diff --git a/.github/workflows/test_eessi.yml b/.github/workflows/test_eessi.yml index 92b1f71cad..04195dd619 100644 --- a/.github/workflows/test_eessi.yml +++ b/.github/workflows/test_eessi.yml @@ -40,4 +40,33 @@ jobs: 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/pilot.eessi-hpc.org/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_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 diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh index 2830754b29..ef6e2b805b 100755 --- a/EESSI-pilot-install-software.sh +++ b/EESSI-pilot-install-software.sh @@ -1,5 +1,5 @@ #!/bin/bash -# + # Script to install EESSI pilot software stack (version set through init/eessi_defaults) # see example parsing of command line arguments at @@ -137,7 +137,11 @@ else echo_green ">> MODULEPATH set up: ${MODULEPATH}" fi -REQ_EB_VERSION='4.5.0' +echo "EESSI_CVMFS_REPO=${EESSI_CVMFS_REPO}" + +REQ_EB_VERSION='4.7.1' +echo "REQ_EB_VERSION=${REQ_EB_VERSION}" +module avail 2>&1 | grep -i easybuild echo ">> Checking for EasyBuild module..." ml_av_easybuild_out=$TMPDIR/ml_av_easybuild.out @@ -165,10 +169,6 @@ else eb --install-latest-eb-release &> ${eb_install_out} check_exit_code $? "${ok_msg}" "${fail_msg}" - # restore origin $PATH and $PYTHONPATH values - export PATH=${ORIG_PATH} - export PYTHONPATH=${ORIG_PYTHONPATH} - eb --search EasyBuild-${REQ_EB_VERSION}.eb | grep EasyBuild-${REQ_EB_VERSION}.eb > /dev/null if [[ $? -eq 0 ]]; then ok_msg="EasyBuild v${REQ_EB_VERSION} installed, alright!" @@ -177,6 +177,10 @@ else check_exit_code $? "${ok_msg}" "${fail_msg}" fi + # restore origin $PATH and $PYTHONPATH values + export PATH=${ORIG_PATH} + export PYTHONPATH=${ORIG_PYTHONPATH} + module avail easybuild/${REQ_EB_VERSION} &> ${ml_av_easybuild_out} if [[ $? -eq 0 ]]; then echo_green ">> EasyBuild module installed!" @@ -205,233 +209,10 @@ else fi echo_green "All set, let's start installing some software in ${EASYBUILD_INSTALLPATH}..." +eb_install_easystack_out=${TMPDIR}/eb_install_easystack.out +${EB:-eb} --robot --easystack eessi-${EESSI_PILOT_VERSION}.yml --experimental | tee ${eb_install_easystack_out} -# install Java with fixed custom easyblock that uses patchelf to ensure right glibc is picked up, -# see https://github.com/EESSI/software-layer/issues/123 -# and https://github.com/easybuilders/easybuild-easyblocks/pull/2557 -ok_msg="Java installed, off to a good (?) start!" -fail_msg="Failed to install Java, woopsie..." -$EB Java-11.eb --robot --include-easyblocks-from-pr 2557 -check_exit_code $? "${ok_msg}" "${fail_msg}" - -# install GCC for foss/2020a -export GCC_EC="GCC-9.3.0.eb" -echo ">> Starting slow with ${GCC_EC}..." -ok_msg="${GCC_EC} installed, yippy! Off to a good start..." -fail_msg="Installation of ${GCC_EC} failed!" -# pull in easyconfig from https://github.com/easybuilders/easybuild-easyconfigs/pull/14453, -# which includes patch to fix build of GCC 9.3 when recent kernel headers are in place -$EB ${GCC_EC} --robot --from-pr 14453 GCCcore-9.3.0.eb -check_exit_code $? "${ok_msg}" "${fail_msg}" - -# install CMake with custom easyblock that patches CMake when --sysroot is used -echo ">> Install CMake with fixed easyblock to take into account --sysroot" -ok_msg="CMake installed!" -fail_msg="Installation of CMake failed, what the ..." -$EB CMake-3.16.4-GCCcore-9.3.0.eb --robot --include-easyblocks-from-pr 2248 -check_exit_code $? "${ok_msg}" "${fail_msg}" - -# If we're building OpenBLAS for GENERIC, we need https://github.com/easybuilders/easybuild-easyblocks/pull/1946 -echo ">> Installing OpenBLAS..." -ok_msg="Done with OpenBLAS!" -fail_msg="Installation of OpenBLAS failed!" -if [[ $GENERIC -eq 1 ]]; then - echo_yellow ">> Using https://github.com/easybuilders/easybuild-easyblocks/pull/1946 to