Merge branch '2023.06' of https://github.com/EESSI/software-layer int…

…o espresso_2021a

.github/workflows/test_eessi.yml

@@ -29,6 +29,11 @@ jobs:
         - eessi-2023.06-eb-4.8.0-2021a.yml
         - eessi-2023.06-eb-4.8.0-system.yml
         - eessi-2023.06-eb-4.8.0-2021b.yml
+        - eessi-2023.06-eb-4.8.1-system.yml
+        - eessi-2023.06-eb-4.8.1-2021a.yml
+        - eessi-2023.06-eb-4.8.1-2021b.yml
+        - eessi-2023.06-eb-4.8.1-2022a.yml
+        - eessi-2023.06-eb-4.8.1-2023a.yml
     steps:
         - name: Check out software-layer repository
           uses: actions/checkout@93ea575cb5d8a053eaa0ac8fa3b40d7e05a33cc8 # v3.1.0

EESSI-pilot-install-software.sh

@@ -8,10 +8,12 @@
 
 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"
 }
 
 function copy_build_log() {
@@ -39,7 +41,7 @@ function copy_build_log() {
         echo "- working directory: ${PWD}" >> ${build_log_path}
         echo "- Slurm job ID: ${SLURM_OUT}" >> ${build_log_path}
         echo "- EasyBuild version: ${eb_version}" >> ${build_log_path}
-        echo "- easystack file: ${es}" >> ${build_log_path}
+        echo "- easystack file: ${easystack_file}" >> ${build_log_path}
 
         echo "EasyBuild log file ${build_log} copied to ${build_log_path} (with context appended)"
     fi
@@ -70,6 +72,10 @@ while [[ $# -gt 0 ]]; do
       export build_logs_dir="${2}"
       shift 2
       ;;
+    --shared-fs-path)
+      export shared_fs_path="${2}"
+      shift 2
+      ;;
     -*|--*)
       echo "Error: Unknown option: $1" >&2
       exit 1
@@ -160,6 +166,14 @@ 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}:${EASYBUILD_SOURCEPATH}
+fi
+
+${EB} --show-config
+
 echo ">> Setting up \$MODULEPATH..."
 # make sure no modules are loaded
 module --force purge
@@ -172,36 +186,39 @@ else
     echo_green ">> MODULEPATH set up: ${MODULEPATH}"
 fi
 
-for eb_version in '4.7.2' '4.8.0'; do
+# use 'git diff' to determine which easystack files were changed
+for easystack_file in $(git diff --name-only | grep '^eessi.*yml$'); 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}
 
     echo_green "All set, let's start installing some software with EasyBuild v${eb_version} in ${EASYBUILD_INSTALLPATH}..."
 
-    for es in $(ls eessi-${EESSI_PILOT_VERSION}-eb-${eb_version}-*.yml); do
-
-        if [ -f ${es} ]; then
-            echo_green "Feeding easystack file ${es} to EasyBuild..."
-
-            ${EB} --easystack ${TOPDIR}/${es} --robot
-            ec=$?
+    if [ -f ${easystack_file} ]; then
+        echo_green "Feeding easystack file ${easystack_file} to EasyBuild..."
 
-            # copy EasyBuild log file if EasyBuild exited with an error
-            if [ ${ec} -ne 0 ]; then
-                eb_last_log=$(unset EB_VERBOSE; eb --last-log)
-                # copy to current working directory
-                cp -a ${eb_last_log} .
-                echo "Last EasyBuild log file copied from ${eb_last_log} to ${PWD}"
-                # copy to build logs dir (with context added)
-                copy_build_log "${eb_last_log}" "${build_logs_dir}"
-            fi
+        ${EB} --easystack ${TOPDIR}/${easystack_file} --robot
+        ec=$?
 
