From 9e861655020ef8abcc9233dfd69a3d26070c33d8 Mon Sep 17 00:00:00 2001 From: Richard Top Date: Fri, 6 Oct 2023 12:18:34 +0000 Subject: [PATCH 1/3] {2023.06}[foss/2022a] ASE V3.22.1 --- eessi-2023.06-eb-4.8.1-2022a.yml | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 eessi-2023.06-eb-4.8.1-2022a.yml diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml new file mode 100644 index 0000000000..56424735f3 --- /dev/null +++ b/eessi-2023.06-eb-4.8.1-2022a.yml @@ -0,0 +1,2 @@ +easyconfigs: + - ASE-3.22.1-foss-2022a.eb From 17936e88a127c5db3f6256a01a79075989f5aad6 Mon Sep 17 00:00:00 2001 From: Richard Top Date: Fri, 6 Oct 2023 19:37:16 +0000 Subject: [PATCH 2/3] added from-pr to Pillow as a trial --- .github/workflows/test_eessi.yml | 40 +++++++++++++++++++++++--------- EESSI-pilot-install-software.sh | 4 ++-- check_missing_installations.sh | 3 +++ eessi-2023.06-eb-4.7.2-2021a.yml | 4 ++++ eessi-2023.06-eb-4.8.1-2022a.yml | 10 ++++++++ 5 files changed, 48 insertions(+), 13 deletions(-) diff --git a/.github/workflows/test_eessi.yml b/.github/workflows/test_eessi.yml index 72dc642c7d..832d4cf74f 100644 --- a/.github/workflows/test_eessi.yml +++ b/.github/workflows/test_eessi.yml @@ -4,14 +4,14 @@ on: [push, pull_request, workflow_dispatch] permissions: contents: read # to fetch code (actions/checkout) jobs: - eessi_pilot_repo: + pilot: runs-on: ubuntu-20.04 strategy: fail-fast: false matrix: EESSI_VERSION: - 2023.06 - EESSI_SOFTWARE_SUBDIR_OVERRIDE: + EESSI_SOFTWARE_SUBDIR: - aarch64/generic - x86_64/amd/zen2 - x86_64/intel/broadwell @@ -25,6 +25,7 @@ jobs: - eessi-2023.06-eb-4.7.2-2022b.yml - eessi-2023.06-eb-4.7.2-system.yml - eessi-2023.06-eb-4.8.0-system.yml + - eessi-2023.06-eb-4.8.1-2022a.yml steps: - name: Check out software-layer repository uses: actions/checkout@93ea575cb5d8a053eaa0ac8fa3b40d7e05a33cc8 # v3.1.0 @@ -36,38 +37,55 @@ jobs: cvmfs_http_proxy: DIRECT cvmfs_repositories: pilot.nessi.no - - name: Test check_missing_installations.sh script + - name: Test check_missing_installations.sh script with EESSI_SOFTWARE_SUBDIR_OVERRIDE + if: '!cancelled()' + run: | + export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR}} + source /cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}}/init/bash + module load EasyBuild + eb --version + export EESSI_PREFIX=/cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}} + export EESSI_OS_TYPE=linux + env | grep ^EESSI | sort + echo "just run check_missing_installations.sh (should use ${{matrix.EASYSTACK_FILE}})" + ./check_missing_installations.sh ${{matrix.EASYSTACK_FILE}} + + - name: Test check_missing_installations.sh script without EESSI_SOFTWARE_SUBDIR_OVERRIDE + if: '!cancelled()' run: | - export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}} source /cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}}/init/bash module load EasyBuild - which eb eb --version export EESSI_PREFIX=/cvmfs/pilot.nessi.no/versions/${{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)" + echo "just run check_missing_installations.sh (should use ${{matrix.EASYSTACK_FILE}})" ./check_missing_installations.sh ${{matrix.EASYSTACK_FILE}} - name: Test check_missing_installations.sh with missing package (GCC/8.3.0) + if: '!cancelled()' run: | - export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}} source /cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}}/init/bash module load EasyBuild which eb eb --version export EESSI_PREFIX=/cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}} export EESSI_OS_TYPE=linux + export EESSI_SOFTWARE_SUBDIR=${{matrix.EESSI_SOFTWARE_SUBDIR}} env | grep ^EESSI | sort - echo "modify easystack file by adding a missing package (GCC/8.3.0)" - echo " - GCC-8.3.0:" >> ${{matrix.EASYSTACK_FILE}} - tail -n 5 ${{matrix.EASYSTACK_FILE}} + # create dummy easystack file with a single entry (something that is not installed in EESSI) + easystack_file="test.yml" + echo "easyconfigs:" > ${easystack_file} + echo " - GCC-8.3.0:" >> ${easystack_file} + echo "created easystack file '${easystack_file}' with a missing installation (GCC/8.3.0):" + cat ${easystack_file} # 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 ${{matrix.EASYSTACK_FILE}}; then + if ./check_missing_installations.sh ${easystack_file}; then echo "did NOT capture missing package; test FAILED" exit 1 else diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh index c6c51e7abc..026919157f 100755 --- a/EESSI-pilot-install-software.sh +++ b/EESSI-pilot-install-software.sh @@ -172,8 +172,6 @@ if [ ! -z "${shared_fs_path}" ]; then 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 @@ -200,6 +198,8 @@ for easystack_file in $(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[ # 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 diff --git a/check_missing_installations.sh b/check_missing_installations.sh index 3627d1d0b5..e927f14701 100755 --- a/check_missing_installations.sh +++ b/check_missing_installations.sh @@ -22,6 +22,9 @@ source $TOPDIR/scripts/utils.sh source $TOPDIR/configure_easybuild +echo ">> Active EasyBuild configuration when checking for missing installations:" +${EB:-eb} --show-config + echo ">> Checking for missing installations in ${EASYBUILD_INSTALLPATH}..." eb_missing_out=$LOCAL_TMPDIR/eb_missing.out ${EB:-eb} --easystack ${easystack} --missing 2>&1 | tee ${eb_missing_out} diff --git a/eessi-2023.06-eb-4.7.2-2021a.yml b/eessi-2023.06-eb-4.7.2-2021a.yml index dfabf377ea..28612c5566 100644 --- a/eessi-2023.06-eb-4.7.2-2021a.yml +++ b/eessi-2023.06-eb-4.7.2-2021a.yml @@ -21,3 +21,7 @@ easyconfigs: options: from-pr: 18446 - WRF-4.3-foss-2021a-dmpar.eb + - Yambo-5.1.1-foss-2021a.eb: + options: + from-pr: 18905 + diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml index 56424735f3..51ddd53302 100644 --- a/eessi-2023.06-eb-4.8.1-2022a.yml +++ b/eessi-2023.06-eb-4.8.1-2022a.yml @@ -1,2 +1,12 @@ easyconfigs: + - BAMM-2.5.0-foss-2022a.eb + - BamTools-2.5.2-GCC-11.3.0.eb + - BCFtools-1.15.1-GCC-11.3.0.eb + - Bowtie2-2.4.5-GCC-11.3.0.eb + - FastTree-2.1.11-GCCcore-11.3.0.eb + - SAMtools-1.16.1-GCC-11.3.0.eb + - Pillow-9.1.1-GCCcore-11.3.0.eb: + # avoid that hardcoded paths like /usr/include are used in build commands + options: + from-pr: 18881 - ASE-3.22.1-foss-2022a.eb From f8cadf0120473f145717f0c52955e8d2a51e4981 Mon Sep 17 00:00:00 2001 From: Richard Top Date: Fri, 6 Oct 2023 19:44:14 +0000 Subject: [PATCH 3/3] sync local branch with target --- eessi-2023.06-eb-4.8.1-2022a.yml | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml index 9fdaae20b3..e6ea8299f0 100644 --- a/eessi-2023.06-eb-4.8.1-2022a.yml +++ b/eessi-2023.06-eb-4.8.1-2022a.yml @@ -5,14 +5,11 @@ easyconfigs: - Bowtie2-2.4.5-GCC-11.3.0.eb - FastTree-2.1.11-GCCcore-11.3.0.eb - SAMtools-1.16.1-GCC-11.3.0.eb -<<<<<<< HEAD + - gzip-1.12-GCCcore-11.3.0.eb + - lz4-1.9.3-GCCcore-11.3.0.eb + - zstd-1.5.2-GCCcore-11.3.0.eb - Pillow-9.1.1-GCCcore-11.3.0.eb: # avoid that hardcoded paths like /usr/include are used in build commands options: from-pr: 18881 - ASE-3.22.1-foss-2022a.eb -======= - - gzip-1.12-GCCcore-11.3.0.eb - - lz4-1.9.3-GCCcore-11.3.0.eb - - zstd-1.5.2-GCCcore-11.3.0.eb ->>>>>>> 181dd0ac845922c4a35db32e874c75995735dd95