build generic OpenBLAS." - openblas_include_easyblocks_from_pr="--include-easyblocks-from-pr 1946" -else - openblas_include_easyblocks_from_pr='' -fi -$EB $openblas_include_easyblocks_from_pr OpenBLAS-0.3.9-GCC-9.3.0.eb --robot -check_exit_code $? "${ok_msg}" "${fail_msg}" - -echo ">> Installing OpenMPI..." -ok_msg="OpenMPI installed, w00!" -fail_msg="Installation of OpenMPI failed, that's not good..." -$EB OpenMPI-4.0.3-GCC-9.3.0.eb --robot -check_exit_code $? "${ok_msg}" "${fail_msg}" - -# install Python -echo ">> Install Python 2.7.18 and Python 3.8.2..." -ok_msg="Python 2.7.18 and 3.8.2 installed, yaay!" -fail_msg="Installation of Python failed, oh no..." -$EB Python-2.7.18-GCCcore-9.3.0.eb Python-3.8.2-GCCcore-9.3.0.eb --robot -check_exit_code $? "${ok_msg}" "${fail_msg}" - -echo ">> Installing Perl..." -ok_msg="Perl installed, making progress..." -fail_msg="Installation of Perl failed, this never happens..." -# use enhanced Perl easyblock from https://github.com/easybuilders/easybuild-easyblocks/pull/2640 -# to avoid trouble when using long installation prefix (for example with EESSI pilot 2021.12 on skylake_avx512...) -$EB Perl-5.30.2-GCCcore-9.3.0.eb --robot --include-easyblocks-from-pr 2640 -check_exit_code $? "${ok_msg}" "${fail_msg}" - -echo ">> Installing Qt5..." -ok_msg="Qt5 installed, phieuw, that was a big one!" -fail_msg="Installation of Qt5 failed, that's frustrating..." -$EB Qt5-5.14.1-GCCcore-9.3.0.eb --robot -check_exit_code $? "${ok_msg}" "${fail_msg}" - -# skip test step when installing SciPy-bundle on aarch64, -# to dance around problem with broken numpy tests; -# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/11959 -echo ">> Installing SciPy-bundle" -ok_msg="SciPy-bundle installed, yihaa!" -fail_msg="SciPy-bundle installation failed, bummer..." -SCIPY_EC=SciPy-bundle-2020.03-foss-2020a-Python-3.8.2.eb -if [[ "$(uname -m)" == "aarch64" ]]; then - $EB $SCIPY_EC --robot --skip-test-step -else - $EB $SCIPY_EC --robot -fi -check_exit_code $? "${ok_msg}" "${fail_msg}" - -echo ">> Installing GROMACS..." -ok_msg="GROMACS installed, wow!" -fail_msg="Installation of GROMACS failed, damned..." -$EB GROMACS-2020.1-foss-2020a-Python-3.8.2.eb GROMACS-2020.4-foss-2020a-Python-3.8.2.eb --robot -check_exit_code $? "${ok_msg}" "${fail_msg}" - -# note: compiling OpenFOAM is memory hungry (16GB is not enough with 8 cores)! -# 32GB is sufficient to build with 16 cores -echo ">> Installing OpenFOAM (twice!)..." -ok_msg="OpenFOAM installed, now we're talking!" -fail_msg="Installation of OpenFOAM failed, we were so close..." -$EB OpenFOAM-8-foss-2020a.eb OpenFOAM-v2006-foss-2020a.eb --robot -check_exit_code $? "${ok_msg}" "${fail_msg}" - -if [ ! "${EESSI_CPU_FAMILY}" = "ppc64le" ]; then - echo ">> Installing QuantumESPRESSO..." - ok_msg="QuantumESPRESSO installed, let's go quantum!" - fail_msg="Installation of QuantumESPRESSO failed, did somebody observe it?!" - $EB QuantumESPRESSO-6.6-foss-2020a.eb --robot - check_exit_code $? "${ok_msg}" "${fail_msg}" -fi - -echo ">> Installing R 4.0.0 (better be patient)..." -ok_msg="R installed, wow!" -fail_msg="Installation of R failed, so sad..." -$EB R-4.0.0-foss-2020a.eb --robot --parallel-extensions-install --experimental -check_exit_code $? "${ok_msg}" "${fail_msg}" - -echo ">> Installing Bioconductor 3.11 bundle..." -ok_msg="Bioconductor installed, enjoy!" -fail_msg="Installation of Bioconductor failed, that's annoying..." -$EB R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb --robot -check_exit_code $? "${ok_msg}" "${fail_msg}" - -echo ">> Installing TensorFlow 2.3.1..." -ok_msg="TensorFlow 2.3.1 installed, w00!" -fail_msg="Installation of TensorFlow failed, why am I not surprised..." -$EB TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb --robot --include-easyblocks-from-pr 2218 -check_exit_code $? "${ok_msg}" "${fail_msg}" - -echo ">> Installing Horovod 0.21.3..." -ok_msg="Horovod installed! Go do some parallel training!" -fail_msg="Horovod installation failed. There comes the headache..." -$EB Horovod-0.21.3-foss-2020a-TensorFlow-2.3.1-Python-3.8.2.eb --robot -check_exit_code $? "${ok_msg}" "${fail_msg}" - -if [ ! "${EESSI_CPU_FAMILY}" = "ppc64le" ]; then - - echo ">> Installing code-server 3.7.3..." - ok_msg="code-server 3.7.3 installed, now you can use VS Code!" - fail_msg="Installation of code-server failed, that's going to be hard to fix..." - $EB code-server-3.7.3.eb --robot - check_exit_code $? "${ok_msg}" "${fail_msg}" -fi - -echo ">> Installing RStudio-Server 1.3.1093..." -ok_msg="RStudio-Server installed, enjoy!" -fail_msg="Installation of RStudio-Server failed, might be OS deps..." -$EB RStudio-Server-1.3.1093-foss-2020a-Java-11-R-4.0.0.eb --robot -check_exit_code $? "${ok_msg}" "${fail_msg}" - -echo ">> Installing OSU-Micro-Benchmarks 5.6.3..." -ok_msg="OSU-Micro-Benchmarks installed, yihaa!" -fail_msg="Installation of OSU-Micro-Benchmarks failed, that's unexpected..." -$EB OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb -r -check_exit_code $? "${ok_msg}" "${fail_msg}" - -echo ">> Installing Spark 3.1.1..." -ok_msg="Spark installed, set off the fireworks!" -fail_msg="Installation of Spark failed, no fireworks this time..." -$EB Spark-3.1.1-foss-2020a-Python-3.8.2.eb -r -check_exit_code $? "${ok_msg}" "${fail_msg}" - -echo ">> Installing IPython 7.15.0..." -ok_msg="IPython installed, launch your Jupyter Notebooks!" -fail_msg="Installation of IPython failed, that's unexpected..." -$EB IPython-7.15.0-foss-2020a-Python-3.8.2.eb -r -check_exit_code $? "${ok_msg}" "${fail_msg}" - -echo ">> Installing WRF 3.9.1.1..." -ok_msg="WRF installed, it's getting hot in here!" -fail_msg="Installation of WRF failed, that's unexpected..." -OMPI_MCA_pml=ucx UCX_TLS=tcp $EB WRF-3.9.1.1-foss-2020a-dmpar.eb -r --include-easyblocks-from-pr 2648 -check_exit_code $? "${ok_msg}" "${fail_msg}" - -echo ">> Installing R 4.1.0 (better be patient)..." -ok_msg="R installed, wow!" -fail_msg="Installation of R failed, so sad..." -$EB --from-pr 14821 X11-20210518-GCCcore-10.3.0.eb -r && $EB --from-pr 16011 R-4.1.0-foss-2021a.eb --robot --parallel-extensions-install --experimental -check_exit_code $? "${ok_msg}" "${fail_msg}" - -echo ">> Installing Nextflow 22.10.1..." -ok_msg="Nextflow installed, the work must flow..." -fail_msg="Installation of Nextflow failed, that's unexpected..." -$EB -r --from-pr 16531 Nextflow-22.10.1.eb -check_exit_code $? "${ok_msg}" "${fail_msg}" - -echo ">> Installing OSU-Micro-Benchmarks/5.7.1-gompi-2021a..." -ok_msg="OSU-Micro-Benchmarks installed, yihaa!" -fail_msg="Installation of OSU-Micro-Benchmarks failed, that's unexpected..." -$EB OSU-Micro-Benchmarks-5.7.1-gompi-2021a.eb -r -check_exit_code $? "${ok_msg}" "${fail_msg}" - -echo ">> Installing EasyBuild 4.5.1..." -ok_msg="EasyBuild v4.5.1 installed" -fail_msg="EasyBuild v4.5.1 failed to install" -$EB --from-pr 14545 --include-easyblocks-from-pr 2805 -check_exit_code $? "${ok_msg}" "${fail_msg}" - -LMOD_IGNORE_CACHE=1 module swap EasyBuild/4.5.1 -check_exit_code $? "Swapped to EasyBuild/4.5.1" "Couldn't swap to EasyBuild/4.5.1" - -echo ">> Installing SciPy-bundle with foss/2021a..." -ok_msg="SciPy-bundle with foss/2021a installed, welcome to the modern age" -fail_msg="Installation of SciPy-bundle with foss/2021a failed, back to the stone age..." -# use GCCcore easyconfig from https://github.com/easybuilders/easybuild-easyconfigs/pull/14454 -# which includes patch to fix installation with recent Linux kernel headers -$EB --from-pr 14454 