-            $TOPDIR/check_missing_installations.sh ${TOPDIR}/${es}
-        else
-            fatal_error "Easystack file ${es} not found!"
+        # copy EasyBuild log file if EasyBuild exited with an error
+        if [ ${ec} -ne 0 ]; then
+            eb_last_log=$(unset EB_VERBOSE; eb --last-log)
+            # copy to current working directory
+            cp -a ${eb_last_log} .
+            echo "Last EasyBuild log file copied from ${eb_last_log} to ${PWD}"
+            # copy to build logs dir (with context added)
+            copy_build_log "${eb_last_log}" "${build_logs_dir}"
         fi
-    done
+
+        $TOPDIR/check_missing_installations.sh ${TOPDIR}/${easystack_file}
+    else
+        fatal_error "Easystack file ${easystack_file} not found!"
+    fi
 
 done
 

bot/bot-eessi-aws-citc.cfg

@@ -28,7 +28,7 @@ private_key = /mnt/shared/home/bot/eessi-bot-software-layer/eessi-bot-citc-aws.2
 # which GH accounts have the permission to send commands to the bot
 # if value is left/empty everyone can send commands
 # value can be a space delimited list of GH accounts
-command_permission = boegel trz42 bedroge laraPPr ocaisa casparvl satishskamath maxim-masterov TopRichard xinan1911
+command_permission = boegel trz42 bedroge laraPPr ocaisa casparvl satishskamath maxim-masterov TopRichard xinan1911 Neves-P
 
 # format of the response when processing bot commands
 command_response_fmt =
@@ -44,6 +44,10 @@ command_response_fmt =
 # name of the job script used for building an EESSI stack
 build_job_script = /mnt/shared/home/bot/eessi-bot-software-layer/scripts/bot-build.slurm
 
+# path to directory on shared filesystem that can be used for sharing data across build jobs
+# (for example source tarballs used by EasyBuild)
+shared_fs_path = /mnt/shared/home/bot/shared
+
 # Path (directory) to which build logs for (only) failing builds should be copied by bot/build.sh script
 build_logs_dir = /mnt/shared/bot-build-logs
 
@@ -96,7 +100,7 @@ submit_command = /usr/bin/sbatch
 # the label 'bot:build' (apparently this cannot be restricted on GitHub)
 # if value is left/empty everyone can trigger the build
 # value can be a space delimited list of GH accounts
-build_permission = boegel trz42 bedroge laraPPr ocaisa casparvl satishskamath maxim-masterov TopRichard xinan1911
+build_permission = boegel trz42 bedroge laraPPr ocaisa casparvl satishskamath maxim-masterov TopRichard xinan1911 Neves-P
 
 # template for comment when user who set a label has no permission to trigger build jobs
 no_build_permission_comment = Label `bot:build` has been set by user `{build_labeler}`, but only users `{build_permission_users}` have permission to trigger the action

bot/build.sh

@@ -57,11 +57,27 @@ echo "bot/build.sh: LOCAL_TMP='${LOCAL_TMP}'"
 BUILD_LOGS_DIR=$(cfg_get_value "site_config" "build_logs_dir")
 echo "bot/build.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
-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}"
+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=$(cfg_get_value "site_config" "shared_fs_path")
+echo "bot/build.sh: SHARED_FS_PATH='${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")
@@ -167,6 +183,7 @@ 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}")
 
 # create tmp file for output of build step
 build_outerr=$(mktemp build.outerr.XXXX)

eb_hooks.py

@@ -18,6 +18,8 @@
     from distutils.version import LooseVersion
 
 
+CPU_TARGET_NEOVERSE_V1 = 'aarch64/neoverse_v1'
+
 EESSI_RPATH_OVERRIDE_ATTR = 'orig_rpath_override_dirs'
 
 
@@ -160,13 +162,14 @@ def parse_hook_fontconfig_add_fonts(ec, eprefix):
 
