Merge branch 'nessi.no-2023.06' of https://github.com/NorESSI/softwar…

…e-layer into nessi.no-2023.06-Yambo/5.1.1-foss/2021a

.github/workflows/test_eessi.yml

@@ -23,6 +23,7 @@ jobs:
         - eessi-2023.06-eb-4.7.2-2021b.yml
         - eessi-2023.06-eb-4.7.2-2022a.yml
         - eessi-2023.06-eb-4.7.2-2022b.yml
+        - eessi-2023.06-eb-4.7.2-system.yml
     steps:
         - name: Check out software-layer repository
           uses: actions/checkout@93ea575cb5d8a053eaa0ac8fa3b40d7e05a33cc8 # v3.1.0

EESSI-pilot-install-software.sh

@@ -8,10 +8,43 @@
 
 display_help() {
   echo "usage: $0 [OPTIONS]"
+  echo "  --build-logs-dir       -  location to copy EasyBuild logs to for failed builds"
   echo "  -g | --generic         -  instructs script to build for generic architecture target"
   echo "  -h | --help            -  display this usage information"
   echo "  -x | --http-proxy URL  -  provides URL for the environment variable http_proxy"
   echo "  -y | --https-proxy URL -  provides URL for the environment variable https_proxy"
+  echo "  --shared-fs-path       -  path to directory on shared filesystem that can be used"
+}
+
+function copy_build_log() {
+    # copy specified build log to specified directory, with some context added
+    build_log=${1}
+    build_logs_dir=${2}
+
+    # also copy to build logs directory, if specified
+    if [ ! -z "${build_logs_dir}" ]; then
+        log_filename="$(basename ${build_log})"
+        if [ ! -z "${SLURM_JOB_ID}" ]; then
+            # use subdirectory for build log in context of a Slurm job
+            build_log_path="${build_logs_dir}/jobs/${SLURM_JOB_ID}/${log_filename}"
+        else
+            build_log_path="${build_logs_dir}/non-jobs/${log_filename}"
+        fi
+        mkdir -p $(dirname ${build_log_path})
+        cp -a ${build_log} ${build_log_path}
+        chmod 0644 ${build_log_path}
+
+        # add context to end of copied log file
+        echo >> ${build_log_path}
+        echo "Context from which build log was copied:" >> ${build_log_path}
+        echo "- original path of build log: ${build_log}" >> ${build_log_path}
+        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: ${easystack_file}" >> ${build_log_path}
+
+        echo "EasyBuild log file ${build_log} copied to ${build_log_path} (with context appended)"
+    fi
 }
 
 POSITIONAL_ARGS=()
@@ -35,6 +68,14 @@ while [[ $# -gt 0 ]]; do
       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
@@ -99,7 +140,7 @@ 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})
+# 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
@@ -125,6 +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
@@ -137,25 +186,42 @@ else
     echo_green ">> MODULEPATH set up: ${MODULEPATH}"
 fi
 
-for eb_version in '4.7.2'; do
+# assume there's only one diff file that corresponds to the PR patch file
+pr_diff=$(ls [0-9]*.diff | head -1)
+
+# use PR patch file to determine in which easystack files stuff was added
+for easystack_file in $(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^eessi.*yml$'); 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..."
+    if [ -f ${easystack_file} ]; then
+        echo_green "Feeding easystack file ${easystack_file} to EasyBuild..."
 
-            ${EB} --easystack ${TOPDIR}/${es} --robot
+        ${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
 

eessi-2023.06-eb-4.7.2-2021a.yml

@@ -12,10 +12,11 @@ easyconfigs:
   - Rust-1.52.1-GCCcore-10.3.0.eb
   - foss-2021a.eb
   - QuantumESPRESSO-6.7-foss-2021a.eb
-  - GROMACS-2021.3-foss-2021a.eb:  
-        options:
-          download-timeout: 1000
+  - GROMACS-2021.3-foss-2021a.eb:
+       options:
+         download-timeout: 1000
   - libGLU-9.0.1-GCCcore-10.3.0.eb
+  # since the BAGEL ec file is new we have to keep the from-pr or eb fails
   - BAGEL-1.2.2-foss-2021a.eb:
         options:
           from-pr: 18446

eessi-2023.06-eb-4.7.2-2021b.yml

@@ -9,6 +9,8 @@ easyconfigs:
   - FFTW-3.3.10-gompi-2021b.eb
   - BLIS-0.8.1-GCC-11.2.0.eb
   - foss-2021b.eb
+  # note, the below CMake has never been installed, just put here to use the
+  # same version as easy does
   # - CMake-3.22.1-GCCcore-11.2.0.eb:
   #     options:
   #       include-easyblocks-from-pr: 2248

eessi-2023.06-eb-4.7.2-system.yml

@@ -0,0 +1,4 @@
+easyconfigs:
+  - EasyBuild-4.8.0.eb:
+      options:
+        from-pr: 18282