_TMPDIR}/overlay-work
 
@@ -627,6 +627,12 @@ if [ ! -z ${EESSI_SOFTWARE_SUBDIR_OVERRIDE} ]; then
     export APPTAINERENV_EESSI_SOFTWARE_SUBDIR_OVERRIDE=${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
 fi
 
+if [[ ! -z ${JOB_CFG_FILE} ]]; then
+    echo "Removing software by launching container with command (next line):"
+    echo "singularity ${RUN_QUIET} exec --fakeroot ${ADDITIONAL_CONTAINER_OPTIONS[@]} ${EESSI_FUSE_MOUNTS[@]} ${CONTAINER} ./EESSI-remove-software.sh"
+    singularity ${RUN_QUIET} exec --fakeroot "${ADDITIONAL_CONTAINER_OPTIONS[@]}" "${EESSI_FUSE_MOUNTS[@]}" ${CONTAINER} ./EESSI-remove-software.sh
+fi
+
 echo "Launching container with command (next line):"
 echo "singularity ${RUN_QUIET} ${MODE} ${ADDITIONAL_CONTAINER_OPTIONS[@]} ${EESSI_FUSE_MOUNTS[@]} ${CONTAINER} $@"
 singularity ${RUN_QUIET} ${MODE} "${ADDITIONAL_CONTAINER_OPTIONS[@]}" "${EESSI_FUSE_MOUNTS[@]}" ${CONTAINER} "$@"

From 499328d70e3c6275eec9dcaf717a34afaf75a6e0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 5 Mar 2024 15:14:47 +0100
Subject: [PATCH 138/501] undo

---
 install_software_layer.sh | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/install_software_layer.sh b/install_software_layer.sh
index 249140a503..82ca70b73f 100755
--- a/install_software_layer.sh
+++ b/install_software_layer.sh
@@ -1,8 +1,4 @@
 #!/bin/bash
 base_dir=$(dirname $(realpath $0))
 source ${base_dir}/init/eessi_defaults
-if [ $UID -eq 0 ]; then
-    ./EESSI-remove-software.sh "$@"
-    exec runuser -u eessi $( readlink -f "$0" ) -- "$@"
-fi
 ./run_in_compat_layer_env.sh ./EESSI-install-software.sh "$@"

From 8100fed0e6a7105a4f1ffc08f6fca89f35145e0b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 5 Mar 2024 15:32:27 +0100
Subject: [PATCH 139/501] dont use TMPDIR

---
 EESSI-remove-software.sh | 20 +++-----------------
 1 file changed, 3 insertions(+), 17 deletions(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index e55efe823e..91490507c6 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -62,15 +62,6 @@ TOPDIR=$(dirname $(realpath $0))
 
 source $TOPDIR/scripts/utils.sh
 
-# honor $TMPDIR if it is already defined, use /tmp otherwise
-if [ -z $TMPDIR ]; then
-    export WORKDIR=/tmp/$USER
-else
-    export WORKDIR=$TMPDIR/$USER
-fi
-
-TMPDIR=$(mktemp -d)
-
 echo ">> Setting up environment..."
 
 source $TOPDIR/init/minimal_eessi_env
@@ -82,7 +73,7 @@ else
 fi
 
 # avoid that pyc files for EasyBuild are stored in EasyBuild installation directory
-export PYTHONPYCACHEPREFIX=$TMPDIR/pycache
+#export PYTHONPYCACHEPREFIX=$TMPDIR/pycache
 
 DETECTION_PARAMETERS=''
 GENERIC=0
@@ -117,12 +108,11 @@ fi
 
 echo ">> Initializing Lmod..."
 source $EPREFIX/usr/share/Lmod/init/bash
-ml_version_out=$TMPDIR/ml.out
-ml --version &> $ml_version_out
+ml --version
 if [[ $? -eq 0 ]]; then
     echo_green ">> Found Lmod ${LMOD_VERSION}"
 else
-    fatal_error "Failed to initialize Lmod?! (see output in ${ml_version_out}"
+    fatal_error "Failed to initialize Lmod?!"
 fi
 
 echo ">> Configuring EasyBuild..."
@@ -183,7 +173,3 @@ if [ $UID -eq 0 ]; then
 else
     fatal_error "This script can only be run by root!"
 fi
-
-
-#echo ">> Cleaning up ${TMPDIR}..."
-#rm -r ${TMPDIR}

From c758d74bc70d386ea8c1134d5f9edf500b48db5a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 5 Mar 2024 15:42:15 +0100
Subject: [PATCH 140/501] use EUID instead of UID

---
 EESSI-remove-software.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index 91490507c6..4cbc27be98 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -140,7 +140,7 @@ fi
 pr_diff=$(ls [0-9]*.diff | head -1)
 
 # if this script is run as root, use PR patch file to determine if software needs to be removed first
-if [ $UID -eq 0 ]; then
+if [ $EUID -eq 0 ]; then
     changed_easystacks_rebuilds=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | egrep -v 'known-issues|missing' | grep "/rebuilds/")
     if [ -z ${changed_easystacks_rebuilds} ]; then
         echo "No software needs to be removed."

From 78cc503e43cd4731fb5a8c10c4d3499613cb09f9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 5 Mar 2024 15:48:15 +0100
Subject: [PATCH 141/501] do set/override TMPDIR

---
 EESSI-remove-software.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index 4cbc27be98..819c08f8ce 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -60,6 +60,8 @@ set -- "${POSITIONAL_ARGS[@]}"
 
 TOPDIR=$(dirname $(realpath $0))
 
+export TMPDIR=$(mktemp -d /tmp/eessi-remove.XXXXXXXX)
+
 source $TOPDIR/scripts/utils.sh
 
 echo ">> Setting up environment..."

From 0de249e32f6cb2cd1cbb694cbddf37fb93987561 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 5 Mar 2024 18:15:10 +0100
Subject: [PATCH 142/501] Look for site-specific lmodrc file in
 host_injections. If present, set LMOD_RC

---
 init/eessi_environment_variables | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index d3a209630e..1c8a68b1d5 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -82,6 +82,11 @@ if [ -d $EESSI_PREFIX ]; then
           else
             error "Lmod configuration file not found at $LMOD_RC"
           fi
+          # Allow for site-specific lmod configuration
+          host_lmod_rc="$EESSI_CVMFS_REPO"/host_injections/.lmod/lmodrc.lua
+          if [ -f $host_lmod_rc ]; then
+              export LMOD_RC="$host_lmod_rc"
+          fi
 
         else
           error "EESSI software layer at $EESSI_SOFTWARE_PATH not found!"

From c1840dd55f306b20e6d26201990313ad4dc18a3a Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Wed, 6 Mar 2024 15:05:07 +0100
Subject: [PATCH 143/501] Next the local lmodrc within the versioned directory,
 e.g. /cvmfs/software.eessi.io/host_injections/2023.06/.lmod/lmodrc.lua

---
 init/eessi_environment_variables | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index 1c8a68b1d5..5407034191 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -83,7 +83,7 @@ if [ -d $EESSI_PREFIX ]; then
             error "Lmod configuration file not found at $LMOD_RC"
           fi
           # Allow for site-specific lmod configuration
-          host_lmod_rc="$EESSI_CVMFS_REPO"/host_injections/.lmod/lmodrc.lua
+          host_lmod_rc="${EESSI_PREFIX/versions/host_injections}/.lmod/lmodrc.lua
           if [ -f $host_lmod_rc ]; then
               export LMOD_RC="$host_lmod_rc"
           fi

From df4140a74bad2f0af022c10a2d8ada12fa1627df Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Wed, 6 Mar 2024 15:54:28 +0100
Subject: [PATCH 144/501] Update init/eessi_environment_variables

---
 init/eessi_environment_variables | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index 5407034191..f9ca6de408 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -83,7 +83,7 @@ if [ -d $EESSI_PREFIX ]; then
             error "Lmod configuration file not found at $LMOD_RC"
           fi
           # Allow for site-specific lmod configuration
-          host_lmod_rc="${EESSI_PREFIX/versions/host_injections}/.lmod/lmodrc.lua
+          host_lmod_rc="${EESSI_PREFIX/versions/host_injections}"/.lmod/lmodrc.lua
           if [ -f $host_lmod_rc ]; then
               export LMOD_RC="$host_lmod_rc"
           fi

From 78e582ba2c5fd5de813836151a3d256fc6ba5c94 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Wed, 6 Mar 2024 15:59:31 +0100
Subject: [PATCH 145/501] Update init/eessi_environment_variables

---
 init/eessi_environment_variables | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index f9ca6de408..b41dd60924 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -78,9 +78,9 @@ if [ -d $EESSI_PREFIX ]; then
 
           export LMOD_CONFIG_DIR="$EESSI_SOFTWARE_PATH/.lmod"
           if [ -f $LMOD_CONFIG_DIR/lmodrc.lua ]; then
-            show_msg "Found Lmod configuration file at $LMOD_RC"
+            show_msg "Found Lmod configuration file at $LMOD_CONFIG_DIR/lmodrc.lua"
           else
-            error "Lmod configuration file not found at $LMOD_RC"
+            error "Lmod configuration file not found at $LMOD_CONFIG_DIR/lmodrc.lua"
           fi
           # Allow for site-specific lmod configuration
           host_lmod_rc="${EESSI_PREFIX/versions/host_injections}"/.lmod/lmodrc.lua

From 77c97235f0291dff7b98f2f1958e345a7afb48ee Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Wed, 6 Mar 2024 16:00:42 +0100
Subject: [PATCH 146/501] Update init/eessi_environment_variables

---
 init/eessi_environment_variables | 1 +
 1 file changed, 1 insertion(+)

diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index b41dd60924..d4c113c67a 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -85,6 +85,7 @@ if [ -d $EESSI_PREFIX ]; then
           # Allow for site-specific lmod configuration
           host_lmod_rc="${EESSI_PREFIX/versions/host_injections}"/.lmod/lmodrc.lua
           if [ -f $host_lmod_rc ]; then
+              show_msg "Found site Lmod configuration file at $LMOD_RC"
               export LMOD_RC="$host_lmod_rc"
           fi
 

From 276a64c66347e24b94ace71914547cc0abd75381 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Thu, 7 Mar 2024 07:54:23 +0000
Subject: [PATCH 147/501] {2023.06}[gompi/2023b] CDO v2.2.2

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 4dd31dbd5d..2664d8f417 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -8,3 +8,6 @@ easyconfigs:
   - matplotlib-3.8.2-gfbf-2023b.eb:
       options:
         from-pr: 19552
+  - CDO-2.2.2-gompi-2023b.eb:
+      options:
+        from-pr: 19792   

From e33938f1a8424d28966827c4a8942f82b8043bed Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Thu, 7 Mar 2024 14:52:25 +0100
Subject: [PATCH 148/501] Revert changes in eessi_environment_variables. Limit
 this PR to the bug fix only. We can follow up properly using SitePackage.lua
 instead

---
 init/eessi_environment_variables | 14 ++++----------
 1 file changed, 4 insertions(+), 10 deletions(-)

diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index d4c113c67a..af5222e7b9 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -76,17 +76,11 @@ if [ -d $EESSI_PREFIX ]; then
             false
           fi
 
-          export LMOD_CONFIG_DIR="$EESSI_SOFTWARE_PATH/.lmod"
-          if [ -f $LMOD_CONFIG_DIR/lmodrc.lua ]; then
-            show_msg "Found Lmod configuration file at $LMOD_CONFIG_DIR/lmodrc.lua"
+          export LMOD_RC="$EESSI_SOFTWARE_PATH/.lmod/lmodrc.lua"
+          if [ -f $LMOD_RC ]; then
+            show_msg "Found Lmod configuration file at $LMOD_RC"
           else
-            error "Lmod configuration file not found at $LMOD_CONFIG_DIR/lmodrc.lua"
-          fi
-          # Allow for site-specific lmod configuration
-          host_lmod_rc="${EESSI_PREFIX/versions/host_injections}"/.lmod/lmodrc.lua
-          if [ -f $host_lmod_rc ]; then
-              show_msg "Found site Lmod configuration file at $LMOD_RC"
-              export LMOD_RC="$host_lmod_rc"
+            error "Lmod configuration file not found at $LMOD_RC"
           fi
 
         else

From c660a4259c7e391502167203e4a9bc31bbac692e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 8 Mar 2024 10:40:40 +0100
Subject: [PATCH 149/501] dont set fakeroot here

---
 eessi_container.sh | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index 09cec8964f..ad6d68640c 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -627,11 +627,11 @@ if [ ! -z ${EESSI_SOFTWARE_SUBDIR_OVERRIDE} ]; then
     export APPTAINERENV_EESSI_SOFTWARE_SUBDIR_OVERRIDE=${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
 fi
 
-if [[ ! -z ${JOB_CFG_FILE} ]]; then
-    echo "Removing software by launching container with command (next line):"
-    echo "singularity ${RUN_QUIET} exec --fakeroot ${ADDITIONAL_CONTAINER_OPTIONS[@]} ${EESSI_FUSE_MOUNTS[@]} ${CONTAINER} ./EESSI-remove-software.sh"
-    singularity ${RUN_QUIET} exec --fakeroot "${ADDITIONAL_CONTAINER_OPTIONS[@]}" "${EESSI_FUSE_MOUNTS[@]}" ${CONTAINER} ./EESSI-remove-software.sh
-fi
+#if [[ ! -z ${JOB_CFG_FILE} ]]; then
+#    echo "Removing software by launching container with command (next line):"
+#    echo "singularity ${RUN_QUIET} exec --fakeroot ${ADDITIONAL_CONTAINER_OPTIONS[@]} ${EESSI_FUSE_MOUNTS[@]} ${CONTAINER} ./EESSI-remove-software.sh"
+#    singularity ${RUN_QUIET} exec --fakeroot "${ADDITIONAL_CONTAINER_OPTIONS[@]}" "${EESSI_FUSE_MOUNTS[@]}" ${CONTAINER} ./EESSI-remove-software.sh
+#fi
 
 echo "Launching container with command (next line):"
 echo "singularity ${RUN_QUIET} ${MODE} ${ADDITIONAL_CONTAINER_OPTIONS[@]} ${EESSI_FUSE_MOUNTS[@]} ${CONTAINER} $@"

From be5aa374e0aea043f97a709afae6fba58c556a59 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 8 Mar 2024 10:40:51 +0100
Subject: [PATCH 150/501] run build step with fakeroot

---
 bot/build.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/bot/build.sh b/bot/build.sh
index 1622e757e2..ef9b34ab88 100755
--- a/bot/build.sh
+++ b/bot/build.sh
@@ -181,6 +181,8 @@ BUILD_STEP_ARGS+=("--nvidia" "all")
 if [[ ! -z ${SHARED_FS_PATH} ]]; then
     BUILD_STEP_ARGS+=("--host-injections" "${SHARED_FS_PATH}/host-injections")
 fi
+# add fakeroot option in order to be able to remove software
+BUILD_STEP_ARGS+=("--fakeroot")
 
 # prepare arguments to install_software_layer.sh (specific to build step)
 declare -a INSTALL_SCRIPT_ARGS=()

From 4946b085eb6bff9515aa8e2257d3320f778ab6f4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 8 Mar 2024 10:41:21 +0100
Subject: [PATCH 151/501] if run as root, run the removal script

---
 install_software_layer.sh | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/install_software_layer.sh b/install_software_layer.sh
index 82ca70b73f..8137ec78e3 100755
--- a/install_software_layer.sh
+++ b/install_software_layer.sh
@@ -1,4 +1,8 @@
 #!/bin/bash
 base_dir=$(dirname $(realpath $0))
 source ${base_dir}/init/eessi_defaults
+if [ $EUID -eq 0 ]; then
+    ./EESSI-remove-software.sh "$@"
+    exec runuser -u eessi $( readlink -f "$0" ) -- "$@"
+fi
 ./run_in_compat_layer_env.sh ./EESSI-install-software.sh "$@"

From 123c47a84ff20e35c2fbe7dba6a7f371b9a1c694 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 8 Mar 2024 10:51:16 +0100
Subject: [PATCH 152/501] add fakeroot option

---
 eessi_container.sh | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/eessi_container.sh b/eessi_container.sh
index ad6d68640c..af8618f4b8 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -73,6 +73,7 @@ display_help() {
   echo "  -a | --access {ro,rw}  - ro (read-only), rw (read & write) [default: ro]"
   echo "  -c | --container IMG   - image file or URL defining the container to use"
   echo "                           [default: docker://ghcr.io/eessi/build-node:debian11]"
+  echo "  -f | --fakeroot        - run the container with --fakeroot [default: false]"
   echo "  -g | --storage DIR     - directory space on host machine (used for"
   echo "                           temporary data) [default: 1. TMPDIR, 2. /tmp]"
   echo "  -h | --help            - display this usage information [default: false]"
@@ -113,6 +114,7 @@ display_help() {
 ACCESS="ro"
 CONTAINER="docker://ghcr.io/eessi/build-node:debian11"
 #DRY_RUN=0
+FAKEROOT=0
 VERBOSE=0
 STORAGE=
 LIST_REPOS=0
@@ -140,6 +142,10 @@ while [[ $# -gt 0 ]]; do
 #      DRY_RUN=1
 #      shift 1
 #      ;;
+    -f|--fakeroot)
+      FAKEROOT=1
+      shift 1
+      ;;
     -g|--storage)
       STORAGE="$2"
       shift 2
@@ -460,6 +466,11 @@ if [[ ${SETUP_NVIDIA} -eq 1 ]]; then
     fi
 fi
 
+# Configure the fakeroot setting for the container
+if [[ ${FAKEROOT} -eq 1 ]]; then
+  ADDITIONAL_CONTAINER_OPTIONS+=("--fakeroot")
+fi
+
 # set up repository config (always create directory repos_cfg and populate it with info when
 # arg -r|--repository is used)
 mkdir -p ${EESSI_TMPDIR}/repos_cfg

From 93ccf68c0fcb5f48aeba2339f09bdf892d4547d4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 8 Mar 2024 11:13:46 +0100
Subject: [PATCH 153/501] add echo

---
 install_software_layer.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/install_software_layer.sh b/install_software_layer.sh
index 8137ec78e3..c5cf40bb5a 100755
--- a/install_software_layer.sh
+++ b/install_software_layer.sh
@@ -1,6 +1,9 @@
 #!/bin/bash
 base_dir=$(dirname $(realpath $0))
 source ${base_dir}/init/eessi_defaults
+
+echo "User ID: $EUID"
+
 if [ $EUID -eq 0 ]; then
     ./EESSI-remove-software.sh "$@"
     exec runuser -u eessi $( readlink -f "$0" ) -- "$@"

From 017803bbf1705045b84a4bf8c8b4e479fffada5b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 8 Mar 2024 11:18:57 +0100
Subject: [PATCH 154/501] add echo

---
 EESSI-install-software.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index ab91d2c6de..4d26b30b53 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -87,6 +87,8 @@ while [[ $# -gt 0 ]]; do
   esac
 done
 
+echo "Software installation user: $EUID $UID"
+
 set -- "${POSITIONAL_ARGS[@]}"
 
 TOPDIR=$(dirname $(realpath $0))

From c49240680190081b1e0cc6ac8b9e57bffde415c1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 8 Mar 2024 11:51:42 +0100
Subject: [PATCH 155/501] add removal step

---
 bot/build.sh | 41 ++++++++++++++++++++++++++++++-----------
 1 file changed, 30 insertions(+), 11 deletions(-)

diff --git a/bot/build.sh b/bot/build.sh
index ef9b34ab88..bc1cd27770 100755
--- a/bot/build.sh
+++ b/bot/build.sh
@@ -168,9 +168,34 @@ COMMON_ARGS+=("--mode" "run")
 # make sure to use the same parent dir for storing tarballs of tmp
 PREVIOUS_TMP_DIR=${PWD}/previous_tmp
 
-# prepare directory to store tarball of tmp for build step
+# prepare directory to store tarball of tmp for removal and build steps
+TARBALL_TMP_REMOVE_STEP_DIR=${PREVIOUS_TMP_DIR}/remove_step
 TARBALL_TMP_BUILD_STEP_DIR=${PREVIOUS_TMP_DIR}/build_step
-mkdir -p ${TARBALL_TMP_BUILD_STEP_DIR}
+mkdir -p ${TARBALL_TMP_BUILD_STEP_DIR} ${TARBALL_TMP_REMOVE_STEP_DIR}
+
+# prepare arguments to install_software_layer.sh (specific to build step)
+declare -a INSTALL_SCRIPT_ARGS=()
+if [[ ${EESSI_SOFTWARE_SUBDIR_OVERRIDE} =~ .*/generic$ ]]; then
+    INSTALL_SCRIPT_ARGS+=("--generic")
+fi
+[[ ! -z ${BUILD_LOGS_DIR} ]] && INSTALL_SCRIPT_ARGS+=("--build-logs-dir" "${BUILD_LOGS_DIR}")
+[[ ! -z ${SHARED_FS_PATH} ]] && INSTALL_SCRIPT_ARGS+=("--shared-fs-path" "${SHARED_FS_PATH}")
+
+# prepare arguments to eessi_container.sh specific to remove step
+declare -a REMOVE_STEP_ARGS=()
+REMOVE_STEP_ARGS+=("--save" "${TARBALL_TMP_BUILD_STEP_DIR}")
+REMOVE_STEP_ARGS+=("--storage" "${STORAGE}")
+# add fakeroot option in order to be able to remove software
+REMOVE_STEP_ARGS+=("--fakeroot")
+
+# create tmp file for output of removal step
+remove_outerr=$(mktemp remove.outerr.XXXX)
+
+echo "Executing command to remove software:"
+echo "./eessi_container.sh ${COMMON_ARGS[@]} ${REMOVE_STEP_ARGS[@]}"
+echo "                     -- ./install_software_layer.sh \"${INSTALL_SCRIPT_ARGS[@]}\" \"$@\" 2>&1 | tee -a ${remove_outerr}"
+./eessi_container.sh "${COMMON_ARGS[@]}" "${REMOVE_STEP_ARGS[@]}" \
+                     -- ./install_software_layer.sh "${INSTALL_SCRIPT_ARGS[@]}" "$@" 2>&1 | tee -a ${remove_outerr}
 
 # prepare arguments to eessi_container.sh specific to build step
 declare -a BUILD_STEP_ARGS=()
@@ -181,16 +206,10 @@ BUILD_STEP_ARGS+=("--nvidia" "all")
 if [[ ! -z ${SHARED_FS_PATH} ]]; then
     BUILD_STEP_ARGS+=("--host-injections" "${SHARED_FS_PATH}/host-injections")
 fi
-# add fakeroot option in order to be able to remove software
-BUILD_STEP_ARGS+=("--fakeroot")
 
-# prepare arguments to install_software_layer.sh (specific to build step)
-declare -a INSTALL_SCRIPT_ARGS=()
-if [[ ${EESSI_SOFTWARE_SUBDIR_OVERRIDE} =~ .*/generic$ ]]; then
-    INSTALL_SCRIPT_ARGS+=("--generic")
-fi
-[[ ! -z ${BUILD_LOGS_DIR} ]] && INSTALL_SCRIPT_ARGS+=("--build-logs-dir" "${BUILD_LOGS_DIR}")
-[[ ! -z ${SHARED_FS_PATH} ]] && INSTALL_SCRIPT_ARGS+=("--shared-fs-path" "${SHARED_FS_PATH}")
+# determine temporary directory to resume from; this is important in case software was removed for a rebuild
+REMOVE_TMPDIR=$(grep ' as tmp directory ' ${remove_outerr} | cut -d ' ' -f 2)
+BUILD_STEP_ARGS+=("--resume" "${REMOVE_TMPDIR}")
 
 # create tmp file for output of build step
 build_outerr=$(mktemp build.outerr.XXXX)

From 7b57e8130ca9a03cc2fab3a8b74bda0c59d1c6e5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 8 Mar 2024 11:52:05 +0100
Subject: [PATCH 156/501] remove removal step

---
 install_software_layer.sh | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/install_software_layer.sh b/install_software_layer.sh
index c5cf40bb5a..82ca70b73f 100755
--- a/install_software_layer.sh
+++ b/install_software_layer.sh
@@ -1,11 +1,4 @@
 #!/bin/bash
 base_dir=$(dirname $(realpath $0))
 source ${base_dir}/init/eessi_defaults
-
-echo "User ID: $EUID"
-
-if [ $EUID -eq 0 ]; then
-    ./EESSI-remove-software.sh "$@"
-    exec runuser -u eessi $( readlink -f "$0" ) -- "$@"
-fi
 ./run_in_compat_layer_env.sh ./EESSI-install-software.sh "$@"

From 485ff46bd4e87d2c9e35d1e42b12d8c884e782f9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 8 Mar 2024 11:52:50 +0100
Subject: [PATCH 157/501] call EESSI-remove-software.sh for removal step

---
 bot/build.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bot/build.sh b/bot/build.sh
index bc1cd27770..208209ab28 100755
--- a/bot/build.sh
+++ b/bot/build.sh
@@ -193,9 +193,9 @@ remove_outerr=$(mktemp remove.outerr.XXXX)
 
 echo "Executing command to remove software:"
 echo "./eessi_container.sh ${COMMON_ARGS[@]} ${REMOVE_STEP_ARGS[@]}"
-echo "                     -- ./install_software_layer.sh \"${INSTALL_SCRIPT_ARGS[@]}\" \"$@\" 2>&1 | tee -a ${remove_outerr}"
+echo "                     -- ./EESSI-remove-software.sh \"${INSTALL_SCRIPT_ARGS[@]}\" \"$@\" 2>&1 | tee -a ${remove_outerr}"
 ./eessi_container.sh "${COMMON_ARGS[@]}" "${REMOVE_STEP_ARGS[@]}" \
-                     -- ./install_software_layer.sh "${INSTALL_SCRIPT_ARGS[@]}" "$@" 2>&1 | tee -a ${remove_outerr}
+                     -- ./EESSI-remove-software.sh "${INSTALL_SCRIPT_ARGS[@]}" "$@" 2>&1 | tee -a ${remove_outerr}
 
 # prepare arguments to eessi_container.sh specific to build step
 declare -a BUILD_STEP_ARGS=()

From 8204a529b4d73aa082bcc0a785555a3f1119fe70 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 8 Mar 2024 12:00:49 +0100
Subject: [PATCH 158/501] remove echo command

---
 EESSI-install-software.sh | 2 --
 1 file changed, 2 deletions(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 4d26b30b53..ab91d2c6de 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -87,8 +87,6 @@ while [[ $# -gt 0 ]]; do
   esac
 done
 
-echo "Software installation user: $EUID $UID"
-
 set -- "${POSITIONAL_ARGS[@]}"
 
 TOPDIR=$(dirname $(realpath $0))

From 15eb765405f65966f7c16c2756d7062bbcb4d4a5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 8 Mar 2024 12:02:43 +0100
Subject: [PATCH 159/501] remove unused code

---
 eessi_container.sh | 12 ------------
 1 file changed, 12 deletions(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index af8618f4b8..d084fe5fab 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -596,12 +596,6 @@ if [[ "${ACCESS}" == "ro" ]]; then
 fi
 
 if [[ "${ACCESS}" == "rw" ]]; then
-  #if [[ ! -z ${JOB_CFG_FILE} ]]; then
-    # always launch build jobs triggered by the job with --fakeroot in order to be able to remove existing installations, see:
-    # https://github.com/EESSI/software-layer/issues/312
-    # we drop back to a regular user in the build script
-    #ADDITIONAL_CONTAINER_OPTIONS+=("--fakeroot")
-  #fi
   mkdir -p ${EESSI_TMPDIR}/overlay-upper
   mkdir -p ${EESSI_TMPDIR}/overlay-work
 
@@ -638,12 +632,6 @@ if [ ! -z ${EESSI_SOFTWARE_SUBDIR_OVERRIDE} ]; then
     export APPTAINERENV_EESSI_SOFTWARE_SUBDIR_OVERRIDE=${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
 fi
 
-#if [[ ! -z ${JOB_CFG_FILE} ]]; then
-#    echo "Removing software by launching container with command (next line):"
-#    echo "singularity ${RUN_QUIET} exec --fakeroot ${ADDITIONAL_CONTAINER_OPTIONS[@]} ${EESSI_FUSE_MOUNTS[@]} ${CONTAINER} ./EESSI-remove-software.sh"
-#    singularity ${RUN_QUIET} exec --fakeroot "${ADDITIONAL_CONTAINER_OPTIONS[@]}" "${EESSI_FUSE_MOUNTS[@]}" ${CONTAINER} ./EESSI-remove-software.sh
-#fi
-
 echo "Launching container with command (next line):"
 echo "singularity ${RUN_QUIET} ${MODE} ${ADDITIONAL_CONTAINER_OPTIONS[@]} ${EESSI_FUSE_MOUNTS[@]} ${CONTAINER} $@"
 singularity ${RUN_QUIET} ${MODE} "${ADDITIONAL_CONTAINER_OPTIONS[@]}" "${EESSI_FUSE_MOUNTS[@]}" ${CONTAINER} "$@"

From 1f7501f2e1aad58abb5d85430d8fed95aaa55576 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 8 Mar 2024 13:02:14 +0100
Subject: [PATCH 160/501] rename remove to removal, resume tarball step from
 removal dir

---
 bot/build.sh | 29 ++++++++++++++---------------
 1 file changed, 14 insertions(+), 15 deletions(-)

diff --git a/bot/build.sh b/bot/build.sh
index 208209ab28..8f3439b3ad 100755
--- a/bot/build.sh
+++ b/bot/build.sh
@@ -169,9 +169,9 @@ COMMON_ARGS+=("--mode" "run")
 PREVIOUS_TMP_DIR=${PWD}/previous_tmp
 
 # prepare directory to store tarball of tmp for removal and build steps
-TARBALL_TMP_REMOVE_STEP_DIR=${PREVIOUS_TMP_DIR}/remove_step
+TARBALL_TMP_REMOVAL_STEP_DIR=${PREVIOUS_TMP_DIR}/removal_step
 TARBALL_TMP_BUILD_STEP_DIR=${PREVIOUS_TMP_DIR}/build_step
-mkdir -p ${TARBALL_TMP_BUILD_STEP_DIR} ${TARBALL_TMP_REMOVE_STEP_DIR}
+mkdir -p ${TARBALL_TMP_BUILD_STEP_DIR} ${TARBALL_TMP_REMOVAL_STEP_DIR}
 
 # prepare arguments to install_software_layer.sh (specific to build step)
 declare -a INSTALL_SCRIPT_ARGS=()
@@ -182,20 +182,20 @@ fi
 [[ ! -z ${SHARED_FS_PATH} ]] && INSTALL_SCRIPT_ARGS+=("--shared-fs-path" "${SHARED_FS_PATH}")
 
 # prepare arguments to eessi_container.sh specific to remove step
-declare -a REMOVE_STEP_ARGS=()
-REMOVE_STEP_ARGS+=("--save" "${TARBALL_TMP_BUILD_STEP_DIR}")
-REMOVE_STEP_ARGS+=("--storage" "${STORAGE}")
+declare -a REMOVAL_STEP_ARGS=()
+REMOVAL_STEP_ARGS+=("--save" "${TARBALL_TMP_BUILD_STEP_DIR}")
+REMOVAL_STEP_ARGS+=("--storage" "${STORAGE}")
 # add fakeroot option in order to be able to remove software
-REMOVE_STEP_ARGS+=("--fakeroot")
+REMOVAL_STEP_ARGS+=("--fakeroot")
 
 # create tmp file for output of removal step
-remove_outerr=$(mktemp remove.outerr.XXXX)
+removal_outerr=$(mktemp remove.outerr.XXXX)
 
 echo "Executing command to remove software:"
-echo "./eessi_container.sh ${COMMON_ARGS[@]} ${REMOVE_STEP_ARGS[@]}"
-echo "                     -- ./EESSI-remove-software.sh \"${INSTALL_SCRIPT_ARGS[@]}\" \"$@\" 2>&1 | tee -a ${remove_outerr}"
-./eessi_container.sh "${COMMON_ARGS[@]}" "${REMOVE_STEP_ARGS[@]}" \
-                     -- ./EESSI-remove-software.sh "${INSTALL_SCRIPT_ARGS[@]}" "$@" 2>&1 | tee -a ${remove_outerr}
+echo "./eessi_container.sh ${COMMON_ARGS[@]} ${REMOVAL_STEP_ARGS[@]}"
+echo "                     -- ./EESSI-remove-software.sh \"${INSTALL_SCRIPT_ARGS[@]}\" \"$@\" 2>&1 | tee -a ${removal_outerr}"
+./eessi_container.sh "${COMMON_ARGS[@]}" "${REMOVAL_STEP_ARGS[@]}" \
+                     -- ./EESSI-remove-software.sh "${INSTALL_SCRIPT_ARGS[@]}" "$@" 2>&1 | tee -a ${removal_outerr}
 
 # prepare arguments to eessi_container.sh specific to build step
 declare -a BUILD_STEP_ARGS=()
@@ -208,8 +208,8 @@ if [[ ! -z ${SHARED_FS_PATH} ]]; then
 fi
 
 # determine temporary directory to resume from; this is important in case software was removed for a rebuild
-REMOVE_TMPDIR=$(grep ' as tmp directory ' ${remove_outerr} | cut -d ' ' -f 2)
-BUILD_STEP_ARGS+=("--resume" "${REMOVE_TMPDIR}")
+REMOVAL_TMPDIR=$(grep ' as tmp directory ' ${removal_outerr} | cut -d ' ' -f 2)
+BUILD_STEP_ARGS+=("--resume" "${REMOVAL_TMPDIR}")
 
 # create tmp file for output of build step
 build_outerr=$(mktemp build.outerr.XXXX)
@@ -232,8 +232,7 @@ declare -a TARBALL_STEP_ARGS=()
 TARBALL_STEP_ARGS+=("--save" "${TARBALL_TMP_TARBALL_STEP_DIR}")
 
 # determine temporary directory to resume from
-BUILD_TMPDIR=$(grep ' as tmp directory ' ${build_outerr} | cut -d ' ' -f 2)
-TARBALL_STEP_ARGS+=("--resume" "${BUILD_TMPDIR}")
+TARBALL_STEP_ARGS+=("--resume" "${REMOVAL_TMPDIR}")
 
 timestamp=$(date +%s)
 # to set EESSI_VERSION we need to source init/eessi_defaults now

From 45022b6b47c3046ea3e2d4033197fdd80dc63850 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 8 Mar 2024 17:30:55 +0100
Subject: [PATCH 161/501] Allow for open PRs when checking missing
 installations in build script

---
 EESSI-install-software.sh      |  2 +-
 check_missing_installations.sh | 20 +++++++++++++++++---
 2 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 69de9d1997..75b4f71178 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -237,7 +237,7 @@ else
                 copy_build_log "${eb_last_log}" "${build_logs_dir}"
             fi
     
-            $TOPDIR/check_missing_installations.sh ${TOPDIR}/${easystack_file}
+            $TOPDIR/check_missing_installations.sh ${TOPDIR}/${easystack_file} ${TOPDIR}/${pr_diff}
         else
             fatal_error "Easystack file ${easystack_file} not found!"
         fi
diff --git a/check_missing_installations.sh b/check_missing_installations.sh
index c902fa8184..623c46c74f 100755
--- a/check_missing_installations.sh
+++ b/check_missing_installations.sh
@@ -10,8 +10,15 @@
 
 TOPDIR=$(dirname $(realpath $0))
 
-if [ $# -ne 1 ]; then
-    echo "ERROR: Usage: $0 <path to easystack file>" >&2
+if [ "$#" -eq 1 ]; then
+    true
+elif [ "$#" -eq 2 ]; then
+    echo "Using $2 to give create exceptions for PR filtering of easystack"
+    # Find lines that are added and use from-pr, make them unique, grab the
+    # PR numbers and use them to construct something we can use within awk
+    pr_exceptions=$(grep ^+ $2 | grep from-pr | uniq | awk '{print $3}' | xargs -i echo " || /'{}'/")
+else
+    echo "ERROR: Usage: $0 <path to easystack file> (<optional path to PR diff>)" >&2
     exit 1
 fi
 easystack=$1
@@ -24,7 +31,10 @@ export EASYBUILD_ROBOT_PATHS=$LOCAL_TMPDIR/easyconfigs/easybuild/easyconfigs
 
 # All PRs used in EESSI are supposed to be merged, so we can strip out all cases of from-pr
 tmp_easystack=${LOCAL_TMPDIR}/$(basename ${easystack})
-grep -v from-pr ${easystack} > ${tmp_easystack} 
+# Let's use awk so we can allow for exceptions if we are given a PR diff file
+awk_command="awk '\!/'from-pr'/ EXCEPTIONS' $easystack"
+awk_command=${awk_command/\\/}  # Strip out the backslash we needed for !
+eval ${awk_command/EXCEPTIONS/$pr_exceptions} > ${tmp_easystack}
 
 source $TOPDIR/scripts/utils.sh
 
@@ -40,6 +50,10 @@ exit_code=${PIPESTATUS[0]}
 
 ok_msg="Command 'eb --missing ...' succeeded, analysing output..."
 fail_msg="Command 'eb --missing ...' failed, check log '${eb_missing_out}'"
+if [ "$#" -eq 1 ]; then
+    fail_msg="$fail_msg (are you sure all PRs referenced have been merged in EasyBuild?)"
+fi
+
 check_exit_code ${exit_code} "${ok_msg}" "${fail_msg}"
 
 # the above assesses the installed software for each easyconfig provided in

From 723fce82b272cccd75a1d1841ef301be419461e6 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Sat, 9 Mar 2024 11:39:33 +0100
Subject: [PATCH 162/501] Check for unmerged EasyConfig output pattern

---
 bot/check-build.sh | 143 ++++++++++++++++++++++++++++-----------------
 1 file changed, 90 insertions(+), 53 deletions(-)

diff --git a/bot/check-build.sh b/bot/check-build.sh
index ec1ca56bba..e737363f35 100755
--- a/bot/check-build.sh
+++ b/bot/check-build.sh
@@ -98,15 +98,15 @@ job_dir=${PWD}
 job_out="slurm-${SLURM_JOB_ID}.out"
 [[ ${VERBOSE} -ne 0 ]] && echo ">> searching for job output file(s) matching '"${job_out}"'"
 if  [[ -f ${job_out} ]]; then
-    SLURM=1
+    SLURM_OUTPUT_FOUND=1
     [[ ${VERBOSE} -ne 0 ]] && echo "   found slurm output file '"${job_out}"'"
 else
-    SLURM=0
+    SLURM_OUTPUT_FOUND=0
     [[ ${VERBOSE} -ne 0 ]] && echo "   Slurm output file '"${job_out}"' NOT found"
 fi
 
 ERROR=-1
-if [[ ${SLURM} -eq 1 ]]; then
+if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]]; then
   GP_error='ERROR: '
   grep_out=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_error}")
   [[ $? -eq 0 ]] && ERROR=1 || ERROR=0
@@ -116,7 +116,7 @@ if [[ ${SLURM} -eq 1 ]]; then
 fi
 
 FAILED=-1
-if [[ ${SLURM} -eq 1 ]]; then
+if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]]; then
   GP_failed='FAILED: '
   grep_out=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_failed}")
   [[ $? -eq 0 ]] && FAILED=1 || FAILED=0
@@ -126,7 +126,7 @@ if [[ ${SLURM} -eq 1 ]]; then
 fi
 
 MISSING=-1
-if [[ ${SLURM} -eq 1 ]]; then
+if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]]; then
   GP_req_missing=' required modules missing:'
   grep_out=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_req_missing}")
   [[ $? -eq 0 ]] && MISSING=1 || MISSING=0
@@ -136,7 +136,7 @@ if [[ ${SLURM} -eq 1 ]]; then
 fi
 
 NO_MISSING=-1
-if [[ ${SLURM} -eq 1 ]]; then
+if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]]; then
   GP_no_missing='No missing installations'
   grep_out=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_no_missing}")
   [[ $? -eq 0 ]] && NO_MISSING=1 || NO_MISSING=0
@@ -147,7 +147,7 @@ fi
 
 TGZ=-1
 TARBALL=
-if [[ ${SLURM} -eq 1 ]]; then
+if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]]; then
   GP_tgz_created="\.tar\.gz created!"
   grep_out=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${GP_tgz_created}" | sort -u)
   if [[ $? -eq 0 ]]; then
@@ -169,9 +169,27 @@ fi
 [[ ${VERBOSE} -ne 0 ]] && echo "  NO_MISSING.: $([[ $NO_MISSING -eq 1 ]] && echo 'yes' || echo 'no') (yes)"
 [[ ${VERBOSE} -ne 0 ]] && echo "  TGZ_CREATED: $([[ $TGZ -eq 1 ]] && echo 'yes' || echo 'no') (yes)"
 
+# Here, we try to do some additional analysis on the output file
+# to see if we can print a more clear 'reason' for the failure
+# For now, we only analyse unmerged EasyConfigs as potential cause, but we can easily add checks for other
+# specific scenarios below
+
+# Check for the pattern being added here https://github.com/EESSI/software-layer/pull/493 to the output to
+# see if EasyConfigs might have been unmerged, and that's causing a failure
+UNMERGED_EASYCONFIG=-1
+if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]]; then
+  gp_unmerged="are you sure all PRs referenced have been merged in EasyBuild"
+  grep_unmerged=$(grep -v "^>> searching for " ${job_dir}/${job_out} | grep "${gp_unmerged}")
+  [[ $? -eq 0 ]] && UNMERGED_EASYCONFIG=1 || UNMERGED_EASYCONFIG=0
+  # have to be careful to not add searched for pattern into slurm out file
+  [[ ${VERBOSE} -ne 0 ]] && echo ">> searching for '"${gp_unmerged}"'"
+  [[ ${VERBOSE} -ne 0 ]] && echo "${grep_unmerged}"
+fi
+
 job_result_file=_bot_job${SLURM_JOB_ID}.result
 
-if [[ ${SLURM} -eq 1 ]] && \
+# Default reason:
+if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]] && \
    [[ ${ERROR} -eq 0 ]] && \
    [[ ${FAILED} -eq 0 ]] && \
    [[ ${MISSING} -eq 0 ]] && \
@@ -180,7 +198,12 @@ if [[ ${SLURM} -eq 1 ]] && \
    [[ ! -z ${TARBALL} ]]; then
     # SUCCESS
     status="SUCCESS"
+    reason=""
     summary=":grin: SUCCESS"
+elif [[ ${UNMERGED_EASYCONFIG} -eq 1 ]]; then
+    status="FAILURE"
+    reason="EasyConfig not found during missing installation check. Are you sure all PRs referenced have been merged in EasyBuild?"
+    summary=":cry: FAILURE"
 else
     # FAILURE
     status="FAILURE"
@@ -253,14 +276,6 @@ fi
 # </details>
 ###
 
-# construct and write complete PR comment details: implements third alternative
-comment_template="<details>__SUMMARY_FMT__<dl>__DETAILS_FMT____ARTEFACTS_FMT__</dl></details>"
-comment_summary_fmt="<summary>__SUMMARY__ _(click triangle for details)_</summary>"
-comment_details_fmt="<dt>_Details_</dt><dd>__DETAILS_LIST__</dd>"
-comment_success_item_fmt=":white_check_mark: __ITEM__"
-comment_failure_item_fmt=":x: __ITEM__"
-comment_artefacts_fmt="<dt>_Artefacts_</dt><dd>__ARTEFACTS_LIST__</dd>"
-comment_artefact_details_fmt="<details>__ARTEFACT_SUMMARY____ARTEFACT_DETAILS__</details>"
 
 function print_br_item() {
     format="${1}"
@@ -332,42 +347,65 @@ echo -n "comment_description = " >> ${job_result_file}
 # - __DETAILS_FMT__ -> variable $comment_details
 # - __ARTEFACTS_FMT__ -> variable $comment_artefacts
 
+# construct and write complete PR comment details: implements third alternative
+comment_template="<details>__SUMMARY_FMT__<dl>__REASON_FMT____DETAILS_FMT____ARTEFACTS_FMT__</dl></details>"
+comment_success_item_fmt=":white_check_mark: __ITEM__"
+comment_failure_item_fmt=":x: __ITEM__"
+
+# Initialize comment_description
+comment_description=${comment_template}
+
+# Now, start replacing template items one by one
+# Replace the summary template (__SUMMARY_FMT__)
+comment_summary_fmt="<summary>__SUMMARY__ _(click triangle for details)_</summary>"
 comment_summary="${comment_summary_fmt/__SUMMARY__/${summary}}"
+comment_description=${comment_template/__SUMMARY_FMT__/${comment_summary}}
+
+# Only add if there is a reason (e.g. no reason for successful runs)
+if [[ ! -z ${reason} ]]; then
+    comment_reason_fmt="<dt>_Reason_</dt><dd>__REASONS__</dd>"
+    reason_details="${comment_reason_fmt/__REASONS__/${reason}}"
+    comment_description=${comment_description/__REASON_FMT__/${reason_details}}
+else
+    comment_description=${comment_description/__REASON_FMT__/""}
+fi
 
-# first construct comment_details_list, abbreviated CoDeList
+# Replace the details template (__DETAILS_FMT__)
+# first construct comment_details_list, abbreviated comment_details_list
 # then use it to set comment_details
-CoDeList=""
+comment_details_list=""
 
 success_msg="job output file <code>${job_out}</code>"
 failure_msg="no job output file <code>${job_out}</code>"
-CoDeList=${CoDeList}$(add_detail ${SLURM} 1 "${success_msg}" "${failure_msg}")
+comment_details_list=${comment_details_list}$(add_detail ${SLURM_OUTPUT_FOUND} 1 "${success_msg}" "${failure_msg}")
 
 success_msg="no message matching <code>${GP_error}</code>"
 failure_msg="found message matching <code>${GP_error}</code>"
-CoDeList=${CoDeList}$(add_detail ${ERROR} 0 "${success_msg}" "${failure_msg}")
+comment_details_list=${comment_details_list}$(add_detail ${ERROR} 0 "${success_msg}" "${failure_msg}")
 
 success_msg="no message matching <code>${GP_failed}</code>"
 failure_msg="found message matching <code>${GP_failed}</code>"
-CoDeList=${CoDeList}$(add_detail ${FAILED} 0 "${success_msg}" "${failure_msg}")
+comment_details_list=${comment_details_list}$(add_detail ${FAILED} 0 "${success_msg}" "${failure_msg}")
 
 success_msg="no message matching <code>${GP_req_missing}</code>"
 failure_msg="found message matching <code>${GP_req_missing}</code>"
-CoDeList=${CoDeList}$(add_detail ${MISSING} 0 "${success_msg}" "${failure_msg}")
+comment_details_list=${comment_details_list}$(add_detail ${MISSING} 0 "${success_msg}" "${failure_msg}")
 
 success_msg="found message(s) matching <code>${GP_no_missing}</code>"
 failure_msg="no message matching <code>${GP_no_missing}</code>"
-CoDeList=${CoDeList}$(add_detail ${NO_MISSING} 1 "${success_msg}" "${failure_msg}")
+comment_details_list=${comment_details_list}$(add_detail ${NO_MISSING} 1 "${success_msg}" "${failure_msg}")
 
 success_msg="found message matching <code>${GP_tgz_created}</code>"
 failure_msg="no message matching <code>${GP_tgz_created}</code>"
-CoDeList=${CoDeList}$(add_detail ${TGZ} 1 "${success_msg}" "${failure_msg}")
-
-comment_details="${comment_details_fmt/__DETAILS_LIST__/${CoDeList}}"
-
+comment_details_list=${comment_details_list}$(add_detail ${TGZ} 1 "${success_msg}" "${failure_msg}")
+# Now, do the actual repalcement of __DETAILS_FMT__
+comment_details_fmt="<dt>_Details_</dt><dd>__DETAILS_LIST__</dd>"
+comment_details="${comment_details_fmt/__DETAILS_LIST__/${comment_details_list}}"
+comment_description=${comment_description/__DETAILS_FMT__/${comment_details}}
 
-# first construct comment_artefacts_list, abbreviated CoArList
+# first construct comment_artefacts_list
 # then use it to set comment_artefacts
-CoArList=""
+comment_artifacts_list=""
 
 # TARBALL should only contain a single tarball
 if [[ ! -z ${TARBALL} ]]; then
@@ -427,50 +465,49 @@ if [[ ! -z ${TARBALL} ]]; then
     software_pkgs=$(echo "${software_entries}" | sed -e "s@${prefix}/software/@@" | awk -F/ '{if (NR >= 2) {print $1 "/" $2}}' | sort -u)
 
     artefact_summary="<summary>$(print_code_item '__ITEM__' ${TARBALL})</summary>"
-    CoArList=""
-    CoArList="${CoArList}$(print_br_item2 'size: __ITEM__ MiB (__ITEM2__ bytes)' ${size_mib} ${size})"
-    CoArList="${CoArList}$(print_br_item 'entries: __ITEM__' ${entries})"
-    CoArList="${CoArList}$(print_br_item 'modules under ___ITEM___' ${prefix}/modules/all)"
-    CoArList="${CoArList}<pre>"
+    comment_artifacts_list=""
+    comment_artifacts_list="${comment_artifacts_list}$(print_br_item2 'size: __ITEM__ MiB (__ITEM2__ bytes)' ${size_mib} ${size})"
+    comment_artifacts_list="${comment_artifacts_list}$(print_br_item 'entries: __ITEM__' ${entries})"
+    comment_artifacts_list="${comment_artifacts_list}$(print_br_item 'modules under ___ITEM___' ${prefix}/modules/all)"
+    comment_artifacts_list="${comment_artifacts_list}<pre>"
     if [[ ! -z ${modules} ]]; then
         while IFS= read -r mod ; do
-            CoArList="${CoArList}$(print_br_item '<code>__ITEM__</code>' ${mod})"
+            comment_artifacts_list="${comment_artifacts_list}$(print_br_item '<code>__ITEM__</code>' ${mod})"
         done <<< "${modules}"
     else
-        CoArList="${CoArList}$(print_br_item '__ITEM__' 'no module files in tarball')"
+        comment_artifacts_list="${comment_artifacts_list}$(print_br_item '__ITEM__' 'no module files in tarball')"
     fi
-    CoArList="${CoArList}</pre>"
-    CoArList="${CoArList}$(print_br_item 'software under ___ITEM___' ${prefix}/software)"
-    CoArList="${CoArList}<pre>"
+    comment_artifacts_list="${comment_artifacts_list}</pre>"
+    comment_artifacts_list="${comment_artifacts_list}$(print_br_item 'software under ___ITEM___' ${prefix}/software)"
+    comment_artifacts_list="${comment_artifacts_list}<pre>"
     if [[ ! -z ${software_pkgs} ]]; then
         while IFS= read -r sw_pkg ; do
-            CoArList="${CoArList}$(print_br_item '<code>__ITEM__</code>' ${sw_pkg})"
+            comment_artifacts_list="${comment_artifacts_list}$(print_br_item '<code>__ITEM__</code>' ${sw_pkg})"
         done <<< "${software_pkgs}"
     else
-        CoArList="${CoArList}$(print_br_item '__ITEM__' 'no software packages in tarball')"
+        comment_artifacts_list="${comment_artifacts_list}$(print_br_item '__ITEM__' 'no software packages in tarball')"
     fi
-    CoArList="${CoArList}</pre>"
-    CoArList="${CoArList}$(print_br_item 'other under ___ITEM___' ${prefix})"
-    CoArList="${CoArList}<pre>"
+    comment_artifacts_list="${comment_artifacts_list}</pre>"
+    comment_artifacts_list="${comment_artifacts_list}$(print_br_item 'other under ___ITEM___' ${prefix})"
+    comment_artifacts_list="${comment_artifacts_list}<pre>"
     if [[ ! -z ${other_shortened} ]]; then
         while IFS= read -r other ; do
-            CoArList="${CoArList}$(print_br_item '<code>__ITEM__</code>' ${other})"
+            comment_artifacts_list="${comment_artifacts_list}$(print_br_item '<code>__ITEM__</code>' ${other})"
         done <<< "${other_shortened}"
     else
-        CoArList="${CoArList}$(print_br_item '__ITEM__' 'no other files in tarball')"
+        comment_artifacts_list="${comment_artifacts_list}$(print_br_item '__ITEM__' 'no other files in tarball')"
     fi
-    CoArList="${CoArList}</pre>"
+    comment_artifacts_list="${comment_artifacts_list}</pre>"
 else
-    CoArList="${CoArList}$(print_dd_item 'No artefacts were created or found.' '')"
+    comment_artifacts_list="${comment_artifacts_list}$(print_dd_item 'No artefacts were created or found.' '')"
 fi
 
+comment_artefact_details_fmt="<details>__ARTEFACT_SUMMARY____ARTEFACT_DETAILS__</details>"
 comment_artefacts_details="${comment_artefact_details_fmt/__ARTEFACT_SUMMARY__/${artefact_summary}}"
-comment_artefacts_details="${comment_artefacts_details/__ARTEFACT_DETAILS__/${CoArList}}"
-comment_artefacts="${comment_artefacts_fmt/__ARTEFACTS_LIST__/${comment_artefacts_details}}"
+comment_artefacts_details="${comment_artefacts_details/__ARTEFACT_DETAILS__/${comment_artifacts_list}}"
 
-# now put all pieces together creating comment_details from comment_template
-comment_description=${comment_template/__SUMMARY_FMT__/${comment_summary}}
-comment_description=${comment_description/__DETAILS_FMT__/${comment_details}}
+comment_artefacts_fmt="<dt>_Artefacts_</dt><dd>__ARTEFACTS_LIST__</dd>"
+comment_artefacts="${comment_artefacts_fmt/__ARTEFACTS_LIST__/${comment_artefacts_details}}"
 comment_description=${comment_description/__ARTEFACTS_FMT__/${comment_artefacts}}
 
 echo "${comment_description}" >> ${job_result_file}

From f4f277605a17aea824f940ae1de0727b190be47d Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Sat, 9 Mar 2024 13:22:18 +0100
Subject: [PATCH 163/501] First, try without --from-pr. If that fails, try with
 --from-pr, but only for items added to the EasyStack file in _this_ PR to
 software-layer. If that succeeds, the reason must be that one of the
 EasyBuild PRs wasn't merged yet, and we can add that information to the
 fail_msg to make it more explicit

---
 check_missing_installations.sh | 22 +++++++++++++++++++++-
 1 file changed, 21 insertions(+), 1 deletion(-)

diff --git a/check_missing_installations.sh b/check_missing_installations.sh
index 623c46c74f..fd2c0d34bb 100755
--- a/check_missing_installations.sh
+++ b/check_missing_installations.sh
@@ -31,6 +31,8 @@ export EASYBUILD_ROBOT_PATHS=$LOCAL_TMPDIR/easyconfigs/easybuild/easyconfigs
 
 # All PRs used in EESSI are supposed to be merged, so we can strip out all cases of from-pr
 tmp_easystack=${LOCAL_TMPDIR}/$(basename ${easystack})
+grep -v from-pr ${easystack} > ${tmp_easystack}
+
 # Let's use awk so we can allow for exceptions if we are given a PR diff file
 awk_command="awk '\!/'from-pr'/ EXCEPTIONS' $easystack"
 awk_command=${awk_command/\\/}  # Strip out the backslash we needed for !
@@ -51,7 +53,25 @@ exit_code=${PIPESTATUS[0]}
 ok_msg="Command 'eb --missing ...' succeeded, analysing output..."
 fail_msg="Command 'eb --missing ...' failed, check log '${eb_missing_out}'"
 if [ "$#" -eq 1 ]; then
-    fail_msg="$fail_msg (are you sure all PRs referenced have been merged in EasyBuild?)"
+    # We might have failed due to unmerged PRs. Try to make exceptions for --from-pr added in this PR
+    # to software-layer, and see if then it passes. If so, we can report a more specific fail_msg
+
+    # Let's use awk so we can allow for exceptions if we are given a PR diff file
+    awk_command="awk '\!/'from-pr'/ EXCEPTIONS' $easystack"
+    awk_command=${awk_command/\\/}  # Strip out the backslash we needed for !
+    eval ${awk_command/EXCEPTIONS/$pr_exceptions} > ${tmp_easystack}
+
+    msg=">> Checking for missing installations in ${EASYBUILD_INSTALLPATH},"
+    msg="${msg} allowing for --from-pr's that were added in this PR..."
+    echo ${msg}
+    eb_missing_out=$LOCAL_TMPDIR/eb_missing_with_from_pr.out
+    ${EB:-eb} --easystack ${tmp_easystack} --missing 2>&1 | tee ${eb_missing_out}
+    exit_code=${PIPESTATUS[0]}
+
+    # If now we succeeded, the reason must be that we originally stripped the --from-pr's
+    if [ "$#" -eq 0 ]; then
+        fail_msg="$fail_msg (are you sure all PRs referenced have been merged in EasyBuild?)"
+    fi
 fi
 
 check_exit_code ${exit_code} "${ok_msg}" "${fail_msg}"

From b7891087072ab05b50d93295b0f8990e27b50edf Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Sat, 9 Mar 2024 13:24:08 +0100
Subject: [PATCH 164/501] Add CFITSIO as a test example, see if we can get a
 clear error message printed on a build failure here

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml                 | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 2664d8f417..51e96f1fac 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -10,4 +10,7 @@ easyconfigs:
         from-pr: 19552
   - CDO-2.2.2-gompi-2023b.eb:
       options:
-        from-pr: 19792   
+        from-pr: 19792
+  - CFITSIO-4.3.1-GCCcore-13.2.0.eb:
+      options:
+        from-pr: 19840

From d178a8f14d6e16f5bcddcd7af0bb7978f647d823 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Sat, 9 Mar 2024 13:34:33 +0100
Subject: [PATCH 165/501] Added clarifying comment

---
 bot/check-build.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/bot/check-build.sh b/bot/check-build.sh
index e737363f35..24c608b04a 100755
--- a/bot/check-build.sh
+++ b/bot/check-build.sh
@@ -207,6 +207,8 @@ elif [[ ${UNMERGED_EASYCONFIG} -eq 1 ]]; then
 else
     # FAILURE
     status="FAILURE"
+    # General failure, we don't know a more specific reason
+    reason=""
     summary=":cry: FAILURE"
 fi
 

From 9123c9c8f483cf5f6b1e931cfe5a4484fc978faa Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Sat, 9 Mar 2024 13:37:08 +0100
Subject: [PATCH 166/501] Correct mistake: I meant to _move_ the awk part, not
 duplicate it

---
 check_missing_installations.sh | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/check_missing_installations.sh b/check_missing_installations.sh
index fd2c0d34bb..4781ecc72a 100755
--- a/check_missing_installations.sh
+++ b/check_missing_installations.sh
@@ -33,11 +33,6 @@ export EASYBUILD_ROBOT_PATHS=$LOCAL_TMPDIR/easyconfigs/easybuild/easyconfigs
 tmp_easystack=${LOCAL_TMPDIR}/$(basename ${easystack})
 grep -v from-pr ${easystack} > ${tmp_easystack}
 
-# Let's use awk so we can allow for exceptions if we are given a PR diff file
-awk_command="awk '\!/'from-pr'/ EXCEPTIONS' $easystack"
-awk_command=${awk_command/\\/}  # Strip out the backslash we needed for !
-eval ${awk_command/EXCEPTIONS/$pr_exceptions} > ${tmp_easystack}
-
 source $TOPDIR/scripts/utils.sh
 
 source $TOPDIR/configure_easybuild

From 7e4422335f1c2f3ad682362a060906866b9b90f4 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Sat, 9 Mar 2024 13:54:07 +0100
Subject: [PATCH 167/501] Now actually check against the exit code of the
 pipe...

---
 check_missing_installations.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/check_missing_installations.sh b/check_missing_installations.sh
index 4781ecc72a..51a328b50c 100755
--- a/check_missing_installations.sh
+++ b/check_missing_installations.sh
@@ -47,7 +47,7 @@ exit_code=${PIPESTATUS[0]}
 
 ok_msg="Command 'eb --missing ...' succeeded, analysing output..."
 fail_msg="Command 'eb --missing ...' failed, check log '${eb_missing_out}'"
-if [ "$#" -eq 1 ]; then
+if [ "$exit_code" -eq 1 ]; then
     # We might have failed due to unmerged PRs. Try to make exceptions for --from-pr added in this PR
     # to software-layer, and see if then it passes. If so, we can report a more specific fail_msg
 

From da749a111320720773d648d4a55caa2ba1a826e3 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Sat, 9 Mar 2024 14:08:27 +0100
Subject: [PATCH 168/501] Make seperate exit code for the run that allows
 --from-pr

---
 check_missing_installations.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/check_missing_installations.sh b/check_missing_installations.sh
index 51a328b50c..6d84384fd7 100755
--- a/check_missing_installations.sh
+++ b/check_missing_installations.sh
@@ -61,10 +61,10 @@ if [ "$exit_code" -eq 1 ]; then
     echo ${msg}
     eb_missing_out=$LOCAL_TMPDIR/eb_missing_with_from_pr.out
     ${EB:-eb} --easystack ${tmp_easystack} --missing 2>&1 | tee ${eb_missing_out}
-    exit_code=${PIPESTATUS[0]}
+    exit_code_with_from_pr=${PIPESTATUS[0]}
 
     # If now we succeeded, the reason must be that we originally stripped the --from-pr's
-    if [ "$#" -eq 0 ]; then
+    if [ "$exit_code_with_from_pr" -eq 0 ]; then
         fail_msg="$fail_msg (are you sure all PRs referenced have been merged in EasyBuild?)"
     fi
 fi

From 86d8a36c52a9a3dfe9af25662bc6c95968804024 Mon Sep 17 00:00:00 2001
From: Tim Kok <tim.kok@surf.nl>
Date: Mon, 11 Mar 2024 11:46:32 +0100
Subject: [PATCH 169/501] Remove ineffective DP3 hook

---
 eb_hooks.py | 27 ---------------------------
 1 file changed, 27 deletions(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index 1478f1a508..d93ee37067 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -186,32 +186,6 @@ def parse_hook_casacore_disable_vectorize(ec, eprefix):
         raise EasyBuildError("casacore-specific hook triggered for non-casacore easyconfig?!")
 