GCCcore-10.3.0.eb --robot -# use enhanced Perl easyblock from https://github.com/easybuilders/easybuild-easyblocks/pull/2640 -# to avoid trouble when using long installation prefix (for example with EESSI pilot 2021.12 on skylake_avx512...) -$EB Perl-5.32.1-GCCcore-10.3.0.eb --robot --include-easyblocks-from-pr 2640 -# use enhanced CMake easyblock to patch CMake's UnixPaths.cmake script if --sysroot is set -# from https://github.com/easybuilders/easybuild-easyblocks/pull/2248 -$EB CMake-3.20.1-GCCcore-10.3.0.eb --robot --include-easyblocks-from-pr 2248 -# use Rust easyconfig from https://github.com/easybuilders/easybuild-easyconfigs/pull/14584 -# that includes patch to fix bootstrap problem when using alternate sysroot -$EB --from-pr 14584 Rust-1.52.1-GCCcore-10.3.0.eb --robot -# use OpenBLAS easyconfig from https://github.com/easybuilders/easybuild-easyconfigs/pull/15885 -# which includes a patch to fix installation on POWER -$EB $openblas_include_easyblocks_from_pr --from-pr 15885 OpenBLAS-0.3.15-GCC-10.3.0.eb --robot -# ignore failing FlexiBLAS tests when building on POWER; -# some tests are failing due to a segmentation fault due to "invalid memory reference", -# see also https://github.com/easybuilders/easybuild-easyconfigs/pull/12476; -# using -fstack-protector-strong -fstack-clash-protection should fix that, -# but it doesn't for some reason when building for ppc64le/generic... -if [ "${EESSI_SOFTWARE_SUBDIR}" = "ppc64le/generic" ]; then - $EB FlexiBLAS-3.0.4-GCC-10.3.0.eb --ignore-test-failure -else - $EB FlexiBLAS-3.0.4-GCC-10.3.0.eb -fi - -$EB SciPy-bundle-2021.05-foss-2021a.eb --robot -check_exit_code $? "${ok_msg}" "${fail_msg}" - -### add packages here - -echo ">> Creating/updating Lmod cache..." +echo ">> Creating/updating Lmod cache on $(date) (nr 1) ..." export LMOD_RC="${EASYBUILD_INSTALLPATH}/.lmod/lmodrc.lua" if [ ! -f $LMOD_RC ]; then python3 $TOPDIR/create_lmodrc.py ${EASYBUILD_INSTALLPATH} @@ -442,5 +223,9 @@ $TOPDIR/update_lmod_cache.sh ${EPREFIX} ${EASYBUILD_INSTALLPATH} $TOPDIR/check_missing_installations.sh +# TODO do not clean up by default (or provide a cmd line arg and when run +# from bot, do not clean up) echo ">> Cleaning up ${TMPDIR}..." rm -r ${TMPDIR} + +exit 0 diff --git a/bot/check-result.sh b/bot/check-result.sh new file mode 100755 index 0000000000..e13db38821 --- /dev/null +++ b/bot/check-result.sh @@ -0,0 +1,292 @@ +#!/bin/bash +# +# Script to check the result of building the EESSI software layer. +# Intended use is that it is called by a (batch) job running on a compute +# node. +# +# This script is part of the EESSI software layer, see +# https://github.com/EESSI/software-layer.git +# +# author: Thomas Roeblitz (@trz42) +# +# license: GPLv2 +# + +# result cases + +# - SUCCESS (all of) +# - working directory contains slurm-JOBID.out file +# - working directory contains eessi*tar.gz +# - no message ERROR +# - no message FAILED +# - no message ' required modules missing:' +# - one or more of 'No missing modules!' +# - message regarding created tarball +# - FAILED (one of ... implemented as NOT SUCCESS) +# - no slurm-JOBID.out file +# - no tarball +# - message with ERROR +# - message with FAILED +# - message with ' required modules missing:' +# - no message regarding created tarball + +# stop as soon as something fails +# set -e + +TOPDIR=$(dirname $(realpath $0)) + +source ${TOPDIR}/../scripts/utils.sh +source ${TOPDIR}/../scripts/cfg_files.sh + +display_help() { + echo "usage: $0 [OPTIONS]" + echo " OPTIONS:" + echo " -h | --help - display this usage information [default: false]" + echo " -v | --verbose - display more information [default: false]" +} + +# set defaults for command line arguments +VERBOSE=0 + +POSITIONAL_ARGS=() + +while [[ $# -gt 0 ]]; do + case $1 in + -h|--help) + display_help + exit 0 + ;; + -v|--verbose) + VERBOSE=1 + shift 1 + ;; + --) + shift + POSITIONAL_ARGS+=("$@") # save positional args + break + ;; + -*|--*) + fatal_error "Unknown option: $1" "${CMDLINE_ARG_UNKNOWN_EXITCODE}" + ;; + *) # No more options + POSITIONAL_ARGS+=("$1") # save positional arg + shift + ;; + esac +done + +set -- "${POSITIONAL_ARGS[@]}" + +job_dir=${PWD} + +[[ ${VERBOSE} -ne 0 ]] && echo ">> analysing job in directory ${job_dir}" + +GP_slurm_out="slurm-${SLURM_JOB_ID}.out" +job_out=$(ls ${job_dir} | grep "${GP_slurm_out}") +[[ $? -eq 0 ]] && SLURM=1 || SLURM=0 +# have to be careful to not add searched for pattern into slurm out file +[[ ${VERBOSE} -ne 0 ]] && echo ">> searching for job output file(s) matching '"${GP_slurm_out}"'" +[[ ${VERBOSE} -ne 0 ]] && echo " found slurm output file '"${job_out}"'" + +ERROR=-1 +if [[ ${SLURM} -eq 1 ]]; then + GP_error='ERROR: ' + grep_out=$(grep "${GP_error}" ${job_dir}/${job_out}) + [[ $? -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 + +FAILED=-1 +if [[ ${SLURM} -eq 1 ]]; then + GP_failed='FAILED: ' + grep_out=$(grep "${GP_failed}" ${job_dir}/${job_out}) + [[ $? -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 + +MISSING=-1 +if [[ ${SLURM} -eq 1 ]]; then + GP_req_missing=' required modules missing:' + grep_out=$(grep "${GP_req_missing}" ${job_dir}/${job_out}) + [[ $? -eq 0 ]] && MISSING=1 || MISSING=0 + # have to be careful to not add searched for pattern into slurm out file + [[ ${VERBOSE} -ne 0 ]] && echo ">> searching for '"${GP_req_missing}"'" + [[ ${VERBOSE} -ne 0 ]] && echo "${grep_out}" +fi + +NO_MISSING=-1 +if [[ ${SLURM} -eq 1 ]]; then + GP_no_missing='No missing modules!' + grep_out=$(grep "${GP_no_missing}" ${job_dir}/${job_out}) + [[ $? -eq 0 ]] && NO_MISSING=1 || NO_MISSING=0 + # have to be careful to not add searched for pattern into slurm out file + [[ ${VERBOSE} -ne 0 ]] && echo ">> searching for '"${GP_no_missing}"'" + [[ ${VERBOSE} -ne 0 ]] && echo "${grep_out}" +fi + +TGZ=-1 +TARBALL= +if [[ ${SLURM} -eq 1 ]]; then + GP_tgz_created="tar.gz created!" + grep_out=$(grep "${GP_tgz_created}" ${job_dir}/${job_out}) + if [[ $? -eq 0 ]]; then + TGZ=1 + TARBALL=$(echo ${grep_out} | sed -e 's@^.*\(eessi[^/ ]*\) .*$@\1@') + else + TGZ=0 + fi + # have to be careful to not add searched for pattern into slurm out file + [[ ${VERBOSE} -ne 0 ]] && echo ">> searching for '"${GP_tgz_created}"'" + [[ ${VERBOSE} -ne 0 ]] && echo "${grep_out}" +fi + +[[ ${VERBOSE} -ne 0 ]] && echo "SUMMARY: ${job_dir}/${job_out}" +[[ ${VERBOSE} -ne 0 ]] && echo " test name : result (expected result)" +[[ ${VERBOSE} -ne 0 ]] && echo " ERROR......: $([[ $ERROR -eq 1 ]] && echo 'yes' || echo 'no') (no)" +[[ ${VERBOSE} -ne 0 ]] && echo " FAILED.....: $([[ $FAILED -eq 1 ]] && echo 'yes' || echo 'no') (no)" +[[ ${VERBOSE} -ne 0 ]] && echo " REQ_MISSING: $([[ $MISSING -eq 1 ]] && echo 'yes' || echo 'no') (no)" +[[ ${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 + +if [[ ${SLURM} -eq 1 ]] && \ + [[ ${ERROR} -eq 0 ]] && \ + [[ ${FAILED} -eq 0 ]] && \ + [[ ${MISSING} -eq 0 ]] && \ + [[ ${NO_MISSING} -eq 1 ]] && \ + [[ ${TGZ} -eq 1 ]] && \ + [[ ! -z ${TARBALL} ]]; then + # SUCCESS + summary=":grin: SUCCESS" + status="success" +else + # FAILURE + summary=":cry: FAILURE" + status="failure" +fi + +### Example details/descriptions +# +#
:cry: FAILURE _(click triangle for detailed information)_Details:
    :heavy_check_mark: job output file slurm-470503.out
    :heavy_multiplication_x: found message matching ERROR:
    :heavy_multiplication_x: found message matching FAILED:
    :heavy_multiplication_x: found message matching required modules missing:
    :heavy_check_mark: found message(s) matching No missing modules!