 
 def parse_hook_openblas_relax_lapack_tests_num_errors(ec, eprefix):
-    """Relax number of failing numerical LAPACK tests on Arm 64-bit systems."""
+    """Relax number of failing numerical LAPACK tests for aarch64/neoverse_v1 CPU target."""
+    cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
     if ec.name == 'OpenBLAS':
-        # relax maximum number of failed numerical LAPACK tests on Arm 64-bit systems,
-        # since the default setting of 150 that works well on x86_64 is a bit too strict
+        # relax maximum number of failed numerical LAPACK tests for aarch64/neoverse_v1 CPU target
+        # since the default setting of 150 that works well on other aarch64 targets and x86_64 is a bit too strict
         # See https://github.com/EESSI/software-layer/issues/314
         cfg_option = 'max_failing_lapack_tests_num_errors'
-        if get_cpu_architecture() == AARCH64:
+        if cpu_target == CPU_TARGET_NEOVERSE_V1:
             orig_value = ec[cfg_option]
             ec[cfg_option] = 400
             print_msg("Maximum number of failing LAPACK tests with numerical errors for %s relaxed to %s (was %s)",
@@ -270,10 +273,46 @@ def pre_test_hook_ignore_failing_tests_SciPybundle(self, *args, **kwargs):
     In previous versions we were not as strict yet on the numpy/SciPy tests
     """
     cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
-    if self.name == 'SciPy-bundle' and self.version == '2021.10' and cpu_target == 'aarch64/neoverse_v1':
+    if self.name == 'SciPy-bundle' and self.version == '2021.10' 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."""
+    if ext.name in PRE_SINGLE_EXTENSION_HOOKS:
+        PRE_SINGLE_EXTENSION_HOOKS[ext.name](ext, *args, **kwargs)
+
+
+def pre_single_extension_testthat(ext, *args, **kwargs):
+    """
+    Pre-extension hook for testthat R package, to fix build on top of recent glibc.
+    """
+    if ext.name == 'testthat' and LooseVersion(ext.version) < LooseVersion('3.1.0'):
+        # use constant value instead of SIGSTKSZ for stack size,
+        # cfr. https://github.com/r-lib/testthat/issues/1373 + https://github.com/r-lib/testthat/pull/1403
+        ext.cfg['preinstallopts'] = "sed -i 's/SIGSTKSZ/32768/g' inst/include/testthat/vendor/catch.h && "
+
+
+def pre_single_extension_isoband(ext, *args, **kwargs):
+    """
+    Pre-extension hook for isoband R package, to fix build on top of recent glibc.
+    """
+    if ext.name == 'isoband' and LooseVersion(ext.version) < LooseVersion('0.2.5'):
+        # use constant value instead of SIGSTKSZ for stack size in vendored testthat included in isoband sources,
+        # cfr. https://github.com/r-lib/isoband/commit/6984e6ce8d977f06e0b5ff73f5d88e5c9a44c027
+        ext.cfg['preinstallopts'] = "sed -i 's/SIGSTKSZ/32768/g' src/testthat/vendor/catch.h && "
+
+
+def pre_test_hook_ignore_failing_tests_FFTWMPI(self, *args, **kwargs):
+    """
+    Pre-test hook for FFTW.MPI: skip failing tests for FFTW.MPI 3.3.10 on neoverse_v1
+    cfr. https://github.com/EESSI/software-layer/issues/325
+    """
+    cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
+    if self.name == 'FFTW.MPI' and self.version == '3.3.10' and cpu_target == CPU_TARGET_NEOVERSE_V1:
+        self.cfg['testopts'] = "|| echo ignoring failing tests"
+
+
 PARSE_HOOKS = {
     'CGAL': parse_hook_cgal_toolchainopts_precise,
     'fontconfig': parse_hook_fontconfig_add_fonts,
@@ -295,4 +334,10 @@ def pre_test_hook_ignore_failing_tests_SciPybundle(self, *args, **kwargs):
 
 PRE_TEST_HOOKS = {
     'SciPy-bundle': pre_test_hook_ignore_failing_tests_SciPybundle,
+    'FFTW.MPI': pre_test_hook_ignore_failing_tests_FFTWMPI,
+}
+
+PRE_SINGLE_EXTENSION_HOOKS = {
+    'isoband': pre_single_extension_isoband,
+    'testthat': pre_single_extension_testthat,
 }

eessi-2023.06-eb-4.8.0-system.yml

@@ -5,3 +5,6 @@ easyconfigs:
       # + https://github.com/easybuilders/easybuild-easyblocks/pull/2995
       options:
         include-easyblocks-from-pr: 2995
+  - EasyBuild-4.8.1.eb:
+      options:
+        from-pr: 18761