 
-def parse_hook_dp3_enable_relaxed_vector_conversions(ec, eprefix):
-    """
-    Enable lax vector conversion for DP3 on aarch64/neoverse_v1
-    Compiling DP3 6.0 with GCC 13.2.0 (foss-2023b) gives a conversion error when building for aarch64/neoverse_v1.
-    See also, https://github.com/EESSI/software-layer/pull/479
-    """
-    if ec.name == 'DP3':
-        tcname, tcversion = ec['toolchain']['name'], ec['toolchain']['version']
-        if (
-            LooseVersion(ec.version) == LooseVersion('6.0') and
-            tcname == 'foss' and tcversion == '2023b'
-        ):
-            cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
-            if cpu_target == CPU_TARGET_NEOVERSE_V1:
-                if not hasattr(ec, 'configopts'):
-                    ec['configopts'] = ""
-                ec['configopts'] += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -flax-vector-conversions" '
-                print_msg("Changed configopts for %s: %s", ec.name, ec['configopts'])
-            else:
-                print_msg("Not changing configopts for %s on non-neoverse_v1", ec.name)
-        else:
-            print_msg("Not changing configopts for %s %s %s", ec.name, ec.version, ec.toolchain)
-    else:
-        raise EasyBuildError("DP3-specific hook triggered for non-DP3 easyconfig?!")
-
-
 def parse_hook_cgal_toolchainopts_precise(ec, eprefix):
     """Enable 'precise' rather than 'strict' toolchain option for CGAL on POWER."""
     if ec.name == 'CGAL':
@@ -633,7 +607,6 @@ def inject_gpu_property(ec):
 PARSE_HOOKS = {
     'casacore': parse_hook_casacore_disable_vectorize,
     'CGAL': parse_hook_cgal_toolchainopts_precise,
-    'DP3': parse_hook_dp3_enable_relaxed_vector_conversions,
     'fontconfig': parse_hook_fontconfig_add_fonts,
     'OpenBLAS': parse_hook_openblas_relax_lapack_tests_num_errors,
     'pybind11': parse_hook_pybind11_replace_catch2,

From f8816acf3c0c0022bbba3e123f6d0239469728d3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 11 Mar 2024 14:19:15 +0100
Subject: [PATCH 170/501] {2023.06}[2023a] JupyterNotebook v7.0.2

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 0d8e71e86c..cb207e50ea 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -36,3 +36,4 @@ easyconfigs:
   - dask-2023.9.2-foss-2023a.eb
   - OSU-Micro-Benchmarks-7.2-gompi-2023a-CUDA-12.1.1.eb
   - OSU-Micro-Benchmarks-7.2-gompi-2023b.eb
+  - JupyterNotebook-7.0.2-GCCcore-12.3.0.eb

From 310e1e3a36df67c5d51b9bb0dbe80fc97abf1fa7 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Mon, 11 Mar 2024 15:34:50 +0100
Subject: [PATCH 171/501] Initial attempt at splitting off the LMOD hooks into
 a seperate SitePackage.lua file

---
 EESSI-install-software.sh        |  15 +++-
 create_lmodrc.py                 | 108 -----------------------
 create_lmodsitepackage.py        | 141 +++++++++++++++++++++++++++++++
 init/eessi_environment_variables |  17 +++-
 4 files changed, 166 insertions(+), 115 deletions(-)
 create mode 100755 create_lmodsitepackage.py

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 69de9d1997..ed137c522d 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -248,11 +248,20 @@ fi
 ### add packages here
 
 echo ">> Creating/updating Lmod cache..."
-export LMOD_RC="${EASYBUILD_INSTALLPATH}/.lmod/lmodrc.lua"
+export LMOD_CONFIG_DIR="${EASYBUILD_INSTALLPATH}/.lmod"
+lmod_rc_file="$LMOD_CONFIG_DIR/lmodrc.lua"
 lmodrc_changed=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^create_lmodrc.py$' > /dev/null; echo $?)
-if [ ! -f $LMOD_RC ] || [ ${lmodrc_changed} == '0' ]; then
+if [ ! -f $lmod_rc_file ] || [ ${lmodrc_changed} == '0' ]; then
     python3 $TOPDIR/create_lmodrc.py ${EASYBUILD_INSTALLPATH}
-    check_exit_code $? "$LMOD_RC created" "Failed to create $LMOD_RC"
+    check_exit_code $? "$lmod_rc_file created" "Failed to create $lmod_rc_file"
+fi
+
+echo ">> Creating/updating Lmod SitePackage.lua ..."
+export LMOD_PACKAGE_PATH=${EASYBUILD_INSTALLPATH}/.lmod"
+lmod_sitepackage_file="$LMOD_PACKAGE_PATH/SitePackage.lua"
+if [ ! -f $lmod_sitepackage_file ] || [ ${sitepackage_changed} == '0' ]; then
+    python3 $TOPDIR/create_lmodsitepackage.py ${EASYBUILD_INSTALLPATH}
+    check_exit_code $? "$lmod_sitepackage_file created" "Failed to create $lmod_sitepackage_file"
 fi
 
 $TOPDIR/update_lmod_cache.sh ${EPREFIX} ${EASYBUILD_INSTALLPATH}
diff --git a/create_lmodrc.py b/create_lmodrc.py
index 621c8e271a..ae65153a20 100755
--- a/create_lmodrc.py
+++ b/create_lmodrc.py
@@ -17,113 +17,6 @@
 }
 """
 
-GPU_LMOD_RC ="""require("strict")
-local hook = require("Hook")
-local open = io.open
-
-local function read_file(path)
-    local file = open(path, "rb") -- r read mode and b binary mode
-    if not file then return nil end
-    local content = file:read "*a" -- *a or *all reads the whole file
-    file:close()
-    return content
-end
-
-local function eessi_cuda_enabled_load_hook(t)
-    local frameStk  = require("FrameStk"):singleton()
-    local mt        = frameStk:mt()
-    local simpleName = string.match(t.modFullName, "(.-)/")
-    -- If we try to load CUDA itself, check if the full CUDA SDK was installed on the host in host_injections. 
-    -- This is required for end users to build additional CUDA software. If the full SDK isn't present, refuse
-    -- to load the CUDA module and print an informative message on how to set up GPU support for EESSI
-    local refer_to_docs = "For more information on how to do this, see https://www.eessi.io/docs/gpu/.\\n"
-    if simpleName == 'CUDA' then
-        -- get the full host_injections path
-        local hostInjections = string.gsub(os.getenv('EESSI_SOFTWARE_PATH') or "", 'versions', 'host_injections')
-        -- build final path where the CUDA software should be installed
-        local cudaEasyBuildDir = hostInjections .. "/software/" .. t.modFullName .. "/easybuild"
-        local cudaDirExists = isDir(cudaEasyBuildDir)
-        if not cudaDirExists then
-            local advice = "but while the module file exists, the actual software is not entirely shipped with EESSI "
-            advice = advice .. "due to licencing. You will need to install a full copy of the CUDA SDK where EESSI "
-            advice = advice .. "can find it.\\n"
-            advice = advice .. refer_to_docs
-            LmodError("\\nYou requested to load ", simpleName, " ", advice)
-        end
-    end
-    -- when loading CUDA enabled modules check if the necessary driver libraries are accessible to the EESSI linker,
-    -- otherwise, refuse to load the requested module and print error message
-    local haveGpu = mt:haveProperty(simpleName,"arch","gpu")
-    if haveGpu then
-        local arch = os.getenv("EESSI_CPU_FAMILY") or ""
-        local cudaVersionFile = "/cvmfs/software.eessi.io/host_injections/nvidia/" .. arch .. "/latest/cuda_version.txt"
-        local cudaDriverFile = "/cvmfs/software.eessi.io/host_injections/nvidia/" .. arch .. "/latest/libcuda.so"
-        local cudaDriverExists = isFile(cudaDriverFile)
-        local singularityCudaExists = isFile("/.singularity.d/libs/libcuda.so")
-        if not (cudaDriverExists or singularityCudaExists)  then
-            local advice = "which relies on the CUDA runtime environment and driver libraries. "
-            advice = advice .. "In order to be able to use the module, you will need "
-            advice = advice .. "to make sure EESSI can find the GPU driver libraries on your host system.\\n"
-            advice = advice .. refer_to_docs
-            LmodError("\\nYou requested to load ", simpleName, " ", advice)
-        else
-            -- CUDA driver exists, now we check its version to see if an update is needed
-            if cudaDriverExists then
-                local cudaVersion = read_file(cudaVersionFile)
-                local cudaVersion_req = os.getenv("EESSICUDAVERSION")
-                -- driver CUDA versions don't give a patch version for CUDA
-                local major, minor = string.match(cudaVersion, "(%d+)%.(%d+)")
-                local major_req, minor_req, patch_req = string.match(cudaVersion_req, "(%d+)%.(%d+)%.(%d+)")
-                local driver_libs_need_update = false
-                if major < major_req then
-                    driver_libs_need_update = true
-                elseif major == major_req then
-                    if minor < minor_req then
-                        driver_libs_need_update = true
-                    end
-                end
-                if driver_libs_need_update == true then
-                    local advice = "but the module you want to load requires CUDA  " .. cudaVersion_req .. ". "
-                    advice = advice .. "Please update your CUDA driver libraries and then "
-                    advice = advice .. "let EESSI know about the update.\\n"
-                    advice = advice .. refer_to_docs
-                    LmodError("\\nYour driver CUDA version is ", cudaVersion, " ", advice)
-                end
-            end
-        end
-    end
-end
-
-local function eessi_openmpi_load_hook(t)
-    -- disable smcuda BTL when loading OpenMPI module for aarch64/neoverse_v1,
-    -- to work around hang/crash due to bug in OpenMPI;
-    -- see https://gitlab.com/eessi/support/-/issues/41
-    local frameStk = require("FrameStk"):singleton()
-    local mt = frameStk:mt()
-    local moduleName = string.match(t.modFullName, "(.-)/")
-    local cpuTarget = os.getenv("EESSI_SOFTWARE_SUBDIR") or ""
-    if (moduleName == "OpenMPI") and (cpuTarget == "aarch64/neoverse_v1") then
-        local msg = "Adding '^smcuda' to $OMPI_MCA_btl to work around bug in OpenMPI"
-        LmodMessage(msg .. " (see https://gitlab.com/eessi/support/-/issues/41)")
-	local ompiMcaBtl = os.getenv("OMPI_MCA_btl")
-	if ompiMcaBtl == nil then
-            setenv("OMPI_MCA_btl", "^smcuda")
-        else
-            setenv("OMPI_MCA_btl", ompiMcaBtl .. ",^smcuda")
-	end
-    end
-end
-
--- Combine both functions into a single one, as we can only register one function as load hook in lmod
--- Also: make it non-local, so it can be imported and extended by other lmodrc files if needed
-function eessi_load_hook(t)
-    eessi_cuda_enabled_load_hook(t)
-    eessi_openmpi_load_hook(t)
-end
-
-
-hook.register("load", eessi_load_hook)
-"""
 
 def error(msg):
     sys.stderr.write("ERROR: %s\n" % msg)
@@ -143,7 +36,6 @@ def error(msg):
     'dot_lmod': DOT_LMOD,
     'prefix': prefix,
 }
-lmodrc_txt += '\n' + GPU_LMOD_RC
 try:
     os.makedirs(os.path.dirname(lmodrc_path), exist_ok=True)
     with open(lmodrc_path, 'w') as fp:
diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
new file mode 100755
index 0000000000..9e77eafecf
--- /dev/null
+++ b/create_lmodsitepackage.py
@@ -0,0 +1,141 @@
+#!/usr/bin/env python3
+#
+# Create SitePackage.lua configuration file for Lmod.
+#
+import os
+import sys
+
+DOT_LMOD = '.lmod'
+
+hook_txt ="""require("strict")
+local hook = require("Hook")
+local open = io.open
+
+local function read_file(path)
+    local file = open(path, "rb") -- r read mode and b binary mode
+    if not file then return nil end
+    local content = file:read "*a" -- *a or *all reads the whole file
+    file:close()
+    return content
+end
+
+local function eessi_cuda_enabled_load_hook(t)
+    local frameStk  = require("FrameStk"):singleton()
+    local mt        = frameStk:mt()
+    local simpleName = string.match(t.modFullName, "(.-)/")
+    -- If we try to load CUDA itself, check if the full CUDA SDK was installed on the host in host_injections. 
+    -- This is required for end users to build additional CUDA software. If the full SDK isn't present, refuse
+    -- to load the CUDA module and print an informative message on how to set up GPU support for EESSI
+    local refer_to_docs = "For more information on how to do this, see https://www.eessi.io/docs/gpu/.\\n"
+    if simpleName == 'CUDA' then
+        -- get the full host_injections path
+        local hostInjections = string.gsub(os.getenv('EESSI_SOFTWARE_PATH') or "", 'versions', 'host_injections')
+        -- build final path where the CUDA software should be installed
+        local cudaEasyBuildDir = hostInjections .. "/software/" .. t.modFullName .. "/easybuild"
+        local cudaDirExists = isDir(cudaEasyBuildDir)
+        if not cudaDirExists then
+            local advice = "but while the module file exists, the actual software is not entirely shipped with EESSI "
+            advice = advice .. "due to licencing. You will need to install a full copy of the CUDA SDK where EESSI "
+            advice = advice .. "can find it.\\n"
+            advice = advice .. refer_to_docs
+            LmodError("\\nYou requested to load ", simpleName, " ", advice)
+        end
+    end
+    -- when loading CUDA enabled modules check if the necessary driver libraries are accessible to the EESSI linker,
+    -- otherwise, refuse to load the requested module and print error message
+    local haveGpu = mt:haveProperty(simpleName,"arch","gpu")
+    if haveGpu then
+        local arch = os.getenv("EESSI_CPU_FAMILY") or ""
+        local cudaVersionFile = "/cvmfs/software.eessi.io/host_injections/nvidia/" .. arch .. "/latest/cuda_version.txt"
+        local cudaDriverFile = "/cvmfs/software.eessi.io/host_injections/nvidia/" .. arch .. "/latest/libcuda.so"
+        local cudaDriverExists = isFile(cudaDriverFile)
+        local singularityCudaExists = isFile("/.singularity.d/libs/libcuda.so")
+        if not (cudaDriverExists or singularityCudaExists)  then
+            local advice = "which relies on the CUDA runtime environment and driver libraries. "
+            advice = advice .. "In order to be able to use the module, you will need "
+            advice = advice .. "to make sure EESSI can find the GPU driver libraries on your host system.\\n"
+            advice = advice .. refer_to_docs
+            LmodError("\\nYou requested to load ", simpleName, " ", advice)
+        else
+            -- CUDA driver exists, now we check its version to see if an update is needed
+            if cudaDriverExists then
+                local cudaVersion = read_file(cudaVersionFile)
+                local cudaVersion_req = os.getenv("EESSICUDAVERSION")
+                -- driver CUDA versions don't give a patch version for CUDA
+                local major, minor = string.match(cudaVersion, "(%d+)%.(%d+)")
+                local major_req, minor_req, patch_req = string.match(cudaVersion_req, "(%d+)%.(%d+)%.(%d+)")
+                local driver_libs_need_update = false
+                if major < major_req then
+                    driver_libs_need_update = true
+                elseif major == major_req then
+                    if minor < minor_req then
+                        driver_libs_need_update = true
+                    end
+                end
+                if driver_libs_need_update == true then
+                    local advice = "but the module you want to load requires CUDA  " .. cudaVersion_req .. ". "
+                    advice = advice .. "Please update your CUDA driver libraries and then "
+                    advice = advice .. "let EESSI know about the update.\\n"
+                    advice = advice .. refer_to_docs
+                    LmodError("\\nYour driver CUDA version is ", cudaVersion, " ", advice)
+                end
+            end
+        end
+    end
+end
+
+local function eessi_openmpi_load_hook(t)
+    -- disable smcuda BTL when loading OpenMPI module for aarch64/neoverse_v1,
+    -- to work around hang/crash due to bug in OpenMPI;
+    -- see https://gitlab.com/eessi/support/-/issues/41
+    local frameStk = require("FrameStk"):singleton()
+    local mt = frameStk:mt()
+    local moduleName = string.match(t.modFullName, "(.-)/")
+    local cpuTarget = os.getenv("EESSI_SOFTWARE_SUBDIR") or ""
+    if (moduleName == "OpenMPI") and (cpuTarget == "aarch64/neoverse_v1") then
+        local msg = "Adding '^smcuda' to $OMPI_MCA_btl to work around bug in OpenMPI"
+        LmodMessage(msg .. " (see https://gitlab.com/eessi/support/-/issues/41)")
+	local ompiMcaBtl = os.getenv("OMPI_MCA_btl")
+	if ompiMcaBtl == nil then
+            setenv("OMPI_MCA_btl", "^smcuda")
+        else
+            setenv("OMPI_MCA_btl", ompiMcaBtl .. ",^smcuda")
+	end
+    end
+end
+
+-- Combine both functions into a single one, as we can only register one function as load hook in lmod
+-- Also: make it non-local, so it can be imported and extended by other lmodrc files if needed
+function eessi_load_hook(t)
+    eessi_cuda_enabled_load_hook(t)
+    eessi_openmpi_load_hook(t)
+end
+
+
+hook.register("load", eessi_load_hook)
+"""
+
+def error(msg):
+    sys.stderr.write("ERROR: %s\n" % msg)
+    sys.exit(1)
+
+
+if len(sys.argv) != 2:
+    error("Usage: %s <software prefix>" % sys.argv[0])
+
+prefix = sys.argv[1]
+
+if not os.path.exists(prefix):
+    error("Prefix directory %s does not exist!" % prefix)
+
+sitepackage_path = os.path.join(prefix, DOT_LMOD, 'SitePackage.lua')
+sitepackage_txt += hook_txt
+try:
+    os.makedirs(os.path.dirname(sitepackage_path), exist_ok=True)
+    with open(sitepackage_path, 'w') as fp:
+        fp.write(sitepackage_txt)
+
+except (IOError, OSError) as err:
+    error("Failed to create %s: %s" % (sitepackage_path, err))
+
+print(sitepackage_path)
diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index af5222e7b9..78f01b1921 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -76,11 +76,20 @@ if [ -d $EESSI_PREFIX ]; then
             false
           fi
 
-          export LMOD_RC="$EESSI_SOFTWARE_PATH/.lmod/lmodrc.lua"
-          if [ -f $LMOD_RC ]; then
-            show_msg "Found Lmod configuration file at $LMOD_RC"
+          export LMOD_CONFIG_DIR="$EESSI_SOFTWARE_PATH/.lmod"
+          lmod_rc_file="$LMOD_CONFIG_DIR/lmodrc.lua"
+          if [ -f $lmod_rc_file ]; then
+            show_msg "Found Lmod configuration file at $lmod_rc_file"
           else
-            error "Lmod configuration file not found at $LMOD_RC"
+            error "Lmod configuration file not found at $lmod_rc_file"
+          fi
+
+          export LMOD_PACKAGE_PATH="$EESSI_SOFTWARE_PATH/.lmod"
+          lmod_sitepackage_file="$LMOD_PACKAGE_PATH/SitePackage.lua"
+          if [ -f $lmod_sitepackage_file ]; then
+            show_msg "Found Lmod SitePackage.lua file at $lmod_sitepackage_file"
+          else
+            error "Lmod SitePackage.lua file not found at $lmod_sitepackage_file"
           fi
 
         else

From a8c2883f0c73af0537a834221c3ae439f44c1b2f Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com>
Date: Mon, 11 Mar 2024 15:59:32 +0100
Subject: [PATCH 172/501] Correct typo

Co-authored-by: ocaisa <alan.ocais@cecam.org>
---
 bot/check-build.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bot/check-build.sh b/bot/check-build.sh
index 24c608b04a..10b1ed6a11 100755
--- a/bot/check-build.sh
+++ b/bot/check-build.sh
@@ -400,7 +400,7 @@ comment_details_list=${comment_details_list}$(add_detail ${NO_MISSING} 1 "${succ
 success_msg="found message matching <code>${GP_tgz_created}</code>"
 failure_msg="no message matching <code>${GP_tgz_created}</code>"
 comment_details_list=${comment_details_list}$(add_detail ${TGZ} 1 "${success_msg}" "${failure_msg}")
-# Now, do the actual repalcement of __DETAILS_FMT__
+# Now, do the actual replacement of __DETAILS_FMT__
 comment_details_fmt="<dt>_Details_</dt><dd>__DETAILS_LIST__</dd>"
 comment_details="${comment_details_fmt/__DETAILS_LIST__/${comment_details_list}}"
 comment_description=${comment_description/__DETAILS_FMT__/${comment_details}}

From 6553e294163fb9e117803a2433acba3c14e135f2 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Mon, 11 Mar 2024 16:05:16 +0100
Subject: [PATCH 173/501] Skip the if-condition also if pr_exceptions is empty.
 There is no point in running the eb --missing again in that case, since there
 were no --from-pr's in this PR to begin with, so unmerged PRs cannot be the
 reason for failing

---
 check_missing_installations.sh | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/check_missing_installations.sh b/check_missing_installations.sh
index 6d84384fd7..0ee6ec4385 100755
--- a/check_missing_installations.sh
+++ b/check_missing_installations.sh
@@ -47,9 +47,11 @@ exit_code=${PIPESTATUS[0]}
 
 ok_msg="Command 'eb --missing ...' succeeded, analysing output..."
 fail_msg="Command 'eb --missing ...' failed, check log '${eb_missing_out}'"
-if [ "$exit_code" -eq 1 ]; then
+if [ "$exit_code" -eq 1 ] && [ ! -z $pr_exceptions ]; then
     # We might have failed due to unmerged PRs. Try to make exceptions for --from-pr added in this PR
     # to software-layer, and see if then it passes. If so, we can report a more specific fail_msg
+    # Note that if no --from-pr's were used in this PR, $pr_exceptions will be empty and we might as
+    # well skip this check - unmerged PRs can not be the reason for the non-zero exit code in that scenario
 
     # Let's use awk so we can allow for exceptions if we are given a PR diff file
     awk_command="awk '\!/'from-pr'/ EXCEPTIONS' $easystack"

From 27a12bd2e4a88c486f3dd5b5be57ac16eefd2650 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Mon, 11 Mar 2024 16:09:46 +0100
Subject: [PATCH 174/501] Added missing quote

---
 EESSI-install-software.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index ed137c522d..219fa8680a 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -257,7 +257,7 @@ if [ ! -f $lmod_rc_file ] || [ ${lmodrc_changed} == '0' ]; then
 fi
 
 echo ">> Creating/updating Lmod SitePackage.lua ..."
-export LMOD_PACKAGE_PATH=${EASYBUILD_INSTALLPATH}/.lmod"
+export LMOD_PACKAGE_PATH="${EASYBUILD_INSTALLPATH}/.lmod"
 lmod_sitepackage_file="$LMOD_PACKAGE_PATH/SitePackage.lua"
 if [ ! -f $lmod_sitepackage_file ] || [ ${sitepackage_changed} == '0' ]; then
     python3 $TOPDIR/create_lmodsitepackage.py ${EASYBUILD_INSTALLPATH}

From 81e544f15333b3d3b3ed70f4954f414f262ba6cd Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Mon, 11 Mar 2024 16:11:31 +0100
Subject: [PATCH 175/501] Cant add to a variable that doesnt exist... We don't
 need this intermediate assignment anyway

---
 create_lmodsitepackage.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index 9e77eafecf..9a4a232863 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -129,11 +129,10 @@ def error(msg):
     error("Prefix directory %s does not exist!" % prefix)
 
 sitepackage_path = os.path.join(prefix, DOT_LMOD, 'SitePackage.lua')
-sitepackage_txt += hook_txt
 try:
     os.makedirs(os.path.dirname(sitepackage_path), exist_ok=True)
     with open(sitepackage_path, 'w') as fp:
-        fp.write(sitepackage_txt)
+        fp.write(hook_txt)
 
 except (IOError, OSError) as err:
     error("Failed to create %s: %s" % (sitepackage_path, err))

From 333762b9c1ddab70721826b70a1d432f6d043c49 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 11 Mar 2024 16:41:19 +0100
Subject: [PATCH 176/501] determine whether or not the removal step has to be
 run

---
 bot/build.sh | 60 +++++++++++++++++++++++++++++++---------------------
 1 file changed, 36 insertions(+), 24 deletions(-)

diff --git a/bot/build.sh b/bot/build.sh
index 8f3439b3ad..31d9b576fe 100755
--- a/bot/build.sh
+++ b/bot/build.sh
@@ -168,12 +168,8 @@ COMMON_ARGS+=("--mode" "run")
 # make sure to use the same parent dir for storing tarballs of tmp
 PREVIOUS_TMP_DIR=${PWD}/previous_tmp
 
-# prepare directory to store tarball of tmp for removal and build steps
-TARBALL_TMP_REMOVAL_STEP_DIR=${PREVIOUS_TMP_DIR}/removal_step
-TARBALL_TMP_BUILD_STEP_DIR=${PREVIOUS_TMP_DIR}/build_step
-mkdir -p ${TARBALL_TMP_BUILD_STEP_DIR} ${TARBALL_TMP_REMOVAL_STEP_DIR}
-
 # prepare arguments to install_software_layer.sh (specific to build step)
+declare -a BUILD_STEP_ARGS=()
 declare -a INSTALL_SCRIPT_ARGS=()
 if [[ ${EESSI_SOFTWARE_SUBDIR_OVERRIDE} =~ .*/generic$ ]]; then
     INSTALL_SCRIPT_ARGS+=("--generic")
@@ -181,24 +177,44 @@ fi
 [[ ! -z ${BUILD_LOGS_DIR} ]] && INSTALL_SCRIPT_ARGS+=("--build-logs-dir" "${BUILD_LOGS_DIR}")
 [[ ! -z ${SHARED_FS_PATH} ]] && INSTALL_SCRIPT_ARGS+=("--shared-fs-path" "${SHARED_FS_PATH}")
 
-# prepare arguments to eessi_container.sh specific to remove step
-declare -a REMOVAL_STEP_ARGS=()
-REMOVAL_STEP_ARGS+=("--save" "${TARBALL_TMP_BUILD_STEP_DIR}")
-REMOVAL_STEP_ARGS+=("--storage" "${STORAGE}")
-# add fakeroot option in order to be able to remove software
-REMOVAL_STEP_ARGS+=("--fakeroot")
-
-# create tmp file for output of removal step
-removal_outerr=$(mktemp remove.outerr.XXXX)
+# determine if the removal step has to be run
+# assume there's only one diff file that corresponds to the PR patch file
+pr_diff=$(ls [0-9]*.diff | head -1)
+changed_easystacks_rebuilds=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | grep "/rebuilds/")
+if [[ -z ${changed_easystacks_rebuilds} ]]; then
+    echo "This PR does not add any easystack files in a rebuilds subdirectory, so let's skip the removal step."
+else
+    # prepare directory to store tarball of tmp for removal and build steps
+    TARBALL_TMP_REMOVAL_STEP_DIR=${PREVIOUS_TMP_DIR}/removal_step
+    mkdir -p ${TARBALL_TMP_REMOVAL_STEP_DIR}
+
+    # prepare arguments to eessi_container.sh specific to remove step
+    declare -a REMOVAL_STEP_ARGS=()
+    REMOVAL_STEP_ARGS+=("--save" "${TARBALL_TMP_BUILD_STEP_DIR}")
+    REMOVAL_STEP_ARGS+=("--storage" "${STORAGE}")
+    # add fakeroot option in order to be able to remove software
+    REMOVAL_STEP_ARGS+=("--fakeroot")
+
+    # create tmp file for output of removal step
+    removal_outerr=$(mktemp remove.outerr.XXXX)
+
+    echo "Executing command to remove software:"
+    echo "./eessi_container.sh ${COMMON_ARGS[@]} ${REMOVAL_STEP_ARGS[@]}"
+    echo "                     -- ./EESSI-remove-software.sh \"${INSTALL_SCRIPT_ARGS[@]}\" \"$@\" 2>&1 | tee -a ${removal_outerr}"
+    ./eessi_container.sh "${COMMON_ARGS[@]}" "${REMOVAL_STEP_ARGS[@]}" \
+                         -- ./EESSI-remove-software.sh "${INSTALL_SCRIPT_ARGS[@]}" "$@" 2>&1 | tee -a ${removal_outerr}
+
+    # make sure that the build step resumes from the same temporary directory
+    # this is important, as otherwise the removed software will still be there
+    REMOVAL_TMPDIR=$(grep ' as tmp directory ' ${removal_outerr} | cut -d ' ' -f 2)
+    BUILD_STEP_ARGS+=("--resume" "${REMOVAL_TMPDIR}")
+fi
 
-echo "Executing command to remove software:"
-echo "./eessi_container.sh ${COMMON_ARGS[@]} ${REMOVAL_STEP_ARGS[@]}"
-echo "                     -- ./EESSI-remove-software.sh \"${INSTALL_SCRIPT_ARGS[@]}\" \"$@\" 2>&1 | tee -a ${removal_outerr}"
-./eessi_container.sh "${COMMON_ARGS[@]}" "${REMOVAL_STEP_ARGS[@]}" \
-                     -- ./EESSI-remove-software.sh "${INSTALL_SCRIPT_ARGS[@]}" "$@" 2>&1 | tee -a ${removal_outerr}
+# prepare directory to store tarball of tmp for build step
+TARBALL_TMP_BUILD_STEP_DIR=${PREVIOUS_TMP_DIR}/build_step
+mkdir -p ${TARBALL_TMP_BUILD_STEP_DIR}
 
 # prepare arguments to eessi_container.sh specific to build step
-declare -a BUILD_STEP_ARGS=()
 BUILD_STEP_ARGS+=("--save" "${TARBALL_TMP_BUILD_STEP_DIR}")
 BUILD_STEP_ARGS+=("--storage" "${STORAGE}")
 # add options required to handle NVIDIA support
@@ -207,10 +223,6 @@ if [[ ! -z ${SHARED_FS_PATH} ]]; then
     BUILD_STEP_ARGS+=("--host-injections" "${SHARED_FS_PATH}/host-injections")
 fi
 
-# determine temporary directory to resume from; this is important in case software was removed for a rebuild
-REMOVAL_TMPDIR=$(grep ' as tmp directory ' ${removal_outerr} | cut -d ' ' -f 2)
-BUILD_STEP_ARGS+=("--resume" "${REMOVAL_TMPDIR}")
-
 # create tmp file for output of build step
 build_outerr=$(mktemp build.outerr.XXXX)
 

From 0343684cc8e7b73fc25e160007dc458c2c54e6d0 Mon Sep 17 00:00:00 2001
From: Tim Kok <tim.kok@surf.nl>
Date: Tue, 12 Mar 2024 10:19:33 +0100
Subject: [PATCH 177/501] {2023.06}[foss/2023b] python-casacore 3.5.2 +
 libspatialindex 1.9.3

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml                | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 54011c262e..186f4f86b3 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -43,3 +43,9 @@ easyconfigs:
   - CDO-2.2.2-gompi-2023b.eb:
       options:
         from-pr: 19792
+  - python-casacore-3.5.2-foss-2023b.eb:
+      options:
+        from-pr: 20084
+  - libspatialindex-1.9.3-GCCcore-13.2.0.eb:
+      options:
+        from-pr: 19922

From 3e43b061314bdde685b585804a047802cb95f81a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 12 Mar 2024 14:00:38 +0100
Subject: [PATCH 178/501] add ImageMagick-7.1.1-15-GCCcore-12.3.0.eb

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index cb207e50ea..8165755865 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -37,3 +37,6 @@ easyconfigs:
   - OSU-Micro-Benchmarks-7.2-gompi-2023a-CUDA-12.1.1.eb
   - OSU-Micro-Benchmarks-7.2-gompi-2023b.eb
   - JupyterNotebook-7.0.2-GCCcore-12.3.0.eb
+  - ImageMagick-7.1.1-15-GCCcore-12.3.0.eb:
+      options:
+        from-pr: 20086

From 0b826ae64a31e0b2463c6ea65c9c12e1701922ec Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 12 Mar 2024 16:53:26 +0100
Subject: [PATCH 179/501] remove proxy arguments

Co-authored-by: Kenneth Hoste <kenneth.hoste@ugent.be>
---
 EESSI-remove-software.sh | 2 --
 1 file changed, 2 deletions(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index 819c08f8ce..4786d60fc0 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -11,8 +11,6 @@ display_help() {
   echo "  --build-logs-dir       -  location to copy EasyBuild logs to for failed builds"
   echo "  -g | --generic         -  instructs script to build for generic architecture target"
   echo "  -h | --help            -  display this usage information"
-  echo "  -x | --http-proxy URL  -  provides URL for the environment variable http_proxy"
-  echo "  -y | --https-proxy URL -  provides URL for the environment variable https_proxy"
   echo "  --shared-fs-path       -  path to directory on shared filesystem that can be used"
 }
 

From 0ed12492ed91e0ada5dd142536927a5edc4a817f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 12 Mar 2024 16:58:17 +0100
Subject: [PATCH 180/501] remove code for setting http(s)_proxy

Co-authored-by: Kenneth Hoste <kenneth.hoste@ugent.be>
---
 EESSI-remove-software.sh | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index 4786d60fc0..e995f55a45 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -27,14 +27,6 @@ while [[ $# -gt 0 ]]; do
       # no shifting needed here, we're done.
       exit 0
       ;;
-    -x|--http-proxy)
-      export http_proxy="$2"
-      shift 2
-      ;;
-    -y|--https-proxy)
-      export https_proxy="$2"
-      shift 2
-      ;;
     --build-logs-dir)
       export build_logs_dir="${2}"
       shift 2

From bc4fd890f9ae68b094b164dc85ed217eef420622 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 12 Mar 2024 16:58:42 +0100
Subject: [PATCH 181/501] no need to set build logs dir

Co-authored-by: Kenneth Hoste <kenneth.hoste@ugent.be>
---
 EESSI-remove-software.sh | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index e995f55a45..d3823c7036 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -27,10 +27,6 @@ while [[ $# -gt 0 ]]; do
       # no shifting needed here, we're done.
       exit 0
       ;;
-    --build-logs-dir)
-      export build_logs_dir="${2}"
-      shift 2
-      ;;
     --shared-fs-path)
       export shared_fs_path="${2}"
       shift 2

From fd7a9eadd21fd386beaceb0af211dd2f523a6669 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 12 Mar 2024 16:59:52 +0100
Subject: [PATCH 182/501] remove commented code

Co-authored-by: ocaisa <alan.ocais@cecam.org>
---
 EESSI-remove-software.sh | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index d3823c7036..02e91a43d1 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -60,9 +60,6 @@ else
     fatal_error "$EESSI_CVMFS_REPO is not available!"
 fi
 
-# avoid that pyc files for EasyBuild are stored in EasyBuild installation directory
-#export PYTHONPYCACHEPREFIX=$TMPDIR/pycache
-
 DETECTION_PARAMETERS=''
 GENERIC=0
 EB='eb'

From 994d573759c1c7707952a9d9a125cc6e1d3df47b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 12 Mar 2024 17:00:27 +0100
Subject: [PATCH 183/501] fix comment about purpose of script

Co-authored-by: ocaisa <alan.ocais@cecam.org>
---
 EESSI-remove-software.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index 02e91a43d1..f111be339e 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 #
-# Script to install EESSI software stack (version set through init/eessi_defaults)
+# Script to remove part of the EESSI software stack (version set through init/eessi_defaults)
 
 # see example parsing of command line arguments at
 #   https://wiki.bash-hackers.org/scripting/posparams#using_a_while_loop

From 3d7a959d0a1e62eb4c29c7b6742b82d5eaff4321 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 12 Mar 2024 17:02:10 +0100
Subject: [PATCH 184/501] remove code and parameter for setting shared fs path

---
 EESSI-remove-software.sh | 11 -----------
 1 file changed, 11 deletions(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index f111be339e..1779a7ed58 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -11,7 +11,6 @@ display_help() {
   echo "  --build-logs-dir       -  location to copy EasyBuild logs to for failed builds"
   echo "  -g | --generic         -  instructs script to build for generic architecture target"
   echo "  -h | --help            -  display this usage information"
-  echo "  --shared-fs-path       -  path to directory on shared filesystem that can be used"
 }
 
 POSITIONAL_ARGS=()
@@ -27,10 +26,6 @@ while [[ $# -gt 0 ]]; do
       # no shifting needed here, we're done.
       exit 0
       ;;
-    --shared-fs-path)
-      export shared_fs_path="${2}"
-      shift 2
-      ;;
     -*|--*)
       echo "Error: Unknown option: $1" >&2
       exit 1
@@ -103,12 +98,6 @@ fi
 echo ">> Configuring EasyBuild..."
 source $TOPDIR/configure_easybuild
 
-if [ ! -z "${shared_fs_path}" ]; then
-    shared_eb_sourcepath=${shared_fs_path}/easybuild/sources
-    echo ">> Using ${shared_eb_sourcepath} as shared EasyBuild source path"
-    export EASYBUILD_SOURCEPATH=${shared_eb_sourcepath}:${EASYBUILD_SOURCEPATH}
-fi
-
 echo ">> Setting up \$MODULEPATH..."
 # make sure no modules are loaded
 module --force purge

From 02955711c5600305d8feedece3e85978626ff962 Mon Sep 17 00:00:00 2001
From: Tim Kok <tim.kok@surf.nl>
Date: Tue, 12 Mar 2024 18:33:07 +0100
Subject: [PATCH 185/501] Use PR that sets LD_LIBRARY_PATH for python-casacore

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 186f4f86b3..e2d35276df 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -45,7 +45,7 @@ easyconfigs:
         from-pr: 19792
   - python-casacore-3.5.2-foss-2023b.eb:
       options:
-        from-pr: 20084
+        from-pr: 20089
   - libspatialindex-1.9.3-GCCcore-13.2.0.eb:
       options:
         from-pr: 19922

From dab1ac0f66c6164c9ea9bc3798be7a0673465ac5 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 12 Mar 2024 19:12:15 +0100
Subject: [PATCH 186/501] Create generic function to compare (and if needed
 copy) files based on an explicit list from one dir to another. Use that
 generic function to replace the existing code copying the scripts dir, and
 the scripts/gpu_support/nvidia dir. Add to that a copy of the init dir and
 the current subdirs, again listing the files to copy explicitely for safety.

---
 install_scripts.sh | 80 +++++++++++++++++++++++++++++++++-------------
 1 file changed, 57 insertions(+), 23 deletions(-)

diff --git a/install_scripts.sh b/install_scripts.sh
index 6e6cd825ac..ac1741428e 100755
--- a/install_scripts.sh
+++ b/install_scripts.sh
@@ -25,6 +25,35 @@ compare_and_copy() {
     fi
 }
 
+copy_files_by_list() {
+# Compares and copies listed files from a source to a target directory
+    if [ "$#" -ne 3 ]; then
+        echo "Usage of function: copy_files_by_list <source_dir> <destination_dir> <file_list>"
+        echo "Here, file_list is an (expanded) bash array"
+        echo "Example:"
+        echo "my_files=(file1 file2)"
+        echo 'copy_files_by_list /my/source /my/target "${my_files[@]}"'
+        return 1
+    fi
+    source_dir="$1"
+    target_dir="$2"
+    # Need to shift all arguments to the left twice. Then, rebuild the array with the rest of the arguments
+    shift
+    shift
+    file_list=("$@")
+
+    # Create target dir
+    mkdir -p ${target_dir}
+
+    # Copy from source to target
+    echo "Copying files: ${file_list[@]}"
+    echo "From directory: ${source_dir}"
+    echo "To directory: ${target_dir}"
+
+    for file in ${file_list[@]}; do
+        compare_and_copy ${source_dir}/${file} ${target_dir}/${file}
+    done
+}
 
 POSITIONAL_ARGS=()
 
@@ -54,28 +83,33 @@ set -- "${POSITIONAL_ARGS[@]}"
 
 TOPDIR=$(dirname $(realpath $0))
 
-# Subdirs for generic scripts
-SCRIPTS_DIR_SOURCE=${TOPDIR}/scripts  # Source dir
-SCRIPTS_DIR_TARGET=${INSTALL_PREFIX}/scripts  # Target dir
+# Copy for init directory
+init_files=(
+    bash eessi_archdetect.sh eessi_defaults eessi_environment_variables eessi_software_subdir_for_host.py
+    minimal_eessi_env README.md test.py
+)
+copy_files_by_list ${TOPDIR}/init ${INSTALL_PREFIX}/init "${init_files[@]}"
 
-# Create target dir
-mkdir -p ${SCRIPTS_DIR_TARGET}
+# Copy for the init/arch_specs directory
+arch_specs_files=(
+   eessi_arch_arm.spec eessi_arch_ppc.spec eessi_arch_x86.spec
+)
+copy_files_by_list ${TOPDIR}/init/arch_specs ${INSTALL_PREFIX}/init/arch_specs "${arch_specs_files[@]}"
 
-# Copy scripts into this prefix
-echo "copying scripts from ${SCRIPTS_DIR_SOURCE} to ${SCRIPTS_DIR_TARGET}"
-for file in utils.sh; do
-    compare_and_copy ${SCRIPTS_DIR_SOURCE}/${file} ${SCRIPTS_DIR_TARGET}/${file}
-done
-# Subdirs for GPU support
-NVIDIA_GPU_SUPPORT_DIR_SOURCE=${SCRIPTS_DIR_SOURCE}/gpu_support/nvidia  # Source dir
-NVIDIA_GPU_SUPPORT_DIR_TARGET=${SCRIPTS_DIR_TARGET}/gpu_support/nvidia  # Target dir
-
-# Create target dir
-mkdir -p ${NVIDIA_GPU_SUPPORT_DIR_TARGET}
-
-# Copy files from this directory into the prefix
-# To be on the safe side, we dont do recursive copies, but we are explicitely copying each individual file we want to add
-echo "copying scripts from ${NVIDIA_GPU_SUPPORT_DIR_SOURCE} to ${NVIDIA_GPU_SUPPORT_DIR_TARGET}"
-for file in install_cuda_host_injections.sh link_nvidia_host_libraries.sh; do
-    compare_and_copy ${NVIDIA_GPU_SUPPORT_DIR_SOURCE}/${file} ${NVIDIA_GPU_SUPPORT_DIR_TARGET}/${file}
-done
+# Copy for init/Magic_castle directory
+mc_files=(
+   bash eessi_python3
+)
+copy_files_by_list ${TOPDIR}/init/Magic_Castle ${INSTALL_PREFIX}/init/Magic_Castle "${mc_files[@]}"
+
+# Copy for the scripts directory
+script_files=(
+    utils.sh
+)
+copy_files_by_list ${TOPDIR}/scripts ${INSTALL_PREFIX}/scripts "${script_files[@]}"
+
+# Copy files for the scripts/gpu_support/nvidia directory
+nvidia_files=(
+    install_cuda_host_injections.sh link_nvidia_host_libraries.sh
+)
+copy_files_by_list ${TOPDIR}/gpu_support/nvidia ${INSTALL_PREFIX}/gpu_support/nvidia "${nvidia_files[@]}"

From 0abedef29ffceb22a5cafa88869bf48b38f3fbb3 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 12 Mar 2024 19:17:47 +0100
Subject: [PATCH 187/501] An expanded bash array counts as extra arguments.
 Thus, we cannot check for three arguments, it can be anything greater than 2

---
 install_scripts.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/install_scripts.sh b/install_scripts.sh
index ac1741428e..e8077aa242 100755
--- a/install_scripts.sh
+++ b/install_scripts.sh
@@ -27,7 +27,7 @@ compare_and_copy() {
 
 copy_files_by_list() {
 # Compares and copies listed files from a source to a target directory
-    if [ "$#" -ne 3 ]; then
+    if [ ! "$#" -ge 3 ]; then
         echo "Usage of function: copy_files_by_list <source_dir> <destination_dir> <file_list>"
         echo "Here, file_list is an (expanded) bash array"
         echo "Example:"

From 11c7525e03069c0a5aa85d36a9cca5a1aeaff381 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 12 Mar 2024 19:21:06 +0100
Subject: [PATCH 188/501] Forgot to check the diff if the
 create_lmodsitepackage.py actually changed

---
 EESSI-install-software.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 219fa8680a..2d5912736b 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -259,6 +259,7 @@ fi
 echo ">> Creating/updating Lmod SitePackage.lua ..."
 export LMOD_PACKAGE_PATH="${EASYBUILD_INSTALLPATH}/.lmod"
 lmod_sitepackage_file="$LMOD_PACKAGE_PATH/SitePackage.lua"
+sitepackage_changed=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^create_lmodsitepackage.py$' > /dev/null; echo $?)
 if [ ! -f $lmod_sitepackage_file ] || [ ${sitepackage_changed} == '0' ]; then
     python3 $TOPDIR/create_lmodsitepackage.py ${EASYBUILD_INSTALLPATH}
     check_exit_code $? "$lmod_sitepackage_file created" "Failed to create $lmod_sitepackage_file"

From a07b8a8accc23666be71f36ce0d09e82e9ffdc30 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 12 Mar 2024 19:22:01 +0100
Subject: [PATCH 189/501] Is quoting the problem

---
 EESSI-install-software.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 2d5912736b..c51459967d 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -260,7 +260,7 @@ echo ">> Creating/updating Lmod SitePackage.lua ..."
 export LMOD_PACKAGE_PATH="${EASYBUILD_INSTALLPATH}/.lmod"
 lmod_sitepackage_file="$LMOD_PACKAGE_PATH/SitePackage.lua"
 sitepackage_changed=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^create_lmodsitepackage.py$' > /dev/null; echo $?)
-if [ ! -f $lmod_sitepackage_file ] || [ ${sitepackage_changed} == '0' ]; then
+if [ ! -f $lmod_sitepackage_file ] || [ "${sitepackage_changed}" == '0' ]; then
     python3 $TOPDIR/create_lmodsitepackage.py ${EASYBUILD_INSTALLPATH}
     check_exit_code $? "$lmod_sitepackage_file created" "Failed to create $lmod_sitepackage_file"
 fi

From 90b3ce068aa787715d82a20656c99f656f561a44 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 12 Mar 2024 19:23:57 +0100
Subject: [PATCH 190/501] Try quoting

---
 EESSI-install-software.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index c51459967d..2a4f7182cd 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -260,7 +260,7 @@ echo ">> Creating/updating Lmod SitePackage.lua ..."
 export LMOD_PACKAGE_PATH="${EASYBUILD_INSTALLPATH}/.lmod"
 lmod_sitepackage_file="$LMOD_PACKAGE_PATH/SitePackage.lua"
 sitepackage_changed=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^create_lmodsitepackage.py$' > /dev/null; echo $?)
-if [ ! -f $lmod_sitepackage_file ] || [ "${sitepackage_changed}" == '0' ]; then
+if [ ! -f "$lmod_sitepackage_file" ] || [ "${sitepackage_changed}" == '0' ]; then
     python3 $TOPDIR/create_lmodsitepackage.py ${EASYBUILD_INSTALLPATH}
     check_exit_code $? "$lmod_sitepackage_file created" "Failed to create $lmod_sitepackage_file"
 fi

From 9c707e4a69ad385474067f2adee599632ffda882 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 12 Mar 2024 19:25:30 +0100
Subject: [PATCH 191/501] Correct prefix for the gpu_support scripts

---
 install_scripts.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/install_scripts.sh b/install_scripts.sh
index e8077aa242..508735975c 100755
--- a/install_scripts.sh
+++ b/install_scripts.sh
@@ -112,4 +112,4 @@ copy_files_by_list ${TOPDIR}/scripts ${INSTALL_PREFIX}/scripts "${script_files[@
 nvidia_files=(
     install_cuda_host_injections.sh link_nvidia_host_libraries.sh
 )
-copy_files_by_list ${TOPDIR}/gpu_support/nvidia ${INSTALL_PREFIX}/gpu_support/nvidia "${nvidia_files[@]}"
+copy_files_by_list ${TOPDIR}/scripts/gpu_support/nvidia ${INSTALL_PREFIX}/scripts/gpu_support/nvidia "${nvidia_files[@]}"

From 743860fc06d5be09e9b15d62514f91ac2fb4aebc Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 13 Mar 2024 11:29:07 +0100
Subject: [PATCH 192/501] {2023.06}[foss/2023b] GROMACS 2024.1

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index e2d35276df..f906811a73 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -49,3 +49,6 @@ easyconfigs:
   - libspatialindex-1.9.3-GCCcore-13.2.0.eb:
       options:
         from-pr: 19922
+  - GROMACS-2024.1-foss-2023b.eb:
+      options:
+        from-pr: 20102

From c08831ee060d153bb1da466cfaa00e4103c37e31 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Wed, 13 Mar 2024 15:46:24 +0100
Subject: [PATCH 193/501] Update bot/check-build.sh

Co-authored-by: Kenneth Hoste <kenneth.hoste@ugent.be>
---
 bot/check-build.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bot/check-build.sh b/bot/check-build.sh
index 10b1ed6a11..e075518421 100755
--- a/bot/check-build.sh
+++ b/bot/check-build.sh
@@ -174,7 +174,7 @@ fi
 # For now, we only analyse unmerged EasyConfigs as potential cause, but we can easily add checks for other
 # specific scenarios below
 
-# Check for the pattern being added here https://github.com/EESSI/software-layer/pull/493 to the output to
+# Check for the pattern being added here by check_missing_installations.sh to the output to
 # see if EasyConfigs might have been unmerged, and that's causing a failure
 UNMERGED_EASYCONFIG=-1
 if [[ ${SLURM_OUTPUT_FOUND} -eq 1 ]]; then

From 992b11dc782d391899862f80033f08b1efba4634 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Wed, 13 Mar 2024 15:47:37 +0100
Subject: [PATCH 194/501] Remove PR to trigger comment

Co-authored-by: Kenneth Hoste <kenneth.hoste@ugent.be>
---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 2b5844289d..e2d35276df 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -49,6 +49,3 @@ easyconfigs:
   - libspatialindex-1.9.3-GCCcore-13.2.0.eb:
       options:
         from-pr: 19922
-  - CFITSIO-4.3.1-GCCcore-13.2.0.eb:
-      options:
-        from-pr: 19840

From 8d6493ea05422ee443f10bc9230c3ff3884af998 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Wed, 13 Mar 2024 15:48:08 +0100
Subject: [PATCH 195/501] Trigger on any non-zero exit code

Co-authored-by: Kenneth Hoste <kenneth.hoste@ugent.be>
---
 check_missing_installations.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/check_missing_installations.sh b/check_missing_installations.sh
index 0ee6ec4385..7c29228416 100755
--- a/check_missing_installations.sh
+++ b/check_missing_installations.sh
@@ -47,7 +47,7 @@ exit_code=${PIPESTATUS[0]}
 
 ok_msg="Command 'eb --missing ...' succeeded, analysing output..."
 fail_msg="Command 'eb --missing ...' failed, check log '${eb_missing_out}'"
-if [ "$exit_code" -eq 1 ] && [ ! -z $pr_exceptions ]; then
+if [ "$exit_code" -ne 0 ] && [ ! -z $pr_exceptions ]; then
     # We might have failed due to unmerged PRs. Try to make exceptions for --from-pr added in this PR
     # to software-layer, and see if then it passes. If so, we can report a more specific fail_msg
     # Note that if no --from-pr's were used in this PR, $pr_exceptions will be empty and we might as

From a148920b35a4a70d03ce5f0175b3c730ae279db0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 13 Mar 2024 22:35:09 +0100
Subject: [PATCH 196/501] remove openmpi hook that provided a temporary
 workaround

---
 create_lmodrc.py | 21 ---------------------
 1 file changed, 21 deletions(-)

diff --git a/create_lmodrc.py b/create_lmodrc.py
index bc69dd4396..0e738a530e 100755
--- a/create_lmodrc.py
+++ b/create_lmodrc.py
@@ -94,28 +94,7 @@
     end
 end
 
-local function openmpi_load_hook(t)
-    -- disable smcuda BTL when loading OpenMPI module for aarch64/neoverse_v1,
-    -- to work around hang/crash due to bug in OpenMPI;
-    -- see https://gitlab.com/eessi/support/-/issues/41
-    local frameStk = require("FrameStk"):singleton()
-    local mt = frameStk:mt()
-    local moduleName = string.match(t.modFullName, "(.-)/")
-    local cpuTarget = os.getenv("EESSI_SOFTWARE_SUBDIR") or ""
-    if (moduleName == "OpenMPI") and (cpuTarget == "aarch64/neoverse_v1") then
-        local msg = "Adding '^smcuda' to $OMPI_MCA_btl to work around bug in OpenMPI"
-        LmodMessage(msg .. " (see https://gitlab.com/eessi/support/-/issues/41)")
-	local ompiMcaBtl = os.getenv("OMPI_MCA_btl")
-	if ompiMcaBtl == nil then
-            setenv("OMPI_MCA_btl", "^smcuda")
-        else
-            setenv("OMPI_MCA_btl", ompiMcaBtl .. ",^smcuda")
-	end
-    end
-end
-
 hook.register("load", cuda_enabled_load_hook)
-hook.register("load", openmpi_load_hook)
 """
 
 def error(msg):

From 5d4542e5a73962da0032427bba7ee7ed19b79ef0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 13 Mar 2024 22:38:33 +0100
Subject: [PATCH 197/501] remove hook.register for cuda hook

---
 create_lmodrc.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/create_lmodrc.py b/create_lmodrc.py
index 2175f885d2..133743c844 100755
--- a/create_lmodrc.py
+++ b/create_lmodrc.py
@@ -94,8 +94,6 @@
     end
 end
 
-hook.register("load", cuda_enabled_load_hook)
-
 -- Combine both functions into a single one, as we can only register one function as load hook in lmod
 -- Also: make it non-local, so it can be imported and extended by other lmodrc files if needed
 function eessi_load_hook(t)

From 54bb3ec1cdd6cae823068a67cdfdb5d443d4e69b Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Thu, 14 Mar 2024 09:38:29 +0100
Subject: [PATCH 198/501] Make sure the changed init scripts also end up in the
 tarball

---
 create_tarball.sh | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/create_tarball.sh b/create_tarball.sh
index a619df9439..5bd8eeb110 100755
--- a/create_tarball.sh
+++ b/create_tarball.sh
@@ -51,6 +51,13 @@ if [ -d ${eessi_version}/scripts ]; then
     find ${eessi_version}/scripts -type f | grep -v '/\.wh\.' >> ${files_list}
 fi
 
+# also include init, which is also copied by install_scripts.sh
+if [ -d ${eessi_version}/init ]; then
+    find ${eessi_version}/init -type f | grep -v '/\.wh\.' >> ${files_list}
+fi
+
+
+
 if [ -d ${eessi_version}/software/${os}/${cpu_arch_subdir}/modules ]; then
     # module files
     find ${eessi_version}/software/${os}/${cpu_arch_subdir}/modules -type f | grep -v '/\.wh\.' >> ${files_list}

From 0fdbd3a3be714c116b76f72c694406ea03e513fe Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Thu, 14 Mar 2024 11:35:35 +0100
Subject: [PATCH 199/501] Add Z3 with new module name

Via https://github.com/easybuilders/easybuild-easyconfigs/pull/20050 , the different Z3 easyconfigs have been consolidated. This means the version used as a dependency for PyTorch has been "corrected" so we need to dance around that for our CI purposes
---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023a.yml                | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 8165755865..5a46cf5fb2 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -40,3 +40,9 @@ easyconfigs:
   - ImageMagick-7.1.1-15-GCCcore-12.3.0.eb:
       options:
         from-pr: 20086
+  - Z3-4.12.2-GCCcore-12.3.0.eb:
+      options:
+        # The Z3 dependency of PyTorch had it's versionsuffix removed
+        # and we need to workaround the problem this creates,
+        # see https://github.com/EESSI/software-layer/pull/501 for details
+        from-pr: 20050

From 5a6bfd149bd59894e51adec5b2e8e9dc00873977 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Thu, 14 Mar 2024 17:47:18 +0100
Subject: [PATCH 200/501] Remove whitspace

---
 create_tarball.sh | 2 --
 1 file changed, 2 deletions(-)

diff --git a/create_tarball.sh b/create_tarball.sh
index 5bd8eeb110..2d77acfc43 100755
--- a/create_tarball.sh
+++ b/create_tarball.sh
@@ -56,8 +56,6 @@ if [ -d ${eessi_version}/init ]; then
     find ${eessi_version}/init -type f | grep -v '/\.wh\.' >> ${files_list}
 fi
 
-
-
 if [ -d ${eessi_version}/software/${os}/${cpu_arch_subdir}/modules ]; then
     # module files
     find ${eessi_version}/software/${os}/${cpu_arch_subdir}/modules -type f | grep -v '/\.wh\.' >> ${files_list}

From d097189aa07f2d323779212e4451a2df2466193d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 14 Mar 2024 22:55:43 +0100
Subject: [PATCH 201/501] {2023.06}[2023a] PyOpenGL 3.1.7

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 5a46cf5fb2..1d3119e5c2 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -46,3 +46,4 @@ easyconfigs:
         # and we need to workaround the problem this creates,
         # see https://github.com/EESSI/software-layer/pull/501 for details
         from-pr: 20050
+  - PyOpenGL-3.1.7-GCCcore-12.3.0.eb

From 8245aff4b7f4dd178924cd42eda76c21eed146fa Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 15 Mar 2024 00:02:09 +0100
Subject: [PATCH 202/501] add from-pr=20007

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023a.yml                  | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 1d3119e5c2..65b4265ff7 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -46,4 +46,6 @@ easyconfigs:
         # and we need to workaround the problem this creates,
         # see https://github.com/EESSI/software-layer/pull/501 for details
         from-pr: 20050
-  - PyOpenGL-3.1.7-GCCcore-12.3.0.eb
+  - PyOpenGL-3.1.7-GCCcore-12.3.0.eb:
+      options:
+        from-pr: 20007

From af58e1a5fc00ab311eab185a91302d0c735c8978 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 15 Mar 2024 20:48:12 +0100
Subject: [PATCH 203/501] {2023.06}[2023a] ipympl 0.9.3

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 65b4265ff7..384aa04a9c 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -49,3 +49,6 @@ easyconfigs:
   - PyOpenGL-3.1.7-GCCcore-12.3.0.eb:
       options:
         from-pr: 20007
+  - ipympl-0.9.3-foss-2023a.eb:
+      options:
+        from-pr: 20126

From a12b9a340e17953a8e6fe741245663c69ece813b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 15 Mar 2024 21:13:32 +0100
Subject: [PATCH 204/501] fix check_missing_installations.sh when unmerged PR
 is used

---
 check_missing_installations.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/check_missing_installations.sh b/check_missing_installations.sh
index 7c29228416..d8135ea3cb 100755
--- a/check_missing_installations.sh
+++ b/check_missing_installations.sh
@@ -47,7 +47,7 @@ exit_code=${PIPESTATUS[0]}
 
 ok_msg="Command 'eb --missing ...' succeeded, analysing output..."
 fail_msg="Command 'eb --missing ...' failed, check log '${eb_missing_out}'"
-if [ "$exit_code" -ne 0 ] && [ ! -z $pr_exceptions ]; then
+if [ "$exit_code" -ne 0 ] && [ ! -z "$pr_exceptions" ]; then
     # We might have failed due to unmerged PRs. Try to make exceptions for --from-pr added in this PR
     # to software-layer, and see if then it passes. If so, we can report a more specific fail_msg
     # Note that if no --from-pr's were used in this PR, $pr_exceptions will be empty and we might as

From 54e30859248035fb70694f68a6b6c6c695b196c9 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Wed, 20 Mar 2024 23:27:16 +0100
Subject: [PATCH 205/501] Add libxc and ELPA

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml  | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 384aa04a9c..4fa3d8a29e 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -52,3 +52,5 @@ easyconfigs:
   - ipympl-0.9.3-foss-2023a.eb:
       options:
         from-pr: 20126
+  - ELPA-2023.05.001-foss-2023a.eb
+  - libxc-6.2.2-GCC-12.3.0.eb

From 9d62787eb90dcd6a42e5c9e8b9f51f87c4d84d31 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 26 Mar 2024 09:19:44 +0100
Subject: [PATCH 206/501] source init/bash instead of minimal eessi env

---
 EESSI-remove-software.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index 1779a7ed58..010ee365af 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -47,7 +47,7 @@ source $TOPDIR/scripts/utils.sh
 
 echo ">> Setting up environment..."
 
-source $TOPDIR/init/minimal_eessi_env
+source $TOPDIR/init/bash
 
 if [ -d $EESSI_CVMFS_REPO ]; then
     echo_green "$EESSI_CVMFS_REPO available, OK!"

From 229ce93ac4c2db86b8fbd29da38f1e78f2d5c167 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 26 Mar 2024 09:20:35 +0100
Subject: [PATCH 207/501] remove GENERIC variable

---
 EESSI-remove-software.sh | 2 --
 1 file changed, 2 deletions(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index 010ee365af..6d0c9e3800 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -56,12 +56,10 @@ else
 fi
 
 DETECTION_PARAMETERS=''
-GENERIC=0
 EB='eb'
 if [[ "$EASYBUILD_OPTARCH" == "GENERIC" ]]; then
     echo_yellow ">> GENERIC build requested, taking appropriate measures!"
     DETECTION_PARAMETERS="$DETECTION_PARAMETERS --generic"
-    GENERIC=1
     EB='eb --optarch=GENERIC'
 fi
 

From 977bcaad3f5ba29d5d38ef95dc5f2acc782c573b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 26 Mar 2024 09:26:41 +0100
Subject: [PATCH 208/501] clean up eb optarch=generic settings

---
 EESSI-remove-software.sh | 12 +++---------
 1 file changed, 3 insertions(+), 9 deletions(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index 6d0c9e3800..cdf4ae3b7b 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -18,7 +18,9 @@ POSITIONAL_ARGS=()
 while [[ $# -gt 0 ]]; do
   case $1 in
     -g|--generic)
+      echo_yellow ">> GENERIC build requested, taking appropriate measures!"
       EASYBUILD_OPTARCH="GENERIC"
+      DETECTION_PARAMETERS="--generic"
       shift
       ;;
     -h|--help)
@@ -55,14 +57,6 @@ else
     fatal_error "$EESSI_CVMFS_REPO is not available!"
 fi
 
-DETECTION_PARAMETERS=''
-EB='eb'
-if [[ "$EASYBUILD_OPTARCH" == "GENERIC" ]]; then
-    echo_yellow ">> GENERIC build requested, taking appropriate measures!"
-    DETECTION_PARAMETERS="$DETECTION_PARAMETERS --generic"
-    EB='eb --optarch=GENERIC'
-fi
-
 echo ">> Determining software subdirectory to use for current build host..."
 if [ -z $EESSI_SOFTWARE_SUBDIR_OVERRIDE ]; then
   export EESSI_SOFTWARE_SUBDIR_OVERRIDE=$(python3 $TOPDIR/eessi_software_subdir.py $DETECTION_PARAMETERS)
@@ -129,7 +123,7 @@ if [ $EUID -eq 0 ]; then
                 # we need to remove existing installation directories first,
                 # so let's figure out which modules have to be rebuilt by doing a dry-run and grepping "someapp/someversion" for the relevant lines (with [R])
                 #  * [R] $CFGS/s/someapp/someapp-someversion.eb (module: someapp/someversion)
-                rebuild_apps=$(${EB} --allow-use-as-root-and-accept-consequences --dry-run-short --rebuild --easystack ${easystack_file} | grep "^ \* \[R\]" | grep -o "module: .*[^)]" | awk '{print $2}')
+                rebuild_apps=$(eb --allow-use-as-root-and-accept-consequences --dry-run-short --rebuild --easystack ${easystack_file} | grep "^ \* \[R\]" | grep -o "module: .*[^)]" | awk '{print $2}')
                 for app in ${rebuild_apps}; do
                     app_dir=${EASYBUILD_INSTALLPATH}/software/${app}
                     app_module=${EASYBUILD_INSTALLPATH}/modules/all/${app}.lua

From f1cfc1b1f4f9f32d3669b46af781b2ab648d9c52 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 26 Mar 2024 09:38:48 +0100
Subject: [PATCH 209/501] source init/bash and clean up redundant code

---
 EESSI-remove-software.sh | 30 ++++++++----------------------
 1 file changed, 8 insertions(+), 22 deletions(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index cdf4ae3b7b..c1f0bcb3d0 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -47,6 +47,14 @@ export TMPDIR=$(mktemp -d /tmp/eessi-remove.XXXXXXXX)
 
 source $TOPDIR/scripts/utils.sh
 
+echo ">> Determining software subdirectory to use for current build host..."
+if [ -z $EESSI_SOFTWARE_SUBDIR_OVERRIDE ]; then
+  export EESSI_SOFTWARE_SUBDIR_OVERRIDE=$(python3 $TOPDIR/eessi_software_subdir.py $DETECTION_PARAMETERS)
+  echo ">> Determined \$EESSI_SOFTWARE_SUBDIR_OVERRIDE via 'eessi_software_subdir.py $DETECTION_PARAMETERS' script"
+else
+  echo ">> Picking up pre-defined \$EESSI_SOFTWARE_SUBDIR_OVERRIDE: ${EESSI_SOFTWARE_SUBDIR_OVERRIDE}"
+fi
+
 echo ">> Setting up environment..."
 
 source $TOPDIR/init/bash
@@ -57,19 +65,6 @@ else
     fatal_error "$EESSI_CVMFS_REPO is not available!"
 fi
 
-echo ">> Determining software subdirectory to use for current build host..."
-if [ -z $EESSI_SOFTWARE_SUBDIR_OVERRIDE ]; then
-  export EESSI_SOFTWARE_SUBDIR_OVERRIDE=$(python3 $TOPDIR/eessi_software_subdir.py $DETECTION_PARAMETERS)
-  echo ">> Determined \$EESSI_SOFTWARE_SUBDIR_OVERRIDE via 'eessi_software_subdir.py $DETECTION_PARAMETERS' script"
-else
-  echo ">> Picking up pre-defined \$EESSI_SOFTWARE_SUBDIR_OVERRIDE: ${EESSI_SOFTWARE_SUBDIR_OVERRIDE}"
-fi
-
-# Set all the EESSI environment variables (respecting $EESSI_SOFTWARE_SUBDIR_OVERRIDE)
-# $EESSI_SILENT - don't print any messages
-# $EESSI_BASIC_ENV - give a basic set of environment variables
-EESSI_SILENT=1 EESSI_BASIC_ENV=1 source $TOPDIR/init/eessi_environment_variables
-
 if [[ -z ${EESSI_SOFTWARE_SUBDIR} ]]; then
     fatal_error "Failed to determine software subdirectory?!"
 elif [[ "${EESSI_SOFTWARE_SUBDIR}" != "${EESSI_SOFTWARE_SUBDIR_OVERRIDE}" ]]; then
@@ -78,15 +73,6 @@ else
     echo_green ">> Using ${EESSI_SOFTWARE_SUBDIR} as software subdirectory!"
 fi
 
-echo ">> Initializing Lmod..."
-source $EPREFIX/usr/share/Lmod/init/bash
-ml --version
-if [[ $? -eq 0 ]]; then
-    echo_green ">> Found Lmod ${LMOD_VERSION}"
-else
-    fatal_error "Failed to initialize Lmod?!"
-fi
-
 echo ">> Configuring EasyBuild..."
 source $TOPDIR/configure_easybuild
 

From aa4a82dd3c87eccf155715eee9797532f9ed8dd0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 26 Mar 2024 09:48:48 +0100
Subject: [PATCH 210/501] set EB variable

---
 EESSI-remove-software.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index c1f0bcb3d0..9993986904 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -74,6 +74,7 @@ else
 fi
 
 echo ">> Configuring EasyBuild..."
+EB="eb"
 source $TOPDIR/configure_easybuild
 
 echo ">> Setting up \$MODULEPATH..."