    :heavy_check_mark: found message matching tar.gz created!
Artefacts:
  • eessi-2023.04-software-linux-x86_64-amd-zen2-1682384569.tar.gz
  • +# +#
    :grin: SUCCESS _(click triangle for detailed information)_Details:
        :heavy_check_mark: job output file slurm-470503.out
        :heavy_check_mark: found message matching ERROR:
        :heavy_check_mark: found message matching FAILED:
        :heavy_check_mark: found message matching required modules missing:
        :heavy_check_mark: found message(s) matching No missing modules!
        :heavy_check_mark: found message matching tar.gz created!
    Artefacts:
  • eessi-2023.04-software-linux-x86_64-amd-zen2-1682384569.tar.gz
  • +# +### + +# construct and write complete PR comment details +comment_template="
    __SUMMARY_FMT____DETAILS_FMT____ARTEFACTS_FMT__
    " +comment_summary_fmt="__SUMMARY__ _(click triangle for detailed information)_" +comment_details_fmt="Details:
    __DETAILS_LIST__" +comment_artefacts_fmt="Artefacts:
    __ARTEFACTS_LIST__" +comment_success_item_fmt=":heavy_check_mark: __ITEM__" +comment_failure_item_fmt=":heavy_multiplication_x: __ITEM__" + +function print_br_item() { + format="${1}" + item="${2}" + echo -n "    ${format//__ITEM__/${item}}
    " +} + +function print_list_item() { + format="${1}" + item="${2}" + echo -n "
  • ${format//__ITEM__/${item}}
  • " +} + +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=${2} + success_msg="${3}" + failure_msg="${4}" + if [[ ${actual} -eq ${expected} ]]; then + success "${success_msg}" + else + failure "${failure_msg}" + fi +} + +echo "[RESULT]" > ${job_result_file} +echo -n "comment_description = " >> ${job_result_file} + +# construct values for placeholders in comment_template: +# - __SUMMARY_FMT__ -> variable $comment_summary +# - __DETAILS_FMT__ -> variable $comment_details +# - __ARTEFACTS_FMT__ -> variable $comment_artefacts + +comment_summary="${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 ${job_out}" +failure_msg="no job output file matching ${GP_slurm_out}" +CoDeList=${CoDeList}$(add_detail ${SLURM} 1 "${success_msg}" "${failure_msg}") + +success_msg="no message matching ${GP_error}" +failure_msg="found message matching ${GP_error}" +CoDeList=${CoDeList}$(add_detail ${ERROR} 0 "${success_msg}" "${failure_msg}") + +success_msg="no message matching ${GP_failed}" +failure_msg="found message matching ${GP_failed}" +CoDeList=${CoDeList}$(add_detail ${FAILED} 0 "${success_msg}" "${failure_msg}") + +success_msg="no message matching ${GP_req_missing}" +failure_msg="found message matching ${GP_req_missing}" +CoDeList=${CoDeList}$(add_detail ${MISSING} 0 "${success_msg}" "${failure_msg}") + +success_msg="found message(s) matching ${GP_no_missing}" +failure_msg="no message matching ${GP_no_missing}" +CoDeList=${CoDeList}$(add_detail ${NO_MISSING} 1 "${success_msg}" "${failure_msg}") + +success_msg="found message matching ${GP_tgz_created}" +failure_msg="no message matching ${GP_tgz_created}" +CoDeList=${CoDeList}$(add_detail ${TGZ} 1 "${success_msg}" "${failure_msg}") + +comment_details="${comment_details_fmt/__DETAILS_LIST__/${CoDeList}}" + + +# first construct comment_artefacts_list, abbreviated CoArList +# then use it to set comment_artefacts +CoArList="" + +# TARBALL should only contain a single tarball +if [[ ! -z ${TARBALL} ]]; then + CoArList="${CoArList}$(print_list_item '__ITEM__' ${TARBALL})" +else + CoArList="${CoArList}$(print_list_item 'No artefacts were created/found.' '')" +fi +comment_artefacts="${comment_artefacts_fmt/__ARTEFACTS_LIST__/${CoArList}}" + +# now put all pieces