eessi-2023.06-eb-4.8.1-2021a.yml

@@ -0,0 +1,7 @@
+easyconfigs:
+  - Xvfb-1.20.11-GCCcore-10.3.0.eb:
+       # fix permission issues for xvfb-run script,
+       # see https://github.com/easybuilders/easybuild-easyconfigs/pull/18834
+       options:
+         from-pr: 18834
+  - R-4.1.0-foss-2021a.eb

eessi-2023.06-eb-4.8.1-2021b.yml

@@ -0,0 +1,7 @@
+easyconfigs:
+  - Xvfb-1.20.13-GCCcore-11.2.0.eb:
+      # enable exec permissions for xvfb-run after copying;
+      # need to also enable user write permissions on xvfb-run to ensure that copying with preserved permissions works
+      options:
+        from-pr: 18834
+  - R-4.2.0-foss-2021b.eb

eessi-2023.06-eb-4.8.1-2022a.yml

@@ -0,0 +1,7 @@
+easyconfigs:
+  - OpenBLAS-0.3.20-GCC-11.3.0:
+      # use easyconfig that includes patch to fix detection of Neoverse V1 CPUs,
+      # see https://github.com/easybuilders/easybuild-easyconfigs/pull/18870
+      options:
+        from-pr: 18870
+  - foss-2022a

eessi-2023.06-eb-4.8.1-2023a.yml

@@ -0,0 +1,10 @@
+easyconfigs:
+  - GCC-12.3.0
+  - OpenBLAS-0.3.23-GCC-12.3.0:
+      # add patch to disable flaky DDRGES3 LAPACK test,
+      # see https://github.com/easybuilders/easybuild-easyconfigs/pull/18887;
+      # also pulls in patch to avoid hang when running OpenBLAS test suite,
+      # see https://github.com/easybuilders/easybuild-easyconfigs/pull/18790
+      options:
+        from-pr: 18887
+  - foss-2023a

eessi-2023.06-eb-4.8.1-system.yml

@@ -0,0 +1,6 @@
+easyconfigs:
+  # rebuilt with EasyBuild v4.8.1 (now wraps around Java/11.0.20)
+  - Java-11.eb
+  - ReFrame-4.3.3.eb:
+      options:
+        from-pr: 18851

eessi-2023.06-known-issues.yml

@@ -0,0 +1,22 @@
+- aarch64/neoverse_v1:
+  - FFTW/3.3.10-3.3.10-GCC-11.3.0:
+      - issue: https://github.com/EESSI/software-layer/issues/325
+      - info: "Flaky FFTW tests, random failures"
+  - FFTW/3.3.10-3.3.10-gompi-2021b:
+      - issue: https://github.com/EESSI/software-layer/issues/325
+      - info: "Flaky FFTW tests, random failures"
+  - OpenBLAS/0.3.18-GCC-11.2.0:
+    - issue: https://github.com/EESSI/software-layer/issues/314
+    - info: "Increased number of non-numerical failures in OpenBLAS test suite (238 vs max. 150 on x86_64/*)"
+  - OpenBLAS/0.3.20-GCC-11.3.0:
+    - issue: https://github.com/EESSI/software-layer/issues/314
+    - info: "Increased number of non-numerical failures in OpenBLAS test suite (238 vs max. 150 on x86_64/*)"
+  - OpenBLAS/0.3.21-GCC-12.2.0:
+    - issue: https://github.com/EESSI/software-layer/issues/314
+    - info: "Increased number of non-numerical failures in OpenBLAS test suite (344 vs max. 150 on x86_64/*)"
+  - SciPy-bundle/2021.05-foss-2021a:
+    - issue: https://github.com/EESSI/software-layer/issues/318
+    - info: "2 failing tests (vs 30554 passed) in scipy test suite"
+  - SciPy-bundle/2021.10-foss-2021b:
+    - issue: https://github.com/EESSI/software-layer/issues/318
+    - info: "20 failing tests (vs 14429 passed) in numpy test suite + 55 failing tests (vs 32438 passed) in scipy test suite"