From 6ca6a70671a019db0e83f54cb74e6049cba2a0f9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 26 Mar 2024 09:57:32 +0100
Subject: [PATCH 211/501] remove build-dir argument from display_help

---
 EESSI-remove-software.sh | 1 -
 1 file changed, 1 deletion(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index 9993986904..10cea933db 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -8,7 +8,6 @@
 
 display_help() {
   echo "usage: $0 [OPTIONS]"
-  echo "  --build-logs-dir       -  location to copy EasyBuild logs to for failed builds"
   echo "  -g | --generic         -  instructs script to build for generic architecture target"
   echo "  -h | --help            -  display this usage information"
 }

From e89cb05d3bdcdb8df9c16cfdcea24afa81f8abf1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 26 Mar 2024 10:08:12 +0100
Subject: [PATCH 212/501] export the EASYBUILD_OPTARCH variable

Co-authored-by: Kenneth Hoste <kenneth.hoste@ugent.be>
---
 EESSI-remove-software.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index 10cea933db..f465aff304 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -18,7 +18,7 @@ while [[ $# -gt 0 ]]; do
   case $1 in
     -g|--generic)
       echo_yellow ">> GENERIC build requested, taking appropriate measures!"
-      EASYBUILD_OPTARCH="GENERIC"
+      export EASYBUILD_OPTARCH="GENERIC"
       DETECTION_PARAMETERS="--generic"
       shift
       ;;

From 502c02311cae893ef7983b340481c47684716997 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 26 Mar 2024 10:19:46 +0100
Subject: [PATCH 213/501] remove EASYBUILD_OPTARCH

---
 EESSI-remove-software.sh | 1 -
 1 file changed, 1 deletion(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index f465aff304..1cd291b16c 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -18,7 +18,6 @@ while [[ $# -gt 0 ]]; do
   case $1 in
     -g|--generic)
       echo_yellow ">> GENERIC build requested, taking appropriate measures!"
-      export EASYBUILD_OPTARCH="GENERIC"
       DETECTION_PARAMETERS="--generic"
       shift
       ;;

From 3206a0ffa0b8759d8db5d67b5c3525d8b25ed674 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 26 Mar 2024 10:24:19 +0100
Subject: [PATCH 214/501] remove echo_yellow call for generic builds

---
 EESSI-remove-software.sh | 1 -
 1 file changed, 1 deletion(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index 1cd291b16c..446a156cb8 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -17,7 +17,6 @@ POSITIONAL_ARGS=()
 while [[ $# -gt 0 ]]; do
   case $1 in
     -g|--generic)
-      echo_yellow ">> GENERIC build requested, taking appropriate measures!"
       DETECTION_PARAMETERS="--generic"
       shift
       ;;

From ee1c2cefd1b6461aa675288bef0cd2faa1163d31 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 26 Mar 2024 10:27:20 +0100
Subject: [PATCH 215/501] use separate variable for removal script arguments

---
 bot/build.sh | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/bot/build.sh b/bot/build.sh
index 31d9b576fe..c76285faf4 100755
--- a/bot/build.sh
+++ b/bot/build.sh
@@ -171,8 +171,10 @@ PREVIOUS_TMP_DIR=${PWD}/previous_tmp
 # prepare arguments to install_software_layer.sh (specific to build step)
 declare -a BUILD_STEP_ARGS=()
 declare -a INSTALL_SCRIPT_ARGS=()
+declare -a REMOVAL_SCRIPT_ARGS=()
 if [[ ${EESSI_SOFTWARE_SUBDIR_OVERRIDE} =~ .*/generic$ ]]; then
     INSTALL_SCRIPT_ARGS+=("--generic")
+    REMOVAL_SCRIPT_ARGS+=("--generic")
 fi
 [[ ! -z ${BUILD_LOGS_DIR} ]] && INSTALL_SCRIPT_ARGS+=("--build-logs-dir" "${BUILD_LOGS_DIR}")
 [[ ! -z ${SHARED_FS_PATH} ]] && INSTALL_SCRIPT_ARGS+=("--shared-fs-path" "${SHARED_FS_PATH}")
@@ -200,9 +202,9 @@ else
 
     echo "Executing command to remove software:"
     echo "./eessi_container.sh ${COMMON_ARGS[@]} ${REMOVAL_STEP_ARGS[@]}"
-    echo "                     -- ./EESSI-remove-software.sh \"${INSTALL_SCRIPT_ARGS[@]}\" \"$@\" 2>&1 | tee -a ${removal_outerr}"
+    echo "                     -- ./EESSI-remove-software.sh \"${REMOVAL_SCRIPT_ARGS[@]}\" \"$@\" 2>&1 | tee -a ${removal_outerr}"
     ./eessi_container.sh "${COMMON_ARGS[@]}" "${REMOVAL_STEP_ARGS[@]}" \
-                         -- ./EESSI-remove-software.sh "${INSTALL_SCRIPT_ARGS[@]}" "$@" 2>&1 | tee -a ${removal_outerr}
+                         -- ./EESSI-remove-software.sh "${REMOVAL_SCRIPT_ARGS[@]}" "$@" 2>&1 | tee -a ${removal_outerr}
 
     # make sure that the build step resumes from the same temporary directory
     # this is important, as otherwise the removed software will still be there

From 330db7a02cf011c2115babf598991217f87bd022 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 26 Mar 2024 10:32:49 +0100
Subject: [PATCH 216/501] also dump status to test result file

---
 bot/check-test.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index 4b5f7575e5..f045b9500a 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -200,5 +200,6 @@ comment_description=${comment_description/__DETAILS_FMT__/${comment_details}}
 
 # Actually writing the comment description to the result file
 echo "${comment_description}" >> ${job_test_result_file}
+echo "status = ${status}" >> ${job_test_result_file}
 
 exit 0

From f3c62077c40e299bb6a3f157adfd2c1f5a32d067 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 26 Mar 2024 10:33:24 +0100
Subject: [PATCH 217/501] add Caspar as author in `bot/test.sh` script

---
 bot/test.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/bot/test.sh b/bot/test.sh
index 89c1a6a8bf..66c2cef129 100755
--- a/bot/test.sh
+++ b/bot/test.sh
@@ -8,6 +8,7 @@
 # https://github.com/EESSI/software-layer.git
 #
 # author: Thomas Roeblitz (@trz42)
+# author: Caspar van Leeuwen (@casparvl)
 #
 # license: GPLv2
 #

From c55ee6b6075786fd0dfd657ba3e2e667a215b9da Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 26 Mar 2024 10:33:44 +0100
Subject: [PATCH 218/501] clarify why we need fakeroot, add link to issue

---
 bot/build.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/bot/build.sh b/bot/build.sh
index c76285faf4..b007b80172 100755
--- a/bot/build.sh
+++ b/bot/build.sh
@@ -194,7 +194,8 @@ else
     declare -a REMOVAL_STEP_ARGS=()
     REMOVAL_STEP_ARGS+=("--save" "${TARBALL_TMP_BUILD_STEP_DIR}")
     REMOVAL_STEP_ARGS+=("--storage" "${STORAGE}")
-    # add fakeroot option in order to be able to remove software
+    # add fakeroot option in order to be able to remove software, see:
+    # https://github.com/EESSI/software-layer/issues/312
     REMOVAL_STEP_ARGS+=("--fakeroot")
 
     # create tmp file for output of removal step

From 13072df707b96cad40b4d21cbedd6666af756b0d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 26 Mar 2024 10:34:09 +0100
Subject: [PATCH 219/501] use read-only mode to access software installations
 via container

---
 bot/test.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bot/test.sh b/bot/test.sh
index 66c2cef129..925b91d49a 100755
--- a/bot/test.sh
+++ b/bot/test.sh
@@ -180,7 +180,7 @@ echo "bot/test.sh: EESSI_OS_TYPE='${EESSI_OS_TYPE}'"
 # prepare arguments to eessi_container.sh common to build and tarball steps
 declare -a COMMON_ARGS=()
 COMMON_ARGS+=("--verbose")
-COMMON_ARGS+=("--access" "rw")
+COMMON_ARGS+=("--access" "ro")
 COMMON_ARGS+=("--mode" "run")
 [[ ! -z ${CONTAINER} ]] && COMMON_ARGS+=("--container" "${CONTAINER}")
 [[ ! -z ${HTTP_PROXY} ]] && COMMON_ARGS+=("--http-proxy" "${HTTP_PROXY}")

From 1fa323ada6d0fddc312ad102cba8619d073f9fb0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 26 Mar 2024 10:34:53 +0100
Subject: [PATCH 220/501] fix typo: build -> test

---
 bot/test.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bot/test.sh b/bot/test.sh
index 925b91d49a..4984340e6e 100755
--- a/bot/test.sh
+++ b/bot/test.sh
@@ -190,7 +190,7 @@ COMMON_ARGS+=("--mode" "run")
 # make sure to use the same parent dir for storing tarballs of tmp
 PREVIOUS_TMP_DIR=${PWD}/previous_tmp
 
-# prepare directory to store tarball of tmp for build step
+# prepare directory to store tarball of tmp for test step
 TARBALL_TMP_TEST_STEP_DIR=${PREVIOUS_TMP_DIR}/test_step
 mkdir -p ${TARBALL_TMP_TEST_STEP_DIR}
 
@@ -216,7 +216,7 @@ fi
 # create tmp file for output of build step
 test_outerr=$(mktemp test.outerr.XXXX)
 
-echo "Executing command to build software:"
+echo "Executing command to test software:"
 echo "./eessi_container.sh ${COMMON_ARGS[@]} ${TEST_STEP_ARGS[@]}"
 echo "                     -- ./run_tests.sh \"${TEST_SUITE_ARGS[@]}\" \"$@\" 2>&1 | tee -a ${test_outerr}"
 ./eessi_container.sh "${COMMON_ARGS[@]}" "${TEST_STEP_ARGS[@]}" \

From 8d05473eb5eedf0cdaba75f6b4d4a40f38a3182d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 26 Mar 2024 10:35:30 +0100
Subject: [PATCH 221/501] disable CPU auto-detection in template ReFrame
 configuration script used for running test suite

---
 reframe_config_bot.py.tmpl | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/reframe_config_bot.py.tmpl b/reframe_config_bot.py.tmpl
index b2f7916e79..0cc3e9f530 100644
--- a/reframe_config_bot.py.tmpl
+++ b/reframe_config_bot.py.tmpl
@@ -51,9 +51,8 @@ site_configuration = {
         {
             'purge_environment': True,
             'resolve_module_conflicts': False,  # avoid loading the module before submitting the job
-            # Enable automatic detection of CPU architecture
-            # See https://reframe-hpc.readthedocs.io/en/stable/configure.html#auto-detecting-processor-information
-            'remote_detect': True,
+            # disable automatic detection of CPU architecture (since we're using local scheduler)
+            'remote_detect': False,
         }
     ],
     'logging': common_logging_config(),

From c53f578687e43ae0c7876c3a9d5c48fc2432ad49 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 26 Mar 2024 10:37:09 +0100
Subject: [PATCH 222/501] pass down --generic to script used for running test
 suite, so tests are run with generic software installations when intended

---
 run_tests.sh  | 2 +-
 test_suite.sh | 9 ++++-----
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/run_tests.sh b/run_tests.sh
index de7fd8c2e1..1dbb47db9d 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -21,4 +21,4 @@ source ${base_dir}/init/eessi_defaults
 ./run_in_compat_layer_env.sh "git clone https://github.com/EESSI/test-suite EESSI-test-suite"
 
 # Run the test suite
-./test_suite.sh
+./test_suite.sh "$@"
diff --git a/test_suite.sh b/test_suite.sh
index e3bab04aec..95eb9daa2a 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -23,7 +23,7 @@ POSITIONAL_ARGS=()
 while [[ $# -gt 0 ]]; do
   case $1 in
     -g|--generic)
-      EASYBUILD_OPTARCH="GENERIC"
+      DETECTION_PARAMETERS="--generic"
       shift
       ;;
     -h|--help)
@@ -75,10 +75,9 @@ TMPDIR=$(mktemp -d)
 
 echo ">> Setting up environment..."
 module --force purge
-# Make sure defaults are set for EESSI_CVMFS_REPO and EESSI_VERSION, before initializing EESSI
-source $TOPDIR/init/eessi_defaults
-# Initialize EESSI
-source ${EESSI_CVMFS_REPO}/versions/${EESSI_VERSION}/init/bash
+export EESSI_SOFTWARE_SUBDIR_OVERRIDE=$(python3 $TOPDIR/eessi_software_subdir.py $DETECTION_PARAMETERS)
+
+source $TOPDIR/init/bash
 
 # Load the ReFrame module
 # Currently, we load the default version. Maybe we should somehow make this configurable in the future?

From 57d8b6fd4eceaf951c69cac9f325d5aa5eb113ef Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 26 Mar 2024 10:54:13 +0100
Subject: [PATCH 223/501] remove openmpi hook for smcuda workaround

---
 create_lmodsitepackage.py | 21 ---------------------
 1 file changed, 21 deletions(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index 9a4a232863..5a7a915494 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -84,31 +84,10 @@
     end
 end
 
-local function eessi_openmpi_load_hook(t)
-    -- disable smcuda BTL when loading OpenMPI module for aarch64/neoverse_v1,
-    -- to work around hang/crash due to bug in OpenMPI;
-    -- see https://gitlab.com/eessi/support/-/issues/41
-    local frameStk = require("FrameStk"):singleton()
-    local mt = frameStk:mt()
-    local moduleName = string.match(t.modFullName, "(.-)/")
-    local cpuTarget = os.getenv("EESSI_SOFTWARE_SUBDIR") or ""
-    if (moduleName == "OpenMPI") and (cpuTarget == "aarch64/neoverse_v1") then
-        local msg = "Adding '^smcuda' to $OMPI_MCA_btl to work around bug in OpenMPI"
-        LmodMessage(msg .. " (see https://gitlab.com/eessi/support/-/issues/41)")
-	local ompiMcaBtl = os.getenv("OMPI_MCA_btl")
-	if ompiMcaBtl == nil then
-            setenv("OMPI_MCA_btl", "^smcuda")
-        else
-            setenv("OMPI_MCA_btl", ompiMcaBtl .. ",^smcuda")
-	end
-    end
-end
-
 -- Combine both functions into a single one, as we can only register one function as load hook in lmod
 -- Also: make it non-local, so it can be imported and extended by other lmodrc files if needed
 function eessi_load_hook(t)
     eessi_cuda_enabled_load_hook(t)
-    eessi_openmpi_load_hook(t)
 end
 
 

From bef38bafea82a15300e6c9ded9d2dd2843c3dadf Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 26 Mar 2024 10:55:57 +0100
Subject: [PATCH 224/501] {2023.06}[2023a] OpenJPEG 2.5.0

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 384aa04a9c..0a1343295e 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -52,3 +52,4 @@ easyconfigs:
   - ipympl-0.9.3-foss-2023a.eb:
       options:
         from-pr: 20126
+  - OpenJPEG-2.5.0-GCCcore-12.3.0.eb

From a0dc2815c4f45162aed56bf2c5e7bfcdc8b0eaf3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 26 Mar 2024 11:03:33 +0100
Subject: [PATCH 225/501] fix comment for creating lmod rc code block

---
 EESSI-install-software.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 31ce30d4fc..b2984af856 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -247,7 +247,7 @@ fi
 
 ### add packages here
 
-echo ">> Creating/updating Lmod cache..."
+echo ">> Creating/updating Lmod RC file..."
 export LMOD_CONFIG_DIR="${EASYBUILD_INSTALLPATH}/.lmod"
 lmod_rc_file="$LMOD_CONFIG_DIR/lmodrc.lua"
 lmodrc_changed=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^create_lmodrc.py$' > /dev/null; echo $?)

From b2570ed8cca9d7f87d3c506ec33d7b0c7b033671 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 26 Mar 2024 11:03:50 +0100
Subject: [PATCH 226/501] don't update lmod cache here anymore

---
 EESSI-install-software.sh | 2 --
 1 file changed, 2 deletions(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index b2984af856..7b7a60686c 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -265,7 +265,5 @@ if [ ! -f "$lmod_sitepackage_file" ] || [ "${sitepackage_changed}" == '0' ]; the
     check_exit_code $? "$lmod_sitepackage_file created" "Failed to create $lmod_sitepackage_file"
 fi
 
-$TOPDIR/update_lmod_cache.sh ${EPREFIX} ${EASYBUILD_INSTALLPATH}
-
 echo ">> Cleaning up ${TMPDIR}..."
 rm -r ${TMPDIR}

From 56e4b87d1c0de54f374ca77d7c316be173d8bb9f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 26 Mar 2024 14:56:15 +0100
Subject: [PATCH 227/501] add LittleCMS, giflib, OpenJPEG to fix check_missing
 CI

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index e2d35276df..380c0107c6 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -49,3 +49,6 @@ easyconfigs:
   - libspatialindex-1.9.3-GCCcore-13.2.0.eb:
       options:
         from-pr: 19922
+  - LittleCMS-2.15-GCCcore-13.2.0.eb
+  - giflib-5.2.1-GCCcore-13.2.0.eb
+  - OpenJPEG-2.5.0-GCCcore-13.2.0.eb

From 32f04020a1b3e3c7061107d221dc4faf155c7fb0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 26 Mar 2024 15:38:05 +0100
Subject: [PATCH 228/501] also add libwebp-1.3.2-GCCcore-13.2.0.eb

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml  | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 380c0107c6..25cdde27e6 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -52,3 +52,5 @@ easyconfigs:
   - LittleCMS-2.15-GCCcore-13.2.0.eb
   - giflib-5.2.1-GCCcore-13.2.0.eb
   - OpenJPEG-2.5.0-GCCcore-13.2.0.eb
+  - libwebp-1.3.2-GCCcore-13.2.0.eb
+

From f2844fb210aa865155989811c88d85b7d8b3c1a5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 26 Mar 2024 17:09:49 +0100
Subject: [PATCH 229/501] remove OpenMPI, which has been rebuilt in #488

---
 .../2023.06/eessi-2023.06-eb-4.8.2-2023a.yml                  | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
index b971c5adad..1c3ea8fd78 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
@@ -55,8 +55,4 @@ easyconfigs:
   - gnuplot-5.4.8-GCCcore-12.3.0.eb: 
       options:
         from-pr: 19261
-  - OpenMPI-4.1.5-GCC-12.3.0.eb:
-      options:
-        from-pr: 19940
-        rebuild: True
   - OpenFOAM-10-foss-2023a.eb

From 5a43f9ef8d8d66dfa2bd0226f28a8bdf7521892b Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Tue, 26 Mar 2024 19:16:00 +0100
Subject: [PATCH 230/501] Don't need gnuplot, install with EasyBuild 4.9.0

---
 .../2023.06/eessi-2023.06-eb-4.8.2-2023a.yml                  | 4 ----
 .../2023.06/eessi-2023.06-eb-4.9.0-2023a.yml                  | 1 +
 2 files changed, 1 insertion(+), 4 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
index 1c3ea8fd78..7244219dc3 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.8.2-2023a.yml
@@ -52,7 +52,3 @@ easyconfigs:
   - BWA-0.7.17-20220923-GCCcore-12.3.0.eb:
       options: 
         from-pr: 19820 
-  - gnuplot-5.4.8-GCCcore-12.3.0.eb: 
-      options:
-        from-pr: 19261
-  - OpenFOAM-10-foss-2023a.eb
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 157a47a49e..13d7ebdc02 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -29,3 +29,4 @@ easyconfigs:
       # see https://github.com/easybuilders/easybuild-easyconfigs/pull/19554
       options:
         from-pr: 19554
+  - OpenFOAM-10-foss-2023a.eb

From 7c7e1b1ff18c960db5f1233438295d9c60dd6431 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Tue, 26 Mar 2024 20:18:03 +0100
Subject: [PATCH 231/501] use older apptainer (1.2.4)

---
 install_apptainer_ubuntu.sh | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/install_apptainer_ubuntu.sh b/install_apptainer_ubuntu.sh
index c35c34cda6..6cf9a6f48e 100755
--- a/install_apptainer_ubuntu.sh
+++ b/install_apptainer_ubuntu.sh
@@ -5,8 +5,11 @@ set -e
 # see https://github.com/apptainer/singularity/issues/5390#issuecomment-899111181
 sudo apt-get install alien
 alien --version
-apptainer_rpm=$(curl --silent -L https://dl.fedoraproject.org/pub/epel/8/Everything/x86_64/Packages/a/ | grep 'apptainer-[0-9]' | sed 's/.*\(apptainer[0-9._a-z-]*.rpm\).*/\1/g')
-curl -OL https://dl.fedoraproject.org/pub/epel/8/Everything/x86_64/Packages/a/${apptainer_rpm}
+#apptainer_rpm=$(curl --silent -L https://dl.fedoraproject.org/pub/epel/8/Everything/x86_64/Packages/a/ | grep 'apptainer-[0-9]' | sed 's/.*\(apptainer[0-9._a-z-]*.rpm\).*/\1/g')
+#curl -OL https://dl.fedoraproject.org/pub/epel/8/Everything/x86_64/Packages/a/${apptainer_rpm}
+#/pub/archive/epel/8.8/Everything/x86_64/Packages/a
+apptainer_rpm=$(curl --silent -L https://dl.fedoraproject.org/pub/archive/epel/8.8/Everything/x86_64/Packages/a/ | grep 'apptainer-[0-9]' | sed 's/.*\(apptainer[0-9._a-z-]*.rpm\).*/\1/g')
+curl -OL https://dl.fedoraproject.org/pub/archive/epel/8.8/Everything/x86_64/Packages/a/${apptainer_rpm}
 sudo alien -d ${apptainer_rpm}
 sudo apt install ./apptainer*.deb
 apptainer --version

From deb12e9fef3103b8c07504e745b14fe366ed618d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 26 Mar 2024 20:35:40 +0100
Subject: [PATCH 232/501] clean up downloading RPM for Apptainer < 1.3.0 RPM
 from EPEL 8.8 archive, for now

---
 install_apptainer_ubuntu.sh | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/install_apptainer_ubuntu.sh b/install_apptainer_ubuntu.sh
index 6cf9a6f48e..5eb513db2c 100755
--- a/install_apptainer_ubuntu.sh
+++ b/install_apptainer_ubuntu.sh
@@ -5,11 +5,13 @@ set -e
 # see https://github.com/apptainer/singularity/issues/5390#issuecomment-899111181
 sudo apt-get install alien
 alien --version
-#apptainer_rpm=$(curl --silent -L https://dl.fedoraproject.org/pub/epel/8/Everything/x86_64/Packages/a/ | grep 'apptainer-[0-9]' | sed 's/.*\(apptainer[0-9._a-z-]*.rpm\).*/\1/g')
-#curl -OL https://dl.fedoraproject.org/pub/epel/8/Everything/x86_64/Packages/a/${apptainer_rpm}
-#/pub/archive/epel/8.8/Everything/x86_64/Packages/a
-apptainer_rpm=$(curl --silent -L https://dl.fedoraproject.org/pub/archive/epel/8.8/Everything/x86_64/Packages/a/ | grep 'apptainer-[0-9]' | sed 's/.*\(apptainer[0-9._a-z-]*.rpm\).*/\1/g')
-curl -OL https://dl.fedoraproject.org/pub/archive/epel/8.8/Everything/x86_64/Packages/a/${apptainer_rpm}
+# stick to Apptainer < 1.3.0 by downloading from EPEL 8.8 archive,
+# since CI workflow for testing scripts hangs/fails when using Apptainer 1.3.0
+# cfr. https://github.com/EESSI/software-layer/pull/514
+epel_subdir="pub/epel/8"
+epel_subdir="pub/archive/epel/8.8"
+apptainer_rpm=$(curl --silent -L https://dl.fedoraproject.org/${epel_subdir}/Everything/x86_64/Packages/a/ | grep 'apptainer-[0-9]' | sed 's/.*\(apptainer[0-9._a-z-]*.rpm\).*/\1/g')
+curl -OL https://dl.fedoraproject.org/${epel_subdir}/Everything/x86_64/Packages/a/${apptainer_rpm}
 sudo alien -d ${apptainer_rpm}
 sudo apt install ./apptainer*.deb
 apptainer --version

From 547386f9180687627ce506cab0cacc91ed808025 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 27 Mar 2024 10:08:14 +0100
Subject: [PATCH 233/501] dont fail if grep doesnt find rebuild easystack files

---
 bot/build.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bot/build.sh b/bot/build.sh
index b007b80172..2438adbcd9 100755
--- a/bot/build.sh
+++ b/bot/build.sh
@@ -182,7 +182,7 @@ fi
 # determine if the removal step has to be run
 # assume there's only one diff file that corresponds to the PR patch file
 pr_diff=$(ls [0-9]*.diff | head -1)
-changed_easystacks_rebuilds=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | grep "/rebuilds/")
+changed_easystacks_rebuilds=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | grep "/rebuilds/" || true)
 if [[ -z ${changed_easystacks_rebuilds} ]]; then
     echo "This PR does not add any easystack files in a rebuilds subdirectory, so let's skip the removal step."
 else

From c2fad0032008d0ca73f6603ad7fbae6c2391a6a1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 27 Mar 2024 10:08:32 +0100
Subject: [PATCH 234/501] add quotes around variable in if statement

---
 bot/build.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bot/build.sh b/bot/build.sh
index 2438adbcd9..e9f8ecfbb9 100755
--- a/bot/build.sh
+++ b/bot/build.sh
@@ -183,7 +183,7 @@ fi
 # assume there's only one diff file that corresponds to the PR patch file
 pr_diff=$(ls [0-9]*.diff | head -1)
 changed_easystacks_rebuilds=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | grep "/rebuilds/" || true)
-if [[ -z ${changed_easystacks_rebuilds} ]]; then
+if [[ -z "${changed_easystacks_rebuilds}" ]]; then
     echo "This PR does not add any easystack files in a rebuilds subdirectory, so let's skip the removal step."
 else
     # prepare directory to store tarball of tmp for removal and build steps

From bce1067e0b9962c591804c87ea150e38123822be Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 27 Mar 2024 10:13:32 +0100
Subject: [PATCH 235/501] use proper tmp dir for removal step

---
 bot/build.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bot/build.sh b/bot/build.sh
index e9f8ecfbb9..0ebd55692e 100755
--- a/bot/build.sh
+++ b/bot/build.sh
@@ -192,7 +192,7 @@ else
 
     # prepare arguments to eessi_container.sh specific to remove step
     declare -a REMOVAL_STEP_ARGS=()
-    REMOVAL_STEP_ARGS+=("--save" "${TARBALL_TMP_BUILD_STEP_DIR}")
+    REMOVAL_STEP_ARGS+=("--save" "${TARBALL_TMP_REMOVAL_STEP_DIR}")
     REMOVAL_STEP_ARGS+=("--storage" "${STORAGE}")
     # add fakeroot option in order to be able to remove software, see:
     # https://github.com/EESSI/software-layer/issues/312

From 4a9d9aeedd5fc7dc719bbc9612c6b5e2213a673b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 27 Mar 2024 10:20:16 +0100
Subject: [PATCH 236/501] let the tarball step resume from the right directory

---
 bot/build.sh | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/bot/build.sh b/bot/build.sh
index 0ebd55692e..0d23f59b66 100755
--- a/bot/build.sh
+++ b/bot/build.sh
@@ -247,7 +247,14 @@ declare -a TARBALL_STEP_ARGS=()
 TARBALL_STEP_ARGS+=("--save" "${TARBALL_TMP_TARBALL_STEP_DIR}")
 
 # determine temporary directory to resume from
-TARBALL_STEP_ARGS+=("--resume" "${REMOVAL_TMPDIR}")
+if [[ -z ${REMOVAL_TMPDIR} ]]; then
+    # no rebuild step was done, so the tarball step should resume from the build directory
+    BUILD_TMPDIR=$(grep ' as tmp directory ' ${build_outerr} | cut -d ' ' -f 2)
+    TARBALL_STEP_ARGS+=("--resume" "${BUILD_TMPDIR}")
+else
+    # a removal step was done, so resume from its temporary directory (which was also used for the build step)
+    TARBALL_STEP_ARGS+=("--resume" "${REMOVAL_TMPDIR}")
+fi
 
 timestamp=$(date +%s)
 # to set EESSI_VERSION we need to source init/eessi_defaults now

From 2ba8513f770f2f23961a05bc64b98488e4aaaa8d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 27 Mar 2024 11:14:05 +0100
Subject: [PATCH 237/501] group grep and true commands

Co-authored-by: Kenneth Hoste <kenneth.hoste@ugent.be>
---
 bot/build.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bot/build.sh b/bot/build.sh
index 0d23f59b66..ff933a447d 100755
--- a/bot/build.sh
+++ b/bot/build.sh
@@ -182,7 +182,7 @@ fi
 # determine if the removal step has to be run
 # assume there's only one diff file that corresponds to the PR patch file
 pr_diff=$(ls [0-9]*.diff | head -1)
-changed_easystacks_rebuilds=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | grep "/rebuilds/" || true)
+changed_easystacks_rebuilds=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | (grep "/rebuilds/" || true))
 if [[ -z "${changed_easystacks_rebuilds}" ]]; then
     echo "This PR does not add any easystack files in a rebuilds subdirectory, so let's skip the removal step."
 else

From 0e38a4769d7db0e893f9a4eb058ec9333a0e648e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 27 Mar 2024 11:16:35 +0100
Subject: [PATCH 238/501] add comment about true command

---
 bot/build.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/bot/build.sh b/bot/build.sh
index ff933a447d..dcc61c19d4 100755
--- a/bot/build.sh
+++ b/bot/build.sh
@@ -182,6 +182,8 @@ fi
 # determine if the removal step has to be run
 # assume there's only one diff file that corresponds to the PR patch file
 pr_diff=$(ls [0-9]*.diff | head -1)
+# the true at the end of the next command is important: grep will expectedly return 1 if there is no easystack file being added under rebuilds,
+# but due to "set -e" the entire script would otherwise fail
 changed_easystacks_rebuilds=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | (grep "/rebuilds/" || true))
 if [[ -z "${changed_easystacks_rebuilds}" ]]; then
     echo "This PR does not add any easystack files in a rebuilds subdirectory, so let's skip the removal step."

From e9bb5b8da5e7634396fca503bdafbe11861c0f42 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Wed, 27 Mar 2024 14:25:47 +0000
Subject: [PATCH 239/501] {2023.06}[GCCcore/13.2.0] Wayland v1.22.0

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 25cdde27e6..6710c07b49 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -53,4 +53,5 @@ easyconfigs:
   - giflib-5.2.1-GCCcore-13.2.0.eb
   - OpenJPEG-2.5.0-GCCcore-13.2.0.eb
   - libwebp-1.3.2-GCCcore-13.2.0.eb
+  - Wayland-1.22.0-GCCcore-13.2.0.eb
 

From 80609663bf16cf013df9922c2229976c19e821df Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 27 Mar 2024 16:08:52 +0100
Subject: [PATCH 240/501] add quotes around changed_easystacks variable

---
 EESSI-install-software.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 470663e45a..e2d7cf8c51 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -204,7 +204,7 @@ ${EESSI_PREFIX}/scripts/gpu_support/nvidia/install_cuda_host_injections.sh -c 12
 
 # use PR patch file to determine in which easystack files stuff was added
 changed_easystacks=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | egrep -v 'known-issues|missing') 
-if [ -z ${changed_easystacks} ]; then
+if [ -z "${changed_easystacks}" ]; then
     echo "No missing installations, party time!"  # Ensure the bot report success, as there was nothing to be build here
 else
 

From 70935ea4293d0e7a94b99f573a77fe74b4f68fbe Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 27 Mar 2024 16:13:07 +0100
Subject: [PATCH 241/501] first process rebuilds, then new installations

---
 EESSI-install-software.sh | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index e2d7cf8c51..a905d966f6 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -208,7 +208,11 @@ if [ -z "${changed_easystacks}" ]; then
     echo "No missing installations, party time!"  # Ensure the bot report success, as there was nothing to be build here
 else
 
-    for easystack_file in ${changed_easystacks}; do
+    # first process rebuilds, if any, then easystack files for new installations
+    # "|| true" is used to make sure that the grep command always returns success
+    rebuild_easystacks=$(echo "${changed_easystacks}" | (grep "/rebuilds/" || true))
+    new_easystacks=$(echo "${changed_easystacks}" | (grep -v "/rebuilds/" || true))
+    for easystack_file in ${rebuild_easystacks} ${new_easystacks}; do
 
         echo -e "Processing easystack file ${easystack_file}...\n\n"
 

From 005c02c4341f02aedb5a0dc7cf3a3c1e96ca2b56 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Thu, 28 Mar 2024 00:18:12 +0100
Subject: [PATCH 242/501] Rebuild GCCcore-12.3.0 and 13.2.0 to fix aarch64
 vectorization issue

---
 ...eb-4.9.0-GCCcore-fix-aarch64-vectorization.yml | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/rebuilds/20240328-eb-4.9.0-GCCcore-fix-aarch64-vectorization.yml

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240328-eb-4.9.0-GCCcore-fix-aarch64-vectorization.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240328-eb-4.9.0-GCCcore-fix-aarch64-vectorization.yml
new file mode 100644
index 0000000000..f63aa421f5
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240328-eb-4.9.0-GCCcore-fix-aarch64-vectorization.yml
@@ -0,0 +1,15 @@
+# 2024-03-28
+# Rebuild GCCcore to fix a compiler bug in the tree-vectorizer
+# We encountered it in https://github.com/EESSI/software-layer/pull/479#issuecomment-1957091774
+# and https://github.com/EESSI/software-layer/pull/507#issuecomment-2011724613
+# Upstream issue: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=111478
+# Upstream fix: https://gcc.gnu.org/git/gitweb.cgi?p=gcc.git;h=e5f1956498251a4973d52c8aad3faf34d0443169
+# Fix in EasyBuild https://github.com/easybuilders/easybuild-easyconfigs/pull/19974
+# https://github.com/easybuilders/easybuild-easyconfigs/pull/20218
+easyconfigs:
+  - GCCcore-12.3.0.eb:
+      options:
+        from-pr: 20218
+  - GCCcore-13.2.0.eb:
+      options:
+        from-pr: 19974

From 1c1dd06db1a9b52b827b7adc87f412db586714cd Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Thu, 28 Mar 2024 10:27:33 +0100
Subject: [PATCH 243/501] Added Modflow and deps

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml          | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 6710c07b49..d0f1f33914 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -54,4 +54,13 @@ easyconfigs:
   - OpenJPEG-2.5.0-GCCcore-13.2.0.eb
   - libwebp-1.3.2-GCCcore-13.2.0.eb
   - Wayland-1.22.0-GCCcore-13.2.0.eb
-
+  - SuperLU_DIST-8.1.2-foss-2023a.eb:
+      options:
+        from-pr: 20162
+  - PETSc-3.20.3-foss-2023a.eb:
+      options:
+        include-easyblocks-from-pr: 3086
+        from-pr: 19686
+  - MODFLOW-6.4.4-foss-2023a.eb:
+      options:
+        from-pr: 20142

From 1489742eae3de68def89474d40945177cc331cff Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 28 Mar 2024 11:11:07 +0100
Subject: [PATCH 244/501] use easyconfigs PR #20238 for R 4.2.2

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2022b.yml                  | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
index 629023a1cd..3962f63bda 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
@@ -8,4 +8,6 @@ easyconfigs:
   - ImageMagick-7.1.0-53-GCCcore-12.2.0.eb:
       options:
         from-pr: 20086
-  - R-4.2.2-foss-2022b.eb
+  - R-4.2.2-foss-2022b.eb:
+      options:
+        from-pr: 20238

From 6e806faef8879bad179c852aa9ec8dc76eca4a1a Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int6.local.snellius.surf.nl>
Date: Fri, 29 Mar 2024 15:12:06 +0100
Subject: [PATCH 245/501] Make sure EESSI's SitePackage.lua loads host's
 SitePackage.lua's if they exist

---
 create_lmodsitepackage.py | 68 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 68 insertions(+)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index 5a7a915494..4f99f1a614 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -19,6 +19,71 @@
     return content
 end
 
+local function load_sitespecific_hooks()
+    -- This function will be run after the EESSI hooks are registered
+    -- It will load a local SitePackage.lua that is architecture independent (if it exists) from e.g.
+    -- /cvmfs/software.eessi.io/host_injections/2023.06/.lmod/SitePackage.lua
+    -- That can define a new hook
+    --
+    -- function site_specific_load_hook(t)
+    --     <some_action_on_load>
+    -- end
+    --
+    -- And the either append to the existing hook:
+    --
+    -- local function final_load_hook(t)
+    --    eessi_load_hook(t)
+    --    site_specific_load_hook(t)
+    -- end
+    --
+    -- Over overwrite the EESSI hook entirely:
+    --
+    -- hook.register("load", final_load_hook)
+    --
+    -- Note that the appending procedure can be simplified once we have an lmod >= 8.7.36
+    -- See https://github.com/TACC/Lmod/pull/696#issuecomment-1998765722
+    --
+    -- Subsequently, this function will look for an architecture-specific SitePackage.lua, e.g. from
+    -- /cvmfs/software.eessi.io/host_injections/2023.06/software/linux/x86_64/amd/zen2/.lmod/SitePackage.lua
+    -- This can then register an additional hook, e.g.
+    --
+    -- function arch_specific_load_hook(t)
+    --     <some_action_on_load>
+    -- end
+    --
+    -- local function final_load_hook(t)
+    --   eessi_load_hook(t)
+    --   site_specific_load_hook(t)
+    --   arch_specific_load_hook(t)
+    -- end
+    --
+    -- hook.register("load", final_load_hook)
+    --
+    -- Again, the host site could also decide to overwrite by simply doing
+    --
+    -- hook.register("load", arch_specific_load_hook)
+
+    -- get path to to architecture independent SitePackage.lua
+    local prefixHostInjections = string.gsub(os.getenv('EESSI_PREFIX'), 'versions', 'host_injections')
+    local hostSitePackage = prefixHostInjections .. "/.lmod/SitePackage.lua"
+
+    -- If the file exists, run it
+    if isDir(hostSitePackage) then
+        dofile(hostSitePackage)
+    end
+
+    -- build the full architecture specific path in host_injections
+    local archHostInjections = string.gsub(os.getenv('EESSI_SOFTWARE_PATH') or "", 'versions', 'host_injections')
+    local archSitePackage = archHostInjections .. "/.lmod/SitePackage.lua"
+
+    -- If the file exists, run it
+    if isDir(archSitePackage)
+        dofile(archSitePackage)
+    end
+    
+end
+
+
 local function eessi_cuda_enabled_load_hook(t)
     local frameStk  = require("FrameStk"):singleton()
     local mt        = frameStk:mt()
@@ -92,6 +157,9 @@
 
 
 hook.register("load", eessi_load_hook)
+
+-- Note that this needs to happen at the end, so that any EESSI specific hooks can be overwritten by the site
+load_site_specific_hooks()
 """
 
 def error(msg):

From 4bc0369d3505347441167436fb2f8de1a005b6b1 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Fri, 29 Mar 2024 15:14:17 +0100
Subject: [PATCH 246/501] Forgot 'then'

---
 create_lmodsitepackage.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index 4f99f1a614..6b67b4beca 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -77,7 +77,7 @@
     local archSitePackage = archHostInjections .. "/.lmod/SitePackage.lua"
 
     -- If the file exists, run it
-    if isDir(archSitePackage)
+    if isDir(archSitePackage) then
         dofile(archSitePackage)
     end
     

From cd9b2061a2d83669bf42a3c8d4f64de97afae3cc Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Fri, 29 Mar 2024 15:49:51 +0100
Subject: [PATCH 247/501] Don't set LMOD_RC any longer, we set LMOD_CONFIG_DIR
 now, so that sites can add their own properties via LMOD_RC if they want. See
 https://lmod.readthedocs.io/en/latest/145_properties.html

---
 init/eessi_environment_variables | 34 +++++++++++++-------------------
 1 file changed, 14 insertions(+), 20 deletions(-)

diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index a3ff265e77..5450b2bfb4 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -51,14 +51,23 @@ if [ -d $EESSI_PREFIX ]; then
         show_msg "Using ${EESSI_SOFTWARE_SUBDIR} as software subdirectory."
         export EESSI_SOFTWARE_PATH=$EESSI_PREFIX/software/$EESSI_OS_TYPE/$EESSI_SOFTWARE_SUBDIR
 
-        # Configure our LMOD_RC file
-        export LMOD_RC="$EESSI_SOFTWARE_PATH/.lmod/lmodrc.lua"
-        if [ -f $LMOD_RC ]; then
-          show_msg "Found Lmod configuration file at $LMOD_RC"
+        # Configure our LMOD
+        export LMOD_CONFIG_DIR="$EESSI_SOFTWARE_PATH/.lmod"
+        lmod_rc_file="$LMOD_CONFIG_DIR/lmodrc.lua"
+        if [ -f $lmod_rc_file ]; then
+          show_msg "Found Lmod configuration file at $lmod_rc_file"
         else
-          error "Lmod configuration file not found at $LMOD_RC"
+          error "Lmod configuration file not found at $lmod_rc_file"
         fi
 
+        export LMOD_PACKAGE_PATH="$EESSI_SOFTWARE_PATH/.lmod"
+        lmod_sitepackage_file="$LMOD_PACKAGE_PATH/SitePackage.lua"
+        if [ -f $lmod_sitepackage_file ]; then
+          show_msg "Found Lmod SitePackage.lua file at $lmod_sitepackage_file"
+        else
+          error "Lmod SitePackage.lua file not found at $lmod_sitepackage_file"
+        fi
+       
         if [ ! -z $EESSI_BASIC_ENV ]; then
           show_msg "Only setting up basic environment, so we're done"
         elif [ -d $EESSI_SOFTWARE_PATH ]; then
@@ -85,21 +94,6 @@ if [ -d $EESSI_PREFIX ]; then
             false
           fi
 
-          export LMOD_CONFIG_DIR="$EESSI_SOFTWARE_PATH/.lmod"
-          lmod_rc_file="$LMOD_CONFIG_DIR/lmodrc.lua"
-          if [ -f $lmod_rc_file ]; then
-            show_msg "Found Lmod configuration file at $lmod_rc_file"
-          else
-            error "Lmod configuration file not found at $lmod_rc_file"
-          fi
-
-          export LMOD_PACKAGE_PATH="$EESSI_SOFTWARE_PATH/.lmod"
-          lmod_sitepackage_file="$LMOD_PACKAGE_PATH/SitePackage.lua"
-          if [ -f $lmod_sitepackage_file ]; then
-            show_msg "Found Lmod SitePackage.lua file at $lmod_sitepackage_file"
-          else
-            error "Lmod SitePackage.lua file not found at $lmod_sitepackage_file"
-          fi
 
         else
           error "EESSI software layer at $EESSI_SOFTWARE_PATH not found!"

From d2c5dabb735709ef4ab50c3643d5620a7ea97f12 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Fri, 29 Mar 2024 15:52:44 +0100
Subject: [PATCH 248/501] Add some comment, the lmodrc file did not get
 properly deployed in https://github.com/EESSI/software-layer/pull/496 . We
 need to have a change to redeploy it

---
 create_lmodrc.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/create_lmodrc.py b/create_lmodrc.py
index ae65153a20..28ad2a1915 100755
--- a/create_lmodrc.py
+++ b/create_lmodrc.py
@@ -7,6 +7,7 @@
 
 DOT_LMOD = '.lmod'
 
+# LMOD_RC file is the place to define properties, see https://lmod.readthedocs.io/en/latest/145_properties.html
 TEMPLATE_LMOD_RC = """propT = {
 }
 scDescriptT = {

From 70d94a1361eaa02a8dea4c64495480f0a4cc6910 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Sat, 30 Mar 2024 22:58:48 +0100
Subject: [PATCH 249/501] add R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
index 3962f63bda..8a3e82d760 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
@@ -11,3 +11,4 @@ easyconfigs:
   - R-4.2.2-foss-2022b.eb:
       options:
         from-pr: 20238
+  - R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb

From 173332f479d74cd220cb25976a17035317e613ae Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 2 Apr 2024 13:02:46 +0200
Subject: [PATCH 250/501] Try to retrigger issue 517

---
 install_apptainer_ubuntu.sh                                | 6 ++----
 scripts/gpu_support/nvidia/install_cuda_host_injections.sh | 3 +++
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/install_apptainer_ubuntu.sh b/install_apptainer_ubuntu.sh
index 5eb513db2c..8642d62999 100755
--- a/install_apptainer_ubuntu.sh
+++ b/install_apptainer_ubuntu.sh
@@ -5,11 +5,9 @@ set -e
 # see https://github.com/apptainer/singularity/issues/5390#issuecomment-899111181
 sudo apt-get install alien
 alien --version
-# stick to Apptainer < 1.3.0 by downloading from EPEL 8.8 archive,
-# since CI workflow for testing scripts hangs/fails when using Apptainer 1.3.0
-# cfr. https://github.com/EESSI/software-layer/pull/514
+# Switch back to Apptainer >= 1.3.0 to retrigger
+# https://github.com/EESSI/software-layer/pull/514
 epel_subdir="pub/epel/8"
-epel_subdir="pub/archive/epel/8.8"
 apptainer_rpm=$(curl --silent -L https://dl.fedoraproject.org/${epel_subdir}/Everything/x86_64/Packages/a/ | grep 'apptainer-[0-9]' | sed 's/.*\(apptainer[0-9._a-z-]*.rpm\).*/\1/g')
 curl -OL https://dl.fedoraproject.org/${epel_subdir}/Everything/x86_64/Packages/a/${apptainer_rpm}
 sudo alien -d ${apptainer_rpm}
diff --git a/scripts/gpu_support/nvidia/install_cuda_host_injections.sh b/scripts/gpu_support/nvidia/install_cuda_host_injections.sh
index a9310d817a..1f1548f7dd 100755
--- a/scripts/gpu_support/nvidia/install_cuda_host_injections.sh
+++ b/scripts/gpu_support/nvidia/install_cuda_host_injections.sh
@@ -12,6 +12,9 @@
 # installation to be successful, this directory needs to be writeable by the user
 # executing this script.
 
+# TRIGGER SCRIPT CHANGE TO REPRODUCE https://github.com/EESSI/software-layer/issues/517
+# THIS COMMENT SHOULD NEVER BE MERGED!
+
 # Initialise our bash functions
 TOPDIR=$(dirname $(realpath $BASH_SOURCE))
 source "$TOPDIR"/../../utils.sh

From 2ace856380267a9e35c44326d5ad2dd2bc61c9a2 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 2 Apr 2024 13:10:28 +0200
Subject: [PATCH 251/501] Undo change

---
 scripts/gpu_support/nvidia/install_cuda_host_injections.sh | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/scripts/gpu_support/nvidia/install_cuda_host_injections.sh b/scripts/gpu_support/nvidia/install_cuda_host_injections.sh
index 1f1548f7dd..a9310d817a 100755
--- a/scripts/gpu_support/nvidia/install_cuda_host_injections.sh
+++ b/scripts/gpu_support/nvidia/install_cuda_host_injections.sh
@@ -12,9 +12,6 @@
 # installation to be successful, this directory needs to be writeable by the user
 # executing this script.
 
-# TRIGGER SCRIPT CHANGE TO REPRODUCE https://github.com/EESSI/software-layer/issues/517
-# THIS COMMENT SHOULD NEVER BE MERGED!
-
 # Initialise our bash functions
 TOPDIR=$(dirname $(realpath $BASH_SOURCE))
 source "$TOPDIR"/../../utils.sh

From dc986adc8b46f622d2d4d899922f5ef4731c305b Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 2 Apr 2024 13:11:11 +0200
Subject: [PATCH 252/501] Retrigger 517

---
 scripts/utils.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/scripts/utils.sh b/scripts/utils.sh
index b2be3f6221..bbe17584b8 100644
--- a/scripts/utils.sh
+++ b/scripts/utils.sh
@@ -1,3 +1,6 @@
+## THIS COMMENT IS ONLY TO RETRIGGER #517
+## IT SHOULD NEVER BE MERGED
+
 function echo_green() {
     echo -e "\e[32m$1\e[0m"
 }

From 6d5a6ae36e86253b4811e9a9f2ec2ca028558e77 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 2 Apr 2024 14:05:30 +0200
Subject: [PATCH 253/501] Add option to skip CUDA SDK installation, e.g. for CI
 environments

---
 EESSI-install-software.sh | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index a905d966f6..2fff281ff5 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -14,6 +14,7 @@ display_help() {
   echo "  -x | --http-proxy URL  -  provides URL for the environment variable http_proxy"
   echo "  -y | --https-proxy URL -  provides URL for the environment variable https_proxy"
   echo "  --shared-fs-path       -  path to directory on shared filesystem that can be used"
+  echo "  --skip-cuda-install    -  disable installing a full CUDA SDK in the host_injections prefix (e.g. in CI)"
 }
 
 function copy_build_log() {
@@ -76,6 +77,10 @@ while [[ $# -gt 0 ]]; do
       export shared_fs_path="${2}"
       shift 2
       ;;
+    --skip-cuda-install)
+      export skip_cuda_install=True
+      shift 1
+      ;;
     -*|--*)
       echo "Error: Unknown option: $1" >&2
       exit 1
@@ -195,7 +200,10 @@ ${TOPDIR}/install_scripts.sh --prefix ${EESSI_PREFIX}
 # Install full CUDA SDK in host_injections
 # Hardcode this for now, see if it works
 # TODO: We should make a nice yaml and loop over all CUDA versions in that yaml to figure out what to install
-${EESSI_PREFIX}/scripts/gpu_support/nvidia/install_cuda_host_injections.sh -c 12.1.1 --accept-cuda-eula
+# Allow skipping CUDA SDK install in e.g. CI environments
+if [ ! -z "${skip_cuda_install}" ] && [ ! "${skip_cuda_install}" ]; then
+    ${EESSI_PREFIX}/scripts/gpu_support/nvidia/install_cuda_host_injections.sh -c 12.1.1 --accept-cuda-eula
+fi
 
 # Install drivers in host_injections
 # TODO: this is commented out for now, because the script assumes that nvidia-smi is available and works;

From 6155e02b317624f287f5bccb694c7b4285d7e388 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 2 Apr 2024 14:18:40 +0200
Subject: [PATCH 254/501] Make sure the install_software_layer.sh test skips
 installing the CUDA SDK - that is simply too heave for CI

---
 .github/workflows/tests_scripts.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/tests_scripts.yml b/.github/workflows/tests_scripts.yml
index df1884dd8c..b1d2426774 100644
--- a/.github/workflows/tests_scripts.yml
+++ b/.github/workflows/tests_scripts.yml
@@ -83,6 +83,8 @@ jobs:
           export SINGULARITY_BIND="${PWD}:/software-layer"
           # force using x86_64/generic, to avoid triggering an installation from scratch
           sed -i "s@./EESSI-install-software.sh@\"export EESSI_SOFTWARE_SUBDIR_OVERRIDE='x86_64/generic'; ./EESSI-install-software.sh\"@g" install_software_layer.sh
+          # skip installation of CUDA SDKs, since this is too heavy for CI
+          sed -i "s@./EESSI-install-software.sh@./EESSI-install-software.sh --skip-cuda-install@g" install_software_layer.sh
           ./eessi_container.sh --mode run --verbose /software-layer/install_software_layer.sh
 
     - name: test create_directory_tarballs.sh script

From 877f364e677a31f8218a973640269d003f95fa4b Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 2 Apr 2024 14:23:23 +0200
Subject: [PATCH 255/501] Fix logic in EESSI-install-software.sh and prove that
 logic is ok by now first retriggering the issue

---
 .github/workflows/tests_scripts.yml | 2 +-
 EESSI-install-software.sh           | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/tests_scripts.yml b/.github/workflows/tests_scripts.yml
index b1d2426774..a245ee1ad5 100644
--- a/.github/workflows/tests_scripts.yml
+++ b/.github/workflows/tests_scripts.yml
@@ -84,7 +84,7 @@ jobs:
           # force using x86_64/generic, to avoid triggering an installation from scratch
           sed -i "s@./EESSI-install-software.sh@\"export EESSI_SOFTWARE_SUBDIR_OVERRIDE='x86_64/generic'; ./EESSI-install-software.sh\"@g" install_software_layer.sh
           # skip installation of CUDA SDKs, since this is too heavy for CI
-          sed -i "s@./EESSI-install-software.sh@./EESSI-install-software.sh --skip-cuda-install@g" install_software_layer.sh
+          # sed -i "s@./EESSI-install-software.sh@./EESSI-install-software.sh --skip-cuda-install@g" install_software_layer.sh
           ./eessi_container.sh --mode run --verbose /software-layer/install_software_layer.sh
 
     - name: test create_directory_tarballs.sh script
diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 2fff281ff5..0374d8e758 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -201,7 +201,7 @@ ${TOPDIR}/install_scripts.sh --prefix ${EESSI_PREFIX}
 # Hardcode this for now, see if it works
 # TODO: We should make a nice yaml and loop over all CUDA versions in that yaml to figure out what to install
 # Allow skipping CUDA SDK install in e.g. CI environments
-if [ ! -z "${skip_cuda_install}" ] && [ ! "${skip_cuda_install}" ]; then
+if [ -z "${skip_cuda_install}" ] || [ ! "${skip_cuda_install}" ]; then
     ${EESSI_PREFIX}/scripts/gpu_support/nvidia/install_cuda_host_injections.sh -c 12.1.1 --accept-cuda-eula
 fi
 

From ba142caeea7d6223354b3aa7554f605ef4468fe4 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 2 Apr 2024 14:28:16 +0200
Subject: [PATCH 256/501] Now make sure CI skips CUDA SDK installation, to
 prove that this fixes the CI run

---
 .github/workflows/tests_scripts.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests_scripts.yml b/.github/workflows/tests_scripts.yml
index a245ee1ad5..b1d2426774 100644
--- a/.github/workflows/tests_scripts.yml
+++ b/.github/workflows/tests_scripts.yml
@@ -84,7 +84,7 @@ jobs:
           # force using x86_64/generic, to avoid triggering an installation from scratch
           sed -i "s@./EESSI-install-software.sh@\"export EESSI_SOFTWARE_SUBDIR_OVERRIDE='x86_64/generic'; ./EESSI-install-software.sh\"@g" install_software_layer.sh
           # skip installation of CUDA SDKs, since this is too heavy for CI
-          # sed -i "s@./EESSI-install-software.sh@./EESSI-install-software.sh --skip-cuda-install@g" install_software_layer.sh
+          sed -i "s@./EESSI-install-software.sh@./EESSI-install-software.sh --skip-cuda-install@g" install_software_layer.sh
           ./eessi_container.sh --mode run --verbose /software-layer/install_software_layer.sh
 
     - name: test create_directory_tarballs.sh script

From dc915fb0b9ec5577787fa58cd618a44a77ff1ff3 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 2 Apr 2024 16:01:39 +0200
Subject: [PATCH 257/501] Print sensible message to log when the cuda
 installation is skipped

---
 EESSI-install-software.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 0374d8e758..567fed8e79 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -203,6 +203,8 @@ ${TOPDIR}/install_scripts.sh --prefix ${EESSI_PREFIX}
 # Allow skipping CUDA SDK install in e.g. CI environments
 if [ -z "${skip_cuda_install}" ] || [ ! "${skip_cuda_install}" ]; then
     ${EESSI_PREFIX}/scripts/gpu_support/nvidia/install_cuda_host_injections.sh -c 12.1.1 --accept-cuda-eula
+else
+    echo "Skipping installation of CUDA SDK in host_injections, since the --skip-cuda-install flag was passed"
 fi
 
 # Install drivers in host_injections

From 4cf4d76cc80ef5e5aa5df73cef628fca3ad56b99 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 2 Apr 2024 16:03:14 +0200
Subject: [PATCH 258/501] Issue is resolved, so we can use Apptainer 1.3.0

---
 install_apptainer_ubuntu.sh | 2 --
 1 file changed, 2 deletions(-)

diff --git a/install_apptainer_ubuntu.sh b/install_apptainer_ubuntu.sh
index 8642d62999..5c4f37ac2d 100755
--- a/install_apptainer_ubuntu.sh
+++ b/install_apptainer_ubuntu.sh
@@ -5,8 +5,6 @@ set -e
 # see https://github.com/apptainer/singularity/issues/5390#issuecomment-899111181
 sudo apt-get install alien
 alien --version
-# Switch back to Apptainer >= 1.3.0 to retrigger
-# https://github.com/EESSI/software-layer/pull/514
 epel_subdir="pub/epel/8"
 apptainer_rpm=$(curl --silent -L https://dl.fedoraproject.org/${epel_subdir}/Everything/x86_64/Packages/a/ | grep 'apptainer-[0-9]' | sed 's/.*\(apptainer[0-9._a-z-]*.rpm\).*/\1/g')
 curl -OL https://dl.fedoraproject.org/${epel_subdir}/Everything/x86_64/Packages/a/${apptainer_rpm}

From c92ceb2e07ddf37fc12ec86b0f6d90ded0423482 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 2 Apr 2024 16:04:12 +0200
Subject: [PATCH 259/501] Revert changes to utils.sh

---
 scripts/utils.sh | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/scripts/utils.sh b/scripts/utils.sh
index bbe17584b8..b2be3f6221 100644
--- a/scripts/utils.sh
+++ b/scripts/utils.sh
@@ -1,6 +1,3 @@
-## THIS COMMENT IS ONLY TO RETRIGGER #517
-## IT SHOULD NEVER BE MERGED
-
 function echo_green() {
     echo -e "\e[32m$1\e[0m"
 }

From b59d327ecce05ad1e5904fe2581c45c3e0b68d10 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 2 Apr 2024 17:19:14 +0200
Subject: [PATCH 260/501] Changed isDir to isFile

---
 create_lmodsitepackage.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index 6b67b4beca..cddb40da5c 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -68,7 +68,7 @@
     local hostSitePackage = prefixHostInjections .. "/.lmod/SitePackage.lua"
 
     -- If the file exists, run it
-    if isDir(hostSitePackage) then
+    if isFile(hostSitePackage) then
         dofile(hostSitePackage)
     end
 
@@ -77,7 +77,7 @@
     local archSitePackage = archHostInjections .. "/.lmod/SitePackage.lua"
 
     -- If the file exists, run it
-    if isDir(archSitePackage) then
+    if isFile(archSitePackage) then
         dofile(archSitePackage)
     end
     

From 9ff3cfab728cf66177b903aaa0e9d63099da2c2d Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 2 Apr 2024 17:20:23 +0200
Subject: [PATCH 261/501] Account for the possibility that EESSI_PREFIX isn't
 set

---
 create_lmodsitepackage.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index cddb40da5c..30f11c9c6f 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -64,7 +64,7 @@
     -- hook.register("load", arch_specific_load_hook)
 
     -- get path to to architecture independent SitePackage.lua
-    local prefixHostInjections = string.gsub(os.getenv('EESSI_PREFIX'), 'versions', 'host_injections')
+    local prefixHostInjections = string.gsub(os.getenv('EESSI_PREFIX') or "", 'versions', 'host_injections')
     local hostSitePackage = prefixHostInjections .. "/.lmod/SitePackage.lua"
 
     -- If the file exists, run it

From f25bfe09cf46f15d1869c32019640005aab2006b Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 2 Apr 2024 17:31:17 +0200
Subject: [PATCH 262/501] Corrected function name

---
 create_lmodsitepackage.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index 30f11c9c6f..29b2d39bd7 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -19,7 +19,7 @@
     return content
 end
 
-local function load_sitespecific_hooks()
+local function load_site_specific_hooks()
     -- This function will be run after the EESSI hooks are registered
     -- It will load a local SitePackage.lua that is architecture independent (if it exists) from e.g.
     -- /cvmfs/software.eessi.io/host_injections/2023.06/.lmod/SitePackage.lua

From 12d17a4777b2e2aa4f9ddaa1433d75d9c0012c59 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 2 Apr 2024 17:43:01 +0200
Subject: [PATCH 263/501] also test create_lmodsitepackage.py in CI

---
 .github/workflows/tests_scripts.yml | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/.github/workflows/tests_scripts.yml b/.github/workflows/tests_scripts.yml
index df1884dd8c..476be3dc4d 100644
--- a/.github/workflows/tests_scripts.yml
+++ b/.github/workflows/tests_scripts.yml
@@ -5,6 +5,7 @@ on:
     paths:
       - build_container.sh
       - create_directory_tarballs.sh
+      - create_lmodsitepackage.py
       - EESSI-install-software.sh
       - install_software_layer.sh
       - load_easybuild_module.sh
@@ -16,6 +17,7 @@ on:
     paths:
       - build_container.sh
       - create_directory_tarballs.sh
+      - create_lmodsitepackage.py
       - EESSI-install-software.sh
       - install_software_layer.sh
       - load_easybuild_module.sh
@@ -94,3 +96,22 @@ jobs:
           ./eessi_container.sh --mode run --verbose /software-layer/create_directory_tarballs.sh 2023.06
           # check if tarballs have been produced
           ls -l *.tar.gz
+
+    - name: test create_lmodsitepackage.py script
+      run: |
+          # bind current directory into container as /software-layer
+          export SINGULARITY_BIND="${PWD}:/software-layer"
+
+          python3 create_lmodsitepackage.py .
+          export LMOD_PACKAGE_PATH="$PWD/.lmod"
+          # run some commands to make sure that generated Lmod SitePackage file works
+          test_script="${PWD}/test_lmod_sitepackage.sh"
+          echo '#!/bin/bash' > ${test_script}
+          echo 'ml --config' >> ${test_script}
+
+          chmod u+x ${test_script}
+
+          ./eessi_container.sh --mode run --verbose /software-layer/run_in_compat_layer_env.sh /software-layer/test_lmod_sitepackage.sh 2>&1 | tee ${out}
+          for pattern in "^Site Pkg location.*$PWD/.lmod/SitePackage.lua" "LMOD_SITEPACKAGE_LOCATION.*${PWD}/.lmod/SitePackage.lua"; do
+            grep "${pattern}" ${out} || (echo "Pattern '${pattern}' not found in output!" && exit 1)
+          done

From 60c46ce702948e3c97e1dc432f5651f837efb39c Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 2 Apr 2024 18:38:23 +0200
Subject: [PATCH 264/501] Make sure export is done inside test script, as
 environment is lost when running in compat layer env

---
 .github/workflows/tests_scripts.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/tests_scripts.yml b/.github/workflows/tests_scripts.yml
index 476be3dc4d..95baedac08 100644
--- a/.github/workflows/tests_scripts.yml
+++ b/.github/workflows/tests_scripts.yml
@@ -102,11 +102,12 @@ jobs:
           # bind current directory into container as /software-layer
           export SINGULARITY_BIND="${PWD}:/software-layer"
 
+          # Creates .lmod/SitePackage.lua in current dir, which then gets bind-mounted into /software-layer
           python3 create_lmodsitepackage.py .
-          export LMOD_PACKAGE_PATH="$PWD/.lmod"
           # run some commands to make sure that generated Lmod SitePackage file works
           test_script="${PWD}/test_lmod_sitepackage.sh"
           echo '#!/bin/bash' > ${test_script}
+          echo 'export LMOD_PACKAGE_PATH="/software-layer/.lmod"' > ${test_script}
           echo 'ml --config' >> ${test_script}
 
           chmod u+x ${test_script}

From d59238b9643de5d34a301122afef133c231747fa Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 2 Apr 2024 18:46:58 +0200
Subject: [PATCH 265/501] Change expected output - we need to account for the
 fact that this is a bind-mounted location

---
 .github/workflows/tests_scripts.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests_scripts.yml b/.github/workflows/tests_scripts.yml
index 95baedac08..96838b99df 100644
--- a/.github/workflows/tests_scripts.yml
+++ b/.github/workflows/tests_scripts.yml
@@ -113,6 +113,6 @@ jobs:
           chmod u+x ${test_script}
 
           ./eessi_container.sh --mode run --verbose /software-layer/run_in_compat_layer_env.sh /software-layer/test_lmod_sitepackage.sh 2>&1 | tee ${out}
-          for pattern in "^Site Pkg location.*$PWD/.lmod/SitePackage.lua" "LMOD_SITEPACKAGE_LOCATION.*${PWD}/.lmod/SitePackage.lua"; do
+          for pattern in "^Site Pkg location.*/software-layer/.lmod/SitePackage.lua" "LMOD_SITEPACKAGE_LOCATION.*/software-layer/.lmod/SitePackage.lua"; do
             grep "${pattern}" ${out} || (echo "Pattern '${pattern}' not found in output!" && exit 1)
           done

From 1e8eb6eac7a040cf16d2f97d4126b93300da05c7 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Tue, 2 Apr 2024 19:12:20 +0200
Subject: [PATCH 266/501] Output variable was undefined

---
 .github/workflows/tests_scripts.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/tests_scripts.yml b/.github/workflows/tests_scripts.yml
index 96838b99df..ac55231bf0 100644
--- a/.github/workflows/tests_scripts.yml
+++ b/.github/workflows/tests_scripts.yml
@@ -112,6 +112,7 @@ jobs:
 
           chmod u+x ${test_script}
 
+          out="${PWD}/test_create_lmodsitepackage.out"
           ./eessi_container.sh --mode run --verbose /software-layer/run_in_compat_layer_env.sh /software-layer/test_lmod_sitepackage.sh 2>&1 | tee ${out}
           for pattern in "^Site Pkg location.*/software-layer/.lmod/SitePackage.lua" "LMOD_SITEPACKAGE_LOCATION.*/software-layer/.lmod/SitePackage.lua"; do
             grep "${pattern}" ${out} || (echo "Pattern '${pattern}' not found in output!" && exit 1)

From 542022c9e5a4e2109416c4476c621e1b7bb6ed82 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 3 Apr 2024 10:12:50 +0200
Subject: [PATCH 267/501] add hook that disables tests for Highway 1.0.4 on
 neoverse_v1

---
 eb_hooks.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/eb_hooks.py b/eb_hooks.py
index d93ee37067..94591ca91f 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -376,6 +376,18 @@ def pre_configure_hook_atspi2core_filter_ld_library_path(self, *args, **kwargs):
         raise EasyBuildError("at-spi2-core-specific hook triggered for non-at-spi2-core easyconfig?!")
 
 
+def pre_configure_hook_highway_disable_tests((self, *args, **kwargs):
+    """
+    pre-configure hook for Highway: disable tests on neoverse_v1
+    cfr. https://github.com/EESSI/software-layer/issues/469
+    """
+    cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
+    if self.name == 'Highway ' and cpu_target == CPU_TARGET_NEOVERSE_V1:
+        self.cfg.update('configopts', '-DHWY_ENABLE_TESTS=OFF')
+    else:
+        raise EasyBuildError("Highway-specific hook triggered for non-Highway easyconfig?!")
+
+
 def pre_test_hook(self,*args, **kwargs):
     """Main pre-test hook: trigger custom functions based on software name."""
     if self.name in PRE_TEST_HOOKS:
@@ -625,6 +637,7 @@ def inject_gpu_property(ec):
     'OpenBLAS': pre_configure_hook_openblas_optarch_generic,
     'WRF': pre_configure_hook_wrf_aarch64,
     'at-spi2-core': pre_configure_hook_atspi2core_filter_ld_library_path,
+    'Highway': pre_configure_hook_highway_disable_tests,
 }
 
 PRE_TEST_HOOKS = {

From a770536d7122c0bf9da89573082c180988798d93 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 3 Apr 2024 10:12:59 +0200
Subject: [PATCH 268/501] add Highway-1.0.4-GCCcore-12.3.0.eb

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 9b0de81b35..ac9c36fe82 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -54,3 +54,4 @@ easyconfigs:
         from-pr: 20126
   - OpenJPEG-2.5.0-GCCcore-12.3.0.eb
   - OpenFOAM-10-foss-2023a.eb
+  - Highway-1.0.4-GCCcore-12.3.0.eb

From 3cc125d7996b04cea0bcd71e1fff767113666310 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 3 Apr 2024 10:15:40 +0200
Subject: [PATCH 269/501] add known issue about Highway 1.0.4 on neoverse_v1

---
 eessi-2023.06-known-issues.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/eessi-2023.06-known-issues.yml b/eessi-2023.06-known-issues.yml
index 875757559e..d818c85952 100644
--- a/eessi-2023.06-known-issues.yml
+++ b/eessi-2023.06-known-issues.yml
@@ -19,6 +19,9 @@
   - Highway-1.0.3-GCCcore-12.2.0.eb:
     - issue: https://github.com/EESSI/software-layer/issues/469
     - info: "failing SVE test due to wrong expected value"
+  - Highway-1.0.4-GCCcore-12.3.0.eb:
+      - issue: https://github.com/EESSI/software-layer/issues/469
+      - info: "failing to build the tests"
   - netCDF-4.9.2-gompi-2023a.eb:
       - issue: https://github.com/EESSI/software-layer/issues/425
       - info: "netCDF intermittent test failures"

From 098d5253901c4e32e2c5f9f4e331be29efcc04ea Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Wed, 3 Apr 2024 10:46:16 +0200
Subject: [PATCH 270/501] Update eb_hooks.py

---
 eb_hooks.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index 94591ca91f..4b29c84eb2 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -382,7 +382,7 @@ def pre_configure_hook_highway_disable_tests((self, *args, **kwargs):
     cfr. https://github.com/EESSI/software-layer/issues/469
     """
     cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
-    if self.name == 'Highway ' and cpu_target == CPU_TARGET_NEOVERSE_V1:
+    if self.name == 'Highway' and cpu_target == CPU_TARGET_NEOVERSE_V1:
         self.cfg.update('configopts', '-DHWY_ENABLE_TESTS=OFF')
     else:
         raise EasyBuildError("Highway-specific hook triggered for non-Highway easyconfig?!")