together creating comment_details from comment_template +comment_description=${comment_template/__SUMMARY_FMT__/${comment_summary}} +comment_description=${comment_description/__DETAILS_FMT__/${comment_details}} +comment_description=${comment_description/__ARTEFACTS_FMT__/${comment_artefacts}} + +echo "${comment_description}" >> ${job_result_file} + +# add overall result: SUCCESS, FAILURE, UNKNOWN + artefacts +# - this should make use of subsequent steps such as deploying a tarball more +# efficient +echo "status = ${status}" >> ${job_result_file} +echo "artefacts = " >> ${job_result_file} +echo "${TARBALL}" | sed -e 's/^/ /g' >> ${job_result_file} + +exit 0 diff --git a/check_missing_installations.sh b/check_missing_installations.sh index e4c75aebd8..945bf32b19 100755 --- a/check_missing_installations.sh +++ b/check_missing_installations.sh @@ -3,6 +3,7 @@ # Script to check for missing installations in EESSI pilot software stack (version 2021.12) # # author: Kenneth Hoste (@boegel) +# author: Thomas Roeblitz (@trz42) # # license: GPLv2 # @@ -21,11 +22,34 @@ source $TOPDIR/scripts/utils.sh source $TOPDIR/configure_easybuild echo ">> Checking for missing installations in ${EASYBUILD_INSTALLPATH}..." -ok_msg="No missing installations, party time!" -fail_msg="On no, some installations are still missing, how did that happen?!" eb_missing_out=$LOCAL_TMPDIR/eb_missing.out # we need to use --from-pr to pull in some easyconfigs that are not available in EasyBuild version being used # PR #16531: Nextflow-22.10.1.eb -${EB:-eb} --from-pr 16531 --easystack eessi-${EESSI_PILOT_VERSION}.yml --experimental --missing | tee ${eb_missing_out} -grep "No missing modules" ${eb_missing_out} > /dev/null -check_exit_code $? "${ok_msg}" "${fail_msg}" +# ${EB:-eb} --from-pr 16531 --easystack eessi-${EESSI_PILOT_VERSION}.yml --experimental --missing 2>&1 | tee ${eb_missing_out} +# PR 16531 not needed since we use EB v4.7.0 +# this, however, breaks the GHA https://github.com/NorESSI/software-layer/blob/main/.github/workflows/test_eessi.yml +# because it uses the EESSI pilot which only provides EB 4.5.1, so adding it back +${EB:-eb} --from-pr 16531 --easystack eessi-${EESSI_PILOT_VERSION}.yml --experimental --missing 2>&1 | tee ${eb_missing_out} +exit_code=${PIPESTATUS[0]} + +ok_msg="Command 'eb --missing ...' succeeded, analysing output..." +fail_msg="Command 'eb --missing ...' failed, check log '${eb_missing_out}'" +check_exit_code ${exit_code} "${ok_msg}" "${fail_msg}" + +# the above assesses the installed software for each easyconfig provided in +# the easystack file and then print messages such as +# `No missing modules!` +# or +# `2 out of 3 required modules missing:` +# depending on the result of the assessment. Hence, we need to check if the +# output does not contain any line with ` required modules missing:` + +grep " required modules missing:" ${eb_missing_out} > /dev/null +exit_code=$? + +# if grep returns 1 (` required modules missing:` was NOT found), we set +# MODULES_MISSING to 0, otherwise (it was found or another error) we set it to 1 +[[ ${exit_code} -eq 1 ]] && MODULES_MISSING=0 || MODULES_MISSING=1 +ok_msg="No missing installations, party time!" +fail_msg="On no, some installations are still missing, how did that happen?!" +check_exit_code ${MODULES_MISSING} "${ok_msg}" "${fail_msg}" diff --git a/create_tarball.sh b/create_tarball.sh index 56ac8ab7ad..b6c72b341d 100755 --- a/create_tarball.sh +++ b/create_tarball.sh @@ -38,6 +38,7 @@ cd ${overlay_upper_dir}/versions/ echo ">> Collecting list of files/directories to include in tarball via ${PWD}..." files_list=${tmpdir}/files.list.txt +module_files_list=${tmpdir}/module_files.list.txt if [ -d ${pilot_version}/software/${os}/${cpu_arch_subdir}/.lmod ]; then # include Lmod cache and configuration file (lmodrc.lua), @@ -49,12 +50,31 @@ if [ -d ${pilot_version}/software/${os}/${cpu_arch_subdir}/modules ]; then find ${pilot_version}/software/${os}/${cpu_arch_subdir}/modules -type f | grep -v '/\.wh\.' >> ${files_list} # module symlinks find ${pilot_version}/software/${os}/${cpu_arch_subdir}/modules -type l | grep -v '/\.wh\.' >> ${files_list} + # module files and symlinks + find ${pilot_version}/software/${os}/${cpu_arch_subdir}/modules/all -type f -o -type l \ + | grep -v '/\.wh\.' | sed -e 's/.lua$//' | sed -e 's@.*/modules/all/@@g' | sort -u \ + >> ${module_files_list} fi -if [ -d ${pilot_version}/software/${os}/${cpu_arch_subdir}/software ]; then - # installation directories - ls -d ${pilot_version}/software/${os}/${cpu_arch_subdir}/software/*/* | grep -v '/\.wh\.' >> ${files_list} +if [ -d ${pilot_version}/software/${os}/${cpu_arch_subdir}/software -a -r ${module_files_list} ]; then + # installation directories but only those for which module files were created + # Note, we assume that module names (as defined by 'PACKAGE_NAME/VERSION.lua' + # using EasyBuild's standard module naming scheme) match the name of the + # software installation directory (expected to be 'PACKAGE_NAME/VERSION/'). + # If either side changes (module naming scheme or naming of software + # installation directories), the procedure will likely not work. + for package_version in $(cat ${module_files_list}); do + echo "handling ${package_version}" + ls -d ${pilot_version}/software/${os}/${cpu_arch_subdir}/software/${package_version} \ + | grep -v '/\.wh\.' >> ${files_list} + done fi +# add a bit debug output +echo "wrote file list to ${files_list}" +[ -r ${files_list} ] && cat ${files_list} +echo "wrote module file list to ${module_files_list}" +[ -r ${module_files_list} ] && cat ${module_files_list} + topdir=${cvmfs_repo}/versions/ echo ">> Creating tarball ${target_tgz} from ${topdir}..." diff --git a/eessi-2022.11.yml b/eessi-2022.11.yml new file mode 100644 index 0000000000..13bf7989aa --- /dev/null +++ b/eessi-2022.11.yml @@ -0,0 +1,26 @@ +easyconfigs: + - CMake-3.16.4-GCCcore-9.3.0.eb + - CMake-3.20.1-GCCcore-10.3.0.eb + - EasyBuild-4.6.2.eb + - GCC-9.3.0.eb + - GCC-10.3.0.eb + - ImageMagick-7.0.11-14-GCCcore-10.3.0.eb + - Java-11.eb + - Java-17.eb + - Nextflow-22.10.1.eb + - OpenBLAS-0.3.9-GCC-9.3.0.eb + - OpenMPI-4.0.3-GCC-9.3.0.eb + - OpenMPI-4.1.1-GCC-10.3.0.eb + - OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb + - OSU-Micro-Benchmarks-5.7.1-gompi-2021a.eb + - Perl-5.30.2-GCCcore-9.3.0.eb + - Python-2.7.18-GCCcore-9.3.0.eb + - Python-3.8.2-GCCcore-9.3.0.eb + - Python-3.9.5-GCCcore-10.3.0.eb + - Qt5-5.14.1-GCCcore-9.3.0.eb + - R-4.0.0-foss-2020a.eb + - SciPy-bundle-2020.03-foss-2020a-Python-3.8.2.eb + - Spark-3.1.1-foss-2020a-Python-3.8.2.eb + - WRF-3.9.1.1-foss-2020a-dmpar.eb + - QuantumESPRESSO-6.6-foss-2020a.eb + - FlexiBLAS-3.0.4-GCC-10.3.0.eb diff --git a/eessi-2023.04.yml b/eessi-2023.04.yml new file mode 100644 index 0000000000..04db10ba7a --- /dev/null +++ b/eessi-2023.04.yml @@ -0,0 +1,15 @@ +easyconfigs: +# - GCC-9.3.0.eb + - GCC-10.3.0.eb: + options: + include-easyblocks-from-pr: 2921 +# - GCC-11.3.0.eb +# - GCC-12.2.0.eb + - OpenSSL-1.1.eb: + options: + include-easyblocks-from-pr: 2922 + - CMake-3.20.1-GCCcore-10.3.0.eb: + options: + include-easyblocks-from-pr: 2248 + - Perl-5.32.1-GCCcore-10.3.0.eb + - OpenMPI-4.1.1-GCC-10.3.0.eb