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trz42 wants to merge 5 commits into from
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try to fix EESSI/software-layer issue 225 #57

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b2644fa
install BLIS only, add debug output
truib Mar 16, 2023
42425d7
adding OpenBLAS
truib Mar 16, 2023
4478bbc
adding FlexiBLAS
truib Mar 16, 2023
aaa2359
search correct py_cache_path
truib Mar 16, 2023
7203d8b
attempt to fix issue #225
truib Mar 17, 2023
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89 changes: 55 additions & 34 deletions EESSI-pilot-install-software.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -60,6 +60,7 @@ else
fi

TMPDIR=$(mktemp -d)
echo "TMPDIR set to '${TMPDIR}'"

echo ">> Setting up environment..."

Expand All @@ -80,6 +81,9 @@ fi

# avoid that pyc files for EasyBuild are stored in EasyBuild installation directory
export PYTHONPYCACHEPREFIX=$TMPDIR/pycache
echo "check PYTHONPYCACHEPREFIX (${PYTHONPYCACHEPREFIX})"
ls -l $TMPDIR
# mkdir -p ${PYTHONPYCACHEPREFIX}

DETECTION_PARAMETERS=''
GENERIC=0
Expand Down Expand Up @@ -177,10 +181,6 @@ 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!"
Expand All @@ -189,6 +189,10 @@ 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!"
Expand Down Expand Up @@ -281,11 +285,11 @@ echo_green "All set, let's start installing some software in ${EASYBUILD_INSTALL
#$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 --disable-cleanup-tmpdir
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 --disable-cleanup-tmpdir
#check_exit_code $? "${ok_msg}" "${fail_msg}"

# skip test step when installing SciPy-bundle on aarch64,
# to dance around problem with broken numpy tests;
Expand Down Expand Up @@ -368,11 +372,11 @@ check_exit_code $? "${ok_msg}" "${fail_msg}"
#$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}" "${fail_msg}"
#echo ">> Installing Spark 3.1.1..."
#ok_msg="Spark installed, set off the fireworks!"
#fail_msg="Installation of Spark failed, no fireworks this time..."
#$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!"
Expand All @@ -392,12 +396,12 @@ check_exit_code $? "${ok_msg}" "${fail_msg}"
#$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..."
# Comment from Axel: PR 16531 was merged so --from-pr not needed anymore (but was used in this build)
$EB -r --from-pr 16531 Nextflow-22.10.1.eb
check_exit_code $? "${ok_msg}" "${fail_msg}"
#echo ">> Installing Nextflow 22.10.1..."
#ok_msg="Nextflow installed, the work must flow..."
#fail_msg="Installation of Nextflow failed, that's unexpected..."
## Comment from Axel: PR 16531 was merged so --from-pr not needed anymore (but was used in this build)
#$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!"
Expand Down Expand Up @@ -425,7 +429,7 @@ check_exit_code $? "${ok_msg}" "${fail_msg}"
#$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
$EB CMake-3.20.1-GCCcore-10.3.0.eb --robot --include-easyblocks-from-pr 2248
#$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
Expand All @@ -450,10 +454,10 @@ $EB CMake-3.20.1-GCCcore-10.3.0.eb --robot --include-easyblocks-from-pr 2248
#####################
### add packages here
#####################
$EB Python-3.9.5-GCCcore-10.3.0.eb --robot
$EB OpenMPI-4.1.1-GCC-10.3.0.eb --robot
#$EB Python-3.9.5-GCCcore-10.3.0.eb --robot
#$EB OpenMPI-4.1.1-GCC-10.3.0.eb --robot
# this Package has been added to reduce the complexity of building large packages such as R
$EB ImageMagick-7.0.11-14-GCCcore-10.3.0.eb --robot
#$EB ImageMagick-7.0.11-14-GCCcore-10.3.0.eb --robot
# example block showing a few debugging means
#echo "Installing CaDiCaL/1.3.0 for GCC/9.3.0..."
#ok_msg="CaDiCaL installed. Nice!"
Expand All @@ -465,17 +469,34 @@ $EB ImageMagick-7.0.11-14-GCCcore-10.3.0.eb --robot
#check_exit_code $exit_code "${ok_msg}" "${fail_msg}"

# add latest EasyBuild to stack
echo ">> Adding latest EasyBuild to stack..."
ok_msg="Latest EasyBuild got installed ... great!"
fail_msg="Installation of latest EasyBuild failed! Disappointed."
if [[ ${EESSI_CVMFS_REPO} == /cvmfs/pilot.eessi-hpc.org ]]; then
$EB --from-pr 14545 --include-easyblocks-from-pr 2805 --robot --install-latest-eb-release
else
$EB --robot --install-latest-eb-release
fi
exit_code=$?
check_exit_code ${exit_code} "${ok_msg}" "${fail_msg}"
#echo ">> Adding latest EasyBuild to stack..."
#ok_msg="Latest EasyBuild got installed ... great!"
#fail_msg="Installation of latest EasyBuild failed! Disappointed."
#if [[ ${EESSI_CVMFS_REPO} == /cvmfs/pilot.eessi-hpc.org ]]; then
# $EB --from-pr 14545 --include-easyblocks-from-pr 2805 --robot --install-latest-eb-release
##else
# $EB --robot --install-latest-eb-release
#fi
#exit_code=$?
#check_exit_code ${exit_code} "${ok_msg}" "${fail_msg}"

echo "BEFORE EB-installing BLIS"
ls -l ${EESSI_SOFTWARE_PATH}/software/Python/3.9.5-GCCcore-10.3.0/easybuild/python/__pycache__/

$EB --robot BLIS-0.8.1-GCC-10.3.0.eb

echo "AFTER EB-installing BLIS"
ls -l ${EESSI_SOFTWARE_PATH}/software/Python/3.9.5-GCCcore-10.3.0/easybuild/python/__pycache__/

$EB --robot OpenBLAS-0.3.15-GCC-10.3.0.eb

echo "AFTER EB-installing OpenBLAS"
ls -l ${EESSI_SOFTWARE_PATH}/software/Python/3.9.5-GCCcore-10.3.0/easybuild/python/__pycache__/

$EB --robot FlexiBLAS-3.0.4-GCC-10.3.0.eb

echo "AFTER EB-installing FlexiBLAS"
ls -l ${EESSI_SOFTWARE_PATH}/software/Python/3.9.5-GCCcore-10.3.0/easybuild/python/__pycache__/

echo ">> Creating/updating Lmod cache..."
export LMOD_RC="${EASYBUILD_INSTALLPATH}/.lmod/lmodrc.lua"
Expand Down
17 changes: 16 additions & 1 deletion create_tarball.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -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),
Expand All @@ -49,12 +50,26 @@ 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}/${cpu_arch_subdir}/modules -type f -o -type l \
| grep -v '/\.wh\.' | sed -e 's/.lua$//' | awk -F'/' '{printf "%s/%s\n", $(NF-1), $NF}' | sort | uniq \
>> ${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}
# ls -d ${pilot_version}/software/${os}/${cpu_arch_subdir}/software/*/* | grep -v '/\.wh\.' >> ${files_list}
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

echo "wrote file list to ${files_list}"
cat ${files_list}
echo "wrote module file list to ${module_files_list}"
cat ${module_files_list}

topdir=${cvmfs_repo}/versions/

echo ">> Creating tarball ${target_tgz} from ${topdir}..."
Expand Down