From 10e1d00ebce2fe8753b2e638e12a8b0f01a33b5f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 3 Apr 2024 10:47:41 +0200
Subject: [PATCH 271/501] fix syntax, remove (

---
 eb_hooks.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index 94591ca91f..78432c7a00 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -376,7 +376,7 @@ def pre_configure_hook_atspi2core_filter_ld_library_path(self, *args, **kwargs):
         raise EasyBuildError("at-spi2-core-specific hook triggered for non-at-spi2-core easyconfig?!")
 
 
-def pre_configure_hook_highway_disable_tests((self, *args, **kwargs):
+def pre_configure_hook_highway_disable_tests(self, *args, **kwargs):
     """
     pre-configure hook for Highway: disable tests on neoverse_v1
     cfr. https://github.com/EESSI/software-layer/issues/469

From 24d5bcfe80061958699ea8376f8ed08780c630a1 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Wed, 3 Apr 2024 11:33:10 +0200
Subject: [PATCH 272/501] Move software builds to the easystack file for the
 right toolchain...

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023a.yml          | 10 ++++++++++
 .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml          | 11 +----------
 2 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 9b0de81b35..0c260cea5c 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -54,3 +54,13 @@ easyconfigs:
         from-pr: 20126
   - OpenJPEG-2.5.0-GCCcore-12.3.0.eb
   - OpenFOAM-10-foss-2023a.eb
+  - SuperLU_DIST-8.1.2-foss-2023a.eb:
+      options:
+        from-pr: 20162
+  - PETSc-3.20.3-foss-2023a.eb:
+      options:
+        include-easyblocks-from-pr: 3086
+        from-pr: 19686
+  - MODFLOW-6.4.4-foss-2023a.eb:
+      options:
+        from-pr: 20142
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 94303fd2b4..1e94f7be78 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -57,13 +57,4 @@ easyconfigs:
   - Qt5-5.15.13-GCCcore-13.2.0.eb:
       options:
         from-pr: 20201
-  - SuperLU_DIST-8.1.2-foss-2023a.eb:
-      options:
-        from-pr: 20162
-  - PETSc-3.20.3-foss-2023a.eb:
-      options:
-        include-easyblocks-from-pr: 3086
-        from-pr: 19686
-  - MODFLOW-6.4.4-foss-2023a.eb:
-      options:
-        from-pr: 20142
+

From 5509f6c33fd15c6f7b6dfdf7f182fe839a44c758 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Wed, 3 Apr 2024 11:36:19 +0200
Subject: [PATCH 273/501] Remove stray blank line

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml   | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 1e94f7be78..86c5106c85 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -57,4 +57,3 @@ easyconfigs:
   - Qt5-5.15.13-GCCcore-13.2.0.eb:
       options:
         from-pr: 20201
-

From abfe1bf536e91938b4fba50c33585962e8d07042 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 3 Apr 2024 12:04:33 +0200
Subject: [PATCH 274/501] add toolchain and version check to Highway hook that
 disables the tests

---
 eb_hooks.py | 31 +++++++++++++++++--------------
 1 file changed, 17 insertions(+), 14 deletions(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index eee2a4dfde..9ccd984de4 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -289,6 +289,21 @@ def parse_hook_lammps_remove_deps_for_CI_aarch64(ec, *args, **kwargs):
         raise EasyBuildError("LAMMPS-specific hook triggered for non-LAMMPS easyconfig?!")
 
 
+def parse_hook_highway_disable_tests(ec, eprefix):):
+    """
+    pre-configure hook for Highway: disable tests on neoverse_v1 for Highway 1.0.4 and GCC 12.3.0
+    cfr. https://github.com/EESSI/software-layer/issues/469
+    """
+    if ec.name == 'Highway':
+        tcname, tcversion = ec['toolchain']['name'], ec['toolchain']['version']
+        cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
+        if ec.version in ['1.0.4'] and tcname == 'GCCcore' and tcversion == '12.3.0':
+            if cpu_target == CPU_TARGET_NEOVERSE_V1:
+                ec.update('configopts', '-DHWY_ENABLE_TESTS=OFF')
+    else:
+        raise EasyBuildError("Highway-specific hook triggered for non-Highway easyconfig?!")
+
+
 def pre_configure_hook(self, *args, **kwargs):
     """Main pre-configure hook: trigger custom functions based on software name."""
     if self.name in PRE_CONFIGURE_HOOKS:
@@ -376,18 +391,6 @@ def pre_configure_hook_atspi2core_filter_ld_library_path(self, *args, **kwargs):
         raise EasyBuildError("at-spi2-core-specific hook triggered for non-at-spi2-core easyconfig?!")
 
 
-def pre_configure_hook_highway_disable_tests(self, *args, **kwargs):
-    """
-    pre-configure hook for Highway: disable tests on neoverse_v1
-    cfr. https://github.com/EESSI/software-layer/issues/469
-    """
-    cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
-    if self.name == 'Highway' and cpu_target == CPU_TARGET_NEOVERSE_V1:
-        self.cfg.update('configopts', '-DHWY_ENABLE_TESTS=OFF')
-    else:
-        raise EasyBuildError("Highway-specific hook triggered for non-Highway easyconfig?!")
-
-
 def pre_test_hook(self,*args, **kwargs):
     """Main pre-test hook: trigger custom functions based on software name."""
     if self.name in PRE_TEST_HOOKS:
@@ -620,11 +623,12 @@ def inject_gpu_property(ec):
     'casacore': parse_hook_casacore_disable_vectorize,
     'CGAL': parse_hook_cgal_toolchainopts_precise,
     'fontconfig': parse_hook_fontconfig_add_fonts,
+    'Highway': parse_hook_highway_disable_tests,
+    'LAMMPS': parse_hook_lammps_remove_deps_for_CI_aarch64,
     'OpenBLAS': parse_hook_openblas_relax_lapack_tests_num_errors,
     'pybind11': parse_hook_pybind11_replace_catch2,
     'Qt5': parse_hook_qt5_check_qtwebengine_disable,
     'UCX': parse_hook_ucx_eprefix,
-    'LAMMPS': parse_hook_lammps_remove_deps_for_CI_aarch64,
 }
 
 POST_PREPARE_HOOKS = {
@@ -637,7 +641,6 @@ def inject_gpu_property(ec):
     'OpenBLAS': pre_configure_hook_openblas_optarch_generic,
     'WRF': pre_configure_hook_wrf_aarch64,
     'at-spi2-core': pre_configure_hook_atspi2core_filter_ld_library_path,
-    'Highway': pre_configure_hook_highway_disable_tests,
 }
 
 PRE_TEST_HOOKS = {

From ae74707573fea4f1f210955e311c391f982c1f88 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 3 Apr 2024 12:15:49 +0200
Subject: [PATCH 275/501] syntax fix

---
 eb_hooks.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index 9ccd984de4..902a37a599 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -289,7 +289,7 @@ def parse_hook_lammps_remove_deps_for_CI_aarch64(ec, *args, **kwargs):
         raise EasyBuildError("LAMMPS-specific hook triggered for non-LAMMPS easyconfig?!")
 
 
-def parse_hook_highway_disable_tests(ec, eprefix):):
+def parse_hook_highway_disable_tests(ec, eprefix):
     """
     pre-configure hook for Highway: disable tests on neoverse_v1 for Highway 1.0.4 and GCC 12.3.0
     cfr. https://github.com/EESSI/software-layer/issues/469

From 3ccecf97e9008ddf98640d3a0ab970607c5b5779 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Wed, 3 Apr 2024 12:58:22 +0200
Subject: [PATCH 276/501] Add possibility to ignore certain hooks on local
 modules. E.g. we don't want to be prevented from loading local CUDA modules
 because of the EESSI hook. See
 https://github.com/EESSI/software-layer/issues/523

---
 create_lmodsitepackage.py | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index 29b2d39bd7..ffbe7a1531 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -19,6 +19,18 @@
     return content
 end
 
+local function from_eessi_prefix(t)
+    local eessi_prefix = os.getenv("EESSI_PREFIX")
+    -- If EESSI_PREFIX wasn't defined, we cannot check if this module was from the EESSI environment
+    -- In that case, we assume it isn't, otherwise EESSI_PREFIX would (probably) have been set
+    if eessi_prefix == nil then
+        return False
+    else
+        -- Check if the full modulepath starts with the eessi_prefix
+        return t.fn:find( "^" .. eessi_prefix) ~= nil
+    end
+end
+
 local function load_site_specific_hooks()
     -- This function will be run after the EESSI hooks are registered
     -- It will load a local SitePackage.lua that is architecture independent (if it exists) from e.g.
@@ -152,10 +164,13 @@
 -- Combine both functions into a single one, as we can only register one function as load hook in lmod
 -- Also: make it non-local, so it can be imported and extended by other lmodrc files if needed
 function eessi_load_hook(t)
-    eessi_cuda_enabled_load_hook(t)
+    -- Only apply CUDA hooks if the loaded module is in the EESSI prefix
+    -- This avoids getting an Lmod Error when trying to load a CUDA module from a local software stack
+    if from_eessi_prefix(t) then
+        eessi_cuda_enabled_load_hook(t)
+    end
 end
 
-
 hook.register("load", eessi_load_hook)
 
 -- Note that this needs to happen at the end, so that any EESSI specific hooks can be overwritten by the site

From 92aad04bfa1810d313e476be5d89e13217cce9d3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 3 Apr 2024 13:02:33 +0200
Subject: [PATCH 277/501] also disable Highway 1.0.4 tests for neoverse_n1

---
 eb_hooks.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index 902a37a599..64671a5889 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -20,6 +20,7 @@
     from distutils.version import LooseVersion
 
 
+CPU_TARGET_NEOVERSE_N1 = 'aarch64/neoverse_n1'
 CPU_TARGET_NEOVERSE_V1 = 'aarch64/neoverse_v1'
 CPU_TARGET_AARCH64_GENERIC = 'aarch64/generic'
 
@@ -173,7 +174,7 @@ def parse_hook_casacore_disable_vectorize(ec, eprefix):
             tcname == 'foss' and tcversion == '2023b'
         ):
             cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
-            if cpu_target == CPU_TARGET_NEOVERSE_V1:
+            if cpu_target in [CPU_TARGET_NEOVERSE_V1, CPU_TARGET_NEOVERSE_N1]:
                 if not hasattr(ec, 'toolchainopts'):
                     ec['toolchainopts'] = {}
                 ec['toolchainopts']['vectorize'] = False

From f2954ef909353b8c0a782b745324b523a612a1cb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 3 Apr 2024 13:26:11 +0200
Subject: [PATCH 278/501] oops, changed the wrong hook... fixed

---
 eb_hooks.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index 64671a5889..7b1eb5cec2 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -174,7 +174,7 @@ def parse_hook_casacore_disable_vectorize(ec, eprefix):
             tcname == 'foss' and tcversion == '2023b'
         ):
             cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
-            if cpu_target in [CPU_TARGET_NEOVERSE_V1, CPU_TARGET_NEOVERSE_N1]:
+            if cpu_target == CPU_TARGET_NEOVERSE_V1:
                 if not hasattr(ec, 'toolchainopts'):
                     ec['toolchainopts'] = {}
                 ec['toolchainopts']['vectorize'] = False
@@ -299,7 +299,7 @@ def parse_hook_highway_disable_tests(ec, eprefix):
         tcname, tcversion = ec['toolchain']['name'], ec['toolchain']['version']
         cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
         if ec.version in ['1.0.4'] and tcname == 'GCCcore' and tcversion == '12.3.0':
-            if cpu_target == CPU_TARGET_NEOVERSE_V1:
+            if cpu_target in [CPU_TARGET_NEOVERSE_V1, CPU_TARGET_NEOVERSE_N1]:
                 ec.update('configopts', '-DHWY_ENABLE_TESTS=OFF')
     else:
         raise EasyBuildError("Highway-specific hook triggered for non-Highway easyconfig?!")

From bb20ab2078b25041011f242673a848b199aedb74 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Wed, 3 Apr 2024 16:36:39 +0200
Subject: [PATCH 279/501] Also use hooks for site extensions in host_injections
 AND for user extensions in /home/casparl/eessi/...

---
 create_lmodsitepackage.py | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index ffbe7a1531..f7d4d06bb9 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -20,14 +20,24 @@
 end
 
 local function from_eessi_prefix(t)
+    -- eessi_prefix is the prefix with official EESSI modules
+    -- e.g. /cvmfs/software.eessi.io/versions/2023.06
     local eessi_prefix = os.getenv("EESSI_PREFIX")
+    -- eessi_prefix_host_injections is the prefix with site-extensions (i.e. additional modules)
+    -- to the official EESSI modules, e.g. /cvmfs/software.eessi.io/host_injections/2023.06
+    local eessi_prefix_host_injections = string.gsub(eessi_prefix, 'versions', 'host_injections')
+    -- eessi_prefix_user_home is the prefix with user-extensions (i.e. additional modules)
+    -- to the offocial EESSI modules, e.g. $HOME/eessi/versions/2023.06
+    local eessi_prefix_user_home = string.gsub(eessi_prefix, os.getenv("EESSI_CVMFS_REPO"), pathJoin(os.getenv("HOME"), "eessi"))
     -- If EESSI_PREFIX wasn't defined, we cannot check if this module was from the EESSI environment
     -- In that case, we assume it isn't, otherwise EESSI_PREFIX would (probably) have been set
     if eessi_prefix == nil then
         return False
     else
-        -- Check if the full modulepath starts with the eessi_prefix
-        return t.fn:find( "^" .. eessi_prefix) ~= nil
+        -- Check if the full modulepath starts with the eessi_prefix_*
+        return string.find(t.fn, "^" .. eessi_prefix) ~= nil or
+        string.find(t.fn, "^" .. eessi_prefix_host_injections) ~= nil or
+        string.find(t.fn, "^" .. eessi_prefix_user_home) ~= nil
     end
 end
 

From 838920bd332819b1e50706873ee53f2469cf3794 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Wed, 3 Apr 2024 16:38:24 +0200
Subject: [PATCH 280/501] Leave breadcrumb to notify that paths may need to be
 changed in the future

---
 create_lmodsitepackage.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index f7d4d06bb9..ce94a7e311 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -23,6 +23,10 @@
     -- eessi_prefix is the prefix with official EESSI modules
     -- e.g. /cvmfs/software.eessi.io/versions/2023.06
     local eessi_prefix = os.getenv("EESSI_PREFIX")
+
+    -- NOTE: exact paths for site and user extensions aren't final, so may need to be updated later.
+    -- See https://github.com/EESSI/software-layer/pull/371
+
     -- eessi_prefix_host_injections is the prefix with site-extensions (i.e. additional modules)
     -- to the official EESSI modules, e.g. /cvmfs/software.eessi.io/host_injections/2023.06
     local eessi_prefix_host_injections = string.gsub(eessi_prefix, 'versions', 'host_injections')

From 11b7bc2a41d228079f238e361683f2c9da1b28fd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 3 Apr 2024 17:38:06 +0200
Subject: [PATCH 281/501] different actions for neoverse_n1 and _v1 in highway
 hook

---
 eb_hooks.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index 7b1eb5cec2..8bf66427a9 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -290,17 +290,20 @@ def parse_hook_lammps_remove_deps_for_CI_aarch64(ec, *args, **kwargs):
         raise EasyBuildError("LAMMPS-specific hook triggered for non-LAMMPS easyconfig?!")
 
 
-def parse_hook_highway_disable_tests(ec, eprefix):
+def parse_hook_highway_handle_test_compilation_issues(ec, eprefix):
     """
-    pre-configure hook for Highway: disable tests on neoverse_v1 for Highway 1.0.4 and GCC 12.3.0
+    pre-configure hook for Highway that solves issue that arise during the compilation of the tests
+    on both neoverse_n1 and neoverse_v1 with Highway 1.0.4 and GCC 12.3.0
     cfr. https://github.com/EESSI/software-layer/issues/469
     """
     if ec.name == 'Highway':
         tcname, tcversion = ec['toolchain']['name'], ec['toolchain']['version']
         cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
         if ec.version in ['1.0.4'] and tcname == 'GCCcore' and tcversion == '12.3.0':
-            if cpu_target in [CPU_TARGET_NEOVERSE_V1, CPU_TARGET_NEOVERSE_N1]:
+            if cpu_target == CPU_TARGET_NEOVERSE_V1:
                 ec.update('configopts', '-DHWY_ENABLE_TESTS=OFF')
+            if cpu_target == CPU_TARGET_NEOVERSE_N1:
+                update_build_option('optarch', OPTARCH_GENERIC)
     else:
         raise EasyBuildError("Highway-specific hook triggered for non-Highway easyconfig?!")
 
@@ -624,7 +627,7 @@ def inject_gpu_property(ec):
     'casacore': parse_hook_casacore_disable_vectorize,
     'CGAL': parse_hook_cgal_toolchainopts_precise,
     'fontconfig': parse_hook_fontconfig_add_fonts,
-    'Highway': parse_hook_highway_disable_tests,
+    'Highway': parse_hook_highway_handle_test_compilation_issues,
     'LAMMPS': parse_hook_lammps_remove_deps_for_CI_aarch64,
     'OpenBLAS': parse_hook_openblas_relax_lapack_tests_num_errors,
     'pybind11': parse_hook_pybind11_replace_catch2,

From 69d0e9d132dcb6123ca000ead3580fd8f59da8a7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 4 Apr 2024 13:51:08 +0200
Subject: [PATCH 282/501] update docstring of
 parse_hook_highway_handle_test_compilation_issues

---
 eb_hooks.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index 8bf66427a9..0221e98b2a 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -292,8 +292,10 @@ def parse_hook_lammps_remove_deps_for_CI_aarch64(ec, *args, **kwargs):
 
 def parse_hook_highway_handle_test_compilation_issues(ec, eprefix):
     """
-    pre-configure hook for Highway that solves issue that arise during the compilation of the tests
-    on both neoverse_n1 and neoverse_v1 with Highway 1.0.4 and GCC 12.3.0
+    Solve issues with compiling or running the tests on both
+    neoverse_n1 and neoverse_v1 with Highway 1.0.4 and GCC 12.3.0:
+      - for neoverse_n1 we set optarch to GENERIC
+      - for neoverse_v1 we completely disable the tests
     cfr. https://github.com/EESSI/software-layer/issues/469
     """
     if ec.name == 'Highway':

From 7dba052cfee0996a1bce79984e79c37d4caeac64 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 4 Apr 2024 13:52:06 +0200
Subject: [PATCH 283/501] add issue with Highway 1.0.4 on neoverse_n1

---
 eessi-2023.06-known-issues.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/eessi-2023.06-known-issues.yml b/eessi-2023.06-known-issues.yml
index d818c85952..011cb2dc08 100644
--- a/eessi-2023.06-known-issues.yml
+++ b/eessi-2023.06-known-issues.yml
@@ -3,6 +3,9 @@
     - issue: https://github.com/EESSI/software-layer/issues/461
     - info: "8 failing tests (out of 209539) on aarch64/*"
 - aarch64/neoverse_n1:
+  - Highway-1.0.4-GCCcore-12.3.0.eb:
+      - issue: https://github.com/EESSI/software-layer/issues/469
+      - info: "failing to build the tests"
   - PyTorch-2.1.2-foss-2023a:
     - issue: https://github.com/EESSI/software-layer/issues/461
     - info: "8 failing tests (out of 209539) on aarch64/*"

From 6fa335b3868a79dc6fda347b841b2bfe9192509f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 4 Apr 2024 19:58:57 +0200
Subject: [PATCH 284/501] change Highway hook in pre_prepare hook, and reset
 optarch in a post-prepare hook

---
 eb_hooks.py | 31 +++++++++++++++++++++++++------
 1 file changed, 25 insertions(+), 6 deletions(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index 0221e98b2a..e8b890a954 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -116,6 +116,9 @@ def pre_prepare_hook(self, *args, **kwargs):
         print_msg("Updated rpath_override_dirs (to allow overriding MPI family %s): %s",
                   mpi_family, rpath_override_dirs)
 
+    if self.name in PRE_PREPARE_HOOKS:
+        PRE_PREPARE_HOOKS[self.name](self, *args, **kwargs)
+
 
 def post_prepare_hook_gcc_prefixed_ld_rpath_wrapper(self, *args, **kwargs):
     """
@@ -290,7 +293,7 @@ def parse_hook_lammps_remove_deps_for_CI_aarch64(ec, *args, **kwargs):
         raise EasyBuildError("LAMMPS-specific hook triggered for non-LAMMPS easyconfig?!")
 
 
-def parse_hook_highway_handle_test_compilation_issues(ec, eprefix):
+def pre_prepare_hook_highway_handle_test_compilation_issues(self, *args, **kwargs):
     """
     Solve issues with compiling or running the tests on both
     neoverse_n1 and neoverse_v1 with Highway 1.0.4 and GCC 12.3.0:
@@ -298,18 +301,30 @@ def parse_hook_highway_handle_test_compilation_issues(ec, eprefix):
       - for neoverse_v1 we completely disable the tests
     cfr. https://github.com/EESSI/software-layer/issues/469
     """
-    if ec.name == 'Highway':
-        tcname, tcversion = ec['toolchain']['name'], ec['toolchain']['version']
+    if self.name == 'Highway':
+        tcname, tcversion = self.toolchain.name, self.toolchain.version
         cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
-        if ec.version in ['1.0.4'] and tcname == 'GCCcore' and tcversion == '12.3.0':
+        if self.version in ['1.0.4'] and tcname == 'GCCcore' and tcversion == '12.3.0':
             if cpu_target == CPU_TARGET_NEOVERSE_V1:
-                ec.update('configopts', '-DHWY_ENABLE_TESTS=OFF')
+                self.cfg.update('configopts', '-DHWY_ENABLE_TESTS=OFF')
             if cpu_target == CPU_TARGET_NEOVERSE_N1:
+                self.orig_optarch = build_option('optarch')
                 update_build_option('optarch', OPTARCH_GENERIC)
     else:
         raise EasyBuildError("Highway-specific hook triggered for non-Highway easyconfig?!")
 
 
+def post_prepare_hook_highway_handle_test_compilation_issues(self, *args, **kwargs):
+    """
+    Post-prepare hook for Highway to reset optarch build option.
+    """
+    if self.name == 'Highway':
+        tcname, tcversion = self.toolchain.name, self.toolchain.version
+        cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
+        if self.version in ['1.0.4'] and tcname == 'GCCcore' and tcversion == '12.3.0':
+            if cpu_target == CPU_TARGET_NEOVERSE_N1:
+                update_build_option('optarch', self.orig_optarch)
+
 def pre_configure_hook(self, *args, **kwargs):
     """Main pre-configure hook: trigger custom functions based on software name."""
     if self.name in PRE_CONFIGURE_HOOKS:
@@ -629,7 +644,6 @@ def inject_gpu_property(ec):
     'casacore': parse_hook_casacore_disable_vectorize,
     'CGAL': parse_hook_cgal_toolchainopts_precise,
     'fontconfig': parse_hook_fontconfig_add_fonts,
-    'Highway': parse_hook_highway_handle_test_compilation_issues,
     'LAMMPS': parse_hook_lammps_remove_deps_for_CI_aarch64,
     'OpenBLAS': parse_hook_openblas_relax_lapack_tests_num_errors,
     'pybind11': parse_hook_pybind11_replace_catch2,
@@ -637,8 +651,13 @@ def inject_gpu_property(ec):
     'UCX': parse_hook_ucx_eprefix,
 }
 
+PRE_PREPARE_HOOKS = {
+    'Highway': pre_prepare_hook_highway_handle_test_compilation_issues,
+}
+
 POST_PREPARE_HOOKS = {
     'GCCcore': post_prepare_hook_gcc_prefixed_ld_rpath_wrapper,
+    'Highway': post_prepare_hook_highway_handle_test_compilation_issues,
 }
 
 PRE_CONFIGURE_HOOKS = {

From 42e580bf17d24b6a3736dd620dd5206d1d7507a2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 4 Apr 2024 20:33:49 +0200
Subject: [PATCH 285/501] Update eb_hooks.py

Co-authored-by: Kenneth Hoste <kenneth.hoste@ugent.be>
---
 eb_hooks.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/eb_hooks.py b/eb_hooks.py
index e8b890a954..c2075c8574 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -304,6 +304,8 @@ def pre_prepare_hook_highway_handle_test_compilation_issues(self, *args, **kwarg
     if self.name == 'Highway':
         tcname, tcversion = self.toolchain.name, self.toolchain.version
         cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
+        # note: keep condition in sync with the one used in 
+        # post_prepare_hook_highway_handle_test_compilation_issues
         if self.version in ['1.0.4'] and tcname == 'GCCcore' and tcversion == '12.3.0':
             if cpu_target == CPU_TARGET_NEOVERSE_V1:
                 self.cfg.update('configopts', '-DHWY_ENABLE_TESTS=OFF')

From 3c4572cb03c5d5dde7df1a16282c8bb70286918c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 4 Apr 2024 20:33:54 +0200
Subject: [PATCH 286/501] Update eb_hooks.py

Co-authored-by: Kenneth Hoste <kenneth.hoste@ugent.be>
---
 eb_hooks.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/eb_hooks.py b/eb_hooks.py
index c2075c8574..20b5f76cfc 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -323,6 +323,8 @@ def post_prepare_hook_highway_handle_test_compilation_issues(self, *args, **kwar
     if self.name == 'Highway':
         tcname, tcversion = self.toolchain.name, self.toolchain.version
         cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
+        # note: keep condition in sync with the one used in 
+        # pre_prepare_hook_highway_handle_test_compilation_issues
         if self.version in ['1.0.4'] and tcname == 'GCCcore' and tcversion == '12.3.0':
             if cpu_target == CPU_TARGET_NEOVERSE_N1:
                 update_build_option('optarch', self.orig_optarch)

From 7283d086780b7dc9ae224a70bb4f6236a52e94d9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 4 Apr 2024 22:52:41 +0200
Subject: [PATCH 287/501] add from-pr 20238 for R-bundle-CRAN

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023a.yml                  | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 1674bd76d9..a7cabc110a 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -55,4 +55,6 @@ easyconfigs:
   - OpenJPEG-2.5.0-GCCcore-12.3.0.eb
   - OpenFOAM-10-foss-2023a.eb
   - Highway-1.0.4-GCCcore-12.3.0.eb
-  - R-bundle-CRAN-2023.12-foss-2023a.eb
+  - R-bundle-CRAN-2023.12-foss-2023a.eb:
+      options:
+        from-pr: 20238

From f6012f7ae91bfdf862f46e93cf6942067c8b580d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 5 Apr 2024 11:42:40 +0200
Subject: [PATCH 288/501] add comment, retrigger CI

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 7ab9cf7c9b..44952e2765 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -69,4 +69,5 @@ easyconfigs:
         from-pr: 20142
   - R-bundle-CRAN-2023.12-foss-2023a.eb:
       options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20238
         from-pr: 20238

From 145706e751ea7a73202676894cd58be65bea97d1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 5 Apr 2024 11:53:36 +0200
Subject: [PATCH 289/501] add R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index ad3cfddfb6..2dadc5ab28 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -57,3 +57,4 @@ easyconfigs:
   - Highway-1.0.4-GCCcore-12.3.0.eb
   - ELPA-2023.05.001-foss-2023a.eb
   - libxc-6.2.2-GCC-12.3.0.eb
+  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb

From cef7a277ac4092f8ff1256290ad6bb8b244c2443 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 5 Apr 2024 13:03:35 +0200
Subject: [PATCH 290/501] add from-pr to bioconductor

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023a.yml                  | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index facd4230ab..60b9600589 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -67,4 +67,6 @@ easyconfigs:
   - MODFLOW-6.4.4-foss-2023a.eb:
       options:
         from-pr: 20142
-  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb
+  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
+      options:
+        from-pr: 19949

From 03e66d87cb07fb9d7c2f7f0daff93928f6b25f2d Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 5 Apr 2024 20:51:55 +0200
Subject: [PATCH 291/501] {2023.06}[foss/2023a] QuantumESPRESSO 7.3.1

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023a.yml                | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 44952e2765..6cb243556a 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -71,3 +71,9 @@ easyconfigs:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20238
         from-pr: 20238
+  - QuantumESPRESSO-7.3.1-foss-2023a.eb:
+      # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20138
+      # see https://github.com/easybuilders/easybuild-easyblocks/pull/3257
+      options:
+        from-pr: 20138
+        include-easyblocks-from-pr: 3257

From 3745adee2c09aa73d44c7b693baca3ac4c96e70c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 8 Apr 2024 13:52:36 +0200
Subject: [PATCH 292/501] use pr 20316 for Bioconductor

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index d3ac5f1c5b..bfc408e045 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -73,4 +73,4 @@ easyconfigs:
         from-pr: 20238
   - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
       options:
-        from-pr: 19949
+        from-pr: 20316

From 03b708fe7af1fc1aa330bf17bdf3f25a601f093e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 8 Apr 2024 13:54:13 +0200
Subject: [PATCH 293/501] use PR  20316 for Bioconductor

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2022b.yml                  | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
index 8a3e82d760..da89e01a51 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
@@ -11,4 +11,6 @@ easyconfigs:
   - R-4.2.2-foss-2022b.eb:
       options:
         from-pr: 20238
-  - R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb
+  - R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb:
+      options:
+        from-pr: 20316

From 1998a7cfe2904e1b8dacdba4d6eca1fe67eb6354 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 8 Apr 2024 15:16:08 +0200
Subject: [PATCH 294/501] add EB 4.9.1

---
 .../2023.06/eessi-2023.06-eb-4.9.1-001-system.yml             | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
new file mode 100644
index 0000000000..c5a08b5209
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
@@ -0,0 +1,4 @@
+easyconfigs:
+  - EasyBuild-4.9.1.eb:
+      options:
+        from-pr: 20299

From 1910871e228de824978f00b1d995879330745dec Mon Sep 17 00:00:00 2001
From: maxim-masterov <maxim.vadimovich@gmail.com>
Date: Tue, 9 Apr 2024 12:12:18 +0200
Subject: [PATCH 295/501] Add fix for permissions set on Lmod SitePackage

---
 create_lmodsitepackage.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index 29b2d39bd7..38600cb471 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -4,6 +4,7 @@
 #
 import os
 import sys
+from stat import S_IREAD, S_IWRITE, S_IRGRP, S_IWGRP, S_IROTH
 
 DOT_LMOD = '.lmod'
 
@@ -180,6 +181,8 @@ def error(msg):
     os.makedirs(os.path.dirname(sitepackage_path), exist_ok=True)
     with open(sitepackage_path, 'w') as fp:
         fp.write(hook_txt)
+    # Make sure that the created Lmod file has "read" permissions for the "other" UNIX group
+    os.chmod(sitepackage_path, S_IREAD|S_IWRITE|S_IRGRP|S_IWGRP|S_IROTH)
 
 except (IOError, OSError) as err:
     error("Failed to create %s: %s" % (sitepackage_path, err))

From 8f656a4dced151499045dd9c1c49dc6438fb7471 Mon Sep 17 00:00:00 2001
From: Maxim <maxim.vadimovich@gmail.com>
Date: Wed, 10 Apr 2024 16:19:37 +0200
Subject: [PATCH 296/501] Update create_lmodsitepackage.py

Co-authored-by: ocaisa <alan.ocais@cecam.org>
---
 create_lmodsitepackage.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index 38600cb471..0761f2cdf1 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -181,7 +181,7 @@ def error(msg):
     os.makedirs(os.path.dirname(sitepackage_path), exist_ok=True)
     with open(sitepackage_path, 'w') as fp:
         fp.write(hook_txt)
-    # Make sure that the created Lmod file has "read" permissions for the "other" UNIX group
+    # Make sure that the created Lmod file has "read/write" for the user/group and "read" permissions for others
     os.chmod(sitepackage_path, S_IREAD|S_IWRITE|S_IRGRP|S_IWGRP|S_IROTH)
 
 except (IOError, OSError) as err:

From 1a396e03badc537ddf901257bba7efb1cbdc8281 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 12 Apr 2024 13:23:53 +0200
Subject: [PATCH 297/501] Ensure we use instructions introduced with ARM v8.2
 for Neoverse N1

---
 init/arch_specs/eessi_arch_arm.spec | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/init/arch_specs/eessi_arch_arm.spec b/init/arch_specs/eessi_arch_arm.spec
index b5c9275043..1400871f93 100755
--- a/init/arch_specs/eessi_arch_arm.spec
+++ b/init/arch_specs/eessi_arch_arm.spec
@@ -1,6 +1,6 @@
 # ARM CPU architecture specifications
 # Software path in EESSI 	| Vendor ID 	| List of defining CPU features
-"aarch64/neoverse_n1"	"ARM"		"asimd"		# Ampere Altra
-"aarch64/neoverse_n1"	""		"asimd"		# AWS Graviton2
-"aarch64/neoverse_v1"	"ARM"		"asimd svei8mm"
-"aarch64/neoverse_v1"	""		"asimd svei8mm"	# AWS Graviton3
+"aarch64/neoverse_n1"	"ARM"		"asimddp"		# Ampere Altra
+"aarch64/neoverse_n1"	""		"asimddp"		# AWS Graviton2
+"aarch64/neoverse_v1"	"ARM"		"asimddp svei8mm"
+"aarch64/neoverse_v1"	""		"asimddp svei8mm"	# AWS Graviton3

From cedcf73c5da8d51d47c8d8d209cab76222e82820 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Fri, 12 Apr 2024 16:19:43 +0200
Subject: [PATCH 298/501] Update eessi_arch_arm.spec

---
 init/arch_specs/eessi_arch_arm.spec | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/init/arch_specs/eessi_arch_arm.spec b/init/arch_specs/eessi_arch_arm.spec
index 1400871f93..8c1bc34d20 100755
--- a/init/arch_specs/eessi_arch_arm.spec
+++ b/init/arch_specs/eessi_arch_arm.spec
@@ -1,4 +1,4 @@
-# ARM CPU architecture specifications
+# ARM CPU architecture specifications (see https://gpages.juszkiewicz.com.pl/arm-socs-table/arm-socs.html for guidance)
 # Software path in EESSI 	| Vendor ID 	| List of defining CPU features
 "aarch64/neoverse_n1"	"ARM"		"asimddp"		# Ampere Altra
 "aarch64/neoverse_n1"	""		"asimddp"		# AWS Graviton2

From 61a788281119974079712a3ee9b1beeaa7fb24b9 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Sun, 14 Apr 2024 13:53:43 +0200
Subject: [PATCH 299/501] Update eessi-2023.06-eb-4.9.0-2023a.yml

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 6cb243556a..1e1e7fee14 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -76,4 +76,4 @@ easyconfigs:
       # see https://github.com/easybuilders/easybuild-easyblocks/pull/3257
       options:
         from-pr: 20138
-        include-easyblocks-from-pr: 3257
+        include-easyblocks-from-pr: 3306

From 04e04a308829b49f4b925d4420363739c728a58b Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Mon, 15 Apr 2024 11:33:08 +0200
Subject: [PATCH 300/501] Added ncdu

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml  | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
new file mode 100644
index 0000000000..3b51db3b11
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -0,0 +1,2 @@
+easyconfigs:
+  - ncdu-1.18-GCC-12.3.0.eb

From 8f81944b29dfb48edaf30b9466ce9edde4aa748f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 16 Apr 2024 09:04:47 +0200
Subject: [PATCH 301/501] make sure that software directory that corresponds to
 $EESSI_SOFTWARE_SUBDIR_OVERRIDE exists

---
 EESSI-install-software.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 567fed8e79..91effe4aba 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -143,6 +143,8 @@ if [ -z $EESSI_SOFTWARE_SUBDIR_OVERRIDE ]; then
   echo ">> Determined \$EESSI_SOFTWARE_SUBDIR_OVERRIDE via 'eessi_software_subdir.py $DETECTION_PARAMETERS' script"
 else
   echo ">> Picking up pre-defined \$EESSI_SOFTWARE_SUBDIR_OVERRIDE: ${EESSI_SOFTWARE_SUBDIR_OVERRIDE}"
+  # make sure directory exists (since it's expected by init/eessi_environment_variables when using archdetect)
+  mkdir -p ${EESSI_PREFIX}/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
 fi
 
 # Set all the EESSI environment variables (respecting $EESSI_SOFTWARE_SUBDIR_OVERRIDE)

From 8331e4485a5734730b0929be69c3cd3c6beaa4b6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 16 Apr 2024 09:30:02 +0200
Subject: [PATCH 302/501] remove build_container.sh, as we now use
 eessi_container.sh

---
 build_container.sh | 69 ----------------------------------------------
 1 file changed, 69 deletions(-)
 delete mode 100755 build_container.sh

diff --git a/build_container.sh b/build_container.sh
deleted file mode 100755
index 23a9e665c9..0000000000
--- a/build_container.sh
+++ /dev/null
@@ -1,69 +0,0 @@
-#!/bin/bash
-
-base_dir=$(dirname $(realpath $0))
-
-BUILD_CONTAINER="docker://ghcr.io/eessi/build-node:debian11"
-
-if [ $# -lt 2 ]; then
-    echo "Usage: $0 <shell|run> <path for temporary directories>" >&2
-    exit 1
-fi
-SHELL_OR_RUN=$1
-EESSI_TMPDIR=$2
-shift 2
-
-if [ "$SHELL_OR_RUN" == "run" ] && [ $# -eq 0 ]; then
-    echo "ERROR: No command specified to run?!" >&2
-    exit 1
-fi
-
-# make sure specified temporary directory exists
-mkdir -p $EESSI_TMPDIR
-
-echo "Using $EESSI_TMPDIR as parent for temporary directories..."
-
-# create temporary directories
-mkdir -p $EESSI_TMPDIR/{home,overlay-upper,overlay-work}
-mkdir -p $EESSI_TMPDIR/{var-lib-cvmfs,var-run-cvmfs}
-# configure Singularity
-export SINGULARITY_CACHEDIR=$EESSI_TMPDIR/singularity_cache
-
-# take into account that $SINGULARITY_BIND may be defined already, to bind additional paths into the build container
-BIND_PATHS="$EESSI_TMPDIR/var-run-cvmfs:/var/run/cvmfs,$EESSI_TMPDIR/var-lib-cvmfs:/var/lib/cvmfs,$EESSI_TMPDIR"
-if [ -z $SINGULARITY_BIND ]; then
-    export SINGULARITY_BIND="$BIND_PATHS"
-else
-    export SINGULARITY_BIND="$SINGULARITY_BIND,$BIND_PATHS"
-fi
-
-# allow that SINGULARITY_HOME is defined before script is run
-if [ -z $SINGULARITY_HOME ]; then
-    export SINGULARITY_HOME="$EESSI_TMPDIR/home:/home/$USER"
-fi
-
-source ${base_dir}/init/eessi_defaults
-# strip "/cvmfs/" from default setting
-repo_name=${EESSI_CVMFS_REPO/\/cvmfs\//}
-
-# set environment variables for fuse mounts in Singularity container
-export EESSI_PILOT_READONLY="container:cvmfs2 ${repo_name} /cvmfs_ro/${repo_name}"
-export EESSI_PILOT_WRITABLE_OVERLAY="container:fuse-overlayfs -o lowerdir=/cvmfs_ro/${repo_name} -o upperdir=$EESSI_TMPDIR/overlay-upper -o workdir=$EESSI_TMPDIR/overlay-work ${EESSI_CVMFS_REPO}"
-
-# pass $EESSI_SOFTWARE_SUBDIR_OVERRIDE into build container (if set)
-if [ ! -z ${EESSI_SOFTWARE_SUBDIR_OVERRIDE} ]; then
-    export SINGULARITYENV_EESSI_SOFTWARE_SUBDIR_OVERRIDE=${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
-    # also specify via $APPTAINERENV_* (future proof, cfr. https://apptainer.org/docs/user/latest/singularity_compatibility.html#singularity-environment-variable-compatibility)
-    export APPTAINERENV_EESSI_SOFTWARE_SUBDIR_OVERRIDE=${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
-fi
-
-if [ "$SHELL_OR_RUN" == "shell" ]; then
-    # start shell in Singularity container, with EESSI repository mounted with writable overlay
-    echo "Starting Singularity build container..."
-    singularity shell --fusemount "$EESSI_PILOT_READONLY" --fusemount "$EESSI_PILOT_WRITABLE_OVERLAY" $BUILD_CONTAINER
-elif [ "$SHELL_OR_RUN" == "run" ]; then
-    echo "Running '$@' in Singularity build container..."
-    singularity exec --fusemount "$EESSI_PILOT_READONLY" --fusemount "$EESSI_PILOT_WRITABLE_OVERLAY" $BUILD_CONTAINER "$@"
-else
-    echo "ERROR: Unknown action specified: $SHELL_OR_RUN (should be either 'shell' or 'run')" >&2
-    exit 1
-fi

From a7305456f10ca0289d1cbea8b212aa7cb4fb114a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 16 Apr 2024 09:32:23 +0200
Subject: [PATCH 303/501] replace build_container.sh by eessi_container.sh

---
 .github/workflows/tests_scripts.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/tests_scripts.yml b/.github/workflows/tests_scripts.yml
index 4944d9beaa..76d19d29fe 100644
--- a/.github/workflows/tests_scripts.yml
+++ b/.github/workflows/tests_scripts.yml
@@ -3,9 +3,9 @@ name: Tests for scripts
 on:
   push:
     paths:
-      - build_container.sh
       - create_directory_tarballs.sh
       - create_lmodsitepackage.py
+      - eessi_container.sh
       - EESSI-install-software.sh
       - install_software_layer.sh
       - load_easybuild_module.sh
@@ -15,9 +15,9 @@ on:
 
   pull_request:
     paths:
-      - build_container.sh
       - create_directory_tarballs.sh
       - create_lmodsitepackage.py
+      - eessi_container.sh
       - EESSI-install-software.sh
       - install_software_layer.sh
       - load_easybuild_module.sh

From 8593e595ee382a26c8f9621dd39ccb338e937259 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Thu, 18 Apr 2024 23:51:24 +0200
Subject: [PATCH 304/501] No hyphen any more so no need for lua escaping

---
 EESSI-extend-2023.06-easybuild.eb | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index 8993c63cc3..ce55f619fb 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -69,8 +69,7 @@ if (os.getenv("EESSI_CVMFS_INSTALL") ~= nil) then
 elseif (os.getenv("EESSI_SITE_INSTALL") ~= nil) then 
   easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), 'versions', 'host_injections')
 else
-  -- Would have liked to use os.getenv("EESSI_CVMFS_REPO") here but the hypen needs to be escaped
-  easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), "/cvmfs/pilot.eessi%-hpc.org", pathJoin(os.getenv("HOME"), "eessi"))
+  easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), os.getenv("EESSI_CVMFS_REPO"), pathJoin(os.getenv("HOME"), "eessi"))
 end
 if (mode() == "load") then
   LmodMessage("-- To create installations for EESSI, you _must_ have write permissions to " .. easybuild_installpath)

From 8e976c6a2c8fbef7751dbc3f0c434ac431db3c4d Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 19 Apr 2024 00:58:16 +0200
Subject: [PATCH 305/501] Make the hooks part of the init dir

---
 EESSI-extend-2023.06-easybuild.eb | 17 +++--------------
 EESSI-install-software.sh         |  8 ++++++++
 2 files changed, 11 insertions(+), 14 deletions(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index ce55f619fb..6d71693db8 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -1,4 +1,4 @@
-easyblock = 'Binary'
+easyblock = 'Bundle'
 
 name = 'EESSI-extend'
 version = '2023.06'
@@ -22,13 +22,6 @@ description = """
 
 toolchain = SYSTEM
 
-source_urls = None
-sources = ['eb_hooks.py']
-checksums = ['8ae609f99b6953beae89aa1945913686c86c156509dbc55e2b6b8017b13fcf66']
-
-# Don't extend the PATH
-prepend_to_path = None
-
 # All the dependencies we filter in EESSI
 local_deps_to_filter = "Autoconf,Automake,Autotools,binutils,bzip2,DBus,flex,gettext,gperf,help2man,intltool,libreadline,libtool,M4,makeinfo,ncurses,util-linux,XZ,zlib"
 local_arch_specific_deps_to_filter = {'aarch64': ',yasm', 'x86_64': ''}
@@ -45,12 +38,12 @@ modextravars = {
     'EASYBUILD_READ_ONLY_INSTALLDIR': '1',
     'EASYBUILD_MODULE_EXTENSIONS': '1',
     'EASYBUILD_EXPERIMENTAL': '1',
-    'EASYBUILD_HOOKS': '%(installdir)s/eb_hooks.py',
 }
 
 # Need a few other variables, but they are more dynamic
 # EASYBUILD_SYSROOT=${EPREFIX}
 # EASYBUILD_PREFIX=${WORKDIR}/easybuild
+# EASYBUILD_HOOKS=${EESSI_PREFIX}/init/easybuild/eb_hooks.py
 # EASYBUILD_INSTALLPATH=${EESSI_PREFIX}/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR}
 # EASYBUILD_SOURCEPATH=${WORKDIR}/easybuild/sources:${EESSI_SOURCEPATH}
 modluafooter = """
@@ -82,14 +75,10 @@ end
 setenv ("EASYBUILD_SYSROOT", sysroot)
 setenv ("EASYBUILD_PREFIX", pathJoin(working_dir, "easybuild"))
 setenv ("EASYBUILD_INSTALLPATH", easybuild_installpath)
+setenv ("EASYBUILD_HOOKS", pathJoin(os.getenv("EESSI_PREFIX"), "init", "easybuild", "hooks.py"))
 if not ( isloaded("EasyBuild") ) then
     load("EasyBuild")
 end
 """
 
-sanity_check_paths = {
-    'files': ['eb_hooks.py'],
-    'dirs': ['']
-}
-
 moduleclass = 'devel'
diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 91effe4aba..9766c20aa1 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -264,6 +264,14 @@ fi
 
 ### add packages here
 
+# use PR patch file to determine if the EasyBuild hooks have changed
+changed_eb_hooks=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^eb_hooks.py$') 
+if [ -n "${changed_eb_hooks}" ]; then
+    # If the hooks have been changed we need to copy them over to the init directory
+    mkdir -p ${EESSI_PREFIX}/init/easybuild
+    cp eb_hooks.py ${EESSI_PREFIX}/init/easybuild
+fi
+
 echo ">> Creating/updating Lmod RC file..."
 export LMOD_CONFIG_DIR="${EASYBUILD_INSTALLPATH}/.lmod"
 lmod_rc_file="$LMOD_CONFIG_DIR/lmodrc.lua"

From dbe6d6bde6f7e6e498fe0e337836c4114d4bb0c3 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 19 Apr 2024 01:00:43 +0200
Subject: [PATCH 306/501] Actually install the EESSI extension module

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index 3b51db3b11..b7d4370b84 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -1,2 +1,3 @@
 easyconfigs:
   - ncdu-1.18-GCC-12.3.0.eb
+  - EESSI-extend-2023.06-easybuild.eb 

From 5ca2c4a25d702372f0993b57025a7f01459b21d9 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 19 Apr 2024 09:52:39 +0200
Subject: [PATCH 307/501] Copy over hooks along with initi files

---
 EESSI-install-software.sh | 8 --------
 install_scripts.sh        | 6 ++++++
 2 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 9766c20aa1..91effe4aba 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -264,14 +264,6 @@ fi
 
 ### add packages here
 
-# use PR patch file to determine if the EasyBuild hooks have changed
-changed_eb_hooks=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^eb_hooks.py$') 
-if [ -n "${changed_eb_hooks}" ]; then
-    # If the hooks have been changed we need to copy them over to the init directory
-    mkdir -p ${EESSI_PREFIX}/init/easybuild
-    cp eb_hooks.py ${EESSI_PREFIX}/init/easybuild
-fi
-
 echo ">> Creating/updating Lmod RC file..."
 export LMOD_CONFIG_DIR="${EASYBUILD_INSTALLPATH}/.lmod"
 lmod_rc_file="$LMOD_CONFIG_DIR/lmodrc.lua"
diff --git a/install_scripts.sh b/install_scripts.sh
index 508735975c..e6aecf4513 100755
--- a/install_scripts.sh
+++ b/install_scripts.sh
@@ -113,3 +113,9 @@ nvidia_files=(
     install_cuda_host_injections.sh link_nvidia_host_libraries.sh
 )
 copy_files_by_list ${TOPDIR}/scripts/gpu_support/nvidia ${INSTALL_PREFIX}/scripts/gpu_support/nvidia "${nvidia_files[@]}"
+
+# Copy over EasyBuild hooks file used for installations
+hook_files=(
+    eb_hooks.py
+)
+copy_files_by_list ${TOPDIR} ${INSTALL_PREFIX}/easybuild "${hook_files[@]}"

From 148534a3922272b7f6f4f7a3e1b9d210b69ca933 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Fri, 19 Apr 2024 09:58:10 +0200
Subject: [PATCH 308/501] Update install_scripts.sh

---
 install_scripts.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/install_scripts.sh b/install_scripts.sh
index e6aecf4513..17f0b81008 100755
--- a/install_scripts.sh
+++ b/install_scripts.sh
@@ -118,4 +118,4 @@ copy_files_by_list ${TOPDIR}/scripts/gpu_support/nvidia ${INSTALL_PREFIX}/script
 hook_files=(
     eb_hooks.py
 )
-copy_files_by_list ${TOPDIR} ${INSTALL_PREFIX}/easybuild "${hook_files[@]}"
+copy_files_by_list ${TOPDIR} ${INSTALL_PREFIX}/init/easybuild "${hook_files[@]}"

From dee801bbf1dc31c61a51a6e4b6dde702bf6337f8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Apr 2024 10:25:51 +0200
Subject: [PATCH 309/501] move bioconductor to 4.9.1 easystack

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml   | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
index 8a3e82d760..3962f63bda 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
@@ -11,4 +11,3 @@ easyconfigs:
   - R-4.2.2-foss-2022b.eb:
       options:
         from-pr: 20238
-  - R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb

From cbad690f01b417a9a185685d20f7e160808242ad Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Apr 2024 10:26:05 +0200
Subject: [PATCH 310/501] add bioconductor

---
 .../2023.06/eessi-2023.06-eb-4.9.1-2022b.yml                 | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
new file mode 100644
index 0000000000..f80b99f187
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
@@ -0,0 +1,5 @@
+easyconfigs:
+  - R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb:
+      options:
+        from-pr: 20379
+

From b6a222639341313caca5bebb621590f8d0862373 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Apr 2024 10:30:08 +0200
Subject: [PATCH 311/501] move biocondutor to 4.9.1 stack, use pr 20379

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml | 3 ---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml | 3 +++
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index bfc408e045..44952e2765 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -71,6 +71,3 @@ easyconfigs:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20238
         from-pr: 20238
-  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
-      options:
-        from-pr: 20316
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index 3b51db3b11..57cfc00297 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -1,2 +1,5 @@
 easyconfigs:
   - ncdu-1.18-GCC-12.3.0.eb
+  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
+      options:
+        from-pr: 20379

From 786e1e8189d75682c37150d2d7d58e465ec7e9ca Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Apr 2024 10:31:08 +0200
Subject: [PATCH 312/501] remove blank line

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml   | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
index f80b99f187..e547e45f2b 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
@@ -2,4 +2,3 @@ easyconfigs:
   - R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb:
       options:
         from-pr: 20379
-

From d6336e181efb320a74b895e0baf73373e49875f9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Apr 2024 11:50:15 +0200
Subject: [PATCH 313/501] move bioconductor back to 4.9.0 file

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml | 3 +++
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml | 3 ---
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 44952e2765..23d64036f1 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -71,3 +71,6 @@ easyconfigs:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20238
         from-pr: 20238
+  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
+      options:
+        from-pr: 20379
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index 57cfc00297..3b51db3b11 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -1,5 +1,2 @@
 easyconfigs:
   - ncdu-1.18-GCC-12.3.0.eb
-  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
-      options:
-        from-pr: 20379

From 339f358e46dd338649939c31042a0faf15f9e532 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Apr 2024 13:59:23 +0200
Subject: [PATCH 314/501] add rebuild easystack for setuptools_scm fix

---
 ...move-setuptools_scm-from-hatchling-to-Python.yml | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
new file mode 100644
index 0000000000..56ea7a46a1
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
@@ -0,0 +1,13 @@
+# 2024-04-19
+# Move setuptools_scm extension from hatchling to Python by rebuilding
+# all affected modules with EasyBuild 4.9.1.
+# This solves an issue with pyarrow, which is part of the Arrow installation.
+# https://github.com/easybuilders/easybuild-easyconfigs/pull/19777
+# https://github.com/easybuilders/easybuild-easyconfigs/issues/19849
+easyconfigs:
+  - hatchling-1.18.0-GCCcore-12.3.0.eb
+  - hatchling-1.18.0-GCCcore-13.2.0.eb
+  - Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb
+  - Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb
+  - Python-3.11.3-GCCcore-12.3.0.eb
+  - Python-3.11.5-GCCcore-13.2.0.eb

From 4ad271e4891e9c4e1c533e1a04505f16e505bf0a Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Fri, 19 Apr 2024 19:30:27 +0200
Subject: [PATCH 315/501] Update EESSI-extend-2023.06-easybuild.eb

---
 EESSI-extend-2023.06-easybuild.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index 6d71693db8..7acd0f0d36 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -75,7 +75,7 @@ end
 setenv ("EASYBUILD_SYSROOT", sysroot)
 setenv ("EASYBUILD_PREFIX", pathJoin(working_dir, "easybuild"))
 setenv ("EASYBUILD_INSTALLPATH", easybuild_installpath)
-setenv ("EASYBUILD_HOOKS", pathJoin(os.getenv("EESSI_PREFIX"), "init", "easybuild", "hooks.py"))
+setenv ("EASYBUILD_HOOKS", pathJoin(os.getenv("EESSI_PREFIX"), "init", "easybuild", "eb_hooks.py"))
 if not ( isloaded("EasyBuild") ) then
     load("EasyBuild")
 end

From db81fd36358c0430bfc6d3ae2784b7e0958d097a Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sat, 20 Apr 2024 07:05:40 +0200
Subject: [PATCH 316/501] zen4-only {2023.06}[system] EasyBuild v4.9.1

---
 .../2023.06/zen4/eessi-2023.06-eb-4.9.1-001-system.yml        | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-001-system.yml

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-001-system.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-001-system.yml
new file mode 100644
index 0000000000..c5a08b5209
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-001-system.yml
@@ -0,0 +1,4 @@
+easyconfigs:
+  - EasyBuild-4.9.1.eb:
+      options:
+        from-pr: 20299

From 8cb9547b0c2b1b3bd1736b57d754fa9cad01516b Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sat, 20 Apr 2024 14:10:55 +0200
Subject: [PATCH 317/501] make sure lmod cfg files exists early in build
 environment

---
 EESSI-install-software.sh | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 91effe4aba..7f67b883f2 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -147,6 +147,24 @@ else
   mkdir -p ${EESSI_PREFIX}/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
 fi
 
+# if we run the script for the first time, e.g., to start building for a new
+#   stack, we need to ensure certain files are present in
+#   ${EESSI_PREFIX}/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
+# - .lmod/lmodrc.lua
+# - .lmod/SitePackage.lua
+_eessi_software_path=${EESSI_PREFIX}/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
+_lmod_cfg_dir=${_eessi_software_path}/.lmod
+_lmod_rc_file=${_lmod_cfg_dir}/lmodrc.lua
+if [ ! -f ${_lmod_rc_file} ]; then
+    command -V python3
+    python3 ${TOPDIR}/create_lmodrc.py ${_eessi_software_path}
+fi
+_lmod_sitepackage_file=${_lmod_cfg_dir}/SitePackage.lua
+if [ ! -f ${_lmod_sitepackage_file} ]; then
+    command -V python3
+    python3 ${TOPDIR}/create_lmodrc.py ${_eessi_software_path}
+fi
+
 # Set all the EESSI environment variables (respecting $EESSI_SOFTWARE_SUBDIR_OVERRIDE)
 # $EESSI_SILENT - don't print any messages
 # $EESSI_BASIC_ENV - give a basic set of environment variables

From bde1b728c6c39cfffcffbf0480323d5b7348346a Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Sat, 20 Apr 2024 14:16:44 +0200
Subject: [PATCH 318/501] Allow for default site installations, and
 configurable project and/or user installations

---
 EESSI-extend-2023.06-easybuild.eb | 93 ++++++++++++++++++++++++++++---
 init/Magic_Castle/bash            |  2 +-
 init/bash                         |  2 -
 init/eessi_environment_variables  |  2 -
 4 files changed, 87 insertions(+), 12 deletions(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index 7acd0f0d36..3f9b62a494 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -14,10 +14,26 @@ description = """
  personal workstations and cloud infrastructure.
 
