From 38a9692440c01fd26acde2734c9b3f1b661f92ab Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Wed, 4 Oct 2023 00:46:54 +0200 Subject: [PATCH 1/7] rebuilt CMake --- eessi-2023.06-eb-4.7.2-2021a.yml | 8 ++++---- eessi-2023.06-eb-4.7.2-2021b.yml | 8 ++++---- eessi-2023.06-eb-4.7.2-2022a.yml | 8 ++++---- eessi-2023.06-eb-4.7.2-2022b.yml | 8 ++++---- 4 files changed, 16 insertions(+), 16 deletions(-) diff --git a/eessi-2023.06-eb-4.7.2-2021a.yml b/eessi-2023.06-eb-4.7.2-2021a.yml index b7c703369b..ba63f57fc1 100644 --- a/eessi-2023.06-eb-4.7.2-2021a.yml +++ b/eessi-2023.06-eb-4.7.2-2021a.yml @@ -5,10 +5,10 @@ easyconfigs: # include-easyblocks-from-pr: 2922 - git-2.32.0-GCCcore-10.3.0-nodocs.eb - GCC-10.3.0 - - CMake-3.20.1-GCCcore-10.3.0.eb - # - CMake-3.20.1-GCCcore-10.3.0.eb: - # options: - # include-easyblocks-from-pr: 2248 + # - CMake-3.20.1-GCCcore-10.3.0.eb + - CMake-3.20.1-GCCcore-10.3.0.eb: + options: + include-easyblocks-from-pr: 2248 - Rust-1.52.1-GCCcore-10.3.0.eb - foss-2021a.eb - QuantumESPRESSO-6.7-foss-2021a.eb diff --git a/eessi-2023.06-eb-4.7.2-2021b.yml b/eessi-2023.06-eb-4.7.2-2021b.yml index 45776823ea..d4cd591828 100644 --- a/eessi-2023.06-eb-4.7.2-2021b.yml +++ b/eessi-2023.06-eb-4.7.2-2021b.yml @@ -1,10 +1,10 @@ easyconfigs: - GCC-11.2.0 - git-2.33.1-GCCcore-11.2.0-nodocs.eb - - CMake-3.21.1-GCCcore-11.2.0.eb - # - CMake-3.21.1-GCCcore-11.2.0.eb: - # options: - # include-easyblocks-from-pr: 2248 + # - CMake-3.21.1-GCCcore-11.2.0.eb + - CMake-3.21.1-GCCcore-11.2.0.eb: + options: + include-easyblocks-from-pr: 2248 - OpenMPI-4.1.1-GCC-11.2.0.eb - FFTW-3.3.10-gompi-2021b.eb - BLIS-0.8.1-GCC-11.2.0.eb diff --git a/eessi-2023.06-eb-4.7.2-2022a.yml b/eessi-2023.06-eb-4.7.2-2022a.yml index 9991de1508..88c7ccca4d 100644 --- a/eessi-2023.06-eb-4.7.2-2022a.yml +++ b/eessi-2023.06-eb-4.7.2-2022a.yml @@ -1,10 +1,10 @@ easyconfigs: - GCC-11.3.0 - git-2.36.0-GCCcore-11.3.0-nodocs.eb - - CMake-3.23.1-GCCcore-11.3.0.eb - # - CMake-3.23.1-GCCcore-11.3.0.eb: - # options: - # include-easyblocks-from-pr: 2248 + # - CMake-3.23.1-GCCcore-11.3.0.eb + - CMake-3.23.1-GCCcore-11.3.0.eb: + options: + include-easyblocks-from-pr: 2248 - BLIS-0.9.0-GCC-11.3.0.eb - OpenMPI-4.1.4-GCC-11.3.0.eb - FFTW.MPI-3.3.10-gompi-2022a.eb diff --git a/eessi-2023.06-eb-4.7.2-2022b.yml b/eessi-2023.06-eb-4.7.2-2022b.yml index 129b709b1c..42d4cbf476 100644 --- a/eessi-2023.06-eb-4.7.2-2022b.yml +++ b/eessi-2023.06-eb-4.7.2-2022b.yml @@ -1,10 +1,10 @@ easyconfigs: - GCC-12.2.0 - git-2.38.1-GCCcore-12.2.0-nodocs.eb - - CMake-3.24.3-GCCcore-12.2.0.eb - # - CMake-3.24.3-GCCcore-12.2.0.eb: - # options: - # include-easyblocks-from-pr: 2248 + # - CMake-3.24.3-GCCcore-12.2.0.eb + - CMake-3.24.3-GCCcore-12.2.0.eb: + options: + include-easyblocks-from-pr: 2248 - BLIS-0.9.0-GCC-12.2.0.eb - OpenMPI-4.1.4-GCC-12.2.0.eb - FFTW.MPI-3.3.10-gompi-2022b.eb From 25ea19f12f8a5ef47708997eff47d46c6ad8c9f6 Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Wed, 4 Oct 2023 19:35:25 +0200 Subject: [PATCH 2/7] commented all *-from-pr --- eessi-2023.06-eb-4.7.2-2021a.yml | 22 ++++++++++++---------- eessi-2023.06-eb-4.7.2-2021b.yml | 10 ++++++---- eessi-2023.06-eb-4.7.2-2022a.yml | 8 ++++---- eessi-2023.06-eb-4.7.2-2022b.yml | 8 ++++---- 4 files changed, 26 insertions(+), 22 deletions(-) diff --git a/eessi-2023.06-eb-4.7.2-2021a.yml b/eessi-2023.06-eb-4.7.2-2021a.yml index ba63f57fc1..fe4d992841 100644 --- a/eessi-2023.06-eb-4.7.2-2021a.yml +++ b/eessi-2023.06-eb-4.7.2-2021a.yml @@ -5,18 +5,20 @@ easyconfigs: # include-easyblocks-from-pr: 2922 - git-2.32.0-GCCcore-10.3.0-nodocs.eb - GCC-10.3.0 - # - CMake-3.20.1-GCCcore-10.3.0.eb - - CMake-3.20.1-GCCcore-10.3.0.eb: - options: - include-easyblocks-from-pr: 2248 + - CMake-3.20.1-GCCcore-10.3.0.eb + # - CMake-3.20.1-GCCcore-10.3.0.eb: + # options: + # include-easyblocks-from-pr: 2248 - 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: + # - GROMACS-2021.3-foss-2021a.eb: + # options: + # download-timeout: 1000 - libGLU-9.0.1-GCCcore-10.3.0.eb - - BAGEL-1.2.2-foss-2021a.eb: - options: - from-pr: 18446 + - BAGEL-1.2.2-foss-2021a.eb + # - BAGEL-1.2.2-foss-2021a.eb: + # options: + # from-pr: 18446 - WRF-4.3-foss-2021a-dmpar.eb diff --git a/eessi-2023.06-eb-4.7.2-2021b.yml b/eessi-2023.06-eb-4.7.2-2021b.yml index d4cd591828..d838e157b7 100644 --- a/eessi-2023.06-eb-4.7.2-2021b.yml +++ b/eessi-2023.06-eb-4.7.2-2021b.yml @@ -1,14 +1,16 @@ easyconfigs: - GCC-11.2.0 - git-2.33.1-GCCcore-11.2.0-nodocs.eb - # - CMake-3.21.1-GCCcore-11.2.0.eb - - CMake-3.21.1-GCCcore-11.2.0.eb: - options: - include-easyblocks-from-pr: 2248 + - CMake-3.21.1-GCCcore-11.2.0.eb + # - CMake-3.21.1-GCCcore-11.2.0.eb: + # options: + # include-easyblocks-from-pr: 2248 - OpenMPI-4.1.1-GCC-11.2.0.eb - 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 diff --git a/eessi-2023.06-eb-4.7.2-2022a.yml b/eessi-2023.06-eb-4.7.2-2022a.yml index 88c7ccca4d..9991de1508 100644 --- a/eessi-2023.06-eb-4.7.2-2022a.yml +++ b/eessi-2023.06-eb-4.7.2-2022a.yml @@ -1,10 +1,10 @@ easyconfigs: - GCC-11.3.0 - git-2.36.0-GCCcore-11.3.0-nodocs.eb - # - CMake-3.23.1-GCCcore-11.3.0.eb - - CMake-3.23.1-GCCcore-11.3.0.eb: - options: - include-easyblocks-from-pr: 2248 + - CMake-3.23.1-GCCcore-11.3.0.eb + # - CMake-3.23.1-GCCcore-11.3.0.eb: + # options: + # include-easyblocks-from-pr: 2248 - BLIS-0.9.0-GCC-11.3.0.eb - OpenMPI-4.1.4-GCC-11.3.0.eb - FFTW.MPI-3.3.10-gompi-2022a.eb diff --git a/eessi-2023.06-eb-4.7.2-2022b.yml b/eessi-2023.06-eb-4.7.2-2022b.yml index 42d4cbf476..129b709b1c 100644 --- a/eessi-2023.06-eb-4.7.2-2022b.yml +++ b/eessi-2023.06-eb-4.7.2-2022b.yml @@ -1,10 +1,10 @@ easyconfigs: - GCC-12.2.0 - git-2.38.1-GCCcore-12.2.0-nodocs.eb - # - CMake-3.24.3-GCCcore-12.2.0.eb - - CMake-3.24.3-GCCcore-12.2.0.eb: - options: - include-easyblocks-from-pr: 2248 + - CMake-3.24.3-GCCcore-12.2.0.eb + # - CMake-3.24.3-GCCcore-12.2.0.eb: + # options: + # include-easyblocks-from-pr: 2248 - BLIS-0.9.0-GCC-12.2.0.eb - OpenMPI-4.1.4-GCC-12.2.0.eb - FFTW.MPI-3.3.10-gompi-2022b.eb From 3b157a7b78c7c84eb96801ca4ab57019dd295ea4 Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Wed, 4 Oct 2023 19:44:47 +0200 Subject: [PATCH 3/7] sync install script with EESSI/2023.06 --- EESSI-pilot-install-software.sh | 85 ++++++++++++++++++++++++++++----- 1 file changed, 74 insertions(+), 11 deletions(-) diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh index 979156830a..4f473eb82f 100755 --- a/EESSI-pilot-install-software.sh +++ b/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 +186,39 @@ else echo_green ">> MODULEPATH set up: ${MODULEPATH}" fi -for eb_version in '4.7.2'; 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..." + 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 From a3fbcade13c495869cca67ce832f73faa7f7aba5 Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Wed, 4 Oct 2023 20:34:37 +0200 Subject: [PATCH 4/7] need to keep from-pr for BAGEL, keep timeout for GROMACS --- eessi-2023.06-eb-4.7.2-2021a.yml | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/eessi-2023.06-eb-4.7.2-2021a.yml b/eessi-2023.06-eb-4.7.2-2021a.yml index fe4d992841..dfabf377ea 100644 --- a/eessi-2023.06-eb-4.7.2-2021a.yml +++ b/eessi-2023.06-eb-4.7.2-2021a.yml @@ -13,12 +13,11 @@ easyconfigs: - foss-2021a.eb - QuantumESPRESSO-6.7-foss-2021a.eb - GROMACS-2021.3-foss-2021a.eb: - # - GROMACS-2021.3-foss-2021a.eb: - # options: - # download-timeout: 1000 + options: + download-timeout: 1000 - libGLU-9.0.1-GCCcore-10.3.0.eb - - BAGEL-1.2.2-foss-2021a.eb - # - BAGEL-1.2.2-foss-2021a.eb: - # options: - # from-pr: 18446 + # 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 - WRF-4.3-foss-2021a-dmpar.eb From a733f95383daf8c41c0f380b841787e2caee0583 Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Wed, 4 Oct 2023 22:51:07 +0200 Subject: [PATCH 5/7] add EasyBuild/4.8.0 --- eessi-2023.06-eb-4.7.2-system.yml | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 eessi-2023.06-eb-4.7.2-system.yml diff --git a/eessi-2023.06-eb-4.7.2-system.yml b/eessi-2023.06-eb-4.7.2-system.yml new file mode 100644 index 0000000000..a5f84c7cd5 --- /dev/null +++ b/eessi-2023.06-eb-4.7.2-system.yml @@ -0,0 +1,4 @@ +easyconfigs: + - EasyBuild-4.8.0.eb: + options: + from-pr: 18282 From c2d199d0bb1ea0e67ce36bc21b9d8c91f94a5b82 Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Wed, 4 Oct 2023 23:08:04 +0200 Subject: [PATCH 6/7] use original approach to determine changed/new easystack files --- EESSI-pilot-install-software.sh | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh index 4f473eb82f..c6c51e7abc 100755 --- a/EESSI-pilot-install-software.sh +++ b/EESSI-pilot-install-software.sh @@ -186,8 +186,11 @@ else echo_green ">> MODULEPATH set up: ${MODULEPATH}" fi -# use 'git diff' to determine which easystack files were changed -for easystack_file in $(git diff --name-only | grep '^eessi.*yml$'); 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" From a7c66f63092af30f7133391081f040f1dee73095 Mon Sep 17 00:00:00 2001 From: Thomas Roeblitz Date: Thu, 5 Oct 2023 02:14:14 +0200 Subject: [PATCH 7/7] add new easystack file to CI --- .github/workflows/test_eessi.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/test_eessi.yml b/.github/workflows/test_eessi.yml index 2fc071da8b..9d31f2aa90 100644 --- a/.github/workflows/test_eessi.yml +++ b/.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