  This module allows you to extend EESSI using the same configuration for
- EasyBuild as EESSI itself uses. The default installation is the users
- home directory, but this can be overridden for a site installation (by setting
- EESSI_SITE_INSTALL) or for a direct installation under CVMFS (by setting
- EESSI_CVMFS_INSTALL). 
+ EasyBuild as EESSI itself uses. A number of environment variables control the
+ behaviour of the module:
+ - EESSI_USER_INSTALL can be set to a location to install modules for use by
+   the user only. The location must already exist on the filesystem.
+ - EESSI_PROJECT_INSTALL can be set to a location to install modules for use by
+   a project. The location must already exist on the filesystem and you should
+   ensure that the location has the correct Linux group and the SGID permission
+   is set on that directory (`chmod g+s $EESSI_PROJECT_INSTALL`) so that all
+   members of the group have permission to read and write installations.
+ - EESSI_SITE_INSTALL is either defined or not and cannot be used with another
+   environment variable. A site installation is done in a defined location and
+   any installations there are (by default) world readable.
+ - EESSI_CVMFS_INSTALL is either defined or not and cannot be used with another
+   environment variable. A CVMFS installation targets a defined location which
+   will be ingested into CVMFS and is only useful for CVMFS administrators.
+ - If none of the environment variables above are defined, an EESSI_USER_INSTALL
+   is assumed with a value of $HOME/EESSI
+ If both EESSI_USER_INSTALL and EESSI_PROJECT_INSTALL are defined, both sets of
+ installations are exposed, but new installations are created as user
+ installations.
 """
 
 toolchain = SYSTEM
@@ -27,6 +43,7 @@ local_deps_to_filter = "Autoconf,Automake,Autotools,binutils,bzip2,DBus,flex,get
 local_arch_specific_deps_to_filter = {'aarch64': ',yasm', 'x86_64': ''}
 local_deps_to_filter += local_arch_specific_deps_to_filter[ARCH]
 
+# Set the universal EasyBuild variables
 modextravars = {
     'EASYBUILD_FILTER_DEPS': local_deps_to_filter,
     'EASYBUILD_IGNORE_OSDEPS': '1',
@@ -46,6 +63,12 @@ modextravars = {
 # EASYBUILD_HOOKS=${EESSI_PREFIX}/init/easybuild/eb_hooks.py
 # EASYBUILD_INSTALLPATH=${EESSI_PREFIX}/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR}
 # EASYBUILD_SOURCEPATH=${WORKDIR}/easybuild/sources:${EESSI_SOURCEPATH}
+#
+# And also some optional ones based on the kind of installation
+# EASYBUILD_SET_GID_BIT
+# EASYBUILD_GROUP_WRITABLE_INSTALLDIR
+# EASYBUILD_UMASK
+# EASYBUILD_STICKY_BIT
 modluafooter = """
 if (mode() == "load") then
   -- Use a working directory for temporary build files
@@ -58,11 +81,48 @@ working_dir = os.getenv("WORKING_DIR") or pathJoin("/tmp", os.getenv("USER"))
 sysroot = os.getenv("EESSI_EPREFIX")
 -- Use an installation prefix that we _should_ have write access to
 if (os.getenv("EESSI_CVMFS_INSTALL") ~= nil) then
+  -- Make sure no other EESSI install environment variables are set
+  if (os.getenv("EESSI_SITE_INSTALL") ~= nil) or (os.getenv("EESSI_PROJECT_INSTALL") ~= nil) or (os.getenv("EESSI_USER_INSTALL") then
+    LmodError("You cannot use EESSI_CVMFS_INSTALL in combination with any other EESSI_*_INSTALL environment variables")
+  end
+  eessi_cvmfs_install = true
   easybuild_installpath = os.getenv("EESSI_SOFTWARE_PATH")
-elseif (os.getenv("EESSI_SITE_INSTALL") ~= nil) then 
+elseif (os.getenv("EESSI_SITE_INSTALL") ~= nil) then
+  -- Make sure no other EESSI install environment variables are set
+  if (os.getenv("EESSI_PROJECT_INSTALL") ~= nil) or (os.getenv("EESSI_USER_INSTALL") then
+    LmodError("You cannot use EESSI_SITE_INSTALL in combination with any other EESSI_*_INSTALL environment variables")
+  end
   easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), 'versions', 'host_injections')
 else
-  easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), os.getenv("EESSI_CVMFS_REPO"), pathJoin(os.getenv("HOME"), "eessi"))
+  -- Deal with user and project installs
+  project_install = os.getenv("EESSI_PROJECT_INSTALL")
+  project_modulepath = nil
+  if (project_install ~= nil) then
+    -- Check the folder exists
+    if not isDir(project_install) then
+      LmodError("The location of EESSI_PROJECT_INSTALL (" .. project_install .. ") does not exist or is not a folder")
+    end
+    LmodMessage("Configuring for use of EESSI_PROJECT_INSTALL under " .. project_install)
+    easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), os.getenv("EESSI_CVMFS_REPO"), project_install)
+    project_modulepath = pathJoin(easybuild_installpath, 'modules', 'all')
+  end
+  user_install = os.getenv("EESSI_USER_INSTALL")
+  user_modulepath = nil
+  if (project_install == nil) then
+    if (user_install ~= nil) then
+      user_install = pathJoin(os.getenv("HOME"), "eessi")
+    else
+      -- Check the folder exists
+      if not isDir(user_install) then
+        LmodError("The location of EESSI_USER_INSTALL (" .. user_install .. ") does not exist or is not a folder")
+      end
+    end
+  end
+  if (user_install ~= nil) then
+    LmodMessage("Configuring for use of EESSI_USER_INSTALL under " .. user_install)
+    easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), os.getenv("EESSI_CVMFS_REPO"), user_install)
+    user_modulepath = pathJoin(easybuild_installpath, 'modules', 'all')
+  end
 end
 if (mode() == "load") then
   LmodMessage("-- To create installations for EESSI, you _must_ have write permissions to " .. easybuild_installpath)
@@ -71,11 +131,30 @@ if (mode() == "load") then
     LmodMessage("-- You may wish to configure a sources directory for EasyBuild (for example, via setting the environment variable EASYBUILD_SOURCEPATH) to allow you to reuse existing sources for packages.")
   end
 end
--- Set the relevant environment variables for EasyBuild
+-- Set the relevant universal environment variables for EasyBuild
 setenv ("EASYBUILD_SYSROOT", sysroot)
 setenv ("EASYBUILD_PREFIX", pathJoin(working_dir, "easybuild"))
 setenv ("EASYBUILD_INSTALLPATH", easybuild_installpath)
 setenv ("EASYBUILD_HOOKS", pathJoin(os.getenv("EESSI_PREFIX"), "init", "easybuild", "eb_hooks.py"))
+
+-- Set all related environment variables if we have project or user installations (including extending MODULEPATH)
+if (user_modulepath ~= nil) then
+  setenv ("EASYBUILD_SET_GID_BIT", "1")
+  setenv ("EASYBUILD_GROUP_WRITABLE_INSTALLDIR", "1")
+  setenv ("EASYBUILD_UMASK", "002")
+  setenv ("EASYBUILD_STICKY_BIT", "0")
+  -- configure MODULEPATH
+  if (project_modulepath ~= nil) then
+    prepend_path("MODULEPATH", project_modulepath)
+  end
+  prepend_path("MODULEPATH", user_modulepath)
+elseif (project_modulepath ~= nil) then
+  setenv ("EASYBUILD_UMASK", "022")
+  setenv ("EASYBUILD_STICKY_BIT", "1")
+  -- configure MODULEPATH
+  prepend_path("MODULEPATH", project_modulepath)
+end
+-- Make aure EasyBuild itself is loaded
 if not ( isloaded("EasyBuild") ) then
     load("EasyBuild")
 end
diff --git a/init/Magic_Castle/bash b/init/Magic_Castle/bash
index e6c7ff294c..bf625e7e7b 100644
--- a/init/Magic_Castle/bash
+++ b/init/Magic_Castle/bash
@@ -10,7 +10,7 @@ source $(dirname "$BASH_SOURCE")/../eessi_environment_variables
 
 # Provide a clean MODULEPATH
 export MODULEPATH_ROOT=$EESSI_MODULEPATH
-export MODULEPATH=$EESSI_USER_MODULEPATH:$EESSI_SITE_MODULEPATH:$EESSI_MODULEPATH
+export MODULEPATH=$EESSI_SITE_MODULEPATH:$EESSI_MODULEPATH
 
 # Extensions are too many, let's not print them by default (requires Lmod 8.4.12)
 export LMOD_AVAIL_EXTENSIONS=no
diff --git a/init/bash b/init/bash
index 3c6aad47f1..565c37cc65 100644
--- a/init/bash
+++ b/init/bash
@@ -28,8 +28,6 @@ if [ $? -eq 0 ]; then
     module use $EESSI_MODULEPATH
     echo "Prepending site path $EESSI_SITE_MODULEPATH to \$MODULEPATH..." >> $output
     module use $EESSI_SITE_MODULEPATH
-    echo "Prepending user path $EESSI_SITE_MODULEPATH to \$MODULEPATH..." >> $output
-    module use $EESSI_USER_MODULEPATH
 
     #show_msg ""
     #show_msg "*** Known problems in the ${EESSI_VERSION} software stack ***"
diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index 5ae2c5c3c6..dbf01cc9e4 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -91,8 +91,6 @@ if [ -d $EESSI_PREFIX ]; then
             show_msg "Using ${EESSI_MODULEPATH} as the directory to be added to MODULEPATH."
             export EESSI_SITE_MODULEPATH=${EESSI_MODULEPATH/versions/host_injections}
             show_msg "Using ${EESSI_SITE_MODULEPATH} as the site extension directory to be added to MODULEPATH."
-            export EESSI_USER_MODULEPATH=${EESSI_MODULEPATH/${EESSI_CVMFS_REPO}/${HOME}\/eessi}
-            show_msg "Using ${EESSI_USER_MODULEPATH} as the user extension directory to be added to MODULEPATH."
           else
             error "EESSI module path at $EESSI_MODULEPATH not found!"
             false

From da9f206f216c70b8559bdd002235a754125aba2d Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sat, 20 Apr 2024 14:18:58 +0200
Subject: [PATCH 319/501] use create_lmodsitepackage.py

---
 EESSI-install-software.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 7f67b883f2..13e94fb72d 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -162,7 +162,7 @@ fi
 _lmod_sitepackage_file=${_lmod_cfg_dir}/SitePackage.lua
 if [ ! -f ${_lmod_sitepackage_file} ]; then
     command -V python3
-    python3 ${TOPDIR}/create_lmodrc.py ${_eessi_software_path}
+    python3 ${TOPDIR}/create_lmodsitepackage.py ${_eessi_software_path}
 fi
 
 # Set all the EESSI environment variables (respecting $EESSI_SOFTWARE_SUBDIR_OVERRIDE)

From 82f58b24ae4cb2ada19c79ad6c8e7cef2727ed56 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Sat, 20 Apr 2024 14:30:57 +0200
Subject: [PATCH 320/501] Fix conditions

---
 EESSI-extend-2023.06-easybuild.eb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index 3f9b62a494..0f0b4bc9f9 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -82,14 +82,14 @@ sysroot = os.getenv("EESSI_EPREFIX")
 -- Use an installation prefix that we _should_ have write access to
 if (os.getenv("EESSI_CVMFS_INSTALL") ~= nil) then
   -- Make sure no other EESSI install environment variables are set
-  if (os.getenv("EESSI_SITE_INSTALL") ~= nil) or (os.getenv("EESSI_PROJECT_INSTALL") ~= nil) or (os.getenv("EESSI_USER_INSTALL") then
+  if ((os.getenv("EESSI_SITE_INSTALL") ~= nil) or (os.getenv("EESSI_PROJECT_INSTALL") ~= nil) or (os.getenv("EESSI_USER_INSTALL") ~= nil)) then
     LmodError("You cannot use EESSI_CVMFS_INSTALL in combination with any other EESSI_*_INSTALL environment variables")
   end
   eessi_cvmfs_install = true
   easybuild_installpath = os.getenv("EESSI_SOFTWARE_PATH")
 elseif (os.getenv("EESSI_SITE_INSTALL") ~= nil) then
   -- Make sure no other EESSI install environment variables are set
-  if (os.getenv("EESSI_PROJECT_INSTALL") ~= nil) or (os.getenv("EESSI_USER_INSTALL") then
+  if ((os.getenv("EESSI_PROJECT_INSTALL") ~= nil) or (os.getenv("EESSI_USER_INSTALL") ~= nil)) then
     LmodError("You cannot use EESSI_SITE_INSTALL in combination with any other EESSI_*_INSTALL environment variables")
   end
   easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), 'versions', 'host_injections')

From 4ebfc2057d08056a978743f0e63ce630e5912fef Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Sat, 20 Apr 2024 14:35:32 +0200
Subject: [PATCH 321/501] Fix condition

---
 EESSI-extend-2023.06-easybuild.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index 0f0b4bc9f9..900d584720 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -109,7 +109,7 @@ else
   user_install = os.getenv("EESSI_USER_INSTALL")
   user_modulepath = nil
   if (project_install == nil) then
-    if (user_install ~= nil) then
+    if (user_install == nil) then
       user_install = pathJoin(os.getenv("HOME"), "eessi")
     else
       -- Check the folder exists

From 5c5899b3230c64cb40f57e91fa3521b74d83bdd2 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Sat, 20 Apr 2024 14:39:06 +0200
Subject: [PATCH 322/501] Messages only on module load

---
 EESSI-extend-2023.06-easybuild.eb | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index 900d584720..303abe0410 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -102,7 +102,9 @@ else
     if not isDir(project_install) then
       LmodError("The location of EESSI_PROJECT_INSTALL (" .. project_install .. ") does not exist or is not a folder")
     end
-    LmodMessage("Configuring for use of EESSI_PROJECT_INSTALL under " .. project_install)
+    if (mode() == "load") then
+      LmodMessage("Configuring for use of EESSI_PROJECT_INSTALL under " .. project_install)
+    end
     easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), os.getenv("EESSI_CVMFS_REPO"), project_install)
     project_modulepath = pathJoin(easybuild_installpath, 'modules', 'all')
   end
@@ -119,7 +121,9 @@ else
     end
   end
   if (user_install ~= nil) then
-    LmodMessage("Configuring for use of EESSI_USER_INSTALL under " .. user_install)
+    if (mode() == "load") then
+      LmodMessage("Configuring for use of EESSI_USER_INSTALL under " .. user_install)
+    end
     easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), os.getenv("EESSI_CVMFS_REPO"), user_install)
     user_modulepath = pathJoin(easybuild_installpath, 'modules', 'all')
   end

From c4cbcd8b9b6212c830e371aa3013eee8977ff776 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sat, 20 Apr 2024 14:41:02 +0200
Subject: [PATCH 323/501] skip CUDA install if no EasyBuild module is found

---
 EESSI-install-software.sh | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 13e94fb72d..2d401e40ce 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -221,10 +221,21 @@ ${TOPDIR}/install_scripts.sh --prefix ${EESSI_PREFIX}
 # Hardcode this for now, see if it works
 # TODO: We should make a nice yaml and loop over all CUDA versions in that yaml to figure out what to install
 # Allow skipping CUDA SDK install in e.g. CI environments
+# The install_cuda... script uses EasyBuild. So, we need to check if we have EB
+# or skip this step.
+module_avail_out=$TMPDIR/ml.out
+module avail 2>&1 | grep EasyBuild &> ${module_avail_out}
+if [[ $? -eq 0 ]]; then
+    echo_green ">> Found an EasyBuild module"
+else
+    echo_yellow ">> No EasyBuild module found: skipping step to install CUDA (see output in ${module_avail_out})"
+    export skip_cuda_install=True
+fi
+if
 if [ -z "${skip_cuda_install}" ] || [ ! "${skip_cuda_install}" ]; then
     ${EESSI_PREFIX}/scripts/gpu_support/nvidia/install_cuda_host_injections.sh -c 12.1.1 --accept-cuda-eula
 else
-    echo "Skipping installation of CUDA SDK in host_injections, since the --skip-cuda-install flag was passed"
+    echo "Skipping installation of CUDA SDK in host_injections, since the --skip-cuda-install flag was passed OR no EasyBuild module was found"
 fi
 
 # Install drivers in host_injections

From eeb5537e4b8889cbbf183ffd17e4743961357f3c Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sat, 20 Apr 2024 14:45:17 +0200
Subject: [PATCH 324/501] remove extra if

---
 EESSI-install-software.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 2d401e40ce..8a5789c2b2 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -231,7 +231,7 @@ else
     echo_yellow ">> No EasyBuild module found: skipping step to install CUDA (see output in ${module_avail_out})"
     export skip_cuda_install=True
 fi
-if
+
 if [ -z "${skip_cuda_install}" ] || [ ! "${skip_cuda_install}" ]; then
     ${EESSI_PREFIX}/scripts/gpu_support/nvidia/install_cuda_host_injections.sh -c 12.1.1 --accept-cuda-eula
 else

From 8122bbd6bd7f6c44f4db9c955dcbd0bc7d736ad4 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Sat, 20 Apr 2024 14:56:52 +0200
Subject: [PATCH 325/501] fix location of settings

---
 EESSI-extend-2023.06-easybuild.eb | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index 303abe0410..ddf56648b9 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -143,18 +143,18 @@ setenv ("EASYBUILD_HOOKS", pathJoin(os.getenv("EESSI_PREFIX"), "init", "easybuil
 
 -- Set all related environment variables if we have project or user installations (including extending MODULEPATH)
 if (user_modulepath ~= nil) then
-  setenv ("EASYBUILD_SET_GID_BIT", "1")
-  setenv ("EASYBUILD_GROUP_WRITABLE_INSTALLDIR", "1")
-  setenv ("EASYBUILD_UMASK", "002")
-  setenv ("EASYBUILD_STICKY_BIT", "0")
+  setenv ("EASYBUILD_UMASK", "022")
+  setenv ("EASYBUILD_STICKY_BIT", "1")
   -- configure MODULEPATH
   if (project_modulepath ~= nil) then
     prepend_path("MODULEPATH", project_modulepath)
   end
   prepend_path("MODULEPATH", user_modulepath)
 elseif (project_modulepath ~= nil) then
-  setenv ("EASYBUILD_UMASK", "022")
-  setenv ("EASYBUILD_STICKY_BIT", "1")
+  setenv ("EASYBUILD_SET_GID_BIT", "1")
+  setenv ("EASYBUILD_GROUP_WRITABLE_INSTALLDIR", "1")
+  setenv ("EASYBUILD_UMASK", "002")
+  setenv ("EASYBUILD_STICKY_BIT", "0")
   -- configure MODULEPATH
   prepend_path("MODULEPATH", project_modulepath)
 end

From 4d465e9996b61bfb2f2643710bf944ee88bdd355 Mon Sep 17 00:00:00 2001
From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com>
Date: Sun, 21 Apr 2024 17:47:40 +0200
Subject: [PATCH 326/501] Add SAMtools-1.18-GCC-12.3.0

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index 3b51db3b11..ec5fd3c638 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -1,2 +1,3 @@
 easyconfigs:
   - ncdu-1.18-GCC-12.3.0.eb
+  - SAMtools-1.18-GCC-12.3.0.eb

From 04c6f0ee56bde553968da02f7daba36cbb363d78 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Mon, 22 Apr 2024 09:30:11 +0200
Subject: [PATCH 327/501] Always check for dir existence when using
 EESSI_USER_INSTALL

---
 EESSI-extend-2023.06-easybuild.eb | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index ddf56648b9..c06087a940 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -110,15 +110,14 @@ else
   end
   user_install = os.getenv("EESSI_USER_INSTALL")
   user_modulepath = nil
-  if (project_install == nil) then
-    if (user_install == nil) then
-      user_install = pathJoin(os.getenv("HOME"), "eessi")
-    else
-      -- Check the folder exists
-      if not isDir(user_install) then
-        LmodError("The location of EESSI_USER_INSTALL (" .. user_install .. ") does not exist or is not a folder")
-      end
+  if (user_install ~= nil) then
+    -- Check the folder exists
+    if not isDir(user_install) then
+      LmodError("The location of EESSI_USER_INSTALL (" .. user_install .. ") does not exist or is not a folder")
     end
+  elseif (user_install == nil) and (project_install == nil) then
+    -- No need to check for existence when we use a HOME subdir
+    user_install = pathJoin(os.getenv("HOME"), "eessi")
   end
   if (user_install ~= nil) then
     if (mode() == "load") then

From 8cd5d844e872fe58efcdbb49e38689e656f3f9a1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 22 Apr 2024 16:39:45 +0200
Subject: [PATCH 328/501] attempt to fix the hatchling reinstallation issue

---
 EESSI-remove-software.sh | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index 446a156cb8..d8a6dae63e 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -114,6 +114,11 @@ if [ $EUID -eq 0 ]; then
                     echo_yellow "Removing ${app_dir} and ${app_module}..."
                     rm -rf ${app_dir}
                     rm -rf ${app_module}
+                    # if the parent dir of this application is now empty, remove it too to work around a weird issue with the overlay
+                    # see https://github.com/EESSI/software-layer/pull/546#issuecomment-2067018216
+                    if [ ! -n "$(dirname ${app_dir})" ]; then
+                        rmdir "$(dirname ${app_dir})"
+                    fi
                 done
             else
                 fatal_error "Easystack file ${easystack_file} not found!"

From 76ecccf629f6b4dda1b65e4ee1f3f2d9d9b9457c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 22 Apr 2024 17:13:37 +0200
Subject: [PATCH 329/501] use right if condition for checking if dir is empty

---
 EESSI-remove-software.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index d8a6dae63e..f3c4f9e618 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -116,8 +116,9 @@ if [ $EUID -eq 0 ]; then
                     rm -rf ${app_module}
                     # if the parent dir of this application is now empty, remove it too to work around a weird issue with the overlay
                     # see https://github.com/EESSI/software-layer/pull/546#issuecomment-2067018216
-                    if [ ! -n "$(dirname ${app_dir})" ]; then
-                        rmdir "$(dirname ${app_dir})"
+                    app_dir_parent=$(dirname "${app_dir}")
+                    if [ ! -n "$(ls -A ${app_dir_parent})" ]; then
+                        rmdir "${app_dir_parent}"
                     fi
                 done
             else

From 1642621d1b47b804f689280d7c797824d1662a2c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 26 Apr 2024 14:24:46 +0200
Subject: [PATCH 330/501] undo parent dir removal, workaround didn't work

---
 EESSI-remove-software.sh | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index f3c4f9e618..446a156cb8 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -114,12 +114,6 @@ if [ $EUID -eq 0 ]; then
                     echo_yellow "Removing ${app_dir} and ${app_module}..."
                     rm -rf ${app_dir}
                     rm -rf ${app_module}
-                    # if the parent dir of this application is now empty, remove it too to work around a weird issue with the overlay
-                    # see https://github.com/EESSI/software-layer/pull/546#issuecomment-2067018216
-                    app_dir_parent=$(dirname "${app_dir}")
-                    if [ ! -n "$(ls -A ${app_dir_parent})" ]; then
-                        rmdir "${app_dir_parent}"
-                    fi
                 done
             else
                 fatal_error "Easystack file ${easystack_file} not found!"

From a5bf9d3da294fad127aef0dc972af323a0488077 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 26 Apr 2024 14:26:25 +0200
Subject: [PATCH 331/501] only rebuild 2023a easyconfigs

---
 ...eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
index 56ea7a46a1..76dd37e870 100644
--- a/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
@@ -1,13 +1,10 @@
 # 2024-04-19
 # Move setuptools_scm extension from hatchling to Python by rebuilding
-# all affected modules with EasyBuild 4.9.1.
+# the affected modules in the 2023a toolchain with EasyBuild 4.9.1.
 # This solves an issue with pyarrow, which is part of the Arrow installation.
 # https://github.com/easybuilders/easybuild-easyconfigs/pull/19777
 # https://github.com/easybuilders/easybuild-easyconfigs/issues/19849
 easyconfigs:
   - hatchling-1.18.0-GCCcore-12.3.0.eb
-  - hatchling-1.18.0-GCCcore-13.2.0.eb
   - Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb
-  - Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb
   - Python-3.11.3-GCCcore-12.3.0.eb
-  - Python-3.11.5-GCCcore-13.2.0.eb

From c4af218d2c7dd604f10cea7454d1f672b00498ad Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 26 Apr 2024 15:04:02 +0200
Subject: [PATCH 332/501] only try 2023b versions

---
 ...4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
index 76dd37e870..f3484a3486 100644
--- a/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
@@ -1,10 +1,10 @@
 # 2024-04-19
 # Move setuptools_scm extension from hatchling to Python by rebuilding
-# the affected modules in the 2023a toolchain with EasyBuild 4.9.1.
+# the affected modules in the 2023b toolchain with EasyBuild 4.9.1.
 # This solves an issue with pyarrow, which is part of the Arrow installation.
 # https://github.com/easybuilders/easybuild-easyconfigs/pull/19777
 # https://github.com/easybuilders/easybuild-easyconfigs/issues/19849
 easyconfigs:
-  - hatchling-1.18.0-GCCcore-12.3.0.eb
-  - Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb
-  - Python-3.11.3-GCCcore-12.3.0.eb
+  - hatchling-1.18.0-GCCcore-13.2.0.eb
+  - Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb
+  - Python-3.11.5-GCCcore-13.2.0.eb

From 33cb74f5e2f4f63cd286e0d1b71818ccb1eca1a7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 26 Apr 2024 15:33:15 +0200
Subject: [PATCH 333/501] try adding write permissions instead of removing

---
 EESSI-remove-software.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index 446a156cb8..1a488dcb67 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -112,8 +112,9 @@ if [ $EUID -eq 0 ]; then
                     app_dir=${EASYBUILD_INSTALLPATH}/software/${app}
                     app_module=${EASYBUILD_INSTALLPATH}/modules/all/${app}.lua
                     echo_yellow "Removing ${app_dir} and ${app_module}..."
-                    rm -rf ${app_dir}
-                    rm -rf ${app_module}
+                    #rm -rf ${app_dir}
+                    #rm -rf ${app_module}
+                    chmod -R u+w ${app_dir} ${app_module}
                 done
             else
                 fatal_error "Easystack file ${easystack_file} not found!"

From 1e92daf31bca8a879b2888cefc5156c76774f7ec Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 26 Apr 2024 16:12:21 +0200
Subject: [PATCH 334/501] do remove the module to make sure it gets rebuilt

---
 EESSI-remove-software.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index 1a488dcb67..9d82dd8aa6 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -113,8 +113,8 @@ if [ $EUID -eq 0 ]; then
                     app_module=${EASYBUILD_INSTALLPATH}/modules/all/${app}.lua
                     echo_yellow "Removing ${app_dir} and ${app_module}..."
                     #rm -rf ${app_dir}
-                    #rm -rf ${app_module}
-                    chmod -R u+w ${app_dir} ${app_module}
+                    rm -rf ${app_module}
+                    chmod -R u+w ${app_dir}
                 done
             else
                 fatal_error "Easystack file ${easystack_file} not found!"

From d0229ccb3adb03eac5cdddde76858b00d20832bf Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Mon, 29 Apr 2024 14:40:50 +0200
Subject: [PATCH 335/501] Update create_lmodsitepackage.py

---
 create_lmodsitepackage.py | 22 +++++++++-------------
 1 file changed, 9 insertions(+), 13 deletions(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index ce94a7e311..862902d80e 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -24,24 +24,20 @@
     -- e.g. /cvmfs/software.eessi.io/versions/2023.06
     local eessi_prefix = os.getenv("EESSI_PREFIX")
 
-    -- NOTE: exact paths for site and user extensions aren't final, so may need to be updated later.
-    -- See https://github.com/EESSI/software-layer/pull/371
-
-    -- eessi_prefix_host_injections is the prefix with site-extensions (i.e. additional modules)
-    -- to the official EESSI modules, e.g. /cvmfs/software.eessi.io/host_injections/2023.06
-    local eessi_prefix_host_injections = string.gsub(eessi_prefix, 'versions', 'host_injections')
-    -- eessi_prefix_user_home is the prefix with user-extensions (i.e. additional modules)
-    -- to the offocial EESSI modules, e.g. $HOME/eessi/versions/2023.06
-    local eessi_prefix_user_home = string.gsub(eessi_prefix, os.getenv("EESSI_CVMFS_REPO"), pathJoin(os.getenv("HOME"), "eessi"))
     -- If EESSI_PREFIX wasn't defined, we cannot check if this module was from the EESSI environment
     -- In that case, we assume it isn't, otherwise EESSI_PREFIX would (probably) have been set
     if eessi_prefix == nil then
         return False
     else
-        -- Check if the full modulepath starts with the eessi_prefix_*
-        return string.find(t.fn, "^" .. eessi_prefix) ~= nil or
-        string.find(t.fn, "^" .. eessi_prefix_host_injections) ~= nil or
-        string.find(t.fn, "^" .. eessi_prefix_user_home) ~= nil
+        -- NOTE: exact paths for site so may need to be updated later.
+        -- See https://github.com/EESSI/software-layer/pull/371
+
+        -- eessi_prefix_host_injections is the prefix with site-extensions (i.e. additional modules)
+        -- to the official EESSI modules, e.g. /cvmfs/software.eessi.io/host_injections/2023.06
+        local eessi_prefix_host_injections = string.gsub(eessi_prefix, 'versions', 'host_injections')
+        
+       -- Check if the full modulepath starts with the eessi_prefix_*
+        return string.find(t.fn, "^" .. eessi_prefix) ~= nil or string.find(t.fn, "^" .. eessi_prefix_host_injections) ~= nil
     end
 end
 

From b6371d0e2766720a8fbccdb2ed322b5858dc834f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 30 Apr 2024 11:06:30 +0200
Subject: [PATCH 336/501] use easyconfig PR for GROMACS 2024.1 that uses
 backported patch to fix problems with tests

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml                  | 3 ---
 .../2023.06/eessi-2023.06-eb-4.9.1-2023b.yml                  | 4 ++++
 2 files changed, 4 insertions(+), 3 deletions(-)
 create mode 100644 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index d45ebfb9ba..86c5106c85 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -57,6 +57,3 @@ easyconfigs:
   - Qt5-5.15.13-GCCcore-13.2.0.eb:
       options:
         from-pr: 20201
-  - GROMACS-2024.1-foss-2023b.eb:
-      options:
-        from-pr: 20102
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
new file mode 100644
index 0000000000..1392fa2f5a
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
@@ -0,0 +1,4 @@
+easyconfigs:
+  - GROMACS-2024.1-foss-2023b.eb:
+      options:
+        from-pr: 20439

From b94fa6262a2845a03d58a9095b5da4fb84b8e710 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 30 Apr 2024 15:13:53 +0200
Subject: [PATCH 337/501] restore easystack, rebuild all required versions

---
 ...eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
index f3484a3486..56ea7a46a1 100644
--- a/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
@@ -1,10 +1,13 @@
 # 2024-04-19
 # Move setuptools_scm extension from hatchling to Python by rebuilding
-# the affected modules in the 2023b toolchain with EasyBuild 4.9.1.
+# all affected modules with EasyBuild 4.9.1.
 # This solves an issue with pyarrow, which is part of the Arrow installation.
 # https://github.com/easybuilders/easybuild-easyconfigs/pull/19777
 # https://github.com/easybuilders/easybuild-easyconfigs/issues/19849
 easyconfigs:
+  - hatchling-1.18.0-GCCcore-12.3.0.eb
   - hatchling-1.18.0-GCCcore-13.2.0.eb
+  - Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb
   - Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb
+  - Python-3.11.3-GCCcore-12.3.0.eb
   - Python-3.11.5-GCCcore-13.2.0.eb

From 66724f282e405579021811813721aaf79dc35a75 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 30 Apr 2024 15:14:50 +0200
Subject: [PATCH 338/501] undo changes

---
 EESSI-remove-software.sh | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index 9d82dd8aa6..446a156cb8 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -112,9 +112,8 @@ if [ $EUID -eq 0 ]; then
                     app_dir=${EASYBUILD_INSTALLPATH}/software/${app}
                     app_module=${EASYBUILD_INSTALLPATH}/modules/all/${app}.lua
                     echo_yellow "Removing ${app_dir} and ${app_module}..."
-                    #rm -rf ${app_dir}
+                    rm -rf ${app_dir}
                     rm -rf ${app_module}
-                    chmod -R u+w ${app_dir}
                 done
             else
                 fatal_error "Easystack file ${easystack_file} not found!"

From 01c49de45a802aafdc5d0bcf7cd577c0213cfac0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 30 Apr 2024 20:54:28 +0200
Subject: [PATCH 339/501] avoid building GROMACS 2024.1 with SVE on Neoverse
 V1, stick to Neon for now (cfr.
 https://gitlab.com/gromacs/gromacs/-/issues/5057)

---
 eb_hooks.py | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/eb_hooks.py b/eb_hooks.py
index 20b5f76cfc..f02c8db48c 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -335,6 +335,21 @@ def pre_configure_hook(self, *args, **kwargs):
         PRE_CONFIGURE_HOOKS[self.name](self, *args, **kwargs)
 
 
+def pre_configure_hook_gromacs(self, *args, **kwargs):
+    """
+    Pre-configure hook for GROMACS:
+    - avoid building with SVE instructions on Neoverse V1 as workaround for failing tests,
+      see https://gitlab.com/gromacs/gromacs/-/issues/5057 + https://gitlab.com/eessi/support/-/issues/47
+    """
+    if self.name == 'GROMACS':
+        cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
+        if LooseVersion(self.version) <= LooseVersion('2024.1') and cpu_target == CPU_TARGET_NEOVERSE_V1:
+            self.cfg.update('configopts', '-DGMX_SIMD=ARM_NEON_ASIMD')
+            print_msg("Avoiding use of SVE instructions for GROMACS %s by using ARM_NEON_ASIMD as GMX_SIMD value", self.version)
+    else:
+        raise EasyBuildError("GROMACS-specific hook triggered for non-GROMACS easyconfig?!")
+
+
 def pre_configure_hook_openblas_optarch_generic(self, *args, **kwargs):
     """
     Pre-configure hook for OpenBLAS: add DYNAMIC_ARCH=1 to build/test/install options when using --optarch=GENERIC
@@ -665,6 +680,7 @@ def inject_gpu_property(ec):
 }
 
 PRE_CONFIGURE_HOOKS = {
+    'GROMACS': pre_configure_hook_gromacs,
     'libfabric': pre_configure_hook_libfabric_disable_psm3_x86_64_generic,
     'MetaBAT': pre_configure_hook_metabat_filtered_zlib_dep,
     'OpenBLAS': pre_configure_hook_openblas_optarch_generic,

From ac82cc840bfbdae0638438fb85f9a5004e020f2a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 30 Apr 2024 21:21:32 +0200
Subject: [PATCH 340/501] move bioconductor to eb 4.9.1 file

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml | 3 ---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml | 3 +++
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 23d64036f1..44952e2765 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -71,6 +71,3 @@ easyconfigs:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20238
         from-pr: 20238
-  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
-      options:
-        from-pr: 20379
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index ec5fd3c638..e65747e4a5 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -1,3 +1,6 @@
 easyconfigs:
   - ncdu-1.18-GCC-12.3.0.eb
   - SAMtools-1.18-GCC-12.3.0.eb
+  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
+      options:
+        from-pr: 20379

From 3eee364b47b4cae85aa675d020a7bd7a362b47f0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 1 May 2024 11:11:41 +0200
Subject: [PATCH 341/501] register known issue for GROMACS 2024.1 on
 neoverse_v1

---
 eessi-2023.06-known-issues.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/eessi-2023.06-known-issues.yml b/eessi-2023.06-known-issues.yml
index 011cb2dc08..2d1256354f 100644
--- a/eessi-2023.06-known-issues.yml
+++ b/eessi-2023.06-known-issues.yml
@@ -19,6 +19,9 @@
   - FFTW.MPI-3.3.10-gompi-2023b:
       - issue: https://github.com/EESSI/software-layer/issues/325
       - info: "Flaky FFTW tests, random failures"
+  - GROMACS-2024.1-foss-2023b:
+      - issue: https://github.com/EESSI/software-layer/issues/557
+      - info: "SVE disabled due to known bug which causes test failures"
   - Highway-1.0.3-GCCcore-12.2.0.eb:
     - issue: https://github.com/EESSI/software-layer/issues/469
     - info: "failing SVE test due to wrong expected value"

From fe0c7c534db6ce8d369aafaa84b4d0afaf7b3cc2 Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Wed, 1 May 2024 17:14:47 +0200
Subject: [PATCH 342/501] Add Lmod hook for ESPReSso

---
 create_lmodsitepackage.py | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index 0761f2cdf1..ef17448f0c 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+z#!/usr/bin/env python3
 #
 # Create SitePackage.lua configuration file for Lmod.
 #
@@ -150,10 +150,24 @@
     end
 end
 
+local function eessi_espresso_deprecated_warning(t)
+    local frameStk  = require("FrameStk"):singleton()
+    local mt        = frameStk:mt()
+    local simpleName = string.match(t.modFullName, "(.-)/")
+    local version = string.match(t.modFullName, "%d.%d.%d")
+    if simpleName == 'ESPResSo' and version == '4.2.1'
+        local advice = 'Prefer versions  >= 4.2.2 which include important bugfixes.\\n'
+        advice = advice .. 'For details see https://github.com/espressomd/espresso/issues/4856\\n'
+        advice = advice .. 'Use version 4.2.1 at your own risk!\\nn'
+        LmodWarning("\\nESPReSso v4.2.1 has known issues and has been deprecated. ", advice)
+        end
+end
+
 -- Combine both functions into a single one, as we can only register one function as load hook in lmod
 -- Also: make it non-local, so it can be imported and extended by other lmodrc files if needed
 function eessi_load_hook(t)
     eessi_cuda_enabled_load_hook(t)
+    eessi_espresso_deprecated_warning(t)
 end
 
 

From 8f253276033d83d08ea770c1dd8ef946d6675d63 Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Mon, 6 May 2024 09:36:04 +0200
Subject: [PATCH 343/501] Fix typo

---
 create_lmodsitepackage.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index ef17448f0c..61b40c4252 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -1,4 +1,4 @@
-z#!/usr/bin/env python3
+#!/usr/bin/env python3
 #
 # Create SitePackage.lua configuration file for Lmod.
 #

From a9e8ae8192e916b3b6bcbfa6c47206a748d362b8 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Mon, 6 May 2024 16:06:22 +0200
Subject: [PATCH 344/501] Match name stub of files to CUDA allow list to ship

---
 .../2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml | 8 ++++++++
 eb_hooks.py                                               | 4 ++--
 2 files changed, 10 insertions(+), 2 deletions(-)
 create mode 100644 easystacks/software.eessi.io/2023.06/rebuilds/2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml b/easystacks/software.eessi.io/2023.06/rebuilds/2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml
new file mode 100644
index 0000000000..2a9daf7ba6
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml
@@ -0,0 +1,8 @@
+# 2024.05.06
+# Original matching of files we could ship was not done correctly. We were
+# matching the basename for files (e.g., libcudart.so from libcudart.so.12)
+# rather than the name stub (libcudart)
+easyconfigs:
+  - CUDA-12.1.1.eb:
+      options:
+        accept-eula-for: CUDA
diff --git a/eb_hooks.py b/eb_hooks.py
index f02c8db48c..8b0a11b0ed 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -612,8 +612,8 @@ def post_sanitycheck_cuda(self, *args, **kwargs):
                 full_path = os.path.join(dir_path, filename)
                 # we only really care about real files, i.e. not symlinks
                 if not os.path.islink(full_path):
-                    # check if the current file is part of the allowlist
-                    basename = os.path.splitext(filename)[0]
+                    # check if the current file name stub is part of the allowlist
+                    basename = filename.split('.')[0]
                     if basename in allowlist:
                         self.log.debug("%s is found in allowlist, so keeping it: %s", basename, full_path)
                     else:

From 28e5e9c52005cb46855e7fe965cd41997e9c48d6 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Mon, 6 May 2024 18:49:34 +0200
Subject: [PATCH 345/501] Update
 2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml

---
 .../2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml        | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml b/easystacks/software.eessi.io/2023.06/rebuilds/2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml
index 2a9daf7ba6..058ab75e80 100644
--- a/easystacks/software.eessi.io/2023.06/rebuilds/2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml
@@ -2,6 +2,7 @@
 # Original matching of files we could ship was not done correctly. We were
 # matching the basename for files (e.g., libcudart.so from libcudart.so.12)
 # rather than the name stub (libcudart)
+# See https://github.com/EESSI/software-layer/pull/559
 easyconfigs:
   - CUDA-12.1.1.eb:
       options:

From cc91f3411df6010ff29247a94bfe9356e70cf342 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Thomas=20R=C3=B6blitz?= <trz42@users.noreply.github.com>
Date: Tue, 7 May 2024 10:50:48 +0200
Subject: [PATCH 346/501] fix tiny typo

---
 EESSI-extend-2023.06-easybuild.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index c06087a940..e6e540bf45 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -157,7 +157,7 @@ elseif (project_modulepath ~= nil) then
   -- configure MODULEPATH
   prepend_path("MODULEPATH", project_modulepath)
 end
--- Make aure EasyBuild itself is loaded
+-- Make sure EasyBuild itself is loaded
 if not ( isloaded("EasyBuild") ) then
     load("EasyBuild")
 end

From 38a0581480ac284c2802e5e63a0541fae31f786a Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Tue, 7 May 2024 10:55:28 +0200
Subject: [PATCH 347/501] use eessi.io/docs and system easystack file

---
 EESSI-extend-2023.06-easybuild.eb                               | 2 +-
 .../2023.06/eessi-2023.06-eb-4.9.1-001-system.yml               | 1 +
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml  | 1 -
 3 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index e6e540bf45..241cde264b 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -5,7 +5,7 @@ version = '2023.06'
 # May have different ways to extend EESSI in future (manually, other tools,...)
 versionsuffix = '-easybuild'
 
-homepage = 'https://eessi.github.io/docs/'
+homepage = 'https://eessi.io/docs/'
 
 description = """
  The goal of the European Environment for Scientific Software Installations
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
index c5a08b5209..46ac979719 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
@@ -2,3 +2,4 @@ easyconfigs:
   - EasyBuild-4.9.1.eb:
       options:
         from-pr: 20299
+  - EESSI-extend-2023.06-easybuild.eb
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index b7d4370b84..3b51db3b11 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -1,3 +1,2 @@
 easyconfigs:
   - ncdu-1.18-GCC-12.3.0.eb
-  - EESSI-extend-2023.06-easybuild.eb 

From 0ff23347d31156ed4501f49f1a7f187f51257ecf Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Tue, 7 May 2024 12:05:38 +0200
Subject: [PATCH 348/501] Update EESSI-extend-2023.06-easybuild.eb

---
 EESSI-extend-2023.06-easybuild.eb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index 241cde264b..76e96766f9 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -139,9 +139,11 @@ setenv ("EASYBUILD_SYSROOT", sysroot)
 setenv ("EASYBUILD_PREFIX", pathJoin(working_dir, "easybuild"))
 setenv ("EASYBUILD_INSTALLPATH", easybuild_installpath)
 setenv ("EASYBUILD_HOOKS", pathJoin(os.getenv("EESSI_PREFIX"), "init", "easybuild", "eb_hooks.py"))
+setenv ("EASYBUILD_UMASK", "002")
 
 -- Set all related environment variables if we have project or user installations (including extending MODULEPATH)
 if (user_modulepath ~= nil) then
+  -- Use a more restrictive umask for this case
   setenv ("EASYBUILD_UMASK", "022")
   setenv ("EASYBUILD_STICKY_BIT", "1")
   -- configure MODULEPATH
@@ -152,7 +154,6 @@ if (user_modulepath ~= nil) then
 elseif (project_modulepath ~= nil) then
   setenv ("EASYBUILD_SET_GID_BIT", "1")
   setenv ("EASYBUILD_GROUP_WRITABLE_INSTALLDIR", "1")
-  setenv ("EASYBUILD_UMASK", "002")
   setenv ("EASYBUILD_STICKY_BIT", "0")
   -- configure MODULEPATH
   prepend_path("MODULEPATH", project_modulepath)

From 6682c7d36d54641aeb6a5cd9eeaf2cd981ef89d7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 7 May 2024 13:32:25 +0200
Subject: [PATCH 349/501] move OSU-Micro-Benchmarks 2023b to 2023b easystack

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml   | 1 -
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml   | 1 +
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 44952e2765..8f5608d881 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -35,7 +35,6 @@ easyconfigs:
         from-pr: 19996
   - dask-2023.9.2-foss-2023a.eb
   - OSU-Micro-Benchmarks-7.2-gompi-2023a-CUDA-12.1.1.eb
-  - OSU-Micro-Benchmarks-7.2-gompi-2023b.eb
   - JupyterNotebook-7.0.2-GCCcore-12.3.0.eb
   - ImageMagick-7.1.1-15-GCCcore-12.3.0.eb:
       options:
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 86c5106c85..15c02951d7 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -57,3 +57,4 @@ easyconfigs:
   - Qt5-5.15.13-GCCcore-13.2.0.eb:
       options:
         from-pr: 20201
+  - OSU-Micro-Benchmarks-7.2-gompi-2023b.eb

From 298159e516db7c696b12ca57bf51a5328588ebf9 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Tue, 7 May 2024 14:27:24 +0200
Subject: [PATCH 350/501] bumping scorecard-action version to 2.3.1

---
 .github/workflows/scorecards.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/scorecards.yml b/.github/workflows/scorecards.yml
index dc18fd584a..7eff557094 100644
--- a/.github/workflows/scorecards.yml
+++ b/.github/workflows/scorecards.yml
@@ -40,7 +40,7 @@ jobs:
           persist-credentials: false
 
       - name: "Run analysis"
-        uses: ossf/scorecard-action@99c53751e09b9529366343771cc321ec74e9bd3d # v2.0.6
+        uses: ossf/scorecard-action@0864cf19026789058feabb7e87baa5f140aac736 # v2.3.1
         with:
           results_file: results.sarif
           results_format: sarif

From 462adc5cdd5c3f2255f0275e45a7f6a82da584bf Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 7 May 2024 15:28:38 +0200
Subject: [PATCH 351/501] {2023.06,zen4} foss/2023a

---
 .../2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml               | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml
new file mode 100644
index 0000000000..c821df1afb
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -0,0 +1,2 @@
+easyconfigs:
+  - foss-2023a.eb

From 06f88dbbc5f90654fb1d48c888a9575cb768be59 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 7 May 2024 18:15:55 +0200
Subject: [PATCH 352/501] stick to x86_64/amd/zen3 when AMD Genoa (Zen4) is
 detected, until optimized software installations are available for Zen4

---
 init/eessi_environment_variables | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index 5450b2bfb4..e7f8f2faaa 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -48,6 +48,14 @@ if [ -d $EESSI_PREFIX ]; then
     fi
     if [ ! -z $EESSI_SOFTWARE_SUBDIR ]; then
 
+        # use x86_64/amd/zen3 for now when AMD Genoa (Zen4) CPU is detected,
+        # since optimized software installations for Zen4 are a work-in-progress,
+        # see https://gitlab.com/eessi/support/-/issues/37
+        if [[ "${EESSI_SOFTWARE_SUBDIR}" == "x86_64/amd/zen4" ]]; then
+            export EESSI_SOFTWARE_SUBDIR="x86_64/amd/zen3"
+            echo -e "\e[33mSticking to ${EESSI_SOFTWARE_SUBDIR} for now, since optimized installations for AMD Genoa (Zen4) are a work in progress, see https://gitlab.com/eessi/support/-/issues/37 for more information\e[0m"
+        fi
+
         show_msg "Using ${EESSI_SOFTWARE_SUBDIR} as software subdirectory."
         export EESSI_SOFTWARE_PATH=$EESSI_PREFIX/software/$EESSI_OS_TYPE/$EESSI_SOFTWARE_SUBDIR
 

From 8cce17c83ba3230774a56de285de3fe369792595 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 7 May 2024 19:19:54 +0200
Subject: [PATCH 353/501] relax check for existence of software overlay dir in
 script to create tarball to deploy

---
 create_tarball.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/create_tarball.sh b/create_tarball.sh
index 2d77acfc43..0a7669f73f 100755
--- a/create_tarball.sh
+++ b/create_tarball.sh
@@ -28,7 +28,7 @@ fi
 
 overlay_upper_dir="${eessi_tmpdir}/overlay-upper"
 
-software_dir_overlay="${overlay_upper_dir}/versions/${eessi_version}/software/${os}/${cpu_arch_subdir}"
+software_dir_overlay="${overlay_upper_dir}/versions/${eessi_version}"
 if [ ! -d ${software_dir_overlay} ]; then
     echo "Software directory overlay ${software_dir_overlay} does not exist?!" >&2
     exit 3

From 39dddf641af1d59498076154c77c9de500451d9d Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com>
Date: Tue, 7 May 2024 19:29:25 +0200
Subject: [PATCH 354/501] Update init/bash

Co-authored-by: Kenneth Hoste <kenneth.hoste@ugent.be>
---
 init/bash | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/init/bash b/init/bash
index 565c37cc65..655260841d 100644
--- a/init/bash
+++ b/init/bash
@@ -26,7 +26,7 @@ if [ $? -eq 0 ]; then
     # prepend location of modules for EESSI software stack to $MODULEPATH
     show_msg "Prepending $EESSI_MODULEPATH to \$MODULEPATH..."
     module use $EESSI_MODULEPATH
-    echo "Prepending site path $EESSI_SITE_MODULEPATH to \$MODULEPATH..." >> $output
+    echo "Prepending site path $EESSI_SITE_MODULEPATH to \$MODULEPATH..."
     module use $EESSI_SITE_MODULEPATH
 
     #show_msg ""

From 500b1de874a93e523ec308721f85a5824b8260e1 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com>
Date: Tue, 7 May 2024 19:32:03 +0200
Subject: [PATCH 355/501] Update init/bash
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Thomas Röblitz <trz42@users.noreply.github.com>
---
 init/bash | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/init/bash b/init/bash
index 655260841d..93471e075e 100644
--- a/init/bash
+++ b/init/bash
@@ -26,7 +26,7 @@ if [ $? -eq 0 ]; then
     # prepend location of modules for EESSI software stack to $MODULEPATH
     show_msg "Prepending $EESSI_MODULEPATH to \$MODULEPATH..."
     module use $EESSI_MODULEPATH
-    echo "Prepending site path $EESSI_SITE_MODULEPATH to \$MODULEPATH..."
+    show_msg "Prepending site path $EESSI_SITE_MODULEPATH to \$MODULEPATH..."
     module use $EESSI_SITE_MODULEPATH
 
     #show_msg ""

From 999cbd359528edf4feedd822859b9e2d0f922d9b Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Tue, 7 May 2024 19:45:16 +0200
Subject: [PATCH 356/501] relax check or tarball is not created unless also
 software was built

---
 create_tarball.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/create_tarball.sh b/create_tarball.sh
index 2d77acfc43..0a7669f73f 100755
--- a/create_tarball.sh
+++ b/create_tarball.sh
@@ -28,7 +28,7 @@ fi
 
 overlay_upper_dir="${eessi_tmpdir}/overlay-upper"
 
-software_dir_overlay="${overlay_upper_dir}/versions/${eessi_version}/software/${os}/${cpu_arch_subdir}"
+software_dir_overlay="${overlay_upper_dir}/versions/${eessi_version}"
 if [ ! -d ${software_dir_overlay} ]; then
     echo "Software directory overlay ${software_dir_overlay} does not exist?!" >&2
     exit 3

From 78b4e13a230b0b95cb4f41df013bf016c9b286b6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 7 May 2024 15:30:44 +0200
Subject: [PATCH 357/501] {2023.06,zen4} foss/2023b

---
 .../2023.06/zen4/eessi-2023.06-eb-4.9.1-2023b.yml               | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023b.yml

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023b.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023b.yml
new file mode 100644
index 0000000000..75dc4e6602
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023b.yml
@@ -0,0 +1,2 @@
+easyconfigs:
+  - foss-2023b.eb

From ac3e74795c735eb99acf93e0fe9c024d6d81291a Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Wed, 15 May 2024 11:16:49 +0200
Subject: [PATCH 358/501] Only correct the Zen4 software subdirectory if it has
 not been overridden

---
 init/eessi_environment_variables | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index 71e70ee071..78851a9c95 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -52,8 +52,10 @@ if [ -d $EESSI_PREFIX ]; then
         # since optimized software installations for Zen4 are a work-in-progress,
         # see https://gitlab.com/eessi/support/-/issues/37
         if [[ "${EESSI_SOFTWARE_SUBDIR}" == "x86_64/amd/zen4" ]]; then
-            export EESSI_SOFTWARE_SUBDIR="x86_64/amd/zen3"
-            echo -e "\e[33mSticking to ${EESSI_SOFTWARE_SUBDIR} for now, since optimized installations for AMD Genoa (Zen4) are a work in progress, see https://gitlab.com/eessi/support/-/issues/37 for more information\e[0m"
+            if [ -z $EESSI_SOFTWARE_SUBDIR_OVERRIDE ]; then
+                export EESSI_SOFTWARE_SUBDIR="x86_64/amd/zen3"
+                echo -e "\e[33mSticking to ${EESSI_SOFTWARE_SUBDIR} for now, since optimized installations for AMD Genoa (Zen4) are a work in progress, see https://gitlab.com/eessi/support/-/issues/37 for more information\e[0m"
+            fi
         fi
 
         show_msg "Using ${EESSI_SOFTWARE_SUBDIR} as software subdirectory."

From d043d867a3dccce1b978ee2531923e970b6e6176 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Wed, 15 May 2024 12:10:19 +0200
Subject: [PATCH 359/501] Add `psm2` to filtered dependencies for `2023.06`

`PSM2` was introduced as a dependency of `libfabric` in https://github.com/easybuilders/easybuild-easyconfigs/pull/20501.

We already have PSM2 in the compat layer, so we can filter this dependency out, but longer term we probably actually want it since it should be built with accelerator support.
---
 configure_easybuild | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/configure_easybuild b/configure_easybuild
index c67b879cf3..60e3744603 100644
--- a/configure_easybuild
+++ b/configure_easybuild
@@ -32,6 +32,12 @@ if [[ "$EESSI_CPU_FAMILY" == "aarch64" ]]; then
     DEPS_TO_FILTER="${DEPS_TO_FILTER},Yasm"
 fi
 
+# Version 23.06 of EESSI ships PSM2 in the compat layer, so we can filter this out while retaining support for OFA fabric
+# (longer term this is probably not the right move as PSM2 should be configured with accelerator support, hence the restricted version)
+if [[ "$EESSI_VERSION" == "2023.06" ]]; then
+    DEPS_TO_FILTER="${DEPS_TO_FILTER},psm2"
+fi
+
 export EASYBUILD_FILTER_DEPS=$DEPS_TO_FILTER
 
 export EASYBUILD_MODULE_EXTENSIONS=1

From ec2e8bdf04456b85bf9dae3a46ea132acba90df3 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Wed, 15 May 2024 12:14:20 +0200
Subject: [PATCH 360/501] Update configure_easybuild

---
 configure_easybuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/configure_easybuild b/configure_easybuild
index 60e3744603..ed3e651a4c 100644
--- a/configure_easybuild
+++ b/configure_easybuild
@@ -35,7 +35,7 @@ fi
 # Version 23.06 of EESSI ships PSM2 in the compat layer, so we can filter this out while retaining support for OFA fabric
 # (longer term this is probably not the right move as PSM2 should be configured with accelerator support, hence the restricted version)
 if [[ "$EESSI_VERSION" == "2023.06" ]]; then
-    DEPS_TO_FILTER="${DEPS_TO_FILTER},psm2"
+    DEPS_TO_FILTER="${DEPS_TO_FILTER},PSM2"
 fi
 
 export EASYBUILD_FILTER_DEPS=$DEPS_TO_FILTER

From 3cdb7b2653336dd707b65197bf578f4012a6b0ff Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Wed, 15 May 2024 12:43:43 +0200
Subject: [PATCH 361/501] Add a rebuild of GROMACS

---
 ...240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml | 11 +++++++++++
 1 file changed, 11 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml
new file mode 100644
index 0000000000..e767c63f6e
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml
@@ -0,0 +1,11 @@
+# 2024.05.15
+# Originally shipped version forgot to bump the gmxapi version and source
+# tarball, it was still using an older version from the 2023.3 tarball. Looking
+# at https://gitlab.com/gromacs/gromacs/-/blob/v2024.1/python_packaging/gmxapi/src/gmxapi/version.py?ref_type=tags#L68,
+# the 2024.1 release includes gmxapi 0.5.0.
+#
+# See https://github.com/easybuilders/easybuild-easyconfigs/pull/20522
+easyconfigs:
+  - GROMACS-2024.1-foss-2023b.eb:
+      options:
+        from-pr: 20522

From fb329a4bfe535cffc8d70958fc65fa0072180416 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Wed, 15 May 2024 12:57:36 +0200
Subject: [PATCH 362/501] Also add new dependency on scikit-build-core

---
 .../20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml     | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml
index e767c63f6e..4eca76fd66 100644
--- a/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml
@@ -4,8 +4,13 @@
 # at https://gitlab.com/gromacs/gromacs/-/blob/v2024.1/python_packaging/gmxapi/src/gmxapi/version.py?ref_type=tags#L68,
 # the 2024.1 release includes gmxapi 0.5.0.
 #
+# This also introduced a new build dependency on scikit-build-core for GROMACS
+#
 # See https://github.com/easybuilders/easybuild-easyconfigs/pull/20522
 easyconfigs:
+  - scikit-build-core-0.9.3-GCCcore-13.2.0.eb:
+      options:
+        from-pr: 20526
   - GROMACS-2024.1-foss-2023b.eb:
       options:
         from-pr: 20522

From 792ea3ebdbf011665f3b673ecd974b93e961f8c1 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Wed, 15 May 2024 15:01:57 +0200
Subject: [PATCH 363/501] Use from-commit for merged PRs

---
 .../20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml      | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml
index 4eca76fd66..93d87bbcf3 100644
--- a/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml
@@ -10,7 +10,7 @@
 easyconfigs:
   - scikit-build-core-0.9.3-GCCcore-13.2.0.eb:
       options:
-        from-pr: 20526
+        from-commit: 61d07bff09afe63cfe1ae35dc58a0c8be01eed62
   - GROMACS-2024.1-foss-2023b.eb:
       options:
-        from-pr: 20522
+        from-commit: a0a467a88506c765a93a96b20d7a8fcb01d46b24

From 6cf63359d04a7662ae3aa021763765bf01d5f8c7 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Wed, 15 May 2024 16:06:35 +0200
Subject: [PATCH 364/501] Allow EESSI-extend as a loaded module when using
 EasyBuild

---
 EESSI-extend-2023.06-easybuild.eb | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index 76e96766f9..42defbacc8 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -139,12 +139,17 @@ setenv ("EASYBUILD_SYSROOT", sysroot)
 setenv ("EASYBUILD_PREFIX", pathJoin(working_dir, "easybuild"))
 setenv ("EASYBUILD_INSTALLPATH", easybuild_installpath)
 setenv ("EASYBUILD_HOOKS", pathJoin(os.getenv("EESSI_PREFIX"), "init", "easybuild", "eb_hooks.py"))
-setenv ("EASYBUILD_UMASK", "002")
+
+-- Make sure to use the general umask that allows a global read
+setenv ("EASYBUILD_UMASK", "022")
+
+-- All this module to be loaded when running EasyBuild
+setenv ("EASYBUILD_ALLOW_LOADED_MODULES", "EasyBuild,EESSI-extend")
 
 -- Set all related environment variables if we have project or user installations (including extending MODULEPATH)
 if (user_modulepath ~= nil) then
   -- Use a more restrictive umask for this case
-  setenv ("EASYBUILD_UMASK", "022")
+  setenv ("EASYBUILD_UMASK", "077")
   setenv ("EASYBUILD_STICKY_BIT", "1")
   -- configure MODULEPATH
   if (project_modulepath ~= nil) then
@@ -155,6 +160,7 @@ elseif (project_modulepath ~= nil) then
   setenv ("EASYBUILD_SET_GID_BIT", "1")
   setenv ("EASYBUILD_GROUP_WRITABLE_INSTALLDIR", "1")
   setenv ("EASYBUILD_STICKY_BIT", "0")
+  setenv ("EASYBUILD_UMASK", "002")
   -- configure MODULEPATH
   prepend_path("MODULEPATH", project_modulepath)
 end

From fbdb8461fca7dbb28add02b128877d5b59bb24fc Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Wed, 15 May 2024 16:11:17 +0200
Subject: [PATCH 365/501] Rebuild the module

---
 .../20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml         | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/rebuilds/20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml
new file mode 100644
index 0000000000..5cf2bd6b9d
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml
@@ -0,0 +1,5 @@
+# 2024.05.15
+# The module is an EasyBuil created module and therefore needs to be an allowed
+# module when running EasyBuild
+easyconfigs:
+  - EESSI-extend-2023.06-easybuild.eb 

From 375bf370137a33b748ed649625e532d836a962d5 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Wed, 15 May 2024 16:17:53 +0200
Subject: [PATCH 366/501] Update
 20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml

Issues seen when trying to use `from-commit` in https://github.com/EESSI/software-layer/pull/577
---
 .../20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml    | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml
index 93d87bbcf3..eacfad7079 100644
--- a/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml
@@ -10,7 +10,9 @@
 easyconfigs:
   - scikit-build-core-0.9.3-GCCcore-13.2.0.eb:
       options:
-        from-commit: 61d07bff09afe63cfe1ae35dc58a0c8be01eed62
+        # from-commit: 61d07bff09afe63cfe1ae35dc58a0c8be01eed62
+        from-pr: 20526
   - GROMACS-2024.1-foss-2023b.eb:
       options:
-        from-commit: a0a467a88506c765a93a96b20d7a8fcb01d46b24
+        # from-commit: a0a467a88506c765a93a96b20d7a8fcb01d46b24
+        from-pr: 20522

From 2b30e1f2cca0a60b1dbf9ee0680aa48ba3f260da Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Wed, 15 May 2024 17:09:18 +0200
Subject: [PATCH 367/501] Allow overriding the Lmod GPU driver check

---
 EESSI-install-software.sh | 3 +++
 create_lmodsitepackage.py | 9 ++++++---
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 8a5789c2b2..40f0ed8c3d 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -243,6 +243,9 @@ fi
 #       if not, an error is produced, and the bot flags the whole build as failed (even when not installing GPU software)
 # ${EESSI_PREFIX}/scripts/gpu_support/nvidia/link_nvidia_host_libraries.sh
 
+# Don't run the Lmod GPU driver check when doing builds (may not have a GPU, and it's not relevant for vanilla builds anyway)
+export EESSI_OVERRIDE_GPU_CHECK=1 
+
 # use PR patch file to determine in which easystack files stuff was added
 changed_easystacks=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | egrep -v 'known-issues|missing') 
 if [ -z "${changed_easystacks}" ]; then
diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index 47aa20e51e..816302f7fc 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -131,8 +131,9 @@
     end
     -- when loading CUDA enabled modules check if the necessary driver libraries are accessible to the EESSI linker,
     -- otherwise, refuse to load the requested module and print error message
-    local haveGpu = mt:haveProperty(simpleName,"arch","gpu")
-    if haveGpu then
+    local checkGpu = mt:haveProperty(simpleName,"arch","gpu")
+    local overrideGpuCheck = os.getenv("EESSI_OVERRIDE_GPU_CHECK")
+    if checkGpu and (overrideGpuCheck == nil) then
         local arch = os.getenv("EESSI_CPU_FAMILY") or ""
         local cudaVersionFile = "/cvmfs/software.eessi.io/host_injections/nvidia/" .. arch .. "/latest/cuda_version.txt"
         local cudaDriverFile = "/cvmfs/software.eessi.io/host_injections/nvidia/" .. arch .. "/latest/libcuda.so"
@@ -141,7 +142,9 @@
         if not (cudaDriverExists or singularityCudaExists)  then
             local advice = "which relies on the CUDA runtime environment and driver libraries. "
             advice = advice .. "In order to be able to use the module, you will need "
-            advice = advice .. "to make sure EESSI can find the GPU driver libraries on your host system.\\n"
+            advice = advice .. "to make sure EESSI can find the GPU driver libraries on your host system. You can "
+            advice = advice .. "override this check by setting the environment variable EESSI_OVERRIDE_GPU_CHECK but "
+            advice = advice .. "the loaded application will not be able to execute on your system.\\n"
             advice = advice .. refer_to_docs
             LmodError("\\nYou requested to load ", simpleName, " ", advice)
         else

From 705030d6aca132df57e5432aa6ada663f04d682d Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Thu, 16 May 2024 12:48:25 +0200
Subject: [PATCH 368/501] use directory of called script as base dir for other
 scripts

---
 bot/inspect.sh | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/bot/inspect.sh b/bot/inspect.sh
index 9d1fa87e1f..f0589cd827 100755
--- a/bot/inspect.sh
+++ b/bot/inspect.sh
@@ -27,6 +27,8 @@
 # stop as soon as something fails
 set -e
 
+SCRIPT_DIR=$(dirname $(realpath $BASH_SOURCE))
+
 display_help() {
   echo "usage: $0 [OPTIONS]"
   echo "  -h | --help            -  display this usage information"
@@ -81,8 +83,8 @@ done
 set -- "${POSITIONAL_ARGS[@]}"
 
 # source utils.sh and cfg_files.sh
-source scripts/utils.sh
-source scripts/cfg_files.sh
+source ${SCRIPT_DIR}/../scripts/utils.sh
+source ${SCRIPT_DIR}/../scripts/cfg_files.sh
 
 if [[ -z ${resume_tgz} ]]; then
     echo_red "path to tarball for resuming build job is missing"
@@ -432,14 +434,14 @@ echo "Executing command to start interactive session to inspect build job:"
 # These initializations are combined into a single script that is executed when
 # the shell in startprefix is started. We set the env variable BASH_ENV here.
 if [[ -z ${run_in_prefix} ]]; then
-    echo "./eessi_container.sh ${CMDLINE_ARGS[@]}"
+    echo "${SCRIPT_DIR}/../eessi_container.sh ${CMDLINE_ARGS[@]}"
     echo "                     -- ${EESSI_COMPAT_LAYER_DIR}/startprefix"
-    ./eessi_container.sh "${CMDLINE_ARGS[@]}" \
+    ${SCRIPT_DIR}/../eessi_container.sh "${CMDLINE_ARGS[@]}" \
                      -- ${EESSI_COMPAT_LAYER_DIR}/startprefix
 else
-    echo "./eessi_container.sh ${CMDLINE_ARGS[@]}"
+    echo "${SCRIPT_DIR}/../eessi_container.sh ${CMDLINE_ARGS[@]}"
     echo "                     -- ${EESSI_COMPAT_LAYER_DIR}/startprefix <<< ${run_in_prefix}"
-    ./eessi_container.sh "${CMDLINE_ARGS[@]}" \
+    ${SCRIPT_DIR}/../eessi_container.sh "${CMDLINE_ARGS[@]}" \
                      -- ${EESSI_COMPAT_LAYER_DIR}/startprefix <<< ${run_in_prefix}
 fi
 

From 082722eb6cb9028567f2b5af3bbb1c12d9fc5c15 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Thu, 16 May 2024 17:17:01 +0200
Subject: [PATCH 369/501] use single variable for directory containing script;
 use lowercase var name

---
 bot/inspect.sh | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/bot/inspect.sh b/bot/inspect.sh
index f0589cd827..533968bffc 100755
--- a/bot/inspect.sh
+++ b/bot/inspect.sh
@@ -27,7 +27,9 @@
 # stop as soon as something fails
 set -e
 
-SCRIPT_DIR=$(dirname $(realpath $BASH_SOURCE))
+# script_dir is the directory that contains THIS (inspect.sh) script, usually
+# stored in the directory '.../bot'
+script_dir=$(dirname $(realpath $BASH_SOURCE))
 
 display_help() {
   echo "usage: $0 [OPTIONS]"
@@ -83,8 +85,8 @@ done
 set -- "${POSITIONAL_ARGS[@]}"
 
 # source utils.sh and cfg_files.sh
-source ${SCRIPT_DIR}/../scripts/utils.sh
-source ${SCRIPT_DIR}/../scripts/cfg_files.sh
+source ${script_dir}/../scripts/utils.sh
+source ${script_dir}/../scripts/cfg_files.sh
 
 if [[ -z ${resume_tgz} ]]; then
     echo_red "path to tarball for resuming build job is missing"
@@ -257,10 +259,8 @@ CMDLINE_ARGS+=("--storage" "${JOB_STORAGE}")
 
 # make sure some environment settings are available inside the shell started via
 # startprefix
-base_dir=$(dirname $(realpath $0))
-# base_dir of inspect.sh script is '.../bot', 'init' dir is at the same level
 # TODO better use script from tarball???
-source ${base_dir}/../init/eessi_defaults
+source ${script_dir}/../init/eessi_defaults
 
 if [ -z $EESSI_VERSION ]; then
     echo "ERROR: \$EESSI_VERSION must be set!" >&2
@@ -434,14 +434,14 @@ echo "Executing command to start interactive session to inspect build job:"
 # These initializations are combined into a single script that is executed when
 # the shell in startprefix is started. We set the env variable BASH_ENV here.
 if [[ -z ${run_in_prefix} ]]; then
-    echo "${SCRIPT_DIR}/../eessi_container.sh ${CMDLINE_ARGS[@]}"
+    echo "${script_dir}/../eessi_container.sh ${CMDLINE_ARGS[@]}"
     echo "                     -- ${EESSI_COMPAT_LAYER_DIR}/startprefix"
-    ${SCRIPT_DIR}/../eessi_container.sh "${CMDLINE_ARGS[@]}" \
+    ${script_dir}/../eessi_container.sh "${CMDLINE_ARGS[@]}" \
                      -- ${EESSI_COMPAT_LAYER_DIR}/startprefix
 else
-    echo "${SCRIPT_DIR}/../eessi_container.sh ${CMDLINE_ARGS[@]}"
+    echo "${script_dir}/../eessi_container.sh ${CMDLINE_ARGS[@]}"
     echo "                     -- ${EESSI_COMPAT_LAYER_DIR}/startprefix <<< ${run_in_prefix}"
-    ${SCRIPT_DIR}/../eessi_container.sh "${CMDLINE_ARGS[@]}" \
+    ${script_dir}/../eessi_container.sh "${CMDLINE_ARGS[@]}" \
                      -- ${EESSI_COMPAT_LAYER_DIR}/startprefix <<< ${run_in_prefix}
 fi
 

From 9fd84f95e19477a75d781cbf1590fd0068ee7587 Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Fri, 17 May 2024 20:15:44 +0200
Subject: [PATCH 370/501] Fix syntax errors

---
 create_lmodsitepackage.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index 61b40c4252..4817f14181 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -155,12 +155,12 @@
     local mt        = frameStk:mt()
     local simpleName = string.match(t.modFullName, "(.-)/")
     local version = string.match(t.modFullName, "%d.%d.%d")
-    if simpleName == 'ESPResSo' and version == '4.2.1'
+    if simpleName == 'ESPResSo' and version == '4.2.1' then
         local advice = 'Prefer versions  >= 4.2.2 which include important bugfixes.\\n'
         advice = advice .. 'For details see https://github.com/espressomd/espresso/issues/4856\\n'
         advice = advice .. 'Use version 4.2.1 at your own risk!\\nn'
         LmodWarning("\\nESPReSso v4.2.1 has known issues and has been deprecated. ", advice)
-        end
+    end
 end
 
 -- Combine both functions into a single one, as we can only register one function as load hook in lmod

From 9d8dbb9e105b8c325a267cb3e7f1504dccc82d94 Mon Sep 17 00:00:00 2001
From: Bob Droge <b.e.droge@rug.nl>
Date: Tue, 21 May 2024 14:09:04 +0000
Subject: [PATCH 371/501] add (empty) RISC-V spec file

---
 init/arch_specs/eessi_arch_riscv.spec | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 init/arch_specs/eessi_arch_riscv.spec

diff --git a/init/arch_specs/eessi_arch_riscv.spec b/init/arch_specs/eessi_arch_riscv.spec
new file mode 100644
index 0000000000..430dd2e72d
--- /dev/null
+++ b/init/arch_specs/eessi_arch_riscv.spec
@@ -0,0 +1 @@
+# Software path in EESSI 	| Vendor ID 	| List of defining CPU features

From 19d14eeb913fedd61604e1fc44675dbcc2a11799 Mon Sep 17 00:00:00 2001
From: Bob Droge <b.e.droge@rug.nl>
Date: Tue, 21 May 2024 14:09:35 +0000
Subject: [PATCH 372/501] add initial riscv64 support

---
 init/eessi_archdetect.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/init/eessi_archdetect.sh b/init/eessi_archdetect.sh
index 58b79b0f2a..e89bc75e13 100755
--- a/init/eessi_archdetect.sh
+++ b/init/eessi_archdetect.sh
@@ -85,6 +85,7 @@ cpupath(){
         "x86_64") local spec_file="eessi_arch_x86.spec";;
         "aarch64") local spec_file="eessi_arch_arm.spec";;
         "ppc64le") local spec_file="eessi_arch_ppc.spec";;
+        "riscv64") local spec_file="eessi_arch_riscv.spec";;
         *) log "ERROR" "cpupath: Unsupported CPU architecture $machine_type"
     esac
     # spec files are located in a subfolder with this script

From 02683fb5325fc7c599e4bd847a927a4447894e0c Mon Sep 17 00:00:00 2001
From: Bob Droge <b.e.droge@rug.nl>
Date: Tue, 21 May 2024 14:09:56 +0000
Subject: [PATCH 373/501] use different defaults for RISC-V

---
 init/eessi_defaults | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/init/eessi_defaults b/init/eessi_defaults
index d1779a36ae..c1ce82d1ce 100644
--- a/init/eessi_defaults
+++ b/init/eessi_defaults
@@ -8,8 +8,20 @@
 # license: GPLv2
 #
 
-export EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO_OVERRIDE:=/cvmfs/software.eessi.io}"
-export EESSI_VERSION="${EESSI_VERSION_OVERRIDE:=2023.06}"
+# use different defaults for RISC-V, as we want to redirect to the riscv.eessi.io repo
+if [[ $(uname -m) == "riscv64" ]]; then
+    export EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO_OVERRIDE:=/cvmfs/riscv.eessi.io}"
+    export EESSI_VERSION="${EESSI_VERSION_OVERRIDE:=20240402}"
+    if [[ ! -v EESSI_SILENT ]]; then
+        echo "RISC-V architecture detected, but there is no RISC-V support yet in the production repository."
+        echo "Automatically switching to version ${EESSI_VERSION} of the RISC-V development repository ${EESSI_CVMFS_REPO}."
+        echo "For more details about this repository, see https://www.eessi.io/docs/repositories/riscv.eessi.io/."
+        echo ""
+    fi
+else
+    export EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO_OVERRIDE:=/cvmfs/software.eessi.io}"
+    export EESSI_VERSION="${EESSI_VERSION_OVERRIDE:=2023.06}"
+fi
 # use archdetect by default, unless otherwise specified
 export EESSI_USE_ARCHDETECT="${EESSI_USE_ARCHDETECT:=1}"
 export EESSI_USE_ARCHSPEC="${EESSI_USE_ARCHSPEC:=0}"

From 243620e734d1514d9104c85d8c0b835007c9dfd7 Mon Sep 17 00:00:00 2001
From: Bob Droge <b.e.droge@rug.nl>
Date: Tue, 21 May 2024 14:10:23 +0000
Subject: [PATCH 374/501] update comment about CPU families: add RISC-V, remove
 POWER

---
 init/minimal_eessi_env | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/init/minimal_eessi_env b/init/minimal_eessi_env
index 5b3562068d..03b337ccf7 100644
--- a/init/minimal_eessi_env
+++ b/init/minimal_eessi_env
@@ -16,7 +16,7 @@ else
     export EESSI_OS_TYPE='macos'
 fi
 
-# aarch64 (Arm 64-bit), ppc64le (POWER 64-bit), x86_64 (x86 64-bit)
+# aarch64 (Arm 64-bit), riscv64 (RISC-V 64-bit), x86_64 (x86 64-bit)
 export EESSI_CPU_FAMILY=$(uname -m)
 
 # set $EPREFIX since that is basically a standard in Gentoo Prefix

From 84036fa5a262712ccde2bd0bdb9ee5b701e87e20 Mon Sep 17 00:00:00 2001
From: Bob Droge <b.e.droge@rug.nl>
Date: Tue, 21 May 2024 21:06:19 +0000
Subject: [PATCH 375/501] also install RISC-V spec file

---
 install_scripts.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/install_scripts.sh b/install_scripts.sh
index 17f0b81008..ab06e47997 100755
--- a/install_scripts.sh
+++ b/install_scripts.sh
@@ -92,7 +92,7 @@ copy_files_by_list ${TOPDIR}/init ${INSTALL_PREFIX}/init "${init_files[@]}"
 
 # Copy for the init/arch_specs directory
 arch_specs_files=(
-   eessi_arch_arm.spec eessi_arch_ppc.spec eessi_arch_x86.spec
+   eessi_arch_arm.spec eessi_arch_ppc.spec eessi_arch_riscv.spec eessi_arch_x86.spec
 )
 copy_files_by_list ${TOPDIR}/init/arch_specs ${INSTALL_PREFIX}/init/arch_specs "${arch_specs_files[@]}"
 

From 9a185ea42e8d96282f43fc9a90652347da9afb28 Mon Sep 17 00:00:00 2001
From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com>
Date: Wed, 22 May 2024 17:51:15 +0200
Subject: [PATCH 376/501] Add ESPResSo v.4.2.2 to foss/2023a 4.9.1 stack

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index e65747e4a5..2fdc40e284 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -4,3 +4,6 @@ easyconfigs:
   - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
       options:
         from-pr: 20379
+  - ESPResSo-4.2.2-foss-2023a.eb:
+      options:
+        from-pr: 20595

From 20ccd475f61f664fd55cc17b857c750f0821ad19 Mon Sep 17 00:00:00 2001
From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com>
Date: Thu, 23 May 2024 14:14:18 +0200
Subject: [PATCH 377/501] Advice refers to release notes, not single issue

ESPResSo Lmod warning <= v4.2.1 points users to v4.2.2 release notes instead of only one of the bugs fixed
---
 create_lmodsitepackage.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index e0d7b31f9e..84b18d499b 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -179,7 +179,7 @@
     local version = string.match(t.modFullName, "%d.%d.%d")
     if simpleName == 'ESPResSo' and version == '4.2.1' then
         local advice = 'Prefer versions  >= 4.2.2 which include important bugfixes.\\n'
-        advice = advice .. 'For details see https://github.com/espressomd/espresso/issues/4856\\n'
+        advice = advice .. 'For details see https://github.com/espressomd/espresso/releases/tag/4.2.2\\n'
         advice = advice .. 'Use version 4.2.1 at your own risk!\\nn'
         LmodWarning("\\nESPReSso v4.2.1 has known issues and has been deprecated. ", advice)
     end

From 7f328675deec19f88969eee91945f44617f68ab6 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Thu, 23 May 2024 15:51:36 +0200
Subject: [PATCH 378/501] Use EESSI_OVERRIDE_GPU_CHECK everywhere

---
 eessi_container.sh | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index 7d00d1400c..a95a2c87c9 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -464,10 +464,9 @@ if [[ ${SETUP_NVIDIA} -eq 1 ]]; then
         BIND_PATHS="${BIND_PATHS},${EESSI_VAR_LOG}:/var/log,${EESSI_USR_LOCAL_CUDA}:/usr/local/cuda"
         [[ ${VERBOSE} -eq 1 ]] && echo "BIND_PATHS=${BIND_PATHS}"
         if [[ "${NVIDIA_MODE}" == "install" ]] ; then
-            # We need to "trick" our LMOD_RC file to allow us to load CUDA modules even without a CUDA driver
-            # (this works because we build within a container and the LMOD_RC recognises that)
-            touch ${EESSI_TMPDIR}/libcuda.so
-            export SINGULARITY_CONTAINLIBS="${EESSI_TMPDIR}/libcuda.so"
+            # No GPU so we need to "trick" Lmod to allow us to load CUDA modules even without a CUDA driver
+            # (this variable means EESSI_OVERRIDE_GPU_CHECK=1 will be set inside the container)
+            export SINGULARITYENV_EESSI_OVERRIDE_GPU_CHECK=1
         fi
     fi
 fi

From df4ac260e209e9ccc2578562845ceb2a328dbbb0 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Thu, 23 May 2024 16:05:27 +0200
Subject: [PATCH 379/501] Restrict overridding the GPU driver check to when we
 know it is valid

---
 EESSI-install-software.sh | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 40f0ed8c3d..8a5789c2b2 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -243,9 +243,6 @@ fi
 #       if not, an error is produced, and the bot flags the whole build as failed (even when not installing GPU software)
 # ${EESSI_PREFIX}/scripts/gpu_support/nvidia/link_nvidia_host_libraries.sh
 
-# Don't run the Lmod GPU driver check when doing builds (may not have a GPU, and it's not relevant for vanilla builds anyway)
-export EESSI_OVERRIDE_GPU_CHECK=1 
-
 # use PR patch file to determine in which easystack files stuff was added
 changed_easystacks=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | egrep -v 'known-issues|missing') 
 if [ -z "${changed_easystacks}" ]; then

From bee4b001322a0d22c79642b5b1427f2c397a9f3b Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 24 May 2024 10:47:45 +0200
Subject: [PATCH 380/501] Make sure EESSI_OVERRIDE_GPU_CHECK is still set when
 in prefix shell

---
 run_in_compat_layer_env.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/run_in_compat_layer_env.sh b/run_in_compat_layer_env.sh
index f57c4d0749..b8e9cf979b 100755
--- a/run_in_compat_layer_env.sh
+++ b/run_in_compat_layer_env.sh
@@ -26,6 +26,9 @@ fi
 if [ ! -z ${EESSI_VERSION_OVERRIDE} ]; then
     INPUT="export EESSI_VERSION_OVERRIDE=${EESSI_VERSION_OVERRIDE}; ${INPUT}"
 fi
+if [ ! -z ${EESSI_OVERRIDE_GPU_CHECK} ]; then
+    INPUT="export EESSI_OVERRIDE_GPU_CHECK=${EESSI_OVERRIDE_GPU_CHECK}; ${INPUT}"
+fi
 if [ ! -z ${http_proxy} ]; then
     INPUT="export http_proxy=${http_proxy}; ${INPUT}"
 fi

From f788ca3ab94ab384ee2e4a98e5b76e2a9317102f Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 24 May 2024 11:18:04 +0200
Subject: [PATCH 381/501] Only install NVIDIA drivers if nvidia-smi command
 exists

---
 EESSI-install-software.sh | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 8a5789c2b2..7d358e205a 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -17,6 +17,11 @@ display_help() {
   echo "  --skip-cuda-install    -  disable installing a full CUDA SDK in the host_injections prefix (e.g. in CI)"
 }
 
+# Function to check if a command exists
+function command_exists() {
+    command -v "$1" >/dev/null 2>&1
+}
+
 function copy_build_log() {
     # copy specified build log to specified directory, with some context added
     build_log=${1}
@@ -238,10 +243,11 @@ else
     echo "Skipping installation of CUDA SDK in host_injections, since the --skip-cuda-install flag was passed OR no EasyBuild module was found"
 fi
 
-# Install drivers in host_injections
-# TODO: this is commented out for now, because the script assumes that nvidia-smi is available and works;
-#       if not, an error is produced, and the bot flags the whole build as failed (even when not installing GPU software)
-# ${EESSI_PREFIX}/scripts/gpu_support/nvidia/link_nvidia_host_libraries.sh
+# Install NVIDIA drivers in host_injections (if they exist)
+if command_exists "nvidia-smi"; then
+    echo "Command 'nvidia-smi' found. Installing NVIDIA drivers for use in prefix shell..."
+    ${EESSI_PREFIX}/scripts/gpu_support/nvidia/link_nvidia_host_libraries.sh
+fi
 
 # use PR patch file to determine in which easystack files stuff was added
 changed_easystacks=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | egrep -v 'known-issues|missing') 

From f974c34a85b3fb322906b974b7fcf084fa6398df Mon Sep 17 00:00:00 2001
From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com>
Date: Mon, 27 May 2024 09:49:10 +0200
Subject: [PATCH 382/501] Fix typo in create_lmodsitepackage.py ESPReSso
 warning

---
 create_lmodsitepackage.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index 84b18d499b..31c040718d 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -180,7 +180,7 @@
     if simpleName == 'ESPResSo' and version == '4.2.1' then
         local advice = 'Prefer versions  >= 4.2.2 which include important bugfixes.\\n'
         advice = advice .. 'For details see https://github.com/espressomd/espresso/releases/tag/4.2.2\\n'
-        advice = advice .. 'Use version 4.2.1 at your own risk!\\nn'
+        advice = advice .. 'Use version 4.2.1 at your own risk!\\n'
         LmodWarning("\\nESPReSso v4.2.1 has known issues and has been deprecated. ", advice)
     end
 end

From 39c8abac220d428dc60f0fcf016dbcf6e0a2d049 Mon Sep 17 00:00:00 2001
From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com>
Date: Mon, 27 May 2024 09:59:09 +0200
Subject: [PATCH 383/501] ESPReSso -> ESPResSo

---
 create_lmodsitepackage.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index 31c040718d..bca2970e39 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -181,7 +181,7 @@
         local advice = 'Prefer versions  >= 4.2.2 which include important bugfixes.\\n'
         advice = advice .. 'For details see https://github.com/espressomd/espresso/releases/tag/4.2.2\\n'
         advice = advice .. 'Use version 4.2.1 at your own risk!\\n'
-        LmodWarning("\\nESPReSso v4.2.1 has known issues and has been deprecated. ", advice)
+        LmodWarning("\\nESPResSo v4.2.1 has known issues and has been deprecated. ", advice)
     end
 end
 

From b15fc3d58c270ad3e28727f30e92c78744cbeee9 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Mon, 27 May 2024 10:54:00 +0200
Subject: [PATCH 384/501] Update bot build script to support whether GPU is
 available or not

---
 bot/build.sh     | 10 +++++++++-
 scripts/utils.sh |  5 +++++
 2 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/bot/build.sh b/bot/build.sh
index dcc61c19d4..c9a362fdca 100755
--- a/bot/build.sh
+++ b/bot/build.sh
@@ -223,7 +223,15 @@ mkdir -p ${TARBALL_TMP_BUILD_STEP_DIR}
 BUILD_STEP_ARGS+=("--save" "${TARBALL_TMP_BUILD_STEP_DIR}")
 BUILD_STEP_ARGS+=("--storage" "${STORAGE}")
 # add options required to handle NVIDIA support
-BUILD_STEP_ARGS+=("--nvidia" "all")
+if command_exists "nvidia-smi"; then
+    echo "Command 'nvidia-smi' found, using available GPU"
+    BUILD_STEP_ARGS+=("--nvidia" "all")
+else
+    echo "No 'nvidia-smi' found, no available GPU but allowing overriding this check"
+    BUILD_STEP_ARGS+=("--nvidia" "install")
+fi
+# Retain location for host injections so we don't reinstall CUDA
+# (Always need to run the driver installation as available driver may change)
 if [[ ! -z ${SHARED_FS_PATH} ]]; then
     BUILD_STEP_ARGS+=("--host-injections" "${SHARED_FS_PATH}/host-injections")
 fi
diff --git a/scripts/utils.sh b/scripts/utils.sh
index b2be3f6221..962decd20e 100644
--- a/scripts/utils.sh
+++ b/scripts/utils.sh
@@ -78,6 +78,11 @@ function create_directory_structure() {
   return $return_code
 }
 
+# Function to check if a command exists
+function command_exists() {
+    command -v "$1" >/dev/null 2>&1
+}
+
 function get_path_for_tool {
     tool_name=$1
     tool_envvar_name=$2

From bb4b3c1b17e9eb6ca588a64690445a505353c1c9 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Tue, 28 May 2024 20:31:11 +0200
Subject: [PATCH 385/501] {2023.06}[gfbf/2023a] ipympl v0.9.3

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023a.yml           | 10 +++++++---
 .../2023.06/eessi-2023.06-eb-4.9.1-2023a.yml           |  8 ++++++++
 2 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 8f5608d881..4b58cb6106 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -48,9 +48,13 @@ easyconfigs:
   - PyOpenGL-3.1.7-GCCcore-12.3.0.eb:
       options:
         from-pr: 20007
-  - ipympl-0.9.3-foss-2023a.eb:
-      options:
-        from-pr: 20126
+  # removed by https://github.com/easybuilders/easybuild-easyconfigs/pull/20586
+  # adding ipympl-0.9.3-gfbf-2023a.eb as a replacement in
+  # easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+  # comment the below out here or CI will fail
+  # - ipympl-0.9.3-foss-2023a.eb:
+  #    options:
+  #      from-pr: 20126
   - OpenJPEG-2.5.0-GCCcore-12.3.0.eb
   - OpenFOAM-10-foss-2023a.eb
   - Highway-1.0.4-GCCcore-12.3.0.eb
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index e65747e4a5..32b388854d 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -4,3 +4,11 @@ easyconfigs:
   - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
       options:
         from-pr: 20379
+  # replacement for ipympl-0.9.3-foss-2023a.eb which has been built via
+  # easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml and was
+  # later removed in https://github.com/easybuilders/easybuild-easyconfigs/pull/20586
+  # below we use the replacement ec file which is provided by
+  # https://github.com/easybuilders/easybuild-easyconfigs/pull/18852
+  - ipympl-0.9.3-gfbf-2023a.eb:
+     options:
+       from-pr: 18852

From 9a036d8c9059c4eda163279322dda915e601b7e3 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Wed, 29 May 2024 06:34:05 +0200
Subject: [PATCH 386/501] {2023.06}[foss/2023a] GATK v4.5.0.0

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index 8238b379f9..3e5c09090e 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -15,3 +15,4 @@ easyconfigs:
   - ESPResSo-4.2.2-foss-2023a.eb:
       options:
         from-pr: 20595
+  - GATK-4.5.0.0-GCCcore-12.3.0-Java-17.eb

From 7c48321761b291bb68046722f628360837a134e0 Mon Sep 17 00:00:00 2001
From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com>
Date: Fri, 31 May 2024 11:52:11 +0200
Subject: [PATCH 387/501] Print message, not warning

On ESPResSo version 4.2.1 message, don't use `LmodWarning` but use `LmodMessage` instead
---
 create_lmodsitepackage.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index ed98d1f0f0..f159f186eb 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -175,16 +175,18 @@
     end
 end
 
-local function eessi_espresso_deprecated_warning(t)
+local function eessi_espresso_deprecated_message(t)
     local frameStk  = require("FrameStk"):singleton()
     local mt        = frameStk:mt()
     local simpleName = string.match(t.modFullName, "(.-)/")
     local version = string.match(t.modFullName, "%d.%d.%d")
     if simpleName == 'ESPResSo' and version == '4.2.1' then
+    -- Print a message on loading ESPreSso v <= 4.2.1 recommending using v 4.2.2 and above.
+    -- A message and not a warning as the exit code would break CI runs otherwise.
         local advice = 'Prefer versions  >= 4.2.2 which include important bugfixes.\\n'
         advice = advice .. 'For details see https://github.com/espressomd/espresso/releases/tag/4.2.2\\n'
         advice = advice .. 'Use version 4.2.1 at your own risk!\\n'
-        LmodWarning("\\nESPResSo v4.2.1 has known issues and has been deprecated. ", advice)
+        LmodMessage("\\nESPResSo v4.2.1 has known issues and has been deprecated. ", advice)
     end
 end
 

From 76babe873669777a79a30e6abc33517873fa31a3 Mon Sep 17 00:00:00 2001
From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com>
Date: Fri, 31 May 2024 13:57:20 +0200
Subject: [PATCH 388/501] Correctly use `eessi_espresso_deprecated_message()`

---
 create_lmodsitepackage.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index f159f186eb..7e55bce2a5 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -193,7 +193,7 @@
 -- Combine both functions into a single one, as we can only register one function as load hook in lmod
 -- Also: make it non-local, so it can be imported and extended by other lmodrc files if needed
 function eessi_load_hook(t)
-    eessi_espresso_deprecated_warning(t)
+    eessi_espresso_deprecated_message(t)
     -- Only apply CUDA hooks if the loaded module is in the EESSI prefix
     -- This avoids getting an Lmod Error when trying to load a CUDA module from a local software stack
     if from_eessi_prefix(t) then

From 22578c43328a6e6257b5023e0cac52d21c5f637b Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Mon, 3 Jun 2024 09:43:04 +0000
Subject: [PATCH 389/501] {2023.06}[foss/2022b] ParaView v5.11.1

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
index e547e45f2b..d023fbbaf1 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
@@ -2,3 +2,4 @@ easyconfigs:
   - R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb:
       options:
         from-pr: 20379
+  - ParaView-5.11.1-foss-2022b.eb

From c77c2676ce98260b88fc9b23130f82cf693168f3 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Tue, 4 Jun 2024 06:37:24 +0000
Subject: [PATCH 390/501] {2023.06}[foss/2023a] WhatsHap v2.2

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index 3e5c09090e..49a7191121 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -16,3 +16,4 @@ easyconfigs:
       options:
         from-pr: 20595
   - GATK-4.5.0.0-GCCcore-12.3.0-Java-17.eb
+  - WhatsHap-2.2-foss-2023a.eb

From 3d3019db4be7ecda681ae862ab33962cc1d61e37 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Tue, 4 Jun 2024 10:48:27 +0200
Subject: [PATCH 391/501] Update scorecards to latest version

---
 .github/workflows/scorecards.yml | 18 +++++++-----------
 1 file changed, 7 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/scorecards.yml b/.github/workflows/scorecards.yml
index 7eff557094..5b482763f2 100644
--- a/.github/workflows/scorecards.yml
+++ b/.github/workflows/scorecards.yml
@@ -4,24 +4,20 @@
 
 name: Scorecards supply-chain security
 on:
-  # For Branch-Protection check. Only the default branch is supported. See
-  # https://github.com/ossf/scorecard/blob/main/docs/checks.md#branch-protection
-  branch_protection_rule:
   # To guarantee Maintained check is occasionally updated. See
   # https://github.com/ossf/scorecard/blob/main/docs/checks.md#maintained
   schedule:
     - cron: '25 15 * * 3'
   push:
-    branches: [ "main" ]
-  pull_request:
-    branches:    
-      - main
+    branches:
+      - '2023.06-software.eessi.io'
 
 # Declare default permissions as read only.
 permissions: read-all
 
 jobs:
   analysis:
+    if: github.repository_owner == 'EESSI'   # Prevent running on forks
     name: Scorecards analysis
     runs-on: ubuntu-latest
     permissions:
@@ -35,12 +31,12 @@ jobs:
 
     steps:
       - name: "Checkout code"
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
         with:
           persist-credentials: false
 
       - name: "Run analysis"
-        uses: ossf/scorecard-action@0864cf19026789058feabb7e87baa5f140aac736 # v2.3.1
+        uses: ossf/scorecard-action@dc50aa9510b46c811795eb24b2f1ba02a914e534 # v2.3.3
         with:
           results_file: results.sarif
           results_format: sarif
@@ -62,7 +58,7 @@ jobs:
       # Upload the results as artifacts (optional). Commenting out will disable uploads of run results in SARIF
       # format to the repository Actions tab.
       - name: "Upload artifact"
-        uses: actions/upload-artifact@3cea5372237819ed00197afe530f5a7ea3e805c8 # v3.1.0
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
         with:
           name: SARIF file
           path: results.sarif
@@ -70,6 +66,6 @@ jobs:
 
       # Upload the results to GitHub's code scanning dashboard.
       - name: "Upload to code-scanning"
-        uses: github/codeql-action/upload-sarif@807578363a7869ca324a79039e6db9c843e0e100 # v2.1.27
+        uses: github/codeql-action/upload-sarif@9fdb3e49720b44c48891d036bb502feb25684276 # v3.25.6
         with:
           sarif_file: results.sarif

From a111b6db76a816e030b40d9d4e60e93686f80709 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 6 Jun 2024 07:53:55 +0200
Subject: [PATCH 392/501] {2023.06,2023b,zen4} SciPy-bundle v2023.11

---
 .../2023.06/zen4/eessi-2023.06-eb-4.9.1-2023b.yml                | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023b.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023b.yml
index 75dc4e6602..bc736c4056 100644
--- a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023b.yml
@@ -1,2 +1,3 @@
 easyconfigs:
   - foss-2023b.eb
+  - SciPy-bundle-2023.11-gfbf-2023b.eb

From fe809a5228a05c699169fd1280de89ce15a753b8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 6 Jun 2024 07:54:28 +0200
Subject: [PATCH 393/501] {2023.06,2023b,zen4} SciPy-bundle v2023.07

---
 .../2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml                | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml
index c821df1afb..b3afe2b368 100644
--- a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -1,2 +1,3 @@
 easyconfigs:
   - foss-2023a.eb
+  - SciPy-bundle-2023.07-gfbf-2023a.eb

From fa2fd59c37432395ac45dceffdd99c8a4ea08948 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Thu, 6 Jun 2024 06:36:30 +0000
Subject: [PATCH 394/501] {2023.06}[gfbf/2022b] ASE v3.22.1

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
index d023fbbaf1..385f33b5cb 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
@@ -3,3 +3,4 @@ easyconfigs:
       options:
         from-pr: 20379
   - ParaView-5.11.1-foss-2022b.eb
+  - ASE-3.22.1-gfbf-2022b.eb

From 08e09ca1655348b7e08e11a4cca710522509f291 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Fri, 7 Jun 2024 06:14:03 +0000
Subject: [PATCH 395/501] {2023.06}[foss/2023b] NLTK v3.8.1

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
index 1392fa2f5a..b06cb2788e 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
@@ -2,3 +2,4 @@ easyconfigs:
   - GROMACS-2024.1-foss-2023b.eb:
       options:
         from-pr: 20439
+  - NLTK-3.8.1-foss-2023b.eb

From 9b3f02da7e8c1279cf20cb9a37356b7c430e32f7 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Fri, 7 Jun 2024 08:07:14 +0000
Subject: [PATCH 396/501] {2023.06}[foss/2022b] SEPP v4.5.1

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
index 385f33b5cb..57c985b020 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
@@ -4,3 +4,4 @@ easyconfigs:
         from-pr: 20379
   - ParaView-5.11.1-foss-2022b.eb
   - ASE-3.22.1-gfbf-2022b.eb
+  - SEPP-4.5.1-foss-2022b.eb

From 46d9018f40db4ca174f60746102335ba87ad53b5 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Fri, 7 Jun 2024 12:03:50 +0200
Subject: [PATCH 397/501] Apply suggestions from code review
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 EESSI-extend-2023.06-easybuild.eb                               | 2 +-
 .../rebuilds/20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index 42defbacc8..b525ee462d 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -143,7 +143,7 @@ setenv ("EASYBUILD_HOOKS", pathJoin(os.getenv("EESSI_PREFIX"), "init", "easybuil
 -- Make sure to use the general umask that allows a global read
 setenv ("EASYBUILD_UMASK", "022")
 
--- All this module to be loaded when running EasyBuild
+-- Allow this module to be loaded when running EasyBuild
 setenv ("EASYBUILD_ALLOW_LOADED_MODULES", "EasyBuild,EESSI-extend")
 
 -- Set all related environment variables if we have project or user installations (including extending MODULEPATH)
diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml
index 5cf2bd6b9d..93c4950fc8 100644
--- a/easystacks/software.eessi.io/2023.06/rebuilds/20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml
@@ -1,5 +1,5 @@
 # 2024.05.15
-# The module is an EasyBuil created module and therefore needs to be an allowed
+# The module is an EasyBuild created module and therefore needs to be an allowed
 # module when running EasyBuild
 easyconfigs:
   - EESSI-extend-2023.06-easybuild.eb 

From 51118efbea0730b820493ff27dab231f256fb53f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 7 Jun 2024 12:08:09 +0200
Subject: [PATCH 398/501] remove double hyphen in filename

---
 ...loaded.yml => 20240506-eb-4.9.1-EESSI-extend-allow-loaded.yml} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename easystacks/software.eessi.io/2023.06/rebuilds/{20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml => 20240506-eb-4.9.1-EESSI-extend-allow-loaded.yml} (100%)

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240506-eb-4.9.1-EESSI-extend-allow-loaded.yml
similarity index 100%
rename from easystacks/software.eessi.io/2023.06/rebuilds/20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml
rename to easystacks/software.eessi.io/2023.06/rebuilds/20240506-eb-4.9.1-EESSI-extend-allow-loaded.yml

From 3bdfff7a7fe360b066a971a0c29f67414470c12f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 8 Jun 2024 14:33:46 +0200
Subject: [PATCH 399/501] {2023.06,zen4}[foss/2023a] ESPResSo 4.2.1

---
 .../2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml                | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml
index b3afe2b368..a529746676 100644
--- a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -1,3 +1,4 @@
 easyconfigs:
   - foss-2023a.eb
   - SciPy-bundle-2023.07-gfbf-2023a.eb
+  - ESPResSo-4.2.1-foss-2023a.eb

From 0b715d73f2fb7c157a28953de233cf71703b6136 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Mon, 10 Jun 2024 05:52:26 +0000
Subject: [PATCH 400/501] {2023.06}[gompi/2023a] BLAST+ v2.14.1

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index 49a7191121..f53ad9235c 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -17,3 +17,6 @@ easyconfigs:
         from-pr: 20595
   - GATK-4.5.0.0-GCCcore-12.3.0-Java-17.eb
   - WhatsHap-2.2-foss-2023a.eb
+  - BLAST+-2.14.1-gompi-2023a.eb:
+      options:     
+        from-pr: 20751

From c7a2e6e348e99a2ac7ca170c4c2d7b1eddc46a94 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int5.local.snellius.surf.nl>
Date: Mon, 10 Jun 2024 11:06:39 +0200
Subject: [PATCH 401/501] Change smile for failed test runs

---
 bot/check-test.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index f045b9500a..3b16e5c415 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -101,7 +101,7 @@ elif [[ ${ERROR} -eq 1 ]]; then
     reason="EESSI test suite was not run, test step itself failed to execute."
     status="FAILURE"
 else
-    summary=":grin: FAILURE"
+    summary=":cry: FAILURE"
     reason="Failed for unknown reason"
     status="FAILURE"
 fi

From ad17f4384c1e9500c9c34aa71ae6b0d51e3c446e Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int4.local.snellius.surf.nl>
Date: Mon, 10 Jun 2024 11:43:55 +0200
Subject: [PATCH 402/501] Fix emoticon

---
 bot/check-test.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index f045b9500a..3b16e5c415 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -101,7 +101,7 @@ elif [[ ${ERROR} -eq 1 ]]; then
     reason="EESSI test suite was not run, test step itself failed to execute."
     status="FAILURE"
 else
-    summary=":grin: FAILURE"
+    summary=":cry: FAILURE"
     reason="Failed for unknown reason"
     status="FAILURE"
 fi

From 596c70299d3f73098f0e6b711e5b246ffd54766e Mon Sep 17 00:00:00 2001
From: TopRichard <121792457+TopRichard@users.noreply.github.com>
Date: Mon, 10 Jun 2024 15:24:13 +0200
Subject: [PATCH 403/501] Update
 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index f53ad9235c..be3b9c1bbf 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -19,4 +19,4 @@ easyconfigs:
   - WhatsHap-2.2-foss-2023a.eb
   - BLAST+-2.14.1-gompi-2023a.eb:
       options:     
-        from-pr: 20751
+        from-pr: 20784

From f288436f8193c70e87485bce1e3866915525720a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 10 Jun 2024 20:42:07 +0200
Subject: [PATCH 404/501] add Valgrind

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml   | 1 +
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml   | 1 +
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml   | 1 +
 3 files changed, 3 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
index 57c985b020..1805c581c3 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
@@ -5,3 +5,4 @@ easyconfigs:
   - ParaView-5.11.1-foss-2022b.eb
   - ASE-3.22.1-gfbf-2022b.eb
   - SEPP-4.5.1-foss-2022b.eb
+  - Valgrind-3.21.0-gompi-2022b.eb
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index 49a7191121..db9a6d7e36 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -17,3 +17,4 @@ easyconfigs:
         from-pr: 20595
   - GATK-4.5.0.0-GCCcore-12.3.0-Java-17.eb
   - WhatsHap-2.2-foss-2023a.eb
+  - Valgrind-3.21.0-gompi-2023a.eb
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
index b06cb2788e..c071f220cf 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
@@ -3,3 +3,4 @@ easyconfigs:
       options:
         from-pr: 20439
   - NLTK-3.8.1-foss-2023b.eb
+  - Valgrind-3.23.0-gompi-2023b.eb

From c9287ed954484034e94fed5a8b6292d8c135bb1f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 10 Jun 2024 20:44:35 +0200
Subject: [PATCH 405/501] add --from-pr to Valgrind

---
 .../2023.06/eessi-2023.06-eb-4.9.1-2023b.yml                  | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
index c071f220cf..888bddace3 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
@@ -3,4 +3,6 @@ easyconfigs:
       options:
         from-pr: 20439
   - NLTK-3.8.1-foss-2023b.eb
-  - Valgrind-3.23.0-gompi-2023b.eb
+  - Valgrind-3.23.0-gompi-2023b.eb:
+      options:
+        from-pr: 20792

From c4af3895e61781cba2dbb3d5982e024d95a15d77 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Tue, 11 Jun 2024 09:19:04 +0000
Subject: [PATCH 406/501] {2023.06}[foss/2023a] OrthoFinder v2.5.5

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index be3b9c1bbf..1d74452e45 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -20,3 +20,4 @@ easyconfigs:
   - BLAST+-2.14.1-gompi-2023a.eb:
       options:     
         from-pr: 20784
+  - OrthoFinder-2.5.5-foss-2023a.eb

From 525b23e9af30453137617ce27f456279151bc1e7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 13 Jun 2024 10:26:49 +0200
Subject: [PATCH 407/501] add easystack for EB 4.9.2 and install it

---
 .../2023.06/eessi-2023.06-eb-4.9.2-001-system.yml            | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-001-system.yml

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-001-system.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-001-system.yml
new file mode 100644
index 0000000000..cd87626494
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-001-system.yml
@@ -0,0 +1,5 @@
+easyconfigs:
+  - EasyBuild-4.9.2.eb:
+      options:
+        from-pr: 20801
+        include-easyblocks-from-pr: 3358

From 460da691db015a88e00a0df8548f3f0721b0c6ad Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 13 Jun 2024 13:03:30 +0200
Subject: [PATCH 408/501] add EB 4.9.2

---
 .../2023.06/eessi-2023.06-eb-4.9.1-001-system.yml             | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
index 46ac979719..8f96cf9450 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
@@ -3,3 +3,7 @@ easyconfigs:
       options:
         from-pr: 20299
   - EESSI-extend-2023.06-easybuild.eb
+  - EasyBuild-4.9.2.eb:
+      options:
+        from-pr: 20801
+        include-easyblocks-from-pr: 3358

From 911737d2bea6cea92c09262bcfa605e18ba553eb Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int4.local.snellius.surf.nl>
Date: Thu, 13 Jun 2024 14:05:46 +0200
Subject: [PATCH 409/501] Add template field for mem per node

---
 reframe_config_bot.py.tmpl | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/reframe_config_bot.py.tmpl b/reframe_config_bot.py.tmpl
index 0cc3e9f530..607373767a 100644
--- a/reframe_config_bot.py.tmpl
+++ b/reframe_config_bot.py.tmpl
@@ -34,6 +34,11 @@ site_configuration = {
                             'options': ['--mem={size}'],
                         }
                     ],
+                    'extras': {
+                        # Make sure to round down, otherwise a job might ask for more mem than is available
+                        # per node
+                        'mem_per_node': __MEM_PER_NODE__,
+                    },
                     'max_jobs': 1
                     }
                 ]

From e10b227d3299a0945edd5ecede13b9784c4fd748 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int4.local.snellius.surf.nl>
Date: Thu, 13 Jun 2024 14:14:36 +0200
Subject: [PATCH 410/501] Get memory limit for cgroup of current job / UID and
 put this into the ReFrame config file

---
 test_suite.sh | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/test_suite.sh b/test_suite.sh
index 95eb9daa2a..5c157f7a47 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -135,7 +135,7 @@ export RFM_PREFIX=$PWD/reframe_runs
 echo "Configured reframe with the following environment variables:"
 env | grep "RFM_"
 
-# Inject correct CPU properties into the ReFrame config file
+# Inject correct CPU/memory properties into the ReFrame config file
 cpuinfo=$(lscpu)
 if [[ "${cpuinfo}" =~ CPU\(s\):[^0-9]*([0-9]+) ]]; then
     cpu_count=${BASH_REMATCH[1]}
@@ -157,11 +157,19 @@ if [[ "${cpuinfo}" =~ (Core\(s\) per socket:[^0-9]*([0-9]+)) ]]; then
 else
     fatal_error "Failed to get the number of cores per socket for the current test hardware with lscpu."
 fi
+cgroup_mem_bytes=$(cat /sys/fs/cgroup/memory/slurm/uid_${UID}/job_${SLURM_JOB_ID}/memory.limit_in_bytes)
+if [[ $? -eq 0 ]]
+    # Convert to MiB
+    cgroup_mem_mib=$((cgroup_mem_bytes/(1024*1024)))
+else
+    fatal_error "Failed to get the memory limit in bytes from the current cgroup"
+fi
 cp ${RFM_CONFIG_FILE_TEMPLATE} ${RFM_CONFIG_FILES}
 sed -i "s/__NUM_CPUS__/${cpu_count}/g" $RFM_CONFIG_FILES
 sed -i "s/__NUM_SOCKETS__/${socket_count}/g" $RFM_CONFIG_FILES
 sed -i "s/__NUM_CPUS_PER_CORE__/${threads_per_core}/g" $RFM_CONFIG_FILES
 sed -i "s/__NUM_CPUS_PER_SOCKET__/${cores_per_socket}/g" $RFM_CONFIG_FILES
+sed -i "s/__MEM_PER_NODE__/${cgroup_mem_mib/g" $RFM_CONFIG_FILES
 
 # Workaround for https://github.com/EESSI/software-layer/pull/467#issuecomment-1973341966
 export PSM3_DEVICES='self,shm'  # this is enough, since we only run single node for now

From 644eddcb66a46871cdfe93ef54ca70954169f548 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int4.local.snellius.surf.nl>
Date: Thu, 13 Jun 2024 14:16:02 +0200
Subject: [PATCH 411/501] Missing bracket

---
 test_suite.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test_suite.sh b/test_suite.sh
index 5c157f7a47..2d072d3d95 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -169,7 +169,7 @@ sed -i "s/__NUM_CPUS__/${cpu_count}/g" $RFM_CONFIG_FILES
 sed -i "s/__NUM_SOCKETS__/${socket_count}/g" $RFM_CONFIG_FILES
 sed -i "s/__NUM_CPUS_PER_CORE__/${threads_per_core}/g" $RFM_CONFIG_FILES
 sed -i "s/__NUM_CPUS_PER_SOCKET__/${cores_per_socket}/g" $RFM_CONFIG_FILES
-sed -i "s/__MEM_PER_NODE__/${cgroup_mem_mib/g" $RFM_CONFIG_FILES
+sed -i "s/__MEM_PER_NODE__/${cgroup_mem_mib}/g" $RFM_CONFIG_FILES
 
 # Workaround for https://github.com/EESSI/software-layer/pull/467#issuecomment-1973341966
 export PSM3_DEVICES='self,shm'  # this is enough, since we only run single node for now

From bcba10e3553806f4f1dda6d27412f4756464f13c Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int4.local.snellius.surf.nl>
Date: Thu, 13 Jun 2024 14:16:48 +0200
Subject: [PATCH 412/501] Fix if-else syntax

---
 test_suite.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test_suite.sh b/test_suite.sh
index 2d072d3d95..46b43ee78a 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -158,7 +158,7 @@ else
     fatal_error "Failed to get the number of cores per socket for the current test hardware with lscpu."
 fi
 cgroup_mem_bytes=$(cat /sys/fs/cgroup/memory/slurm/uid_${UID}/job_${SLURM_JOB_ID}/memory.limit_in_bytes)
-if [[ $? -eq 0 ]]
+if [[ $? -eq 0 ]]; then
     # Convert to MiB
     cgroup_mem_mib=$((cgroup_mem_bytes/(1024*1024)))
 else

From 70c1b146789d3d0c4d92f0a368ab078c724b898a Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int4.local.snellius.surf.nl>
Date: Thu, 13 Jun 2024 15:18:17 +0200
Subject: [PATCH 413/501] Make sure we bind-mount /sys/fs/cgroup into the
 container, so that we can use it to determine available memory for
 dynamically configuring ReFrame in the test step

---
 bot/test.sh        |  3 ++
 eessi_container.sh | 78 ++++++++++++++++++++++++++--------------------
 test_suite.sh      |  2 +-
 3 files changed, 48 insertions(+), 35 deletions(-)

diff --git a/bot/test.sh b/bot/test.sh
index 4984340e6e..b3f6acf0ea 100755
--- a/bot/test.sh
+++ b/bot/test.sh
@@ -204,6 +204,9 @@ if [[ -z ${RESUME_DIR} ]]; then
 else
   TEST_STEP_ARGS+=("--resume" "${RESUME_DIR}")
 fi
+# Bind mount /sys/fs/cgroup so that we can determine the amount of memory available in our cgroup for
+# Reframe configuration
+TEST_STEP_ARGS+=("--extra-bind-paths /sys/fs/cgroup:/hostsys/fs/cgroup:ro")
 
 # prepare arguments to test_suite.sh (specific to test step)
 declare -a TEST_SUITE_ARGS=()
diff --git a/eessi_container.sh b/eessi_container.sh
index a95a2c87c9..eac8e74c83 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -70,40 +70,43 @@ export EESSI_REPOS_CFG_FILE="${EESSI_REPOS_CFG_DIR}/repos.cfg"
 display_help() {
   echo "usage: $0 [OPTIONS] [[--] SCRIPT or COMMAND]"
   echo " OPTIONS:"
-  echo "  -a | --access {ro,rw}  - ro (read-only), rw (read & write) [default: ro]"
-  echo "  -c | --container IMG   - image file or URL defining the container to use"
-  echo "                           [default: docker://ghcr.io/eessi/build-node:debian11]"
-  echo "  -f | --fakeroot        - run the container with --fakeroot [default: false]"
-  echo "  -g | --storage DIR     - directory space on host machine (used for"
-  echo "                           temporary data) [default: 1. TMPDIR, 2. /tmp]"
-  echo "  -h | --help            - display this usage information [default: false]"
-  echo "  -i | --host-injections - directory to link to for host_injections "
-  echo "                           [default: /..storage../opt-eessi]"
-  echo "  -l | --list-repos      - list available repository identifiers [default: false]"
-  echo "  -m | --mode MODE       - with MODE==shell (launch interactive shell) or"
-  echo "                           MODE==run (run a script or command) [default: shell]"
-  echo "  -n | --nvidia MODE     - configure the container to work with NVIDIA GPUs,"
-  echo "                           MODE==install for a CUDA installation, MODE==run to"
-  echo "                           attach a GPU, MODE==all for both [default: false]"
-  echo "  -r | --repository CFG  - configuration file or identifier defining the"
-  echo "                           repository to use [default: EESSI via"
-  echo "                           default container, see --container]"
-  echo "  -u | --resume DIR/TGZ  - resume a previous run from a directory or tarball,"
-  echo "                           where DIR points to a previously used tmp directory"
-  echo "                           (check for output 'Using DIR as tmp ...' of a previous"
-  echo "                           run) and TGZ is the path to a tarball which is"
-  echo "                           unpacked the tmp dir stored on the local storage space"
-  echo "                           (see option --storage above) [default: not set]"
-  echo "  -s | --save DIR/TGZ    - save contents of tmp directory to a tarball in"
-  echo "                           directory DIR or provided with the fixed full path TGZ"
-  echo "                           when a directory is provided, the format of the"
-  echo "                           tarball's name will be {REPO_ID}-{TIMESTAMP}.tgz"
-  echo "                           [default: not set]"
-  echo "  -v | --verbose         - display more information [default: false]"
-  echo "  -x | --http-proxy URL  - provides URL for the env variable http_proxy"
-  echo "                           [default: not set]; uses env var \$http_proxy if set"
-  echo "  -y | --https-proxy URL - provides URL for the env variable https_proxy"
-  echo "                           [default: not set]; uses env var \$https_proxy if set"
+  echo "  -a | --access {ro,rw}   - ro (read-only), rw (read & write) [default: ro]"
+  echo "  -c | --container IMG    - image file or URL defining the container to use"
+  echo "                            [default: docker://ghcr.io/eessi/build-node:debian11]"
+  echo "  -f | --fakeroot         - run the container with --fakeroot [default: false]"
+  echo "  -g | --storage DIR      - directory space on host machine (used for"
+  echo "                            temporary data) [default: 1. TMPDIR, 2. /tmp]"
+  echo "  -h | --help             - display this usage information [default: false]"
+  echo "  -i | --host-injections  - directory to link to for host_injections "
+  echo "                            [default: /..storage../opt-eessi]"
+  echo "  -l | --list-repos       - list available repository identifiers [default: false]"
+  echo "  -m | --mode MODE        - with MODE==shell (launch interactive shell) or"
+  echo "                            MODE==run (run a script or command) [default: shell]"
+  echo "  -n | --nvidia MODE      - configure the container to work with NVIDIA GPUs,"
+  echo "                            MODE==install for a CUDA installation, MODE==run to"
+  echo "                            attach a GPU, MODE==all for both [default: false]"
+  echo "  -r | --repository CFG   - configuration file or identifier defining the"
+  echo "                            repository to use [default: EESSI via"
+  echo "                            default container, see --container]"
+  echo "  -u | --resume DIR/TGZ   - resume a previous run from a directory or tarball,"
+  echo "                            where DIR points to a previously used tmp directory"
+  echo "                            (check for output 'Using DIR as tmp ...' of a previous"
+  echo "                            run) and TGZ is the path to a tarball which is"
+  echo "                            unpacked the tmp dir stored on the local storage space"
+  echo "                            (see option --storage above) [default: not set]"
+  echo "  -s | --save DIR/TGZ     - save contents of tmp directory to a tarball in"
+  echo "                            directory DIR or provided with the fixed full path TGZ"
+  echo "                            when a directory is provided, the format of the"
+  echo "                            tarball's name will be {REPO_ID}-{TIMESTAMP}.tgz"
+  echo "                            [default: not set]"
+  echo "  -v | --verbose          - display more information [default: false]"
+  echo "  -x | --http-proxy URL   - provides URL for the env variable http_proxy"
+  echo "                            [default: not set]; uses env var \$http_proxy if set"
+  echo "  -y | --https-proxy URL  - provides URL for the env variable https_proxy"
+  echo "                            [default: not set]; uses env var \$https_proxy if set"
+  echo "  -b | --extra-bind-paths - specify extra paths to be bound into the container."
+  echo "                            To specify multiple bind paths, seperate by comma."
+  echo "                            Example: '/src:/dest:ro,/src2:/dest2:rw'"
   echo
   echo " If value for --mode is 'run', the SCRIPT/COMMAND provided is executed. If"
   echo " arguments to the script/command start with '-' or '--', use the flag terminator"
@@ -197,6 +200,10 @@ while [[ $# -gt 0 ]]; do
       export https_proxy=${HTTPS_PROXY}
       shift 2
       ;;
+    -b|--extra-bind-paths)
+      EXTRA_BIND_PATHS="$2"
+      shift 2
+      ;;
     --)
       shift
       POSITIONAL_ARGS+=("$@") # save positional args
@@ -439,6 +446,9 @@ fi
 BIND_PATHS="${EESSI_CVMFS_VAR_LIB}:/var/lib/cvmfs,${EESSI_CVMFS_VAR_RUN}:/var/run/cvmfs,${HOST_INJECTIONS}:/opt/eessi"
 # provide a '/tmp' inside the container
 BIND_PATHS="${BIND_PATHS},${EESSI_TMPDIR}:${TMP_IN_CONTAINER}"
+if [[ ! -z ${EXTRA_BIND_PATHS} ]]; then
+    BIND_PATHS="${BIND_PATHS},${EXTRA_BIND_PATHS}"
+fi
 
 [[ ${VERBOSE} -eq 1 ]] && echo "BIND_PATHS=${BIND_PATHS}"
 
diff --git a/test_suite.sh b/test_suite.sh
index 46b43ee78a..6e73fbd87c 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -157,7 +157,7 @@ if [[ "${cpuinfo}" =~ (Core\(s\) per socket:[^0-9]*([0-9]+)) ]]; then
 else
     fatal_error "Failed to get the number of cores per socket for the current test hardware with lscpu."
 fi
-cgroup_mem_bytes=$(cat /sys/fs/cgroup/memory/slurm/uid_${UID}/job_${SLURM_JOB_ID}/memory.limit_in_bytes)
+cgroup_mem_bytes=$(cat /hostsys/fs/cgroup/memory/slurm/uid_${UID}/job_${SLURM_JOB_ID}/memory.limit_in_bytes)
 if [[ $? -eq 0 ]]; then
     # Convert to MiB
     cgroup_mem_mib=$((cgroup_mem_bytes/(1024*1024)))

From 5bfd7c1c0898ee268530295f794438cd1fd29836 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com>
Date: Thu, 13 Jun 2024 16:45:32 +0200
Subject: [PATCH 414/501] Update eessi_container.sh
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 eessi_container.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index eac8e74c83..55b0aa4c63 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -71,6 +71,9 @@ display_help() {
   echo "usage: $0 [OPTIONS] [[--] SCRIPT or COMMAND]"
   echo " OPTIONS:"
   echo "  -a | --access {ro,rw}   - ro (read-only), rw (read & write) [default: ro]"
+  echo "  -b | --extra-bind-paths - specify extra paths to be bound into the container."
+  echo "                            To specify multiple bind paths, seperate by comma."
+  echo "                            Example: '/src:/dest:ro,/src2:/dest2:rw'"
   echo "  -c | --container IMG    - image file or URL defining the container to use"
   echo "                            [default: docker://ghcr.io/eessi/build-node:debian11]"
   echo "  -f | --fakeroot         - run the container with --fakeroot [default: false]"
@@ -104,9 +107,6 @@ display_help() {
   echo "                            [default: not set]; uses env var \$http_proxy if set"
   echo "  -y | --https-proxy URL  - provides URL for the env variable https_proxy"
   echo "                            [default: not set]; uses env var \$https_proxy if set"
-  echo "  -b | --extra-bind-paths - specify extra paths to be bound into the container."
-  echo "                            To specify multiple bind paths, seperate by comma."
-  echo "                            Example: '/src:/dest:ro,/src2:/dest2:rw'"
   echo
   echo " If value for --mode is 'run', the SCRIPT/COMMAND provided is executed. If"
   echo " arguments to the script/command start with '-' or '--', use the flag terminator"

From a7fca5155a4e9c145d73c416c85e4c1e6f2c2c12 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int4.local.snellius.surf.nl>
Date: Thu, 13 Jun 2024 16:46:33 +0200
Subject: [PATCH 415/501] Sort alphabetically

---
 eessi_container.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index eac8e74c83..aa5df50af6 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -137,6 +137,10 @@ while [[ $# -gt 0 ]]; do
       ACCESS="$2"
       shift 2
       ;;
+    -b|--extra-bind-paths)
+      EXTRA_BIND_PATHS="$2"
+      shift 2
+      ;;
     -c|--container)
       CONTAINER="$2"
       shift 2
@@ -200,10 +204,6 @@ while [[ $# -gt 0 ]]; do
       export https_proxy=${HTTPS_PROXY}
       shift 2
       ;;
-    -b|--extra-bind-paths)
-      EXTRA_BIND_PATHS="$2"
-      shift 2
-      ;;
     --)
       shift
       POSITIONAL_ARGS+=("$@") # save positional args

From 13366e7c3f3c1aa59192f70e8a26e451611a15d6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 13 Jun 2024 16:48:42 +0200
Subject: [PATCH 416/501] fix typo

---
 eessi_container.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index 891b793f9d..fb14e2118f 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -72,7 +72,7 @@ display_help() {
   echo " OPTIONS:"
   echo "  -a | --access {ro,rw}   - ro (read-only), rw (read & write) [default: ro]"
   echo "  -b | --extra-bind-paths - specify extra paths to be bound into the container."
-  echo "                            To specify multiple bind paths, seperate by comma."
+  echo "                            To specify multiple bind paths, separate by comma."
   echo "                            Example: '/src:/dest:ro,/src2:/dest2:rw'"
   echo "  -c | --container IMG    - image file or URL defining the container to use"
   echo "                            [default: docker://ghcr.io/eessi/build-node:debian11]"

From 63c1abfb8d03fbceb23914d3143abef68dd23bdf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 13 Jun 2024 16:55:06 +0200
Subject: [PATCH 417/501] remove EB 4.9.2 from 4.9.1 easystack

---
 .../2023.06/eessi-2023.06-eb-4.9.1-001-system.yml             | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
index 8f96cf9450..46ac979719 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
@@ -3,7 +3,3 @@ easyconfigs:
       options:
         from-pr: 20299
   - EESSI-extend-2023.06-easybuild.eb
-  - EasyBuild-4.9.2.eb:
-      options:
-        from-pr: 20801
-        include-easyblocks-from-pr: 3358

From 7f6cb8d740ef9761cabd65eb221d9cdc52a84f63 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 13 Jun 2024 17:04:18 +0200
Subject: [PATCH 418/501] remove include-easyblocks-from-pr for EB 4.9.2

---
 .../2023.06/eessi-2023.06-eb-4.9.2-001-system.yml                | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-001-system.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-001-system.yml
index cd87626494..a90f565412 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-001-system.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-001-system.yml
@@ -2,4 +2,3 @@ easyconfigs:
   - EasyBuild-4.9.2.eb:
       options:
         from-pr: 20801
-        include-easyblocks-from-pr: 3358

From 1d56c7239aec4a4521f1114c482b95b7b1f8f2c6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 13 Jun 2024 17:21:47 +0200
Subject: [PATCH 419/501] use separate quotes for option and argument

---
 bot/test.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bot/test.sh b/bot/test.sh
index b3f6acf0ea..04bff346cd 100755
--- a/bot/test.sh
+++ b/bot/test.sh
@@ -206,7 +206,7 @@ else
 fi
 # Bind mount /sys/fs/cgroup so that we can determine the amount of memory available in our cgroup for
 # Reframe configuration
-TEST_STEP_ARGS+=("--extra-bind-paths /sys/fs/cgroup:/hostsys/fs/cgroup:ro")
+TEST_STEP_ARGS+=("--extra-bind-paths" "/sys/fs/cgroup:/hostsys/fs/cgroup:ro")
 
 # prepare arguments to test_suite.sh (specific to test step)
 declare -a TEST_SUITE_ARGS=()

From 158f0eb96d2027a51bb8d5ad8ae347405790c8d4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 13 Jun 2024 20:17:44 +0200
Subject: [PATCH 420/501] add EB 4.9.2

---
 .../2023.06/eessi-2023.06-eb-4.9.1-001-system.yml             | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
index 46ac979719..9e6f4ddb1a 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
@@ -3,3 +3,7 @@ easyconfigs:
       options:
         from-pr: 20299
   - EESSI-extend-2023.06-easybuild.eb
+easyconfigs:
+  - EasyBuild-4.9.2.eb:
+      options:
+        from-pr: 20818

From 4c5cc45627041da2526ad9d9f8ca11b8be10580e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 13 Jun 2024 20:19:45 +0200
Subject: [PATCH 421/501] remove 4.9.2 easystack

---
 .../2023.06/eessi-2023.06-eb-4.9.2-001-system.yml             | 4 ----
 1 file changed, 4 deletions(-)
 delete mode 100644 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-001-system.yml

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-001-system.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-001-system.yml
deleted file mode 100644
index a90f565412..0000000000
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-001-system.yml
+++ /dev/null
@@ -1,4 +0,0 @@
-easyconfigs:
-  - EasyBuild-4.9.2.eb:
-      options:
-        from-pr: 20801

From 8581d3f53f5dde36c46152faecb7de2d88521236 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 13 Jun 2024 22:27:29 +0200
Subject: [PATCH 422/501] Remove line

---
 .../2023.06/eessi-2023.06-eb-4.9.1-001-system.yml                | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
index 9e6f4ddb1a..866766a36b 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
@@ -3,7 +3,6 @@ easyconfigs:
       options:
         from-pr: 20299
   - EESSI-extend-2023.06-easybuild.eb
-easyconfigs:
   - EasyBuild-4.9.2.eb:
       options:
         from-pr: 20818

From 39cf7a0395e67e341808f96dbea812576bef5eb1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 14 Jun 2024 13:24:55 +0200
Subject: [PATCH 423/501] {2023.06,zen4}[foss/2023a] ESPResSo 4.2.2

---
 .../2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml               | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
new file mode 100644
index 0000000000..f148a7fdf9
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -0,0 +1,2 @@
+easyconfigs:
+  - ESPResSo-4.2.2-foss-2023a.eb

From eb363eddaccdde1d70a622d77123d480e6b226c9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 14 Jun 2024 15:49:49 +0200
Subject: [PATCH 424/501] {2023.06,zen4}[foss/2023a] TensorFlow 2.13.0

---
 .../2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml                | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
index f148a7fdf9..f2f4c9d1f5 100644
--- a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -1,2 +1,3 @@
 easyconfigs:
   - ESPResSo-4.2.2-foss-2023a.eb
+  - TensorFlow-2.13.0-foss-2023a.eb

From c810b4e3cf420b4c9f0285211da7f83a5a8e8f7b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 14 Jun 2024 21:47:31 +0200
Subject: [PATCH 425/501] {2023.06,zen4}[foss/2023a] R 4.3.2

---
 .../2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml                | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
index f2f4c9d1f5..09f525364f 100644
--- a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -1,3 +1,4 @@
 easyconfigs:
   - ESPResSo-4.2.2-foss-2023a.eb
   - TensorFlow-2.13.0-foss-2023a.eb
+  - R-4.3.2-gfbf-2023a.eb

From c92f941875f91696e305232fdca1e4d13bd2b091 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 14 Jun 2024 23:22:14 +0200
Subject: [PATCH 426/501] {2023.06,zen4}[foss/2023b] GROMACS 2024.1

---
 .../2023.06/zen4/eessi-2023.06-eb-4.9.2-2023b.yml               | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023b.yml

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023b.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023b.yml
new file mode 100644
index 0000000000..af2c3bfca6
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023b.yml
@@ -0,0 +1,2 @@
+easyconfigs:
+  - GROMACS-2024.1-foss-2023b.eb

From ce370806de21ad95fd6825dcad24262bc8d28ec5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 15 Jun 2024 09:35:29 +0200
Subject: [PATCH 427/501] {2023.06,zen4} add missing installations with
 foss/2023b

---
 .../zen4/eessi-2023.06-eb-4.9.2-2023b.yml        | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023b.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023b.yml
index af2c3bfca6..30a6745ccc 100644
--- a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023b.yml
@@ -1,2 +1,18 @@
 easyconfigs:
   - GROMACS-2024.1-foss-2023b.eb
+  - netCDF-4.9.2-gompi-2023b.eb
+  - matplotlib-3.8.2-gfbf-2023b.eb
+  - DP3-6.0-foss-2023b.eb
+  - WSClean-3.4-foss-2023b.eb
+  - CDO-2.2.2-gompi-2023b.eb
+  - python-casacore-3.5.2-foss-2023b.eb
+  - libspatialindex-1.9.3-GCCcore-13.2.0.eb
+  - LittleCMS-2.15-GCCcore-13.2.0.eb
+  - giflib-5.2.1-GCCcore-13.2.0.eb
+  - OpenJPEG-2.5.0-GCCcore-13.2.0.eb
+  - libwebp-1.3.2-GCCcore-13.2.0.eb
+  - Wayland-1.22.0-GCCcore-13.2.0.eb
+  - Qt5-5.15.13-GCCcore-13.2.0.eb
+  - OSU-Micro-Benchmarks-7.2-gompi-2023b.eb
+  - NLTK-3.8.1-foss-2023b.eb
+  - Valgrind-3.23.0-gompi-2023b.eb

From 1183ae9cc174af34792363048f18cd7086c4666c Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Mon, 17 Jun 2024 11:33:11 +0000
Subject: [PATCH 428/501] {2023.06}[GCCcore/13.2.0] IPython v8.17.2

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml  | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
new file mode 100644
index 0000000000..c23b5b001d
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
@@ -0,0 +1,2 @@
+easyconfigs:
+  - IPython-8.17.2-GCCcore-13.2.0.eb

From e8c2d0636e087d4e565d5d5993d2894fa21da6b1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Thomas=20R=C3=B6blitz?= <thomas.roblitz@uib.no>
Date: Mon, 17 Jun 2024 15:10:28 +0200
Subject: [PATCH 429/501] first steps to support multiple CVMFS repositories

---
 eessi_container.sh | 99 +++++++++++++++++++++++++++++++++++-----------
 1 file changed, 77 insertions(+), 22 deletions(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index fb14e2118f..9b1ab69a3b 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -48,7 +48,11 @@ HTTPS_PROXY_ERROR_EXITCODE=$((${ANY_ERROR_EXITCODE} << 10))
 RUN_SCRIPT_MISSING_EXITCODE=$((${ANY_ERROR_EXITCODE} << 11))
 NVIDIA_MODE_UNKNOWN_EXITCODE=$((${ANY_ERROR_EXITCODE} << 12))
 
+# we use an associative array for storing sets of settings per CVMFS repository
+declare -A cvmfs_repo_settings
+
 # CernVM-FS settings
+# TODO may need to put them into repository specific map
 CVMFS_VAR_LIB="var-lib-cvmfs"
 CVMFS_VAR_RUN="var-run-cvmfs"
 
@@ -89,8 +93,9 @@ display_help() {
   echo "                            MODE==install for a CUDA installation, MODE==run to"
   echo "                            attach a GPU, MODE==all for both [default: false]"
   echo "  -r | --repository CFG   - configuration file or identifier defining the"
-  echo "                            repository to use [default: EESSI via"
-  echo "                            default container, see --container]"
+  echo "                            repository to use; can be given multiple times"
+  echo "                            [default: software.eessi.io via CVMFS config available"
+  echo "                            via default container, see --container]"
   echo "  -u | --resume DIR/TGZ   - resume a previous run from a directory or tarball,"
   echo "                            where DIR points to a previously used tmp directory"
   echo "                            (check for output 'Using DIR as tmp ...' of a previous"
@@ -123,7 +128,7 @@ STORAGE=
 LIST_REPOS=0
 MODE="shell"
 SETUP_NVIDIA=0
-REPOSITORY="EESSI"
+REPOSITORIES=()
 RESUME=
 SAVE=
 HTTP_PROXY=${http_proxy:-}
@@ -179,7 +184,7 @@ while [[ $# -gt 0 ]]; do
       shift 2
       ;;
     -r|--repository)
-      REPOSITORY="$2"
+      REPOSITORIES+=("$2")
       shift 2
       ;;
     -s|--save)
@@ -221,22 +226,50 @@ done
 
 set -- "${POSITIONAL_ARGS[@]}"
 
+# define a list of CVMFS repositories that are accessible via the
+# CVMFS config repository which is always mounted
+declare -A eessi_cvmfs_repos=(["dev.eessi.io"]="extra", ["riscv.eessi.io"]="extra", ["software.eessi.io"]="default")
+eessi_default_cvmfs_repo="software.eessi.io"
+
+# if REPOSITORIES is empty add default repository given above
+if [[ ${#REPOSITORIES[@]} -eq 0 ]]; then
+    REPOSITORIES+=(${eessi_default_cvmfs_repo})
+fi
+
+# define a list of CVMFS repositories that are accessible via the
+# configuration file provided via $EESSI_REPOS_CFG_FILE
+declare -A cfg_cvmfs_repos=()
+if [[ -r ${EESSI_REPOS_CFG_FILE} ]]; then
+    cfg_load ${EESSI_REPOS_CFG_FILE}
+    sections=$(cfg_sections)
+    while IFS= read -r repo_id
+    do
+        cfg_cvmfs_repos[${repo_id}]=${EESSI_REPOS_CFG_FILE}
+    done <<< "${sections}"
+fi
+
 if [[ ${LIST_REPOS} -eq 1 ]]; then
-    echo "Listing available repositories with format 'name [source]':"
-    echo "    EESSI [default]"
-    if [[ -r ${EESSI_REPOS_CFG_FILE} ]]; then
-        cfg_load ${EESSI_REPOS_CFG_FILE}
-        sections=$(cfg_sections)
-        while IFS= read -r repo_id
-        do
-            echo "    ${repo_id} [${EESSI_REPOS_CFG_FILE}]"
-        done <<< "${sections}"
-    fi
+    echo "Listing available repositories with format 'name [source[, 'default']]'."
+    echo "Note, without argument '--repository' the one labeled 'default' will be mounted."
+    for cvmfs_repo in "${!eessi_cvmfs_repos[@]}"
+    do
+        if [[ ${eessi_cvmfs_repos[${cvmfs_repo}]} == "default" ]] ; then
+            default_label=", default"
+        else
+            default_label=""
+	fi
+        echo "    ${cvmfs_repo} [CVMFS config repo${default_label}]"
+    done
+    for cfg_repo in "${!cfg_cvmfs_repos[@]}"
+    do
+        echo "    ${cfg_repo} [${cfg_cvmfs_repos[$cfg_repo]}]"
+    done
     exit 0
 fi
 
 # 1. check if argument values are valid
 # (arg -a|--access) check if ACCESS is supported
+# TODO use the value as global setting, suffix to --repository can specify an access mode per repository
 if [[ "${ACCESS}" != "ro" && "${ACCESS}" != "rw" ]]; then
     fatal_error "unknown access method '${ACCESS}'" "${ACCESS_UNKNOWN_EXITCODE}"
 fi
@@ -260,10 +293,16 @@ if [[ ${SETUP_NVIDIA} -eq 1 ]]; then
     fi
 fi
 
-# TODO (arg -r|--repository) check if repository is known
+# TODO (arg -r|--repository) check if all explicitly listed repositories are known
 # REPOSITORY_ERROR_EXITCODE
-if [[ ! -z "${REPOSITORY}" && "${REPOSITORY}" != "EESSI" && ! -r ${EESSI_REPOS_CFG_FILE} ]]; then
-    fatal_error "arg '--repository ${REPOSITORY}' requires a cfg file at '${EESSI_REPOS_CFG_FILE}'" "${REPOSITORY_ERROR_EXITCODE}"
+if [[ ${#REPOSITORIES[@]} -ne 0 ]] ; then
+    # iterate over entries in REPOSITORIES and check if they are known
+    for cvmfs_repo in "${REPOSITORIES[@]}"
+    do
+        if [[ ! -n "${eessi_cvmfs_repos[${cvmfs_repo}]}" && ! -n ${cfg_cvmfs_repos[${cvmfs_repo}]} ]]; then
+            fatal_error "The repository '${cvmfs_repo}' is not an EESSI CVMFS repository or it is not known how to mount it (could be due to a typo or missing configuration). Run '$0 -l' to obtain a list of available repositories." "${REPOSITORY_ERROR_EXITCODE}"
+        fi
+    done
 fi
 
 # TODO (arg -u|--resume) check if it exists, if user has read permission,
@@ -337,22 +376,36 @@ if [[ ! -z ${RESUME} && -f ${RESUME} ]]; then
 fi
 
 # 3. set up common vars and directories
+# TODO change to be able to support multiple CVMFS repositories
 #    directory structure should be:
 #      ${EESSI_HOST_STORAGE}
 #      |-singularity_cache
-#      |-${CVMFS_VAR_LIB}
-#      |-${CVMFS_VAR_RUN}
-#      |-overlay-upper
-#      |-overlay-work
 #      |-home
 #      |-repos_cfg
-#      |-opt-eessi (unless otherwise specificed for host_injections)
+#      |-CVMFS_REPO_1
+#      |   |-repo_settings (name, access_mode, host_injections)
+#      |   |-${CVMFS_VAR_LIB}
+#      |   |-${CVMFS_VAR_RUN}
+#      |   |-overlay-upper
+#      |   |-overlay-work
+#      |   |-opt-eessi (unless otherwise specificed for host_injections)
+#      |-CVMFS_REPO_n
+#          |-repo_settings (name, access_mode, host_injections)
+#          |-${CVMFS_VAR_LIB}
+#          |-${CVMFS_VAR_RUN}
+#          |-overlay-upper
+#          |-overlay-work
+#          |-opt-eessi (unless otherwise specificed for host_injections)
 
 # tmp dir for EESSI
 EESSI_TMPDIR=${EESSI_HOST_STORAGE}
 mkdir -p ${EESSI_TMPDIR}
 [[ ${VERBOSE} -eq 1 ]] && echo "EESSI_TMPDIR=${EESSI_TMPDIR}"
 
+# TODO make this specific to repository
+# TODO move this code to when we already know which repositories we want to access
+#      actually we should know this already here, but we should rather move this to
+#      where repository args are being processed
 # Set host_injections directory and ensure it is a writable directory (if user provided)
 if [ -z ${USER_HOST_INJECTIONS+x} ]; then
     # Not set, so use our default
@@ -486,6 +539,8 @@ if [[ ${FAKEROOT} -eq 1 ]]; then
   ADDITIONAL_CONTAINER_OPTIONS+=("--fakeroot")
 fi
 
+exit 0; # CONTINUE HERE
+# TODO iterate over repositories in array REPOSITORIES
 # set up repository config (always create directory repos_cfg and populate it with info when
 # arg -r|--repository is used)
 mkdir -p ${EESSI_TMPDIR}/repos_cfg

From 4057496eabede14e228fe08d2fec670870411a1b Mon Sep 17 00:00:00 2001
From: julianmorillo <julianmorillo@users.noreply.github.com>
Date: Tue, 18 Jun 2024 12:00:19 +0200
Subject: [PATCH 430/501] Update eessi-2023.06-eb-4.9.2-2023b.yml including DLB

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
index c23b5b001d..38bfa81142 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
@@ -1,2 +1,3 @@
 easyconfigs:
   - IPython-8.17.2-GCCcore-13.2.0.eb
+  - dlb-3.4-gompi-2023b.eb

From c7a1ca2fbbb736b3eea2242c7143aaa3be063fca Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Thomas=20R=C3=B6blitz?= <thomas.roblitz@uib.no>
Date: Tue, 18 Jun 2024 15:05:17 +0200
Subject: [PATCH 431/501] further changes to support multiple repositories

---
 eessi_container.sh | 248 +++++++++++++++++++++++++++------------------
 1 file changed, 148 insertions(+), 100 deletions(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index 9b1ab69a3b..d561d37792 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -228,16 +228,14 @@ set -- "${POSITIONAL_ARGS[@]}"
 
 # define a list of CVMFS repositories that are accessible via the
 # CVMFS config repository which is always mounted
+# TODO instead of hard-coding the 'extra' and 'default' repositories here one
+#      could have another script in the GitHub and/or CVMFS repository which
+#      provides this "configuration"
 declare -A eessi_cvmfs_repos=(["dev.eessi.io"]="extra", ["riscv.eessi.io"]="extra", ["software.eessi.io"]="default")
-eessi_default_cvmfs_repo="software.eessi.io"
-
-# if REPOSITORIES is empty add default repository given above
-if [[ ${#REPOSITORIES[@]} -eq 0 ]]; then
-    REPOSITORIES+=(${eessi_default_cvmfs_repo})
-fi
+eessi_default_cvmfs_repo="software.eessi.io,access=${ACCESS}"
 
 # define a list of CVMFS repositories that are accessible via the
-# configuration file provided via $EESSI_REPOS_CFG_FILE
+#   configuration file provided via $EESSI_REPOS_CFG_FILE
 declare -A cfg_cvmfs_repos=()
 if [[ -r ${EESSI_REPOS_CFG_FILE} ]]; then
     cfg_load ${EESSI_REPOS_CFG_FILE}
@@ -267,6 +265,11 @@ if [[ ${LIST_REPOS} -eq 1 ]]; then
     exit 0
 fi
 
+# if REPOSITORIES is empty add default repository given above
+if [[ ${#REPOSITORIES[@]} -eq 0 ]]; then
+    REPOSITORIES+=(${eessi_default_cvmfs_repo})
+fi
+
 # 1. check if argument values are valid
 # (arg -a|--access) check if ACCESS is supported
 # TODO use the value as global setting, suffix to --repository can specify an access mode per repository
@@ -295,15 +298,45 @@ fi
 
 # TODO (arg -r|--repository) check if all explicitly listed repositories are known
 # REPOSITORY_ERROR_EXITCODE
-if [[ ${#REPOSITORIES[@]} -ne 0 ]] ; then
-    # iterate over entries in REPOSITORIES and check if they are known
-    for cvmfs_repo in "${REPOSITORIES[@]}"
-    do
-        if [[ ! -n "${eessi_cvmfs_repos[${cvmfs_repo}]}" && ! -n ${cfg_cvmfs_repos[${cvmfs_repo}]} ]]; then
-            fatal_error "The repository '${cvmfs_repo}' is not an EESSI CVMFS repository or it is not known how to mount it (could be due to a typo or missing configuration). Run '$0 -l' to obtain a list of available repositories." "${REPOSITORY_ERROR_EXITCODE}"
+# iterate over entries in REPOSITORIES and check if they are known
+for cvmfs_repo in "${REPOSITORIES[@]}"
+do
+    # split into name and access mode if ',access=' in $cvmfs_repo
+    if [[ ${cvmfs_repo} == *",access="* ]] ; then
+        cvmfs_repo_name=${cvmfs_repo/,access=*/} # remove access mode specification
+    else
+        cvmfs_repo_name="${cvmfs_repo}"
+    fi
+    if [[ ! -n "${eessi_cvmfs_repos[${cvmfs_repo_name}]}" && ! -n ${cfg_cvmfs_repos[${cvmfs_repo_name}]} ]]; then
+        fatal_error "The repository '${cvmfs_repo_name}' is not an EESSI CVMFS repository or it is not known how to mount it (could be due to a typo or missing configuration). Run '$0 -l' to obtain a list of available repositories." "${REPOSITORY_ERROR_EXITCODE}"
+    fi
+done
+
+# make sure each repository is only listed once
+declare -A listed_repos=()
+for cvmfs_repo in "${REPOSITORIES[@]}"
+do
+    cvmfs_repo_name=${cvmfs_repo/,access=*/} # remove access mode
+    echo "checking for duplicates: '${cvmfs_repo}' and '${cvmfs_repo_name}'"
+    # if cvmfs_repo_name is not in eessi_cvmfs_repos, assume it's in cfg_cvmfs_repos
+    #   and obtain actual repo_name from config
+    cfg_repo_id=''
+    if [[ ! -n "${eessi_cvmfs_repos[${cvmfs_repo_name}]}" ]] ; then
+        [[ ${VERBOSE} -eq 1 ]] && echo "repo '${cvmfs_repo_name}' is not an EESSI CVMFS repository..."
+        # cvmfs_repo_name is actually a repository ID, use that to obtain
+	#   the actual name from the EESSI_REPOS_CFG_FILE
+        cfg_repo_id=${cvmfs_repo_name}
+        cvmfs_repo_name=$(cfg_get_value ${cfg_repo_id} "repo_name")
+    fi
+    if [[ -n "${listed_repos[${cvmfs_repo_name}]}" ]] ; then
+        via_cfg=""
+        if [[ -n "${cfg_repo_id}" ]] ; then
+            via_cfg=" (via repository ID '${cfg_repo_id}')"
         fi
-    done
-fi
+        fatal_error "CVMFS repository '${cvmfs_repo_name}'${via_cfg} listed multiple times"
+    fi
+    listed_repos+=([${cvmfs_repo_name}]=true)
+done
 
 # TODO (arg -u|--resume) check if it exists, if user has read permission,
 #      if it contains data from a previous run
@@ -382,17 +415,15 @@ fi
 #      |-singularity_cache
 #      |-home
 #      |-repos_cfg
+#      |-${CVMFS_VAR_LIB}
+#      |-${CVMFS_VAR_RUN}
 #      |-CVMFS_REPO_1
 #      |   |-repo_settings (name, access_mode, host_injections)
-#      |   |-${CVMFS_VAR_LIB}
-#      |   |-${CVMFS_VAR_RUN}
 #      |   |-overlay-upper
 #      |   |-overlay-work
 #      |   |-opt-eessi (unless otherwise specificed for host_injections)
 #      |-CVMFS_REPO_n
 #          |-repo_settings (name, access_mode, host_injections)
-#          |-${CVMFS_VAR_LIB}
-#          |-${CVMFS_VAR_RUN}
 #          |-overlay-upper
 #          |-overlay-work
 #          |-opt-eessi (unless otherwise specificed for host_injections)
@@ -402,7 +433,7 @@ EESSI_TMPDIR=${EESSI_HOST_STORAGE}
 mkdir -p ${EESSI_TMPDIR}
 [[ ${VERBOSE} -eq 1 ]] && echo "EESSI_TMPDIR=${EESSI_TMPDIR}"
 
-# TODO make this specific to repository
+# TODO make this specific to repository?
 # TODO move this code to when we already know which repositories we want to access
 #      actually we should know this already here, but we should rather move this to
 #      where repository args are being processed
@@ -481,6 +512,7 @@ fi
 [[ ${VERBOSE} -eq 1 ]] && echo "CONTAINER=${CONTAINER}"
 
 # set env vars and create directories for CernVM-FS
+# TODO need to use separate values for separate repos?
 EESSI_CVMFS_VAR_LIB=${EESSI_TMPDIR}/${CVMFS_VAR_LIB}
 EESSI_CVMFS_VAR_RUN=${EESSI_TMPDIR}/${CVMFS_VAR_RUN}
 mkdir -p ${EESSI_CVMFS_VAR_LIB}
@@ -539,92 +571,106 @@ if [[ ${FAKEROOT} -eq 1 ]]; then
   ADDITIONAL_CONTAINER_OPTIONS+=("--fakeroot")
 fi
 
-exit 0; # CONTINUE HERE
 # TODO iterate over repositories in array REPOSITORIES
 # set up repository config (always create directory repos_cfg and populate it with info when
 # arg -r|--repository is used)
 mkdir -p ${EESSI_TMPDIR}/repos_cfg
-if [[ "${REPOSITORY}" == "EESSI" ]]; then
-  # need to source defaults as late as possible (see other sourcing below)
-  source ${TOPDIR}/init/eessi_defaults
-
-  # strip "/cvmfs/" from default setting
-  repo_name=${EESSI_CVMFS_REPO/\/cvmfs\//}
-else
-  # TODO implement more flexible specification of repo cfgs
-  #      REPOSITORY => repo-id OR repo-cfg-file (with a single section) OR
-  #                    repo-cfg-file:repo-id (repo-id defined in repo-cfg-file)
-  #
-  # for now, assuming repo-id is defined in config file pointed to
-  #   EESSI_REPOS_CFG_FILE, which is to be copied into the working directory
-  #   (could also become part of the software layer to define multiple
-  #    standard EESSI repositories)
-  cfg_load ${EESSI_REPOS_CFG_FILE}
-
-  # copy repos.cfg to job directory --> makes it easier to inspect the job
-  cp -a ${EESSI_REPOS_CFG_FILE} ${EESSI_TMPDIR}/repos_cfg/.
-
-  # cfg file should include: repo_name, repo_version, config_bundle,
-  #   map { local_filepath -> container_filepath }
-  #
-  # repo_name_domain is the domain part of the repo_name, e.g.,
-  #   eessi.io for software.eessi.io
-  #
-  # where config bundle includes the files (-> target location in container)
-  # - default.local -> /etc/cvmfs/default.local
-  #   contains CVMFS settings, e.g., CVMFS_HTTP_PROXY, CVMFS_QUOTA_LIMIT, ...
-  # - ${repo_name_domain}.conf -> /etc/cvmfs/domain.d/${repo_name_domain}.conf
-  #   contains CVMFS settings, e.g., CVMFS_SERVER_URL (Stratum 1s),
-  #   CVMFS_KEYS_DIR, CVMFS_USE_GEOAPI, ...
-  # - ${repo_name_domain}/ -> /etc/cvmfs/keys/${repo_name_domain}
-  #   a directory that contains the public key to access the repository, key
-  #   itself then doesn't need to be BIND mounted
-  # - ${repo_name_domain}/${repo_name}.pub
-  #   (-> /etc/cvmfs/keys/${repo_name_domain}/${repo_name}.pub
-  #   the public key to access the repository, key itself is BIND mounted
-  #   via directory ${repo_name_domain}
-  repo_name=$(cfg_get_value ${REPOSITORY} "repo_name")
-  # derive domain part from repo_name (everything after first '.')
-  repo_name_domain=${repo_name#*.}
-  repo_version=$(cfg_get_value ${REPOSITORY} "repo_version")
-  config_bundle=$(cfg_get_value ${REPOSITORY} "config_bundle")
-  config_map=$(cfg_get_value ${REPOSITORY} "config_map")
-
-  # convert config_map into associative array cfg_file_map
-  cfg_init_file_map "${config_map}"
-  [[ ${VERBOSE} -eq 1 ]] && cfg_print_map
-
-  # use information to set up dir ${EESSI_TMPDIR}/repos_cfg,
-  #     define BIND mounts and override repo name and version
-  # check if config_bundle exists, if so, unpack it into ${EESSI_TMPDIR}/repos_cfg
-  # if config_bundle is relative path (no '/' at start) prepend it with
-  # EESSI_REPOS_CFG_DIR
-  config_bundle_path=
-  if [[ ! "${config_bundle}" =~ ^/ ]]; then
-      config_bundle_path=${EESSI_REPOS_CFG_DIR}/${config_bundle}
-  else
-      config_bundle_path=${config_bundle}
-  fi
+[[ ${VERBOSE} -eq 1 ]] && echo
+[[ ${VERBOSE} -eq 1 ]] && echo -e "BIND_PATHS before processing REPOSITORIES\n  BIND_PATHS=${BIND_PATHS}"
+[[ ${VERBOSE} -eq 1 ]] && echo
+for cvmfs_repo in "${REPOSITORIES[@]}"
+do
+    echo "process CVMFS repo spec '${cvmfs_repo}'"
+    # split into name and access mode if ',access=' in $cvmfs_repo
+    if [[ ${cvmfs_repo} == *",access="* ]] ; then
+        cvmfs_repo_name=${cvmfs_repo/,access=*/} # remove access mode specification
+        cvmfs_repo_access=${cvmfs_repo/*,access=/} # remove repo name part
+    else
+        cvmfs_repo_name="${cvmfs_repo}"
+        cvmfs_repo_access="${ACCESS}" # use globally defined access mode
+    fi
+    # if cvmfs_repo_name is in cfg_cvmfs_repos, it is a "repository ID" and was
+    #   derived from information in EESSI_REPOS_CFG_FILE, namely the section
+    #   names in that .ini-type file
+    # in the if-block below, we'll use cfg_repo_id to refer to that ID
+    # we need to process/provide the config from EESSI_REPOS_CFG_FILE, such
+    #   that the necessary information for accessing a CVMFS repository is made
+    #   available inside the container
+    if [[ -n "${cfg_cvmfs_repos[${cvmfs_repo_name}]}" ]] ; then
+	cfg_repo_id=${cvmfs_repo_name}
+
+	# obtain CVMFS repository name from section for the given ID
+        cfg_repo_name=$(cfg_get_value ${cfg_repo_id} "repo_name")
+	# derive domain part from (cfg_)repo_name (everything after first '.')
+        repo_name_domain=${repo_name#*.}
+
+        # cfg_cvmfs_repos is populated through reading the file pointed to by
+        #   EESSI_REPOS_CFG_FILE. We need to copy that file and data it needs
+        #   into the job's working directory.
+
+        # copy repos.cfg to job directory --> makes it easier to inspect the job
+        cp -a ${EESSI_REPOS_CFG_FILE} ${EESSI_TMPDIR}/repos_cfg/.
+
+	# cfg file should include sections (one per CVMFS repository to be mounted)
+	#   with each section containing the settings:
+	#   - repo_name,
+	#   - repo_version,
+	#   - config_bundle, and
+	#   - a map { filepath_in_bundle -> container_filepath }
+        #
+	# The config_bundle includes the files which are mapped ('->') to a target
+	# location in container:
+        # - default.local -> /etc/cvmfs/default.local
+        #   contains CVMFS settings, e.g., CVMFS_HTTP_PROXY, CVMFS_QUOTA_LIMIT, ...
+        # - ${repo_name_domain}.conf -> /etc/cvmfs/domain.d/${repo_name_domain}.conf
+        #   contains CVMFS settings, e.g., CVMFS_SERVER_URL (Stratum 1s),
+        #   CVMFS_KEYS_DIR, CVMFS_USE_GEOAPI, ...
+        # - ${repo_name_domain}/ -> /etc/cvmfs/keys/${repo_name_domain}
+        #   a directory that contains the public key to access the repository, key
+        #   itself then doesn't need to be BIND mounted
+        # - ${repo_name_domain}/${cfg_repo_name}.pub
+        #   (-> /etc/cvmfs/keys/${repo_name_domain}/${cfg_repo_name}.pub
+        #   the public key to access the repository, key itself is BIND mounted
+        #   via directory ${repo_name_domain}
+        cfg_repo_version=$(cfg_get_value ${cfg_repo_id} "repo_version")
+        cfg_config_bundle=$(cfg_get_value ${cfg_repo_id} "config_bundle")
+        cfg_config_map=$(cfg_get_value ${cfg_repo_id} "config_map")
+
+        # convert cfg_config_map into associative array cfg_file_map
+        cfg_init_file_map "${cfg_config_map}"
+        [[ ${VERBOSE} -eq 1 ]] && cfg_print_map
+
+        # use information to set up dir ${EESSI_TMPDIR}/repos_cfg and define
+        #   BIND mounts
+        # check if config_bundle exists, if so, unpack it into
+	#   ${EESSI_TMPDIR}/repos_cfg; if it doesn't, exit with an error
+        # if config_bundle is relative path (no '/' at start) prepend it with
+        #   EESSI_REPOS_CFG_DIR
+        config_bundle_path=
+        if [[ ! "${cfg_config_bundle}" =~ ^/ ]]; then
+            config_bundle_path=${EESSI_REPOS_CFG_DIR}/${cfg_config_bundle}
+        else
+            config_bundle_path=${cfg_config_bundle}
+        fi
 
-  if [[ ! -r ${config_bundle_path} ]]; then
-    fatal_error "config bundle '${config_bundle_path}' is not readable" ${REPOSITORY_ERROR_EXITCODE}
-  fi
+        if [[ ! -r ${config_bundle_path} ]]; then
+            fatal_error "config bundle '${config_bundle_path}' is not readable" ${REPOSITORY_ERROR_EXITCODE}
+        fi
 
-  # only unpack config_bundle if we're not resuming from a previous run
-  if [[ -z ${RESUME} ]]; then
-    tar xf ${config_bundle_path} -C ${EESSI_TMPDIR}/repos_cfg
-  fi
+        # only unpack cfg_config_bundle if we're not resuming from a previous run
+        if [[ -z ${RESUME} ]]; then
+            tar xf ${config_bundle_path} -C ${EESSI_TMPDIR}/repos_cfg
+        fi
 
-  for src in "${!cfg_file_map[@]}"
-  do
-    target=${cfg_file_map[${src}]}
-    BIND_PATHS="${BIND_PATHS},${EESSI_TMPDIR}/repos_cfg/${src}:${target}"
-  done
-  export EESSI_VERSION_OVERRIDE=${repo_version}
-  export EESSI_CVMFS_REPO_OVERRIDE="/cvmfs/${repo_name}"
-  # need to source defaults as late as possible (after *_OVERRIDEs)
-  source ${TOPDIR}/init/eessi_defaults
-fi
+        for src in "${!cfg_file_map[@]}"
+        do
+            target=${cfg_file_map[${src}]}
+            BIND_PATHS="${BIND_PATHS},${EESSI_TMPDIR}/repos_cfg/${src}:${target}"
+        done
+    fi
+    [[ ${VERBOSE} -eq 1 ]] && echo -e "BIND_PATHS after processing '${cvmfs_repo}'\n  BIND_PATHS=${BIND_PATHS}"
+    [[ ${VERBOSE} -eq 1 ]] && echo
+done
 
 # if http_proxy is not empty, we assume that the machine accesses internet
 # via a proxy. then we need to add CVMFS_HTTP_PROXY to
@@ -650,14 +696,16 @@ if [[ ! -z ${http_proxy} ]]; then
         export BIND_PATHS="${BIND_PATHS},${EESSI_TMPDIR}/repos_cfg/default.local:/etc/cvmfs/default.local"
     fi
 fi
+exit 0; # CONTINUE HERE
 
 # 4. set up vars and dirs specific to a scenario
 
 declare -a EESSI_FUSE_MOUNTS=()
 
-# always mount cvmfs-config repo (to get access to software.eessi.io)
+# always mount cvmfs-config repo (to get access to EESSI repositories such as software.eessi.io)
 EESSI_FUSE_MOUNTS+=("--fusemount" "container:cvmfs2 cvmfs-config.cern.ch /cvmfs/cvmfs-config.cern.ch")
 
+# TODO iterate over REPOSITORIES and either use repository-specific access mode or global setting (possibly a global default)
 if [[ "${ACCESS}" == "ro" ]]; then
   export EESSI_READONLY="container:cvmfs2 ${repo_name} /cvmfs/${repo_name}"
 

From 934059a731f55d5a11cc10b6e3719abf65b1d478 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Thomas=20R=C3=B6blitz?= <thomas.roblitz@uib.no>
Date: Wed, 19 Jun 2024 15:21:27 +0200
Subject: [PATCH 432/501] configure multiple fusemounts

---
 eessi_container.sh | 123 +++++++++++++++++++++++++++------------------
 1 file changed, 74 insertions(+), 49 deletions(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index d561d37792..c549d04d8c 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -52,7 +52,6 @@ NVIDIA_MODE_UNKNOWN_EXITCODE=$((${ANY_ERROR_EXITCODE} << 12))
 declare -A cvmfs_repo_settings
 
 # CernVM-FS settings
-# TODO may need to put them into repository specific map
 CVMFS_VAR_LIB="var-lib-cvmfs"
 CVMFS_VAR_RUN="var-run-cvmfs"
 
@@ -272,7 +271,7 @@ fi
 
 # 1. check if argument values are valid
 # (arg -a|--access) check if ACCESS is supported
-# TODO use the value as global setting, suffix to --repository can specify an access mode per repository
+# use the value as global setting, suffix to --repository can specify an access mode per repository
 if [[ "${ACCESS}" != "ro" && "${ACCESS}" != "rw" ]]; then
     fatal_error "unknown access method '${ACCESS}'" "${ACCESS_UNKNOWN_EXITCODE}"
 fi
@@ -317,7 +316,7 @@ declare -A listed_repos=()
 for cvmfs_repo in "${REPOSITORIES[@]}"
 do
     cvmfs_repo_name=${cvmfs_repo/,access=*/} # remove access mode
-    echo "checking for duplicates: '${cvmfs_repo}' and '${cvmfs_repo_name}'"
+    [[ ${VERBOSE} -eq 1 ]] && echo "checking for duplicates: '${cvmfs_repo}' and '${cvmfs_repo_name}'"
     # if cvmfs_repo_name is not in eessi_cvmfs_repos, assume it's in cfg_cvmfs_repos
     #   and obtain actual repo_name from config
     cfg_repo_id=''
@@ -409,7 +408,6 @@ if [[ ! -z ${RESUME} && -f ${RESUME} ]]; then
 fi
 
 # 3. set up common vars and directories
-# TODO change to be able to support multiple CVMFS repositories
 #    directory structure should be:
 #      ${EESSI_HOST_STORAGE}
 #      |-singularity_cache
@@ -528,14 +526,18 @@ fi
 [[ ${VERBOSE} -eq 1 ]] && echo "SINGULARITY_HOME=${SINGULARITY_HOME}"
 
 # define paths to add to SINGULARITY_BIND (added later when all BIND mounts are defined)
-BIND_PATHS="${EESSI_CVMFS_VAR_LIB}:/var/lib/cvmfs,${EESSI_CVMFS_VAR_RUN}:/var/run/cvmfs,${HOST_INJECTIONS}:/opt/eessi"
+if [[ -z ${SINGULARITY_BIND} ]] ; then
+    SINGULARITY_BIND="${EESSI_CVMFS_VAR_LIB}:/var/lib/cvmfs,${EESSI_CVMFS_VAR_RUN}:/var/run/cvmfs,${HOST_INJECTIONS}:/opt/eessi"
+else
+    SINGULARITY_BIND="${EESSI_CVMFS_VAR_LIB}:/var/lib/cvmfs,${EESSI_CVMFS_VAR_RUN}:/var/run/cvmfs,${HOST_INJECTIONS}:/opt/eessi,${SINGULARITY_BIND}"
+fi
 # provide a '/tmp' inside the container
-BIND_PATHS="${BIND_PATHS},${EESSI_TMPDIR}:${TMP_IN_CONTAINER}"
+SINGULARITY_BIND="${SINGULARITY_BIND},${EESSI_TMPDIR}:${TMP_IN_CONTAINER}"
 if [[ ! -z ${EXTRA_BIND_PATHS} ]]; then
-    BIND_PATHS="${BIND_PATHS},${EXTRA_BIND_PATHS}"
+    SINGULARITY_BIND="${SINGULARITY_BIND},${EXTRA_BIND_PATHS}"
 fi
 
-[[ ${VERBOSE} -eq 1 ]] && echo "BIND_PATHS=${BIND_PATHS}"
+[[ ${VERBOSE} -eq 1 ]] && echo "SINGULARITY_BIND=${SINGULARITY_BIND}"
 
 declare -a ADDITIONAL_CONTAINER_OPTIONS=()
 
@@ -556,8 +558,8 @@ if [[ ${SETUP_NVIDIA} -eq 1 ]]; then
         EESSI_USR_LOCAL_CUDA=${EESSI_TMPDIR}/usr-local-cuda
         mkdir -p ${EESSI_VAR_LOG}
         mkdir -p ${EESSI_USR_LOCAL_CUDA}
-        BIND_PATHS="${BIND_PATHS},${EESSI_VAR_LOG}:/var/log,${EESSI_USR_LOCAL_CUDA}:/usr/local/cuda"
-        [[ ${VERBOSE} -eq 1 ]] && echo "BIND_PATHS=${BIND_PATHS}"
+        SINGULARITY_BIND="${SINGULARITY_BIND},${EESSI_VAR_LOG}:/var/log,${EESSI_USR_LOCAL_CUDA}:/usr/local/cuda"
+        [[ ${VERBOSE} -eq 1 ]] && echo "SINGULARITY_BIND=${SINGULARITY_BIND}"
         if [[ "${NVIDIA_MODE}" == "install" ]] ; then
             # No GPU so we need to "trick" Lmod to allow us to load CUDA modules even without a CUDA driver
             # (this variable means EESSI_OVERRIDE_GPU_CHECK=1 will be set inside the container)
@@ -571,16 +573,16 @@ if [[ ${FAKEROOT} -eq 1 ]]; then
   ADDITIONAL_CONTAINER_OPTIONS+=("--fakeroot")
 fi
 
-# TODO iterate over repositories in array REPOSITORIES
 # set up repository config (always create directory repos_cfg and populate it with info when
 # arg -r|--repository is used)
 mkdir -p ${EESSI_TMPDIR}/repos_cfg
 [[ ${VERBOSE} -eq 1 ]] && echo
-[[ ${VERBOSE} -eq 1 ]] && echo -e "BIND_PATHS before processing REPOSITORIES\n  BIND_PATHS=${BIND_PATHS}"
+[[ ${VERBOSE} -eq 1 ]] && echo -e "SINGULARITY_BIND before processing REPOSITORIES\n  SINGULARITY_BIND=${SINGULARITY_BIND}"
 [[ ${VERBOSE} -eq 1 ]] && echo
+# iterate over repositories in array REPOSITORIES
 for cvmfs_repo in "${REPOSITORIES[@]}"
 do
-    echo "process CVMFS repo spec '${cvmfs_repo}'"
+    [[ ${VERBOSE} -eq 1 ]] && echo "process CVMFS repo spec '${cvmfs_repo}'"
     # split into name and access mode if ',access=' in $cvmfs_repo
     if [[ ${cvmfs_repo} == *",access="* ]] ; then
         cvmfs_repo_name=${cvmfs_repo/,access=*/} # remove access mode specification
@@ -665,17 +667,21 @@ do
         for src in "${!cfg_file_map[@]}"
         do
             target=${cfg_file_map[${src}]}
-            BIND_PATHS="${BIND_PATHS},${EESSI_TMPDIR}/repos_cfg/${src}:${target}"
+            # if target is alreay BIND mounted, exit with an error
+            if [[ ${SINGULARITY_BIND} =~ "${target}" ]]; then
+                fatal_error "target '${target}' is already listed in paths to bind mount into the container ('${SINGULARITY_BIND}')" ${REPOSITORY_ERROR_EXITCODE}
+            fi
+            export SINGULARITY_BIND="${SINGULARITY_BIND},${EESSI_TMPDIR}/repos_cfg/${src}:${target}"
         done
     fi
-    [[ ${VERBOSE} -eq 1 ]] && echo -e "BIND_PATHS after processing '${cvmfs_repo}'\n  BIND_PATHS=${BIND_PATHS}"
+    [[ ${VERBOSE} -eq 1 ]] && echo -e "SINGULARITY_BIND after processing '${cvmfs_repo}'\n  SINGULARITY_BIND=${SINGULARITY_BIND}"
     [[ ${VERBOSE} -eq 1 ]] && echo
 done
 
 # if http_proxy is not empty, we assume that the machine accesses internet
 # via a proxy. then we need to add CVMFS_HTTP_PROXY to
-# ${EESSI_TMPDIR}/repos_cfg/default.local on host (and possibly add a BIND
-# MOUNT if it was not yet in BIND_PATHS)
+# ${EESSI_TMPDIR}/repos_cfg/default.local on the host (and possibly add a BIND
+# MOUNT if it was not yet in SINGULARITY_BIND)
 if [[ ! -z ${http_proxy} ]]; then
     # TODO tolerate other formats for proxy URLs, for now assume format is
     # http://SOME_HOSTNAME:SOME_PORT/
@@ -691,12 +697,14 @@ if [[ ! -z ${http_proxy} ]]; then
     [[ ${VERBOSE} -eq 1 ]] && echo "contents of default.local"
     [[ ${VERBOSE} -eq 1 ]] && cat ${EESSI_TMPDIR}/repos_cfg/default.local
 
-    # if default.local is not BIND mounted into container, add it to BIND_PATHS
-    if [[ ! ${BIND_PATHS} =~ "${EESSI_TMPDIR}/repos_cfg/default.local:/etc/cvmfs/default.local" ]]; then
-        export BIND_PATHS="${BIND_PATHS},${EESSI_TMPDIR}/repos_cfg/default.local:/etc/cvmfs/default.local"
+    # if default.local is not BIND mounted into container, add it to SINGULARITY_BIND
+    src=${EESSI_TMPDIR}/repos_cfg/default.local
+    target=/etc/cvmfs/default.local
+    if [[ ${SINGULARITY_BIND} =~ "${target}" ]]; then
+        fatal_error "BIND target in '${src}:${target}' is already in paths to be bind mounted into the container ('${SINGULARITY_BIND}')" ${REPOSITORY_ERROR_EXITCODE}
     fi
+    export SINGULARITY_BIND="${SINGULARITY_BIND},${src}:${target}"
 fi
-exit 0; # CONTINUE HERE
 
 # 4. set up vars and dirs specific to a scenario
 
@@ -705,42 +713,59 @@ declare -a EESSI_FUSE_MOUNTS=()
 # always mount cvmfs-config repo (to get access to EESSI repositories such as software.eessi.io)
 EESSI_FUSE_MOUNTS+=("--fusemount" "container:cvmfs2 cvmfs-config.cern.ch /cvmfs/cvmfs-config.cern.ch")
 
-# TODO iterate over REPOSITORIES and either use repository-specific access mode or global setting (possibly a global default)
-if [[ "${ACCESS}" == "ro" ]]; then
-  export EESSI_READONLY="container:cvmfs2 ${repo_name} /cvmfs/${repo_name}"
-
-  EESSI_FUSE_MOUNTS+=("--fusemount" "${EESSI_READONLY}")
-  export EESSI_FUSE_MOUNTS
-fi
+# iterate over REPOSITORIES and either use repository-specific access mode or global setting (possibly a global default)
+for cvmfs_repo in "${REPOSITORIES[@]}"
+do
+    [[ ${VERBOSE} -eq 1 ]] && echo "add fusemount options for CVMFS repo '${cvmfs_repo}'"
+    # split into name and access mode if ',access=' in $cvmfs_repo
+    if [[ ${cvmfs_repo} == *",access="* ]] ; then
+        cvmfs_repo_name=${cvmfs_repo/,access=*/} # remove access mode specification
+        cvmfs_repo_access=${cvmfs_repo/*,access=/} # remove repo name part
+    else
+        cvmfs_repo_name="${cvmfs_repo}"
+        cvmfs_repo_access="${ACCESS}" # use globally defined access mode
+    fi
+    # obtain cvmfs_repo_name from EESSI_REPOS_CFG_FILE if cvmfs_repo is in cfg_cvmfs_repos
+    if [[ ${cfg_cvmfs_repos[${cvmfs_repo_name}]} ]]; then
+        [[ ${VERBOSE} -eq 1 ]] && echo "repo '${cvmfs_repo_name}' is not an EESSI CVMFS repository..."
+        # cvmfs_repo_name is actually a repository ID, use that to obtain
+	#   the actual name from the EESSI_REPOS_CFG_FILE
+        cfg_repo_id=${cvmfs_repo_name}
+        cvmfs_repo_name=$(cfg_get_value ${cfg_repo_id} "repo_name")
+    fi
 
-if [[ "${ACCESS}" == "rw" ]]; then
-  mkdir -p ${EESSI_TMPDIR}/overlay-upper
-  mkdir -p ${EESSI_TMPDIR}/overlay-work
+    # add fusemount options depending on requested access mode ('ro' - read-only; 'rw' - read & write)
+    if [[ ${cvmfs_repo_access} == "ro" ]] ; then
+        export EESSI_READONLY="container:cvmfs2 ${cvmfs_repo_name} /cvmfs/${cvmfs_repo_name}"
 
-  # set environment variables for fuse mounts in Singularity container
-  export EESSI_READONLY="container:cvmfs2 ${repo_name} /cvmfs_ro/${repo_name}"
+        EESSI_FUSE_MOUNTS+=("--fusemount" "${EESSI_READONLY}")
+        export EESSI_FUSE_MOUNTS
+    elif [[ ${cvmfs_repo_access} == "rw" ]] ; then
+        # use repo-specific overlay directories
+        mkdir -p ${EESSI_TMPDIR}/${cvmfs_repo_name}/overlay-upper
+        mkdir -p ${EESSI_TMPDIR}/${cvmfs_repo_name}/overlay-work
 
-  EESSI_FUSE_MOUNTS+=("--fusemount" "${EESSI_READONLY}")
+        # set environment variables for fuse mounts in Singularity container
+        export EESSI_READONLY="container:cvmfs2 ${cvmfs_repo_name} /cvmfs_ro/${cvmfs_repo_name}"
 
-  EESSI_WRITABLE_OVERLAY="container:fuse-overlayfs"
-  EESSI_WRITABLE_OVERLAY+=" -o lowerdir=/cvmfs_ro/${repo_name}"
-  EESSI_WRITABLE_OVERLAY+=" -o upperdir=${TMP_IN_CONTAINER}/overlay-upper"
-  EESSI_WRITABLE_OVERLAY+=" -o workdir=${TMP_IN_CONTAINER}/overlay-work"
-  EESSI_WRITABLE_OVERLAY+=" ${EESSI_CVMFS_REPO}"
-  export EESSI_WRITABLE_OVERLAY
+        EESSI_FUSE_MOUNTS+=("--fusemount" "${EESSI_READONLY}")
 
-  EESSI_FUSE_MOUNTS+=("--fusemount" "${EESSI_WRITABLE_OVERLAY}")
-  export EESSI_FUSE_MOUNTS
-fi
+        EESSI_WRITABLE_OVERLAY="container:fuse-overlayfs"
+        EESSI_WRITABLE_OVERLAY+=" -o lowerdir=/cvmfs_ro/${cvmfs_repo_name}"
+        EESSI_WRITABLE_OVERLAY+=" -o upperdir=${TMP_IN_CONTAINER}/${cvmfs_repo_name}/overlay-upper"
+        EESSI_WRITABLE_OVERLAY+=" -o workdir=${TMP_IN_CONTAINER}/${cvmfs_repo_name}/overlay-work"
+        EESSI_WRITABLE_OVERLAY+=" /cvmfs/${cvmfs_repo_name}"
+        export EESSI_WRITABLE_OVERLAY
 
+        EESSI_FUSE_MOUNTS+=("--fusemount" "${EESSI_WRITABLE_OVERLAY}")
+        export EESSI_FUSE_MOUNTS
+    else
+        echo -e "ERROR: access mode '${cvmfs_repo_access}' for CVMFS repository\n  '${cvmfs_repo_name}' is not known"
+	exit ${REPOSITORY_ERROR_EXITCODE}
+    fi
+done
 
 # 5. run container
-# final settings
-if [[ -z ${SINGULARITY_BIND} ]]; then
-    export SINGULARITY_BIND="${BIND_PATHS}"
-else
-    export SINGULARITY_BIND="${SINGULARITY_BIND},${BIND_PATHS}"
-fi
 [[ ${VERBOSE} -eq 1 ]] && echo "SINGULARITY_BIND=${SINGULARITY_BIND}"
 
 # pass $EESSI_SOFTWARE_SUBDIR_OVERRIDE into build container (if set)

From 32f413328cd3b8f1da7ea7521f7458c20cd7232b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Thomas=20R=C3=B6blitz?= <thomas.roblitz@uib.no>
Date: Wed, 19 Jun 2024 16:02:40 +0200
Subject: [PATCH 433/501] revert back changes related to BIND_PATHS and
 SINGULARITY_BIND + some polishing

---
 eessi_container.sh | 46 ++++++++++++++++++++++++----------------------
 1 file changed, 24 insertions(+), 22 deletions(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index c549d04d8c..163792f622 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -416,12 +416,10 @@ fi
 #      |-${CVMFS_VAR_LIB}
 #      |-${CVMFS_VAR_RUN}
 #      |-CVMFS_REPO_1
-#      |   |-repo_settings (name, access_mode, host_injections)
 #      |   |-overlay-upper
 #      |   |-overlay-work
 #      |   |-opt-eessi (unless otherwise specificed for host_injections)
 #      |-CVMFS_REPO_n
-#          |-repo_settings (name, access_mode, host_injections)
 #          |-overlay-upper
 #          |-overlay-work
 #          |-opt-eessi (unless otherwise specificed for host_injections)
@@ -526,18 +524,15 @@ fi
 [[ ${VERBOSE} -eq 1 ]] && echo "SINGULARITY_HOME=${SINGULARITY_HOME}"
 
 # define paths to add to SINGULARITY_BIND (added later when all BIND mounts are defined)
-if [[ -z ${SINGULARITY_BIND} ]] ; then
-    SINGULARITY_BIND="${EESSI_CVMFS_VAR_LIB}:/var/lib/cvmfs,${EESSI_CVMFS_VAR_RUN}:/var/run/cvmfs,${HOST_INJECTIONS}:/opt/eessi"
-else
-    SINGULARITY_BIND="${EESSI_CVMFS_VAR_LIB}:/var/lib/cvmfs,${EESSI_CVMFS_VAR_RUN}:/var/run/cvmfs,${HOST_INJECTIONS}:/opt/eessi,${SINGULARITY_BIND}"
-fi
+BIND_PATHS="${EESSI_CVMFS_VAR_LIB}:/var/lib/cvmfs,${EESSI_CVMFS_VAR_RUN}:/var/run/cvmfs,${HOST_INJECTIONS}:/opt/eessi"
+
 # provide a '/tmp' inside the container
-SINGULARITY_BIND="${SINGULARITY_BIND},${EESSI_TMPDIR}:${TMP_IN_CONTAINER}"
+BIND_PATHS="${BIND_PATHS},${EESSI_TMPDIR}:${TMP_IN_CONTAINER}"
 if [[ ! -z ${EXTRA_BIND_PATHS} ]]; then
-    SINGULARITY_BIND="${SINGULARITY_BIND},${EXTRA_BIND_PATHS}"
+    BIND_PATHS="${BIND_PATHS},${EXTRA_BIND_PATHS}"
 fi
 
-[[ ${VERBOSE} -eq 1 ]] && echo "SINGULARITY_BIND=${SINGULARITY_BIND}"
+[[ ${VERBOSE} -eq 1 ]] && echo "BIND_PATHS=${BIND_PATHS}"
 
 declare -a ADDITIONAL_CONTAINER_OPTIONS=()
 
@@ -558,8 +553,8 @@ if [[ ${SETUP_NVIDIA} -eq 1 ]]; then
         EESSI_USR_LOCAL_CUDA=${EESSI_TMPDIR}/usr-local-cuda
         mkdir -p ${EESSI_VAR_LOG}
         mkdir -p ${EESSI_USR_LOCAL_CUDA}
-        SINGULARITY_BIND="${SINGULARITY_BIND},${EESSI_VAR_LOG}:/var/log,${EESSI_USR_LOCAL_CUDA}:/usr/local/cuda"
-        [[ ${VERBOSE} -eq 1 ]] && echo "SINGULARITY_BIND=${SINGULARITY_BIND}"
+        BIND_PATHS="${BIND_PATHS},${EESSI_VAR_LOG}:/var/log,${EESSI_USR_LOCAL_CUDA}:/usr/local/cuda"
+        [[ ${VERBOSE} -eq 1 ]] && echo "BIND_PATHS=${BIND_PATHS}"
         if [[ "${NVIDIA_MODE}" == "install" ]] ; then
             # No GPU so we need to "trick" Lmod to allow us to load CUDA modules even without a CUDA driver
             # (this variable means EESSI_OVERRIDE_GPU_CHECK=1 will be set inside the container)
@@ -577,7 +572,7 @@ fi
 # arg -r|--repository is used)
 mkdir -p ${EESSI_TMPDIR}/repos_cfg
 [[ ${VERBOSE} -eq 1 ]] && echo
-[[ ${VERBOSE} -eq 1 ]] && echo -e "SINGULARITY_BIND before processing REPOSITORIES\n  SINGULARITY_BIND=${SINGULARITY_BIND}"
+[[ ${VERBOSE} -eq 1 ]] && echo -e "BIND_PATHS before processing REPOSITORIES\n  BIND_PATHS=${BIND_PATHS}"
 [[ ${VERBOSE} -eq 1 ]] && echo
 # iterate over repositories in array REPOSITORIES
 for cvmfs_repo in "${REPOSITORIES[@]}"
@@ -668,20 +663,20 @@ do
         do
             target=${cfg_file_map[${src}]}
             # if target is alreay BIND mounted, exit with an error
-            if [[ ${SINGULARITY_BIND} =~ "${target}" ]]; then
-                fatal_error "target '${target}' is already listed in paths to bind mount into the container ('${SINGULARITY_BIND}')" ${REPOSITORY_ERROR_EXITCODE}
+            if [[ ${BIND_PATHS} =~ "${target}" ]]; then
+                fatal_error "target '${target}' is already listed in paths to bind mount into the container ('${BIND_PATHS}')" ${REPOSITORY_ERROR_EXITCODE}
             fi
-            export SINGULARITY_BIND="${SINGULARITY_BIND},${EESSI_TMPDIR}/repos_cfg/${src}:${target}"
+            BIND_PATHS="${BIND_PATHS},${EESSI_TMPDIR}/repos_cfg/${src}:${target}"
         done
     fi
-    [[ ${VERBOSE} -eq 1 ]] && echo -e "SINGULARITY_BIND after processing '${cvmfs_repo}'\n  SINGULARITY_BIND=${SINGULARITY_BIND}"
+    [[ ${VERBOSE} -eq 1 ]] && echo -e "BIND_PATHS after processing '${cvmfs_repo}'\n  BIND_PATHS=${BIND_PATHS}"
     [[ ${VERBOSE} -eq 1 ]] && echo
 done
 
 # if http_proxy is not empty, we assume that the machine accesses internet
 # via a proxy. then we need to add CVMFS_HTTP_PROXY to
 # ${EESSI_TMPDIR}/repos_cfg/default.local on the host (and possibly add a BIND
-# MOUNT if it was not yet in SINGULARITY_BIND)
+# MOUNT if it was not yet in BIND_PATHS)
 if [[ ! -z ${http_proxy} ]]; then
     # TODO tolerate other formats for proxy URLs, for now assume format is
     # http://SOME_HOSTNAME:SOME_PORT/
@@ -697,13 +692,13 @@ if [[ ! -z ${http_proxy} ]]; then
     [[ ${VERBOSE} -eq 1 ]] && echo "contents of default.local"
     [[ ${VERBOSE} -eq 1 ]] && cat ${EESSI_TMPDIR}/repos_cfg/default.local
 
-    # if default.local is not BIND mounted into container, add it to SINGULARITY_BIND
+    # if default.local is not BIND mounted into container, add it to BIND_PATHS
     src=${EESSI_TMPDIR}/repos_cfg/default.local
     target=/etc/cvmfs/default.local
-    if [[ ${SINGULARITY_BIND} =~ "${target}" ]]; then
-        fatal_error "BIND target in '${src}:${target}' is already in paths to be bind mounted into the container ('${SINGULARITY_BIND}')" ${REPOSITORY_ERROR_EXITCODE}
+    if [[ ${BIND_PATHS} =~ "${target}" ]]; then
+        fatal_error "BIND target in '${src}:${target}' is already in paths to be bind mounted into the container ('${BIND_PATHS}')" ${REPOSITORY_ERROR_EXITCODE}
     fi
-    export SINGULARITY_BIND="${SINGULARITY_BIND},${src}:${target}"
+    BIND_PATHS="${BIND_PATHS},${src}:${target}"
 fi
 
 # 4. set up vars and dirs specific to a scenario
@@ -744,6 +739,7 @@ do
         # use repo-specific overlay directories
         mkdir -p ${EESSI_TMPDIR}/${cvmfs_repo_name}/overlay-upper
         mkdir -p ${EESSI_TMPDIR}/${cvmfs_repo_name}/overlay-work
+	[[ ${VERBOSE} -eq 1 ]] && echo -e "TMP directory contents:\n$(ls -l ${EESSI_TMPDIR})"
 
         # set environment variables for fuse mounts in Singularity container
         export EESSI_READONLY="container:cvmfs2 ${cvmfs_repo_name} /cvmfs_ro/${cvmfs_repo_name}"
@@ -766,6 +762,12 @@ do
 done
 
 # 5. run container
+# final settings
+if [[ -z ${SINGULARITY_BIND} ]]; then
+    export SINGULARITY_BIND="${BIND_PATHS}"
+else
+    export SINGULARITY_BIND="${SINGULARITY_BIND},${BIND_PATHS}"
+fi
 [[ ${VERBOSE} -eq 1 ]] && echo "SINGULARITY_BIND=${SINGULARITY_BIND}"
 
 # pass $EESSI_SOFTWARE_SUBDIR_OVERRIDE into build container (if set)

From 07de7008e60586d146cd4986de9d0a4f7e505731 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Thomas=20R=C3=B6blitz?= <thomas.roblitz@uib.no>
Date: Thu, 20 Jun 2024 09:07:24 +0200
Subject: [PATCH 434/501] store repository settings under tmp

---
 eessi_container.sh | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/eessi_container.sh b/eessi_container.sh
index 163792f622..eaa4f59af9 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -416,10 +416,12 @@ fi
 #      |-${CVMFS_VAR_LIB}
 #      |-${CVMFS_VAR_RUN}
 #      |-CVMFS_REPO_1
+#      |   |-repo_settings.sh (name, id, access, host_injections)
 #      |   |-overlay-upper
 #      |   |-overlay-work
 #      |   |-opt-eessi (unless otherwise specificed for host_injections)
 #      |-CVMFS_REPO_n
+#          |-repo_settings.sh (name, id, access, host_injections)
 #          |-overlay-upper
 #          |-overlay-work
 #          |-opt-eessi (unless otherwise specificed for host_injections)
@@ -711,6 +713,7 @@ EESSI_FUSE_MOUNTS+=("--fusemount" "container:cvmfs2 cvmfs-config.cern.ch /cvmfs/
 # iterate over REPOSITORIES and either use repository-specific access mode or global setting (possibly a global default)
 for cvmfs_repo in "${REPOSITORIES[@]}"
 do
+    unset cfg_repo_id
     [[ ${VERBOSE} -eq 1 ]] && echo "add fusemount options for CVMFS repo '${cvmfs_repo}'"
     # split into name and access mode if ',access=' in $cvmfs_repo
     if [[ ${cvmfs_repo} == *",access="* ]] ; then
@@ -729,6 +732,9 @@ do
         cvmfs_repo_name=$(cfg_get_value ${cfg_repo_id} "repo_name")
     fi
 
+    # always create a directory for the repository (e.g., to store settings, ...)
+    mkdir -p ${EESSI_TMPDIR}/${cvmfs_repo_name}
+
     # add fusemount options depending on requested access mode ('ro' - read-only; 'rw' - read & write)
     if [[ ${cvmfs_repo_access} == "ro" ]] ; then
         export EESSI_READONLY="container:cvmfs2 ${cvmfs_repo_name} /cvmfs/${cvmfs_repo_name}"
@@ -759,6 +765,20 @@ do
         echo -e "ERROR: access mode '${cvmfs_repo_access}' for CVMFS repository\n  '${cvmfs_repo_name}' is not known"
 	exit ${REPOSITORY_ERROR_EXITCODE}
     fi
+    # create repo_settings.sh file in ${EESSI_TMPDIR}/${cvmfs_repo_name} to store
+    #   (intention is that the file could be just sourced to obtain the settings)
+    # repo_name = ${cvmfs_repo_name}
+    # repo_id = ${cfg_repo_id} # empty if not an EESSI repo
+    # repo_access = ${cvmfs_repo_access}
+    # repo_host_injections = [ {"src_path":"target_path"}... ] # TODO
+    settings=
+    #[[ -n ${cfg_repo_id} ]] && settings="[${cvmfs_repo_name}]\n" || settings="[${cfg_repo_id}]\n"
+    settings="${settings}repo_name = ${cvmfs_repo_name}\n"
+    settings="${settings}repo_id = ${cfg_repo_id}\n"
+    settings="${settings}repo_access = ${cvmfs_repo_access}\n"
+    # TODO iterate over host_injections (first need means to define them (globally and/or per repository)
+    # settings="${settings}repo_host_injections = ${host_injections}\n"
+    echo -e "${settings}" > ${EESSI_TMPDIR}/${cvmfs_repo_name}/repo_settings.sh
 done
 
 # 5. run container

From 3da63162f66480d4c4430e6725800fc0769e90f1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 24 Jun 2024 18:18:49 +0200
Subject: [PATCH 435/501] {2023.06,a64fx}[2023a] OpenMPI 4.1.5

---
 .../2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml              | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml

diff --git a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
new file mode 100644
index 0000000000..1475ad0866
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -0,0 +1,2 @@
+easyconfigs:
+  - OpenMPI-4.1.5-GCC-12.3.0.eb

From 871586fbb055a07ad7250a48a3a06c3ffec1d8b2 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 24 Jun 2024 18:49:22 +0200
Subject: [PATCH 436/501] use latest Ubuntu in CI workflows

---
 .github/workflows/test-software.eessi.io.yml      | 2 +-
 .github/workflows/test_eessi_container_script.yml | 2 +-
 .github/workflows/test_licenses.yml               | 2 +-
 .github/workflows/tests.yml                       | 2 +-
 .github/workflows/tests_archdetect.yml            | 2 +-
 .github/workflows/tests_init.yml                  | 2 +-
 .github/workflows/tests_readme.yml                | 2 +-
 .github/workflows/tests_scripts.yml               | 2 +-
 8 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/test-software.eessi.io.yml b/.github/workflows/test-software.eessi.io.yml
index 8cfb023bc6..06c02c8834 100644
--- a/.github/workflows/test-software.eessi.io.yml
+++ b/.github/workflows/test-software.eessi.io.yml
@@ -5,7 +5,7 @@ permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
   check_missing:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
diff --git a/.github/workflows/test_eessi_container_script.yml b/.github/workflows/test_eessi_container_script.yml
index 32120d0087..d31feb23fe 100644
--- a/.github/workflows/test_eessi_container_script.yml
+++ b/.github/workflows/test_eessi_container_script.yml
@@ -5,7 +5,7 @@ permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
   eessi_container_script:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
diff --git a/.github/workflows/test_licenses.yml b/.github/workflows/test_licenses.yml
index 3b9675d523..6b6387d47d 100644
--- a/.github/workflows/test_licenses.yml
+++ b/.github/workflows/test_licenses.yml
@@ -5,7 +5,7 @@ permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
         - name: Check out software-layer repository
           uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index faa7eb82ff..6af6a83e96 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -5,7 +5,7 @@ permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     strategy:
       matrix:
         python: [3.6, 3.7, 3.8, 3.9, '3.10']
diff --git a/.github/workflows/tests_archdetect.yml b/.github/workflows/tests_archdetect.yml
index bee348995d..4f5d3d174d 100644
--- a/.github/workflows/tests_archdetect.yml
+++ b/.github/workflows/tests_archdetect.yml
@@ -5,7 +5,7 @@ permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     strategy:
       matrix:
         proc_cpuinfo:
diff --git a/.github/workflows/tests_init.yml b/.github/workflows/tests_init.yml
index 053acb9730..aabe37de44 100644
--- a/.github/workflows/tests_init.yml
+++ b/.github/workflows/tests_init.yml
@@ -5,7 +5,7 @@ permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     strategy:
       matrix:
         python: [3.6, 3.7, 3.8, 3.9, '3.10']
diff --git a/.github/workflows/tests_readme.yml b/.github/workflows/tests_readme.yml
index efdb796e5e..76f46a8abe 100644
--- a/.github/workflows/tests_readme.yml
+++ b/.github/workflows/tests_readme.yml
@@ -14,7 +14,7 @@ permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
         - name: Check out software-layer repository
           uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
diff --git a/.github/workflows/tests_scripts.yml b/.github/workflows/tests_scripts.yml
index 76d19d29fe..6413fcf86f 100644
--- a/.github/workflows/tests_scripts.yml
+++ b/.github/workflows/tests_scripts.yml
@@ -28,7 +28,7 @@ permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
     - name: checkout
       uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1

From 70878f66586c49b0a2412754a7937482f7910803 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 24 Jun 2024 18:58:42 +0200
Subject: [PATCH 437/501] only run CI workflows with Python >= 3.7

Co-authored-by: ocaisa <alan.ocais@cecam.org>
---
 .github/workflows/tests.yml      | 2 +-
 .github/workflows/tests_init.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 6af6a83e96..8249e50d9b 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python: [3.6, 3.7, 3.8, 3.9, '3.10']
+        python: [3.7, 3.8, 3.9, '3.10']
       fail-fast: false
     steps:
     - name: checkout
diff --git a/.github/workflows/tests_init.yml b/.github/workflows/tests_init.yml
index aabe37de44..6c356a9184 100644
--- a/.github/workflows/tests_init.yml
+++ b/.github/workflows/tests_init.yml
@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python: [3.6, 3.7, 3.8, 3.9, '3.10']
+        python: [3.7, 3.8, 3.9, '3.10']
       fail-fast: false
     steps:
     - name: checkout

From 0cb1d2af5ad9ad8f2ccdb7e9da9d2614c61781d0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 25 Jun 2024 09:29:21 +0200
Subject: [PATCH 438/501] implement hook to inject -DCACHE_SECTOR_SIZE_READONLY
 in $CFLAGS when building BLIS 0.9.0 on A64FX

---
 eb_hooks.py | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index 8b0a11b0ed..fd3e0830ee 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -23,6 +23,7 @@
 CPU_TARGET_NEOVERSE_N1 = 'aarch64/neoverse_n1'
 CPU_TARGET_NEOVERSE_V1 = 'aarch64/neoverse_v1'
 CPU_TARGET_AARCH64_GENERIC = 'aarch64/generic'
+CPU_TARGET_A64FX = 'aarch64/a64fx'
 
 EESSI_RPATH_OVERRIDE_ATTR = 'orig_rpath_override_dirs'
 
@@ -335,6 +336,19 @@ def pre_configure_hook(self, *args, **kwargs):
         PRE_CONFIGURE_HOOKS[self.name](self, *args, **kwargs)
 
 
+def pre_configure_hook_BLIS_a64fx(self, *args, **kwargs):
+    """
+    Pre-configure hook for BLIS when building for A64FX:
+    - add -DCACHE_SECTOR_SIZE_READONLY to $CFLAGS for BLIS 0.9.0, cfr. https://github.com/flame/blis/issues/800
+    """
+    if self.name == 'BLIS':
+        cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
+        if self.version == '0.9.0' and cpu_target == CPU_TARGET_A64FX:
+            self.cfg.update('configopts', 'CFLAGS="$CFLAGS -DCACHE_SECTOR_SIZE_READONLY"')
+    else:
+        raise EasyBuildError("BLIS-specific hook triggered for non-BLIS easyconfig?!")
+
+
 def pre_configure_hook_gromacs(self, *args, **kwargs):
     """
     Pre-configure hook for GROMACS:
@@ -680,12 +694,13 @@ def inject_gpu_property(ec):
 }
 
 PRE_CONFIGURE_HOOKS = {
+    'at-spi2-core': pre_configure_hook_atspi2core_filter_ld_library_path,
+    'BLIS': pre_configure_hook_BLIS_a64fx,
     'GROMACS': pre_configure_hook_gromacs,
     'libfabric': pre_configure_hook_libfabric_disable_psm3_x86_64_generic,
     'MetaBAT': pre_configure_hook_metabat_filtered_zlib_dep,
     'OpenBLAS': pre_configure_hook_openblas_optarch_generic,
     'WRF': pre_configure_hook_wrf_aarch64,
-    'at-spi2-core': pre_configure_hook_atspi2core_filter_ld_library_path,
 }
 
 PRE_TEST_HOOKS = {

From 3aac7ea854e8f4613ad89fc8e15e2ca26df0af6f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 25 Jun 2024 09:29:38 +0200
Subject: [PATCH 439/501] {2023.06,a64fx} foss/2023a

---
 .../2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml               | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
index 1475ad0866..3a060e30a7 100644
--- a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -1,2 +1,3 @@
 easyconfigs:
   - OpenMPI-4.1.5-GCC-12.3.0.eb
+  - foss-2023a.eb

From d9c1fb1104f19e741b8ac2a5a652eb22e07bf241 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Thomas=20R=C3=B6blitz?= <thomas.roblitz@uib.no>
Date: Tue, 25 Jun 2024 10:17:51 +0200
Subject: [PATCH 440/501] removed unnecessary variable

---
 eessi_container.sh | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index eaa4f59af9..4b7b4eb719 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -48,9 +48,6 @@ HTTPS_PROXY_ERROR_EXITCODE=$((${ANY_ERROR_EXITCODE} << 10))
 RUN_SCRIPT_MISSING_EXITCODE=$((${ANY_ERROR_EXITCODE} << 11))
 NVIDIA_MODE_UNKNOWN_EXITCODE=$((${ANY_ERROR_EXITCODE} << 12))
 
-# we use an associative array for storing sets of settings per CVMFS repository
-declare -A cvmfs_repo_settings
-
 # CernVM-FS settings
 CVMFS_VAR_LIB="var-lib-cvmfs"
 CVMFS_VAR_RUN="var-run-cvmfs"

From e25cd1e720a3a0e787409093d561d5892929d10a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Thomas=20R=C3=B6blitz?= <thomas.roblitz@uib.no>
Date: Tue, 25 Jun 2024 10:23:18 +0200
Subject: [PATCH 441/501] add more information about repository-specific access
 modes

---
 eessi_container.sh | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index 4b7b4eb719..9d2ce6c25f 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -70,7 +70,8 @@ export EESSI_REPOS_CFG_FILE="${EESSI_REPOS_CFG_DIR}/repos.cfg"
 display_help() {
   echo "usage: $0 [OPTIONS] [[--] SCRIPT or COMMAND]"
   echo " OPTIONS:"
-  echo "  -a | --access {ro,rw}   - ro (read-only), rw (read & write) [default: ro]"
+  echo "  -a | --access {ro,rw}   - sets access globally for all CVMFS repositories:"
+  echo "                            ro (read-only), rw (read & write) [default: ro]"
   echo "  -b | --extra-bind-paths - specify extra paths to be bound into the container."
   echo "                            To specify multiple bind paths, separate by comma."
   echo "                            Example: '/src:/dest:ro,/src2:/dest2:rw'"
@@ -89,7 +90,9 @@ display_help() {
   echo "                            MODE==install for a CUDA installation, MODE==run to"
   echo "                            attach a GPU, MODE==all for both [default: false]"
   echo "  -r | --repository CFG   - configuration file or identifier defining the"
-  echo "                            repository to use; can be given multiple times"
+  echo "                            repository to use; can be given multiple times;"
+  echo "                            CFG may include a suffix ';access={ro,rw}' to"
+  echo "                            overwrite the global access mode for this repository"
   echo "                            [default: software.eessi.io via CVMFS config available"
   echo "                            via default container, see --container]"
   echo "  -u | --resume DIR/TGZ   - resume a previous run from a directory or tarball,"

From da1b6710152dcf912db34147e88c739914e0290d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 25 Jun 2024 18:16:24 +0200
Subject: [PATCH 442/501] fix hook to tweak BLIS configure command when
 building for A64FX

---
 eb_hooks.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index fd3e0830ee..b14c799eae 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -344,7 +344,12 @@ def pre_configure_hook_BLIS_a64fx(self, *args, **kwargs):
     if self.name == 'BLIS':
         cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
         if self.version == '0.9.0' and cpu_target == CPU_TARGET_A64FX:
-            self.cfg.update('configopts', 'CFLAGS="$CFLAGS -DCACHE_SECTOR_SIZE_READONLY"')
+            # last argument of BLIS' configure command is configuration target (usually 'auto' for auto-detect),
+            # specifying of variables should be done before that
+            config_opts = self.cfg['configopts'].split(' ')
+            cflags_var = 'CFLAGS="$CFLAGS -DCACHE_SECTOR_SIZE_READONLY"'
+            config_target = config_opts[-1]
+            self.cfg['configopts'] = ' '.join(config_opts[:-1] + [cflags_var, config_target])
     else:
         raise EasyBuildError("BLIS-specific hook triggered for non-BLIS easyconfig?!")
 

From 80d8d6e5789a972342fd57532e84d8df3a39bb88 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 26 Jun 2024 11:46:11 +0200
Subject: [PATCH 443/501] ignore scipy test failures when installing
 SciPy-bundle for A64FX

---
 eb_hooks.py                    | 22 ++++++++++++++++------
 eessi-2023.06-known-issues.yml |  7 +++++++
 2 files changed, 23 insertions(+), 6 deletions(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index b14c799eae..e6f0cf0dd2 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -488,20 +488,30 @@ def pre_test_hook_ignore_failing_tests_FFTWMPI(self, *args, **kwargs):
 def pre_test_hook_ignore_failing_tests_SciPybundle(self, *args, **kwargs):
     """
     Pre-test hook for SciPy-bundle: skip failing tests for selected SciPy-bundle versions
-    In version 2021.10, 2 failing tests in scipy 1.6.3:
+    In version 2021.10 on neoverse_v1, 2 failing tests in scipy 1.6.3:
         FAILED optimize/tests/test_linprog.py::TestLinprogIPSparse::test_bug_6139 - A...
         FAILED optimize/tests/test_linprog.py::TestLinprogIPSparsePresolve::test_bug_6139
         = 2 failed, 30554 passed, 2064 skipped, 10992 deselected, 76 xfailed, 7 xpassed, 40 warnings in 380.27s (0:06:20) =
-    In versions 2023.02, 2023.07, and 2023.11, 2 failing tests in scipy (versions 1.10.1, 1.11.1, 1.11.4):
+    In versions 2023.02 + 2023.07 + 2023.11 on neoverse_v1, 2 failing tests in scipy (versions 1.10.1, 1.11.1, 1.11.4):
         FAILED scipy/spatial/tests/test_distance.py::TestPdist::test_pdist_correlation_iris
         FAILED scipy/spatial/tests/test_distance.py::TestPdist::test_pdist_correlation_iris_float32
         = 2 failed, 54409 passed, 3016 skipped, 223 xfailed, 13 xpassed, 10917 warnings in 892.04s (0:14:52) =
-    In previous versions we were not as strict yet on the numpy/SciPy tests
+    In version 2023.07 on a64fx, 4 failing tests in scipy 1.11.1:
+        FAILED scipy/optimize/tests/test_linprog.py::TestLinprogIPSparse::test_bug_6139
+        FAILED scipy/optimize/tests/test_linprog.py::TestLinprogIPSparsePresolve::test_bug_6139
+        FAILED scipy/spatial/tests/test_distance.py::TestPdist::test_pdist_correlation_iris
+        FAILED scipy/spatial/tests/test_distance.py::TestPdist::test_pdist_correlation_iris_float32
+        = 4 failed, 54407 passed, 3016 skipped, 223 xfailed, 13 xpassed, 10917 warnings in 6068.43s (1:41:08) =
+    (in previous versions we were not as strict yet on the numpy/SciPy tests)
     """
     cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
-    scipy_bundle_versions = ('2021.10', '2023.02', '2023.07', '2023.11')
-    if self.name == 'SciPy-bundle' and self.version in scipy_bundle_versions and cpu_target == CPU_TARGET_NEOVERSE_V1:
-        self.cfg['testopts'] = "|| echo ignoring failing tests"
+    scipy_bundle_versions_nv1 = ('2021.10', '2023.02', '2023.07', '2023.11')
+    scipy_bundle_versions_a64fx = ('2023.07', '2023.11')
+    if self.name == 'SciPy-bundle':
+        if cpu_target == CPU_TARGET_NEOVERSE_V1 and self.version in scipy_bundle_versions_nv1:
+            self.cfg['testopts'] = "|| echo ignoring failing tests"
+        elif cpu_target == CPU_TARGET_A64FX and self.version in scipy_bundle_versions_a64fx:
+            self.cfg['testopts'] = "|| echo ignoring failing tests"
 
 def pre_test_hook_ignore_failing_tests_netCDF(self, *args, **kwargs):
     """
diff --git a/eessi-2023.06-known-issues.yml b/eessi-2023.06-known-issues.yml
index 2d1256354f..c5cdc68941 100644
--- a/eessi-2023.06-known-issues.yml
+++ b/eessi-2023.06-known-issues.yml
@@ -1,3 +1,10 @@
+- aarch64/a64x:
+  - SciPy-bundle-2023.07-gfbf-2023a:
+    - issue: https://github.com/EESSI/software-layer/issues/318
+    - info: "4 failing tests (vs 54407 passed) in scipy test suite"
+  - SciPy-bundle-2023.11-gfbf-2023b:
+    - issue: https://github.com/EESSI/software-layer/issues/318
+    - info: "3 failing tests (vs 54875 passed) in scipy test suite"
 - aarch64/generic:
   - PyTorch-2.1.2-foss-2023a:
     - issue: https://github.com/EESSI/software-layer/issues/461

From f07fd8567f1154cb8b4f0ab338979caff4dbfcce Mon Sep 17 00:00:00 2001
From: torri <torri@disroot.org>
Date: Wed, 26 Jun 2024 14:03:51 +0200
Subject: [PATCH 444/501] fix for broken curl installation

---
 init/eessi_environment_variables | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index 78851a9c95..d6e5b75dce 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -15,6 +15,20 @@ function show_msg {
   fi
 }
 
+function check_rhel_ca {
+
+  os=$(grep -oP '(?<=^ID_LIKE=).+' /etc/os-release | tr -d '"')
+
+  version_id=$(grep -oP '(?<=^VERSION_ID=).+' /etc/os-release | tr -d '"')
+  version_major=${version_id%\.*}
+
+  if [[ $os =~ "rhel" ]] && [ $version_major -gt 7 ]
+  then
+        export CURL_CA_BUNDLE=/etc/pki/tls/certs/ca-bundle.crt
+  fi
+}
+
+
 # set up minimal environment: $EESSI_PREFIX, $EESSI_VERSION, $EESSI_OS_TYPE, $EESSI_CPU_FAMILY, $EPREFIX
 source $EESSI_INIT_DIR_PATH/minimal_eessi_env
 
@@ -106,6 +120,8 @@ if [ -d $EESSI_PREFIX ]; then
             false
           fi
 
+        # Fix wrong path for RHEL >=8 libcurl 
+	check_rhel_ca
 
         else
           error "EESSI software layer at $EESSI_SOFTWARE_PATH not found!"

From 8ed871b53b4bcca8a55f9365b7aaaf0288dc36c9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 26 Jun 2024 15:43:38 +0200
Subject: [PATCH 445/501] {2023.06,a64fx}[foss/2023a] SciPy-bundle 2023.07

---
 .../2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml               | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
index 3a060e30a7..5326f6c493 100644
--- a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -1,3 +1,4 @@
 easyconfigs:
   - OpenMPI-4.1.5-GCC-12.3.0.eb
   - foss-2023a.eb
+  - SciPy-bundle-2023.07-gfbf-2023a.eb

From 69c059b758c29400ac7039cf1ee03af5eba2515c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 26 Jun 2024 22:29:52 +0200
Subject: [PATCH 446/501] {2023.06,a64fx}[foss/2023a] ESPResSo 4.2.2

---
 .../2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml               | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
index 5326f6c493..3fe1e43d3f 100644
--- a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -2,3 +2,4 @@ easyconfigs:
   - OpenMPI-4.1.5-GCC-12.3.0.eb
   - foss-2023a.eb
   - SciPy-bundle-2023.07-gfbf-2023a.eb
+  - ESPResSo-4.2.2-foss-2023a.eb

From 69a812962486940fe553facc459939af8f6549fe Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 27 Jun 2024 13:27:48 +0200
Subject: [PATCH 447/501] {2023.06,a64fx} foss/2023b

---
 .../2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023b.yml          | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023b.yml

diff --git a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023b.yml b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023b.yml
new file mode 100644
index 0000000000..c7411ada0a
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023b.yml
@@ -0,0 +1,6 @@
+easyconfigs:
+  - OpenBLAS-0.3.24-GCC-13.2.0.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20820
+        from-commit: 1fc885b35dacdeb2feef4af207a2daa2502bae08
+  - foss-2023b.eb

From 36dea35585cbc86b7044ec454593a00307c130f9 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Mon, 1 Jul 2024 08:45:07 +0000
Subject: [PATCH 448/501] {2023.06}[GCC/12.3.0] BCFtools v1.18

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml  | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
new file mode 100644
index 0000000000..ade226c217
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -0,0 +1,2 @@
+easyconfigs:
+  - BCFtools-1.18-GCC-12.3.0.eb

From 9f841a2cbcf1c27ea6d7517bbb4edba9cb3744b8 Mon Sep 17 00:00:00 2001
From: lara <lara@localhost.localdomain>
Date: Mon, 1 Jul 2024 15:03:18 +0200
Subject: [PATCH 449/501] {2023.06}[foss/2023a] CP2K 2023.1

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
index ade226c217..bd412f1579 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -1,2 +1,3 @@
 easyconfigs:
   - BCFtools-1.18-GCC-12.3.0.eb
+  - CP2K-2023.1-foss-2023a.eb

From 9747ee497161f23dd999094e78bae6c863c5a9fb Mon Sep 17 00:00:00 2001
From: torri <torri@disroot.org>
Date: Mon, 1 Jul 2024 16:31:37 +0200
Subject: [PATCH 450/501] simplified the implementation

---
 init/eessi_environment_variables | 20 +++++---------------
 1 file changed, 5 insertions(+), 15 deletions(-)

diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index d6e5b75dce..c28ddb45d9 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -15,20 +15,6 @@ function show_msg {
   fi
 }
 
-function check_rhel_ca {
-
-  os=$(grep -oP '(?<=^ID_LIKE=).+' /etc/os-release | tr -d '"')
-
-  version_id=$(grep -oP '(?<=^VERSION_ID=).+' /etc/os-release | tr -d '"')
-  version_major=${version_id%\.*}
-
-  if [[ $os =~ "rhel" ]] && [ $version_major -gt 7 ]
-  then
-        export CURL_CA_BUNDLE=/etc/pki/tls/certs/ca-bundle.crt
-  fi
-}
-
-
 # set up minimal environment: $EESSI_PREFIX, $EESSI_VERSION, $EESSI_OS_TYPE, $EESSI_CPU_FAMILY, $EPREFIX
 source $EESSI_INIT_DIR_PATH/minimal_eessi_env
 
@@ -121,7 +107,11 @@ if [ -d $EESSI_PREFIX ]; then
           fi
 
         # Fix wrong path for RHEL >=8 libcurl 
-	check_rhel_ca
+	rhel_libcurl_file="/etc/pki/tls/certs/ca-bundle.crt"
+        if [ -f $rhel_libcurl_file ]; then
+          show_msg "Found libcurl CAs file at RHEL location, setting CURL_CA_BUNDLE"
+          export CURL_CA_BUNDLE=$rhel_libcurl_file
+        fi
 
         else
           error "EESSI software layer at $EESSI_SOFTWARE_PATH not found!"

From ba8de248ef1de35d2eecb359dd33ebcdb3981da0 Mon Sep 17 00:00:00 2001
From: lara <lara@localhost.localdomain>
Date: Tue, 2 Jul 2024 12:22:46 +0200
Subject: [PATCH 451/501] add from-pr 20951 for ARM support

---
 .../2023.06/eessi-2023.06-eb-4.9.2-2023a.yml                 | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
index bd412f1579..5d4aa9a772 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -1,3 +1,6 @@
 easyconfigs:
   - BCFtools-1.18-GCC-12.3.0.eb
-  - CP2K-2023.1-foss-2023a.eb
+  - CP2K-2023.1-foss-2023a.eb:
+      # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20951
+      options:
+        from-pr: 20951

From 51c6b1c998a69d8dd4a75f4f83b101b5ba81f1b4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 3 Jul 2024 10:51:41 +0200
Subject: [PATCH 452/501] improve comment that explains setting of
 `$CURL_CA_BUNDLE` on RHEL-based systems

Co-authored-by: ocaisa <alan.ocais@cecam.org>
---
 init/eessi_environment_variables | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index c28ddb45d9..f5bb387955 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -107,6 +107,9 @@ if [ -d $EESSI_PREFIX ]; then
           fi
 
         # Fix wrong path for RHEL >=8 libcurl 
+	# This is required here because we ship curl in our compat layer. If we only provided
+	# curl as a module file we could instead do this via a `modluafooter` in an EasyBuild
+	# hook (or via an Lmod hook)
 	rhel_libcurl_file="/etc/pki/tls/certs/ca-bundle.crt"
         if [ -f $rhel_libcurl_file ]; then
           show_msg "Found libcurl CAs file at RHEL location, setting CURL_CA_BUNDLE"

From d56cd31a81ae2a88adf8ca6b0d15e11df5624d7a Mon Sep 17 00:00:00 2001
From: lara <lara@localhost.localdomain>
Date: Wed, 3 Jul 2024 12:07:22 +0200
Subject: [PATCH 453/501] add hook for missing installation check on aarch64

---
 eb_hooks.py | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/eb_hooks.py b/eb_hooks.py
index e6f0cf0dd2..b4862cb572 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -294,6 +294,22 @@ def parse_hook_lammps_remove_deps_for_CI_aarch64(ec, *args, **kwargs):
         raise EasyBuildError("LAMMPS-specific hook triggered for non-LAMMPS easyconfig?!")
 
 
+def parse_hook_CP2K_remove_deps_for_aarch64(ec, *args, **kwargs):
+    """
+    Remove x86_64 specific dependencies for the CI and missing installations to pass on aarch64
+    """
+    if ec.name == 'CP2K' and ec.version in ('2023.1',):
+        if os.getenv('EESSI_CPU_FAMILY') == 'aarch64':
+            # LIBXSMM is not supported on ARM with GCC 12.2.0 and 12.3.0
+            # See https://www.cp2k.org/dev:compiler_support
+            # See https://github.com/easybuilders/easybuild-easyconfigs/pull/20951
+            # we need this hook because we check for missing installations for all CPU targets
+            # on an x86_64 VM in GitHub Actions (so condition based on ARCH in LAMMPS easyconfig is always true)
+            ec['dependencies'] = [dep for dep in ec['dependencies'] if dep[0] not in ('libxsmm',)]
+    else:
+        raise EasyBuildError("CP2K-specific hook triggered for non-CP2K easyconfig?!")]
+
+
 def pre_prepare_hook_highway_handle_test_compilation_issues(self, *args, **kwargs):
     """
     Solve issues with compiling or running the tests on both
@@ -693,6 +709,7 @@ def inject_gpu_property(ec):
     'CGAL': parse_hook_cgal_toolchainopts_precise,
     'fontconfig': parse_hook_fontconfig_add_fonts,
     'LAMMPS': parse_hook_lammps_remove_deps_for_CI_aarch64,
+    'CP2K': parse_hook_CP2K_remove_deps_for_aarch64,
     'OpenBLAS': parse_hook_openblas_relax_lapack_tests_num_errors,
     'pybind11': parse_hook_pybind11_replace_catch2,
     'Qt5': parse_hook_qt5_check_qtwebengine_disable,

From 95dd8a02239cbff967a3a5e51e3186398693bfed Mon Sep 17 00:00:00 2001
From: lara <lara@localhost.localdomain>
Date: Wed, 3 Jul 2024 12:56:06 +0200
Subject: [PATCH 454/501] fix CP2K hook

---
 eb_hooks.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index b4862cb572..4dc39c2fe8 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -307,7 +307,7 @@ def parse_hook_CP2K_remove_deps_for_aarch64(ec, *args, **kwargs):
             # on an x86_64 VM in GitHub Actions (so condition based on ARCH in LAMMPS easyconfig is always true)
             ec['dependencies'] = [dep for dep in ec['dependencies'] if dep[0] not in ('libxsmm',)]
     else:
-        raise EasyBuildError("CP2K-specific hook triggered for non-CP2K easyconfig?!")]
+        raise EasyBuildError("CP2K-specific hook triggered for non-CP2K easyconfig?!")
 
 
 def pre_prepare_hook_highway_handle_test_compilation_issues(self, *args, **kwargs):

From 84de38a958417daf880c347dba0e9ae728d0e3f0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 3 Jul 2024 21:37:43 +0200
Subject: [PATCH 455/501] {2023.06,zen4}[foss/2023a] ParaView 5.11.2

---
 .../2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml                | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
index 09f525364f..d4c70c562d 100644
--- a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -2,3 +2,4 @@ easyconfigs:
   - ESPResSo-4.2.2-foss-2023a.eb
   - TensorFlow-2.13.0-foss-2023a.eb
   - R-4.3.2-gfbf-2023a.eb
+  - ParaView-5.11.2-foss-2023a.eb

From c895bf16668c588d7eec827092849d883ce10bf2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 4 Jul 2024 13:24:12 +0200
Subject: [PATCH 456/501] remove TODO for using separate cache dirs for each
 repo

---
 eessi_container.sh | 1 -
 1 file changed, 1 deletion(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index 9d2ce6c25f..94de82df0f 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -510,7 +510,6 @@ fi
 [[ ${VERBOSE} -eq 1 ]] && echo "CONTAINER=${CONTAINER}"
 
 # set env vars and create directories for CernVM-FS
-# TODO need to use separate values for separate repos?
 EESSI_CVMFS_VAR_LIB=${EESSI_TMPDIR}/${CVMFS_VAR_LIB}
 EESSI_CVMFS_VAR_RUN=${EESSI_TMPDIR}/${CVMFS_VAR_RUN}
 mkdir -p ${EESSI_CVMFS_VAR_LIB}

From 417f4dd9b82795520e5923a9c1532ed04f384747 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 4 Jul 2024 13:24:44 +0200
Subject: [PATCH 457/501] fix usage line for access permissions

---
 eessi_container.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index 94de82df0f..e404b7ee18 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -91,7 +91,7 @@ display_help() {
   echo "                            attach a GPU, MODE==all for both [default: false]"
   echo "  -r | --repository CFG   - configuration file or identifier defining the"
   echo "                            repository to use; can be given multiple times;"
-  echo "                            CFG may include a suffix ';access={ro,rw}' to"
+  echo "                            CFG may include a suffix ',access={ro,rw}' to"
   echo "                            overwrite the global access mode for this repository"
   echo "                            [default: software.eessi.io via CVMFS config available"
   echo "                            via default container, see --container]"

From d8cf6a60540b36b5c3e64c687af5d1482df021a5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 4 Jul 2024 13:41:40 +0200
Subject: [PATCH 458/501] check for software.eessi.io in the default
 --list-repos output

---
 .github/workflows/test_eessi_container_script.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test_eessi_container_script.yml b/.github/workflows/test_eessi_container_script.yml
index d31feb23fe..c0346774cb 100644
--- a/.github/workflows/test_eessi_container_script.yml
+++ b/.github/workflows/test_eessi_container_script.yml
@@ -45,7 +45,8 @@ jobs:
               elif [[ ${{matrix.SCRIPT_TEST}} == 'listrepos_default' ]]; then
                 outfile=out_listrepos.txt
                 ./eessi_container.sh --verbose --list-repos | tee ${outfile}
-                grep "EESSI" ${outfile}
+                # make sure that the default EESSI software repository is available
+                grep "software.eessi.io" ${outfile}
 
               # test use of --list-repos with custom repos.cfg
               elif [[ ${{matrix.SCRIPT_TEST}} == 'listrepos_custom' ]]; then

From aa9895e44ac1afd5a44524d004161f3804449a90 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 4 Jul 2024 15:27:27 +0200
Subject: [PATCH 459/501] fix regex to find the custom EESSI version in the
 output of --list-repos

---
 .github/workflows/test_eessi_container_script.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test_eessi_container_script.yml b/.github/workflows/test_eessi_container_script.yml
index c0346774cb..d44788927f 100644
--- a/.github/workflows/test_eessi_container_script.yml
+++ b/.github/workflows/test_eessi_container_script.yml
@@ -58,11 +58,12 @@ jobs:
                 echo "[EESSI/20HT.TP]" >> cfg/repos.cfg
                 echo "repo_version = 20HT.TP" >> cfg/repos.cfg
                 ./eessi_container.sh --verbose --list-repos | tee ${outfile}
-                grep "EESSI" ${outfile}
+                # make sure that the default EESSI software repository is available
+                grep "software.eessi.io" ${outfile}
 
                 export EESSI_REPOS_CFG_DIR_OVERRIDE=${PWD}/cfg
                 ./eessi_container.sh --verbose --list-repos | tee ${outfile2}
-                grep "[EESSI/2023.02]" ${outfile2}
+                grep "EESSI/20AB.CD" ${outfile2}
 
               # test use of --mode run
               elif [[ ${{matrix.SCRIPT_TEST}} == 'run' ]]; then

From cbedafef9f104540151ca9093bc2e95b178036b3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 4 Jul 2024 21:07:39 +0200
Subject: [PATCH 460/501] {2023.06,a64fx}[foss/2023a] ParaView 5.11.2

---
 .../2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml               | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
index 3fe1e43d3f..5521b92398 100644
--- a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -3,3 +3,4 @@ easyconfigs:
   - foss-2023a.eb
   - SciPy-bundle-2023.07-gfbf-2023a.eb
   - ESPResSo-4.2.2-foss-2023a.eb
+  - ParaView-5.11.2-foss-2023a.eb

From c97dd7ed8e9d7cc23436927f4dfff00fae93d623 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 4 Jul 2024 21:58:10 +0200
Subject: [PATCH 461/501] add missing /cvmfs/ in $EESSI_CVMFS_REPO_OVERRIDE
 defined by bot/build.sh and bot/test.sh

---
 bot/build.sh | 2 +-
 bot/test.sh  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/bot/build.sh b/bot/build.sh
index c9a362fdca..145be740d3 100755
--- a/bot/build.sh
+++ b/bot/build.sh
@@ -138,7 +138,7 @@ echo "bot/build.sh: EESSI_VERSION_OVERRIDE='${EESSI_VERSION_OVERRIDE}'"
 # determine CVMFS repo to be used from .repository.repo_name in ${JOB_CFG_FILE}
 # here, just set EESSI_CVMFS_REPO_OVERRIDE, a bit further down
 # "source init/eessi_defaults" via sourcing init/minimal_eessi_env
-export EESSI_CVMFS_REPO_OVERRIDE=$(cfg_get_value "repository" "repo_name")
+export EESSI_CVMFS_REPO_OVERRIDE=/cvmfs/$(cfg_get_value "repository" "repo_name")
 echo "bot/build.sh: EESSI_CVMFS_REPO_OVERRIDE='${EESSI_CVMFS_REPO_OVERRIDE}'"
 
 # determine architecture to be used from entry .architecture in ${JOB_CFG_FILE}
diff --git a/bot/test.sh b/bot/test.sh
index 04bff346cd..d3f3630ea8 100755
--- a/bot/test.sh
+++ b/bot/test.sh
@@ -160,7 +160,7 @@ echo "bot/test.sh: EESSI_PILOT_VERSION_OVERRIDE='${EESSI_PILOT_VERSION_OVERRIDE}
 # determine CVMFS repo to be used from .repository.repo_name in ${JOB_CFG_FILE}
 # here, just set EESSI_CVMFS_REPO_OVERRIDE, a bit further down
 # "source init/eessi_defaults" via sourcing init/minimal_eessi_env
-export EESSI_CVMFS_REPO_OVERRIDE=$(cfg_get_value "repository" "repo_name")
+export EESSI_CVMFS_REPO_OVERRIDE=/cvmfs/$(cfg_get_value "repository" "repo_name")
 echo "bot/test.sh: EESSI_CVMFS_REPO_OVERRIDE='${EESSI_CVMFS_REPO_OVERRIDE}'"
 
 # determine architecture to be used from entry .architecture in ${JOB_CFG_FILE}

From 3bae44ca2c8ee6cf0b53f753b74f47314d532222 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 4 Jul 2024 21:58:10 +0200
Subject: [PATCH 462/501] add missing /cvmfs/ in $EESSI_CVMFS_REPO_OVERRIDE
 defined by bot/build.sh and bot/test.sh

---
 bot/build.sh | 2 +-
 bot/test.sh  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/bot/build.sh b/bot/build.sh
index c9a362fdca..145be740d3 100755
--- a/bot/build.sh
+++ b/bot/build.sh
@@ -138,7 +138,7 @@ echo "bot/build.sh: EESSI_VERSION_OVERRIDE='${EESSI_VERSION_OVERRIDE}'"
 # determine CVMFS repo to be used from .repository.repo_name in ${JOB_CFG_FILE}
 # here, just set EESSI_CVMFS_REPO_OVERRIDE, a bit further down
 # "source init/eessi_defaults" via sourcing init/minimal_eessi_env
-export EESSI_CVMFS_REPO_OVERRIDE=$(cfg_get_value "repository" "repo_name")
+export EESSI_CVMFS_REPO_OVERRIDE=/cvmfs/$(cfg_get_value "repository" "repo_name")
 echo "bot/build.sh: EESSI_CVMFS_REPO_OVERRIDE='${EESSI_CVMFS_REPO_OVERRIDE}'"
 
 # determine architecture to be used from entry .architecture in ${JOB_CFG_FILE}
diff --git a/bot/test.sh b/bot/test.sh
index 04bff346cd..d3f3630ea8 100755
--- a/bot/test.sh
+++ b/bot/test.sh
@@ -160,7 +160,7 @@ echo "bot/test.sh: EESSI_PILOT_VERSION_OVERRIDE='${EESSI_PILOT_VERSION_OVERRIDE}
 # determine CVMFS repo to be used from .repository.repo_name in ${JOB_CFG_FILE}
 # here, just set EESSI_CVMFS_REPO_OVERRIDE, a bit further down
 # "source init/eessi_defaults" via sourcing init/minimal_eessi_env
-export EESSI_CVMFS_REPO_OVERRIDE=$(cfg_get_value "repository" "repo_name")
+export EESSI_CVMFS_REPO_OVERRIDE=/cvmfs/$(cfg_get_value "repository" "repo_name")
 echo "bot/test.sh: EESSI_CVMFS_REPO_OVERRIDE='${EESSI_CVMFS_REPO_OVERRIDE}'"
 
 # determine architecture to be used from entry .architecture in ${JOB_CFG_FILE}

From 3fc6cdc1558e21005470e815adeb3f8620ec53e8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Jul 2024 08:18:27 +0200
Subject: [PATCH 463/501] reduce parallellism when building Qt5 on A64FX
 systems, due to scarce memory

---
 eb_hooks.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index e6f0cf0dd2..40071ea067 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -81,8 +81,11 @@ def post_ready_hook(self, *args, **kwargs):
     """
     # 'parallel' easyconfig parameter is set via EasyBlock.set_parallel in ready step based on available cores.
     # here we reduce parallellism to only use half of that for selected software,
-    # to avoid failing builds/tests due to out-of-memory problems
-    if self.name in ['TensorFlow', 'libxc']:
+    # to avoid failing builds/tests due to out-of-memory problems;
+    memory_hungry_build = self.name in ['libxc', 'TensorFlow']
+    # on A64FX systems, (HBM) memory is typically scarce, so we need to use fewer cores for some builds
+    memory_hungry_build_a64fx = self.name in ['Qt5']
+    if memory_hungry_build or memory_hungry_build_a64fx:
         parallel = self.cfg['parallel']
         if parallel > 1:
             self.cfg['parallel'] = parallel // 2

From a74669585a742ca83e9b976d7f6854a20570460f Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Fri, 5 Jul 2024 12:24:01 +0000
Subject: [PATCH 464/501] {2023.06}[GCCcore/12.3.0-GCC/12.3.0-gompi/2023a]
 bio-packages

---
 .../2023.06/eessi-2023.06-eb-4.9.2-2023a.yml      | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
index ade226c217..7fc42e2e34 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -1,2 +1,17 @@
 easyconfigs:
   - BCFtools-1.18-GCC-12.3.0.eb
+  - BWA-0.7.18-GCCcore-12.3.0.eb
+  - CapnProto-1.0.1-GCCcore-12.3.0.eb
+  - DendroPy-4.6.1-GCCcore-12.3.0.eb
+  - DIAMOND-2.1.8-GCC-12.3.0.eb
+  - FastME-2.1.6.3-GCC-12.3.0.eb
+  - fastp-0.23.4-GCC-12.3.0.eb
+  - HMMER-3.4-gompi-2023a.eb
+  - IQ-TREE-2.3.5-gompi-2023a.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20955
+        from-commit: 185f88b9a03d65a7fb74edc7acb4221e87e90784      
+  - KronaTools-2.8.1-GCCcore-12.3.0.eb
+  - LSD2-2.4.1-GCCcore-12.3.0.eb
+  - MAFFT-7.520-GCC-12.3.0-with-extensions.eb
+  - ncbi-vdb-3.0.10-gompi-2023a.e

From 4d9390ef015f03abe54ca3f61cd84ca6b1164c07 Mon Sep 17 00:00:00 2001
From: TopRichard <121792457+TopRichard@users.noreply.github.com>
Date: Fri, 5 Jul 2024 14:30:32 +0200
Subject: [PATCH 465/501] Update
 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
index 7fc42e2e34..34ec3257e8 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -14,4 +14,4 @@ easyconfigs:
   - KronaTools-2.8.1-GCCcore-12.3.0.eb
   - LSD2-2.4.1-GCCcore-12.3.0.eb
   - MAFFT-7.520-GCC-12.3.0-with-extensions.eb
-  - ncbi-vdb-3.0.10-gompi-2023a.e
+  - ncbi-vdb-3.0.10-gompi-2023a.eb

From 868a8a8c94e932762299aabc6c6ed4eca749ef42 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 5 Jul 2024 16:07:05 +0200
Subject: [PATCH 466/501] /tmp/overlay-upper should now be
 /tmp/<repo-name>/overlay-upper

---
 create_tarball.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/create_tarball.sh b/create_tarball.sh
index 0a7669f73f..ed999cde89 100755
--- a/create_tarball.sh
+++ b/create_tarball.sh
@@ -26,7 +26,7 @@ if [ ! -d ${software_dir} ]; then
     exit 2
 fi
 
-overlay_upper_dir="${eessi_tmpdir}/overlay-upper"
+overlay_upper_dir="${eessi_tmpdir}/${cvmfs_repo}/overlay-upper"
 
 software_dir_overlay="${overlay_upper_dir}/versions/${eessi_version}"
 if [ ! -d ${software_dir_overlay} ]; then

From d5ecd74837cde2feb834275632e327beb182c00f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 5 Jul 2024 21:58:23 +0200
Subject: [PATCH 467/501] remove /cvmfs/ from cvmfs_repo variable

---
 create_tarball.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/create_tarball.sh b/create_tarball.sh
index ed999cde89..2dee665060 100755
--- a/create_tarball.sh
+++ b/create_tarball.sh
@@ -26,7 +26,8 @@ if [ ! -d ${software_dir} ]; then
     exit 2
 fi
 
-overlay_upper_dir="${eessi_tmpdir}/${cvmfs_repo}/overlay-upper"
+cvmfs_repo_name=${cvmfs_repo#/cvmfs/}
+overlay_upper_dir="${eessi_tmpdir}/${cvmfs_repo_name}/overlay-upper"
 
 software_dir_overlay="${overlay_upper_dir}/versions/${eessi_version}"
 if [ ! -d ${software_dir_overlay} ]; then

From 49cbcc8de452e9cc51a3969b860932caf109a9bf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 5 Jul 2024 22:02:31 +0200
Subject: [PATCH 468/501] implement changes from
 https://github.com/EESSI/software-layer/pull/635 and
 https://github.com/EESSI/software-layer/pull/636

---
 create_tarball.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/create_tarball.sh b/create_tarball.sh
index 0a7669f73f..2dee665060 100755
--- a/create_tarball.sh
+++ b/create_tarball.sh
@@ -26,7 +26,8 @@ if [ ! -d ${software_dir} ]; then
     exit 2
 fi
 
-overlay_upper_dir="${eessi_tmpdir}/overlay-upper"
+cvmfs_repo_name=${cvmfs_repo#/cvmfs/}
+overlay_upper_dir="${eessi_tmpdir}/${cvmfs_repo_name}/overlay-upper"
 
 software_dir_overlay="${overlay_upper_dir}/versions/${eessi_version}"
 if [ ! -d ${software_dir_overlay} ]; then

From 88eebb9ee7245c56e4ad623c4055b8f4c365b59a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 6 Jul 2024 11:26:40 +0200
Subject: [PATCH 469/501] rebuild OpenFOAM-10-foss-2023a.eb and
 OpenFOAM-11-foss-2023a.eb without -ftree-vectorize

---
 ...20240706-eb-4.9.2-OpenFOAM-no-ftree-vectorize.yml | 12 ++++++++++++
 1 file changed, 12 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/rebuilds/20240706-eb-4.9.2-OpenFOAM-no-ftree-vectorize.yml

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240706-eb-4.9.2-OpenFOAM-no-ftree-vectorize.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240706-eb-4.9.2-OpenFOAM-no-ftree-vectorize.yml
new file mode 100644
index 0000000000..c12d244790
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240706-eb-4.9.2-OpenFOAM-no-ftree-vectorize.yml
@@ -0,0 +1,12 @@
+# 2024.07.06
+# OpenFOAM 10 and 11 built with GCC 11.3.0 or 12.3.0 and -ftree-vectorize yields incorrect results,
+# see https://github.com/easybuilders/easybuild-easyconfigs/issues/20927
+easyconfigs:
+  - OpenFOAM-10-foss-2023a.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20958
+        from-commit: dbadb2074464d816740ee0e95595c2cb31b6338f
+  - OpenFOAM-11-foss-2023a.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20958
+        from-commit: dbadb2074464d816740ee0e95595c2cb31b6338f

From f2507201e02ea6da362f784fad1bbb5b27caa4a7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 6 Jul 2024 11:29:01 +0200
Subject: [PATCH 470/501] {2023.06,zen4}[foss/2023a] OpenFOAM 10 + 11

---
 .../2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml         | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
index d4c70c562d..65a12695e4 100644
--- a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -3,3 +3,11 @@ easyconfigs:
   - TensorFlow-2.13.0-foss-2023a.eb
   - R-4.3.2-gfbf-2023a.eb
   - ParaView-5.11.2-foss-2023a.eb
+  - OpenFOAM-10-foss-2023a.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20958
+        from-commit: dbadb2074464d816740ee0e95595c2cb31b6338f
+  - OpenFOAM-11-foss-2023a.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20958
+        from-commit: dbadb2074464d816740ee0e95595c2cb31b6338f

From 085e32a603842363607eeb10743f1f20107afd27 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Sat, 6 Jul 2024 12:10:46 +0200
Subject: [PATCH 471/501] {2023.06}[foss/2023a] Extrae 4.2.0

Alternative to #554
---
 .../2023.06/eessi-2023.06-eb-4.9.2-2023b.yml                  | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
index 38bfa81142..fd26743499 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
@@ -1,3 +1,7 @@
 easyconfigs:
   - IPython-8.17.2-GCCcore-13.2.0.eb
   - dlb-3.4-gompi-2023b.eb
+  - Extrae-4.2.0-gompi-2023b.eb:
+      options:
+        from-pr: 20690
+        include-easyblocks-from-pr: 3339

From 7cb667929694c8a330a5e3f4921ea97e258f933a Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Sun, 7 Jul 2024 12:56:29 +0200
Subject: [PATCH 472/501] Re-add hook from #554 but keep running tests

---
 eb_hooks.py | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/eb_hooks.py b/eb_hooks.py
index e6f0cf0dd2..42b230c006 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -1,5 +1,6 @@
 # Hooks to customize how EasyBuild installs software in EESSI
 # see https://docs.easybuild.io/en/latest/Hooks.html
+import glob
 import os
 import re
 
@@ -353,6 +354,31 @@ def pre_configure_hook_BLIS_a64fx(self, *args, **kwargs):
     else:
         raise EasyBuildError("BLIS-specific hook triggered for non-BLIS easyconfig?!")
 
+def pre_configure_hook_extrae(self, *args, **kwargs):
+    """
+    Pre-configure hook for Extrae
+    - avoid use of 'which' in configure script
+    - specify correct path to binutils (in compat layer)
+    """
+    if self.name == 'Extrae':
+
+        # determine path to Prefix installation in compat layer via $EPREFIX
+        eprefix = get_eessi_envvar('EPREFIX')
+
+        binutils_lib_path_glob_pattern = os.path.join(eprefix, 'usr', 'lib*', 'binutils', '*-pc-linux-gnu', '2.*')
+        binutils_lib_path = glob.glob(binutils_lib_path_glob_pattern)
+        if len(binutils_lib_path) == 1:
+            self.cfg.update('configopts', '--with-binutils=' + binutils_lib_path[0])
+        else:
+            raise EasyBuildError("Failed to isolate path for binutils libraries using %s, got %s",
+                                 binutils_lib_path_glob_pattern, binutils_lib_path)
+
+        # replace use of 'which' with 'command -v', since 'which' is broken in EESSI build container;
+        # this must be done *after* running configure script, because initial configuration re-writes configure script,
+        # and problem due to use of which only pops up when running make ?!
+        self.cfg.update('prebuildopts', "cp config/mpi-macros.m4 config/mpi-macros.m4.orig && sed -i 's/`which /`command -v /g' config/mpi-macros.m4 && ")
+    else:
+        raise EasyBuildError("Extrae-specific hook triggered for non-Extrae easyconfig?!")
 
 def pre_configure_hook_gromacs(self, *args, **kwargs):
     """
@@ -711,6 +737,7 @@ def inject_gpu_property(ec):
 PRE_CONFIGURE_HOOKS = {
     'at-spi2-core': pre_configure_hook_atspi2core_filter_ld_library_path,
     'BLIS': pre_configure_hook_BLIS_a64fx,
+    'Extrae': pre_configure_hook_extrae,
     'GROMACS': pre_configure_hook_gromacs,
     'libfabric': pre_configure_hook_libfabric_disable_psm3_x86_64_generic,
     'MetaBAT': pre_configure_hook_metabat_filtered_zlib_dep,

From b07445e75cb874fb87003df1d92a5ba879deac4c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 7 Jul 2024 21:56:20 +0200
Subject: [PATCH 473/501] only use half the cores for Qt5 when building for
 A64FX

---
 eb_hooks.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index 40071ea067..3b381e5963 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -84,7 +84,8 @@ def post_ready_hook(self, *args, **kwargs):
     # to avoid failing builds/tests due to out-of-memory problems;
     memory_hungry_build = self.name in ['libxc', 'TensorFlow']
     # on A64FX systems, (HBM) memory is typically scarce, so we need to use fewer cores for some builds
-    memory_hungry_build_a64fx = self.name in ['Qt5']
+    cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
+    memory_hungry_build_a64fx = cpu_target == CPU_TARGET_A64FX and self.name in ['Qt5']
     if memory_hungry_build or memory_hungry_build_a64fx:
         parallel = self.cfg['parallel']
         if parallel > 1:

From d6d5a2bb5c2eead7cd931ea307ea4cd3b44bf9db Mon Sep 17 00:00:00 2001
From: Helena Vela Beltran <47674829+hvelab@users.noreply.github.com>
Date: Mon, 8 Jul 2024 17:18:02 +0200
Subject: [PATCH 474/501] Update init/eessi_environment_variables

Add bigger comment

Co-authored-by: ocaisa <alan.ocais@cecam.org>
---
 init/eessi_environment_variables | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index f5bb387955..9417d5b2a2 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -106,15 +106,15 @@ if [ -d $EESSI_PREFIX ]; then
             false
           fi
 
-        # Fix wrong path for RHEL >=8 libcurl 
-	# This is required here because we ship curl in our compat layer. If we only provided
-	# curl as a module file we could instead do this via a `modluafooter` in an EasyBuild
-	# hook (or via an Lmod hook)
-	rhel_libcurl_file="/etc/pki/tls/certs/ca-bundle.crt"
-        if [ -f $rhel_libcurl_file ]; then
-          show_msg "Found libcurl CAs file at RHEL location, setting CURL_CA_BUNDLE"
-          export CURL_CA_BUNDLE=$rhel_libcurl_file
-        fi
+          # Fix wrong path for RHEL >=8 libcurl 
+	  # This is required here because we ship curl in our compat layer. If we only provided
+	  # curl as a module file we could instead do this via a `modluafooter` in an EasyBuild
+	  # hook (or via an Lmod hook)
+	  rhel_libcurl_file="/etc/pki/tls/certs/ca-bundle.crt"
+          if [ -f $rhel_libcurl_file ]; then
+            show_msg "Found libcurl CAs file at RHEL location, setting CURL_CA_BUNDLE"
+            export CURL_CA_BUNDLE=$rhel_libcurl_file
+          fi
 
         else
           error "EESSI software layer at $EESSI_SOFTWARE_PATH not found!"

From 0fef63a6ce712956e04b9cb007c21565d624f1fa Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Tue, 9 Jul 2024 00:15:40 +0200
Subject: [PATCH 475/501] Update eb_hooks.py

---
 eb_hooks.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index 42b230c006..f43b695266 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -365,7 +365,7 @@ def pre_configure_hook_extrae(self, *args, **kwargs):
         # determine path to Prefix installation in compat layer via $EPREFIX
         eprefix = get_eessi_envvar('EPREFIX')
 
-        binutils_lib_path_glob_pattern = os.path.join(eprefix, 'usr', 'lib*', 'binutils', '*-pc-linux-gnu', '2.*')
+        binutils_lib_path_glob_pattern = os.path.join(eprefix, 'usr', 'lib*', 'binutils', '*-linux-gnu', '2.*')
         binutils_lib_path = glob.glob(binutils_lib_path_glob_pattern)
         if len(binutils_lib_path) == 1:
             self.cfg.update('configopts', '--with-binutils=' + binutils_lib_path[0])

From 28eabaaefcde5b112b60e8c94f46494ab7b0944e Mon Sep 17 00:00:00 2001
From: Xin An <xina@int5.local.snellius.surf.nl>
Date: Fri, 12 Jul 2024 12:11:19 +0200
Subject: [PATCH 476/501] {2023.06}[gfbf/2023b] Pystencils 1.3.4

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 15c02951d7..3963f79ecd 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -58,3 +58,4 @@ easyconfigs:
       options:
         from-pr: 20201
   - OSU-Micro-Benchmarks-7.2-gompi-2023b.eb
+  - pystencils-1.3.4-gfbf-2023b.eb

From 2ca3684b845165425af638daaea27897fd1cbe7e Mon Sep 17 00:00:00 2001
From: Xin An <34663977+xinan1911@users.noreply.github.com>
Date: Fri, 12 Jul 2024 14:29:19 +0200
Subject: [PATCH 477/501] Update
 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml                 | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 3963f79ecd..8d9779c59c 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -58,4 +58,7 @@ easyconfigs:
       options:
         from-pr: 20201
   - OSU-Micro-Benchmarks-7.2-gompi-2023b.eb
-  - pystencils-1.3.4-gfbf-2023b.eb
+  - pystencils-1.3.4-gfbf-2023b.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20889
+        from-commit: c66c4788a17f7e4f55aa23f9fdb782aad97c9ce7

From 641288af0c2bc1d1e35d411815465abdeb8a1ddc Mon Sep 17 00:00:00 2001
From: Xin An <34663977+xinan1911@users.noreply.github.com>
Date: Fri, 12 Jul 2024 16:08:14 +0200
Subject: [PATCH 478/501] Update eessi-2023.06-eb-4.9.0-2023b.yml

Remove pystencils
---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml                  | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 8d9779c59c..15c02951d7 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -58,7 +58,3 @@ easyconfigs:
       options:
         from-pr: 20201
   - OSU-Micro-Benchmarks-7.2-gompi-2023b.eb
-  - pystencils-1.3.4-gfbf-2023b.eb:
-      options:
-        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20889
-        from-commit: c66c4788a17f7e4f55aa23f9fdb782aad97c9ce7

From bb8b4aa1442c032b88d6cacc94b2d8f42cce3721 Mon Sep 17 00:00:00 2001
From: Xin An <34663977+xinan1911@users.noreply.github.com>
Date: Fri, 12 Jul 2024 16:10:02 +0200
Subject: [PATCH 479/501] add pystencils

update eessi-2023.06-eb-4.9.2-2023b
---
 .../2023.06/eessi-2023.06-eb-4.9.2-2023b.yml                  | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
index 38bfa81142..e0057f18ab 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
@@ -1,3 +1,7 @@
 easyconfigs:
   - IPython-8.17.2-GCCcore-13.2.0.eb
   - dlb-3.4-gompi-2023b.eb
+  - pystencils-1.3.4-gfbf-2023b.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20889
+        from-commit: c66c4788a17f7e4f55aa23f9fdb782aad97c9ce7

From f204afa5d804dee715476ac3d2a96e8e69fa6842 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Mon, 15 Jul 2024 10:47:34 +0200
Subject: [PATCH 480/501] Add MetalWalls to easystack file

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 4b58cb6106..0cdbd4b5b3 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -74,3 +74,4 @@ easyconfigs:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20238
         from-pr: 20238
+  - MetalWalls-21.06.1-foss-2023a.eb

From 58fb56f2a8f2fb11d5df2b8332388ace82eda993 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Tue, 16 Jul 2024 14:41:39 +0200
Subject: [PATCH 481/501] Switch target to EB 4.9.2

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml   | 1 -
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml   | 1 +
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 0cdbd4b5b3..4b58cb6106 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -74,4 +74,3 @@ easyconfigs:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20238
         from-pr: 20238
-  - MetalWalls-21.06.1-foss-2023a.eb
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
index 34ec3257e8..e7730d1eb6 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -15,3 +15,4 @@ easyconfigs:
   - LSD2-2.4.1-GCCcore-12.3.0.eb
   - MAFFT-7.520-GCC-12.3.0-with-extensions.eb
   - ncbi-vdb-3.0.10-gompi-2023a.eb
+  - MetalWalls-21.06.1-foss-2023a.eb

From a7a895408c9b194cd8aeff27dd5f17f54a5fc514 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Wed, 17 Jul 2024 13:45:39 +0200
Subject: [PATCH 482/501] Move changes to latest eb release

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023a.yml                | 6 ------
 .../2023.06/eessi-2023.06-eb-4.9.2-2023a.yml                | 6 ++++++
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 428c1ac77f..4b58cb6106 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -74,9 +74,3 @@ easyconfigs:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20238
         from-pr: 20238
-  - QuantumESPRESSO-7.3.1-foss-2023a.eb:
-      # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20138
-      # see https://github.com/easybuilders/easybuild-easyblocks/pull/3257
-      options:
-        from-pr: 20138
-        include-easyblocks-from-pr: 3257
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
index e7730d1eb6..af69b288e8 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -16,3 +16,9 @@ easyconfigs:
   - MAFFT-7.520-GCC-12.3.0-with-extensions.eb
   - ncbi-vdb-3.0.10-gompi-2023a.eb
   - MetalWalls-21.06.1-foss-2023a.eb
+  - QuantumESPRESSO-7.3.1-foss-2023a.eb:
+      # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20138
+      # see https://github.com/easybuilders/easybuild-easyblocks/pull/3338
+      options:
+        from-pr: 20138
+        include-easyblocks-from-pr: 3338

From 0ab0440e4ee990bbe76d7e8b7d0912701b21e8fa Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Wed, 17 Jul 2024 14:00:00 +0200
Subject: [PATCH 483/501] Allow initialisation scripts to be used with bash <
 4.2

---
 init/bash                        | 2 +-
 init/eessi_defaults              | 2 +-
 init/eessi_environment_variables | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/init/bash b/init/bash
index 93471e075e..4ad09f6a1b 100644
--- a/init/bash
+++ b/init/bash
@@ -1,7 +1,7 @@
 function show_msg {
   # only echo msg if EESSI_SILENT is unset
   msg=$1
-  if [[ ! -v EESSI_SILENT ]]; then
+  if [[ -z ${EESSI_SILENT+x} ]]; then
     echo "$msg"
   fi
 }
diff --git a/init/eessi_defaults b/init/eessi_defaults
index c1ce82d1ce..654a829425 100644
--- a/init/eessi_defaults
+++ b/init/eessi_defaults
@@ -12,7 +12,7 @@
 if [[ $(uname -m) == "riscv64" ]]; then
     export EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO_OVERRIDE:=/cvmfs/riscv.eessi.io}"
     export EESSI_VERSION="${EESSI_VERSION_OVERRIDE:=20240402}"
-    if [[ ! -v EESSI_SILENT ]]; then
+    if [[ -z ${EESSI_SILENT+x} ]]; then
         echo "RISC-V architecture detected, but there is no RISC-V support yet in the production repository."
         echo "Automatically switching to version ${EESSI_VERSION} of the RISC-V development repository ${EESSI_CVMFS_REPO}."
         echo "For more details about this repository, see https://www.eessi.io/docs/repositories/riscv.eessi.io/."
diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index 9417d5b2a2..3e35f845a1 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -10,7 +10,7 @@ function error() {
 function show_msg {
   # only echo msg if EESSI_SILENT is unset
   msg=$1
-  if [[ ! -v EESSI_SILENT ]]; then
+  if [[ -z ${EESSI_SILENT+x} ]]; then
     echo "$msg"
   fi
 }

From 5ff9d1660c736ddf88052035fa7a10a6ac7a33c1 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Thu, 18 Jul 2024 16:02:55 +0200
Subject: [PATCH 484/501] Fixes for ARM

---
 .../2023.06/eessi-2023.06-eb-4.9.2-2023b.yml                 | 4 ++--
 eb_hooks.py                                                  | 5 ++++-
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
index bc7bee302a..3f18d02db5 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
@@ -7,5 +7,5 @@ easyconfigs:
         from-commit: c66c4788a17f7e4f55aa23f9fdb782aad97c9ce7
   - Extrae-4.2.0-gompi-2023b.eb:
       options:
-        from-pr: 20690
-        include-easyblocks-from-pr: 3339
+        from-pr: 21017
+        include-easyblocks-from-pr: 3393
diff --git a/eb_hooks.py b/eb_hooks.py
index ec08e96847..73adce90f1 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -362,7 +362,7 @@ def pre_configure_hook_extrae(self, *args, **kwargs):
     """
     Pre-configure hook for Extrae
     - avoid use of 'which' in configure script
-    - specify correct path to binutils (in compat layer)
+    - specify correct path to binutils/zlib (in compat layer)
     """
     if self.name == 'Extrae':
 
@@ -377,6 +377,9 @@ def pre_configure_hook_extrae(self, *args, **kwargs):
             raise EasyBuildError("Failed to isolate path for binutils libraries using %s, got %s",
                                  binutils_lib_path_glob_pattern, binutils_lib_path)
 
+        # zlib is a filtered dependency, so we need to manually specify it's location to avoid the host version
+        self.cfg.update('configopts', '--with-libz=' + eprefix)
+
         # replace use of 'which' with 'command -v', since 'which' is broken in EESSI build container;
         # this must be done *after* running configure script, because initial configuration re-writes configure script,
         # and problem due to use of which only pops up when running make ?!

From 192e494b56603dcead6b30c19e00064efe7b2769 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Thu, 18 Jul 2024 16:59:47 +0200
Subject: [PATCH 485/501] Update
 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 .../2023.06/eessi-2023.06-eb-4.9.2-2023b.yml                | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
index 3f18d02db5..f118e94adb 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
@@ -7,5 +7,7 @@ easyconfigs:
         from-commit: c66c4788a17f7e4f55aa23f9fdb782aad97c9ce7
   - Extrae-4.2.0-gompi-2023b.eb:
       options:
-        from-pr: 21017
-        include-easyblocks-from-pr: 3393
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21017
+        from-commit: 120f4d56efebd2bc61382db4c84a664a339c66cf
+        # see https://github.com/easybuilders/easybuild-easyblocks/pull/3393
+        include-easyblocks-from-commit: c4951c78d62fa5cf8e9f6fe0ead212d2a4d7cb9c

From 8b350fd435924a18705d1869c0bc87be15d76465 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Thu, 18 Jul 2024 18:02:08 +0200
Subject: [PATCH 486/501] Update eessi-2023.06-eb-4.9.2-2023a.yml

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
index ed9896191b..f40d7d85e1 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -19,4 +19,4 @@ easyconfigs:
   - CP2K-2023.1-foss-2023a.eb:
       # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20951
       options:
-        from-pr: 20951
\ No newline at end of file
+        from-pr: 20951

From c0bec39b3c0528f9bde6f91c853f08b75cee1796 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Fri, 19 Jul 2024 09:28:03 +0200
Subject: [PATCH 487/501] Update
 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 .../2023.06/eessi-2023.06-eb-4.9.2-2023a.yml                  | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
index f40d7d85e1..bd6c767260 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -17,6 +17,6 @@ easyconfigs:
   - ncbi-vdb-3.0.10-gompi-2023a.eb
   - MetalWalls-21.06.1-foss-2023a.eb
   - CP2K-2023.1-foss-2023a.eb:
-      # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20951
       options:
-        from-pr: 20951
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20951
+        from-commit: a92667fe32396bbd4106243658625f7ff2adcd68

From a61925fb430a0e1b1adaf22f8e7e7c81a782dadf Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Fri, 19 Jul 2024 09:34:19 +0200
Subject: [PATCH 488/501] Update
 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 .../2023.06/eessi-2023.06-eb-4.9.2-2023a.yml              | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
index af69b288e8..67cc4bc155 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -17,8 +17,8 @@ easyconfigs:
   - ncbi-vdb-3.0.10-gompi-2023a.eb
   - MetalWalls-21.06.1-foss-2023a.eb
   - QuantumESPRESSO-7.3.1-foss-2023a.eb:
-      # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20138
-      # see https://github.com/easybuilders/easybuild-easyblocks/pull/3338
       options:
-        from-pr: 20138
-        include-easyblocks-from-pr: 3338
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20138
+        from-commit: dbdaacc0739fdee91baa9123864ea4428cf21273
+        # see https://github.com/easybuilders/easybuild-easyblocks/pull/3338
+        include-easyblocks-from-commit: 32e45bd1f2d916732ca5852d55d17fa4d99e388b

From 1660e048811192f8d072815963e960fdd9620828 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Fri, 19 Jul 2024 09:49:39 +0200
Subject: [PATCH 489/501] Remove duplicate testing of PRs

---
 .github/workflows/test-software.eessi.io.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test-software.eessi.io.yml b/.github/workflows/test-software.eessi.io.yml
index 06c02c8834..d4d980901f 100644
--- a/.github/workflows/test-software.eessi.io.yml
+++ b/.github/workflows/test-software.eessi.io.yml
@@ -1,6 +1,10 @@
 # documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
 name: Check for missing software installations in software.eessi.io
-on: [push, pull_request, workflow_dispatch]
+on:
+  push:
+    branches: [ "*-software.eessi.io" ]
+  pull_request:
+  workflow_dispatch:
 permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:

From 4d93a2d87b7289b12ab65daac9ddcc16e69a47ee Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 19 Jul 2024 09:57:54 +0200
Subject: [PATCH 490/501] Restrict tests for all CI

---
 .github/workflows/scorecards.yml                  | 2 +-
 .github/workflows/test_eessi_container_script.yml | 6 +++++-
 .github/workflows/test_licenses.yml               | 5 ++++-
 .github/workflows/tests.yml                       | 5 ++++-
 .github/workflows/tests_archdetect.yml            | 5 ++++-
 .github/workflows/tests_init.yml                  | 5 ++++-
 6 files changed, 22 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/scorecards.yml b/.github/workflows/scorecards.yml
index 5b482763f2..91c2576b7d 100644
--- a/.github/workflows/scorecards.yml
+++ b/.github/workflows/scorecards.yml
@@ -10,7 +10,7 @@ on:
     - cron: '25 15 * * 3'
   push:
     branches:
-      - '2023.06-software.eessi.io'
+      - '*-software.eessi.io'
 
 # Declare default permissions as read only.
 permissions: read-all
diff --git a/.github/workflows/test_eessi_container_script.yml b/.github/workflows/test_eessi_container_script.yml
index d44788927f..fb587ec489 100644
--- a/.github/workflows/test_eessi_container_script.yml
+++ b/.github/workflows/test_eessi_container_script.yml
@@ -1,6 +1,10 @@
 # documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
 name: Tests for eessi_container.sh script
-on: [push, pull_request, workflow_dispatch]
+on:
+  push:
+    branches: [ "*-software.eessi.io" ]
+  pull_request:
+  workflow_dispatch:
 permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
diff --git a/.github/workflows/test_licenses.yml b/.github/workflows/test_licenses.yml
index 6b6387d47d..bf6965c620 100644
--- a/.github/workflows/test_licenses.yml
+++ b/.github/workflows/test_licenses.yml
@@ -1,6 +1,9 @@
 # documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
 name: Test software licenses
-on: [push, pull_request]
+on:
+  push:
+    branches: [ "*-software.eessi.io" ]
+  pull_request:
 permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 8249e50d9b..940614b6bb 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -1,6 +1,9 @@
 # documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
 name: Tests
-on: [push, pull_request]
+on:
+  push:
+    branches: [ "*-software.eessi.io" ]
+  pull_request:
 permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
diff --git a/.github/workflows/tests_archdetect.yml b/.github/workflows/tests_archdetect.yml
index 4f5d3d174d..f5b42b3d55 100644
--- a/.github/workflows/tests_archdetect.yml
+++ b/.github/workflows/tests_archdetect.yml
@@ -1,6 +1,9 @@
 # documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
 name: Tests for eessi_archdetect.sh
-on: [push, pull_request]
+on:
+  push:
+    branches: [ "*-software.eessi.io" ]
+  pull_request:
 permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
diff --git a/.github/workflows/tests_init.yml b/.github/workflows/tests_init.yml
index 6c356a9184..8581681d63 100644
--- a/.github/workflows/tests_init.yml
+++ b/.github/workflows/tests_init.yml
@@ -1,6 +1,9 @@
 # documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
 name: Tests for init scripts
-on: [push, pull_request]
+on:
+  push:
+    branches: [ "*-software.eessi.io" ]
+  pull_request:
 permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:

From 8a2eca3cf3c949cff5fb1f61e1a3ef4e6d2cdfd2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Jul 2024 12:06:20 +0200
Subject: [PATCH 491/501] add a hook for GObject-Introspection that prevents
 environment vars from being set if EB filters them

---
 eb_hooks.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/eb_hooks.py b/eb_hooks.py
index 73adce90f1..deea409cf4 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -387,6 +387,24 @@ def pre_configure_hook_extrae(self, *args, **kwargs):
     else:
         raise EasyBuildError("Extrae-specific hook triggered for non-Extrae easyconfig?!")
 
+
+def pre_configure_hook_gobject_introspection(self, *args, **kwargs):
+    """
+    pre-configure hook for GObject-Introspection:
+    - prevent GObject-Introspection from setting $LD_LIBRARY_PATH if Easybuild is configured to filter it
+      that are configured to be filtered by EasyBuild, see:
+      https://github.com/EESSI/software-layer/issues/196
+    """
+    if self.name == 'GObject-Introspection':
+        # inject a line that removes all items from runtime_path_envvar that are in $EASYBUILD_FILTER_ENVVARS
+        sed_cmd = r'sed -i "s@\(^\s*runtime_path_envvar = \)\(.*\)@'
+        sed_cmd += r'\1\2\n\1 [x for x in runtime_path_envvar if not x in os.environ.get(\'EASYBUILD_FILTER_ENV_VARS\', \'\').split(\',\')]@g"'
+        sed_cmd += ' %(start_dir)s/giscanner/ccompiler.py && '
+        self.cfg.update('preconfigopts', sed_cmd)
+    else:
+        raise EasyBuildError("GObject-Introspection-specific hook triggered for non-GObject-Introspection easyconfig?!")
+
+
 def pre_configure_hook_gromacs(self, *args, **kwargs):
     """
     Pre-configure hook for GROMACS:
@@ -744,6 +762,7 @@ def inject_gpu_property(ec):
 PRE_CONFIGURE_HOOKS = {
     'at-spi2-core': pre_configure_hook_atspi2core_filter_ld_library_path,
     'BLIS': pre_configure_hook_BLIS_a64fx,
+    'GObject-Introspection': pre_configure_hook_gobject_introspection,
     'Extrae': pre_configure_hook_extrae,
     'GROMACS': pre_configure_hook_gromacs,
     'libfabric': pre_configure_hook_libfabric_disable_psm3_x86_64_generic,

From 62c1f7d000473bd53a60fa7d814dcccf11978524 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Jul 2024 13:45:42 +0200
Subject: [PATCH 492/501] rebuild all GObject-Introspection versions to apply
 new hook

---
 ...eb-4.9.2-GObject-Introspection-filter-envvars.yml | 12 ++++++++++++
 1 file changed, 12 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/rebuilds/20240719-eb-4.9.2-GObject-Introspection-filter-envvars.yml

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240719-eb-4.9.2-GObject-Introspection-filter-envvars.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240719-eb-4.9.2-GObject-Introspection-filter-envvars.yml
new file mode 100644
index 0000000000..676a2fe548
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240719-eb-4.9.2-GObject-Introspection-filter-envvars.yml
@@ -0,0 +1,12 @@
+# 2024.07.19
+# GObject-Introspection sets $LD_LIBRARY_PATH (to many different paths, including $EPREFIX/lib)
+# when calling gcc, and this causes a lot of issues for, especially, scripts using /bin/bash.
+#
+# This rebuild ensures (by using a new EasyBuild hook) that GObject-Introspection will not set
+# environment variables that are configured to be filtered by EasyBuild.
+# 
+# See https://github.com/EESSI/software-layer/issues/196
+easyconfigs:
+  - GObject-Introspection-1.74.0-GCCcore-12.2.0.eb
+  - GObject-Introspection-1.76.1-GCCcore-12.3.0.eb
+  - GObject-Introspection-1.78.1-GCCcore-13.2.0.eb

From 6277bc382003651012a8196bc7667ae1a3371704 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Jul 2024 13:58:53 +0200
Subject: [PATCH 493/501] fix comment

Co-authored-by: ocaisa <alan.ocais@cecam.org>
---
 eb_hooks.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index deea409cf4..aa9bde383a 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -391,8 +391,7 @@ def pre_configure_hook_extrae(self, *args, **kwargs):
 def pre_configure_hook_gobject_introspection(self, *args, **kwargs):
     """
     pre-configure hook for GObject-Introspection:
-    - prevent GObject-Introspection from setting $LD_LIBRARY_PATH if Easybuild is configured to filter it
-      that are configured to be filtered by EasyBuild, see:
+    - prevent GObject-Introspection from setting $LD_LIBRARY_PATH if EasyBuild is configured to filter it, see:
       https://github.com/EESSI/software-layer/issues/196
     """
     if self.name == 'GObject-Introspection':

From 5593999aa6acfaef2d235abc987a908643109cff Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Jul 2024 14:39:10 +0200
Subject: [PATCH 494/501] remove the at-spi2-core hook

---
 eb_hooks.py | 16 ----------------
 1 file changed, 16 deletions(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index deea409cf4..00d26df37b 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -486,21 +486,6 @@ def pre_configure_hook_wrf_aarch64(self, *args, **kwargs):
         raise EasyBuildError("WRF-specific hook triggered for non-WRF easyconfig?!")
 
 
-def pre_configure_hook_atspi2core_filter_ld_library_path(self, *args, **kwargs):
-    """
-    pre-configure hook for at-spi2-core:
-    - instruct GObject-Introspection's g-ir-scanner tool to not set $LD_LIBRARY_PATH
-      when EasyBuild is configured to filter it, see:
-      https://github.com/EESSI/software-layer/issues/196
-    """
-    if self.name == 'at-spi2-core':
-        if build_option('filter_env_vars') and 'LD_LIBRARY_PATH' in build_option('filter_env_vars'):
-            sed_cmd = 'sed -i "s/gir_extra_args = \[/gir_extra_args = \[\\n  \'--lib-dirs-envvar=FILTER_LD_LIBRARY_PATH\',/g" %(start_dir)s/atspi/meson.build && '
-            self.cfg.update('preconfigopts', sed_cmd)
-    else:
-        raise EasyBuildError("at-spi2-core-specific hook triggered for non-at-spi2-core easyconfig?!")
-
-
 def pre_test_hook(self,*args, **kwargs):
     """Main pre-test hook: trigger custom functions based on software name."""
     if self.name in PRE_TEST_HOOKS:
@@ -760,7 +745,6 @@ def inject_gpu_property(ec):
 }
 
 PRE_CONFIGURE_HOOKS = {
-    'at-spi2-core': pre_configure_hook_atspi2core_filter_ld_library_path,
     'BLIS': pre_configure_hook_BLIS_a64fx,
     'GObject-Introspection': pre_configure_hook_gobject_introspection,
     'Extrae': pre_configure_hook_extrae,

From 46a9c85149e1a9ff29bc8da9c322eda639c7f923 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Jul 2024 14:39:34 +0200
Subject: [PATCH 495/501] rebuild at-spi2-core with the rebuilt
 GObject-Introspection

---
 .../20240719-eb-4.9.2-GObject-Introspection-filter-envvars.yml  | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240719-eb-4.9.2-GObject-Introspection-filter-envvars.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240719-eb-4.9.2-GObject-Introspection-filter-envvars.yml
index 676a2fe548..a61cd9705b 100644
--- a/easystacks/software.eessi.io/2023.06/rebuilds/20240719-eb-4.9.2-GObject-Introspection-filter-envvars.yml
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240719-eb-4.9.2-GObject-Introspection-filter-envvars.yml
@@ -10,3 +10,5 @@ easyconfigs:
   - GObject-Introspection-1.74.0-GCCcore-12.2.0.eb
   - GObject-Introspection-1.76.1-GCCcore-12.3.0.eb
   - GObject-Introspection-1.78.1-GCCcore-13.2.0.eb
+  - at-spi2-core-2.46.0-GCCcore-12.2.0.eb
+  - at-spi2-core-2.49.91-GCCcore-12.3.0.eb

From bd328a2c357a4f1fe998d4b922363abe4461b904 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 19 Jul 2024 15:03:34 +0200
Subject: [PATCH 496/501] Use  instead of  (CentOS6)

---
 init/eessi_archdetect.sh         | 2 +-
 init/eessi_environment_variables | 2 +-
 init/minimal_eessi_env           | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/init/eessi_archdetect.sh b/init/eessi_archdetect.sh
index e89bc75e13..ddfed1bfae 100755
--- a/init/eessi_archdetect.sh
+++ b/init/eessi_archdetect.sh
@@ -89,7 +89,7 @@ cpupath(){
         *) log "ERROR" "cpupath: Unsupported CPU architecture $machine_type"
     esac
     # spec files are located in a subfolder with this script
-    local base_dir=$(dirname $(realpath $0))
+    local base_dir=$(dirname $(readlink -f $0))
     update_arch_specs "$base_dir/arch_specs/${spec_file}"
   
     # Identify the host CPU vendor
diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index 3e35f845a1..8c10b1fca8 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -1,6 +1,6 @@
 # this script is *sourced*, not executed, so can't rely on $0 to determine path to self
 # $BASH_SOURCE points to correct path, see also http://mywiki.wooledge.org/BashFAQ/028
-EESSI_INIT_DIR_PATH=$(dirname $(realpath $BASH_SOURCE))
+EESSI_INIT_DIR_PATH=$(dirname $(readlink -f $BASH_SOURCE))
 
 function error() {
     echo -e "\e[31mERROR: $1\e[0m" >&2
diff --git a/init/minimal_eessi_env b/init/minimal_eessi_env
index 03b337ccf7..5273f27862 100644
--- a/init/minimal_eessi_env
+++ b/init/minimal_eessi_env
@@ -2,7 +2,7 @@
 #
 # this script is *sourced*, not executed, so can't rely on $0 to determine path to self
 # $BASH_SOURCE points to correct path, see also http://mywiki.wooledge.org/BashFAQ/028
-EESSI_INIT_DIR_PATH=$(dirname $(realpath $BASH_SOURCE))
+EESSI_INIT_DIR_PATH=$(dirname $(readlink -f $BASH_SOURCE))
 
 # set up defaults: EESSI_CVMFS_REPO, EESSI_VERSION
 #   script takes *_OVERRIDEs into account

From 20eafc70aec97f46f311b27fe9b44b845964f723 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Jul 2024 15:30:35 +0200
Subject: [PATCH 497/501] rebuild GObject-Introspection for zen4

---
 ....9.2-GObject-Introspection-filter-envvars-zen4.yml | 11 +++++++++++
 1 file changed, 11 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/rebuilds/20240719-eb-4.9.2-GObject-Introspection-filter-envvars-zen4.yml

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240719-eb-4.9.2-GObject-Introspection-filter-envvars-zen4.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240719-eb-4.9.2-GObject-Introspection-filter-envvars-zen4.yml
new file mode 100644
index 0000000000..2c9b411736
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240719-eb-4.9.2-GObject-Introspection-filter-envvars-zen4.yml
@@ -0,0 +1,11 @@
+# 2024.07.19
+# GObject-Introspection sets $LD_LIBRARY_PATH (to many different paths, including $EPREFIX/lib)
+# when calling gcc, and this causes a lot of issues for, especially, scripts using /bin/bash.
+#
+# This rebuild ensures (by using a new EasyBuild hook) that GObject-Introspection will not set
+# environment variables that are configured to be filtered by EasyBuild.
+# 
+# See https://github.com/EESSI/software-layer/issues/196
+easyconfigs:
+  - GObject-Introspection-1.76.1-GCCcore-12.3.0.eb
+  - GObject-Introspection-1.78.1-GCCcore-13.2.0.eb

From 55a32613d3f6c4a295186cd93e33234e88146e48 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Mon, 22 Jul 2024 13:54:55 +0000
Subject: [PATCH 498/501] {2023.06}[gompi/2022b] BLAST+ V2.14.0

---
 .../2023.06/eessi-2023.06-eb-4.9.2-2022b.yml                  | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml
new file mode 100644
index 0000000000..ce28312e8c
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml
@@ -0,0 +1,4 @@
+easyconfigs:
+  - BLAST+-2.14.0-gompi-2022b.eb:
+      options:
+        from-commit: 1775912a1d36101d560e1355967732b07e82cd24

From 808a9032f942d1a88108a0b7d7067498b7e6e2d5 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Tue, 23 Jul 2024 10:09:09 +0200
Subject: [PATCH 499/501] {2023.06}[gompi/2023a] amdahl 0.3.1

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
index 7e9f4ff05a..d405d17193 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -26,3 +26,4 @@ easyconfigs:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20951
         from-commit: a92667fe32396bbd4106243658625f7ff2adcd68
+  - amdahl-0.3.1-gompi-2023a.eb

From 7d06f13fa83c7774d74ca9a09499ee34f7f1b17b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 23 Jul 2024 15:56:21 +0200
Subject: [PATCH 500/501] add pyMBE 0.8.0

---
 .../2023.06/eessi-2023.06-eb-4.9.2-2023b.yml                  | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
index f118e94adb..883483f5d2 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
@@ -11,3 +11,7 @@ easyconfigs:
         from-commit: 120f4d56efebd2bc61382db4c84a664a339c66cf
         # see https://github.com/easybuilders/easybuild-easyblocks/pull/3393
         include-easyblocks-from-commit: c4951c78d62fa5cf8e9f6fe0ead212d2a4d7cb9c
+  - pyMBE-0.8.0-foss-2023b.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21034
+        from-commit: 76e7fc6657bab64bfbec826540a3a8f0040258f2

From c0c784efbcb98389d6c61c43b2442dd07a981703 Mon Sep 17 00:00:00 2001
From: TopRichard <121792457+TopRichard@users.noreply.github.com>
Date: Fri, 26 Jul 2024 18:25:45 +0200
Subject: [PATCH 501/501] Update eessi-2023.06-eb-4.9.2-2022b.yml

---
 .../2023.06/eessi-2023.06-eb-4.9.2-2022b.yml                  | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml
index ce28312e8c..7a04eaa9d3 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml
@@ -1,4 +1,2 @@
 easyconfigs:
-  - BLAST+-2.14.0-gompi-2022b.eb:
-      options:
-        from-commit: 1775912a1d36101d560e1355967732b07e82cd24
+  - BLAST+-2.14.0-gompi-2022b.eb