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Fix CI tests on R&D ParallelCluster #940

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merged 5 commits into from
Jan 16, 2024
Merged

Fix CI tests on R&D ParallelCluster #940

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1e33456
Update .gitmodules and submodule pointer for spack for code review an…
climbfuji Jan 10, 2024
f64a566
Attempt to fix duplicate packages by installing Intel and GNU stacks …
climbfuji Jan 10, 2024
7be984c
Revert .gitmodules and update submodule pointer for spack
climbfuji Jan 14, 2024
2d23003
Merge branch 'develop' of https://github.com/jcsda/spack-stack into f…
climbfuji Jan 14, 2024
0b06c7f
Fix concretize arguments in .github/workflows/ubuntu-rnd-x86_64.yaml
climbfuji Jan 14, 2024
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127 changes: 83 additions & 44 deletions .github/workflows/ubuntu-rnd-x86_64.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -61,9 +61,6 @@ jobs:
# For buildcaches
spack config add config:install_tree:padded_length:200

# Set compiler and MPI
sed -i "s/\['\%aocc', '\%apple-clang', '\%gcc', '\%intel'\]/\['\%gcc', '\%intel'\]/g" ${ENVDIR}/spack.yaml

# Add additional variants for MET packages, different from config/common/packages.yaml
spack config add "packages:met:variants:+python +grib2 +graphics +lidar2nc +modis"

Expand All @@ -74,28 +71,45 @@ jobs:
spack config add "config:source_cache:/home/ubuntu/spack-stack/CI/tmp/source_cache"
spack config add "config:misc_cache:/home/ubuntu/spack-stack/CI/tmp/misc_cache"

# Concretize and check for duplicates
spack concretize 2>&1 | tee log.concretize.${ENVNAME}
${SPACK_STACK_DIR}/util/show_duplicate_packages.py -c -d log.concretize.${ENVNAME} -i fms -i crtm -i esmf -i mapl

# Update spack source cache
spack mirror create -a -d /mnt/experiments-efs/spack-stack/source-cache

# Add binary cache if requested
if [ "$USE_BINARY_CACHE" = true ] ; then
spack mirror add local-binary file:///mnt/experiments-efs/spack-stack/build-cache/
spack buildcache update-index local-binary
echo "Packages in spack binary cache:"
spack buildcache list
fi

# Create/update binary cache
echo "Create/update build cache for environment ${TEMPLATE} ..."
spack install --fail-fast --source --no-check-signature 2>&1 | tee log.install.${TEMPLATE}
spack buildcache create -a -u /mnt/experiments-efs/spack-stack/build-cache/

# Next steps: synchronize source and build cache to a central/combined mirror?
#echo "Next steps ..."
# Loop over compilers
compilers=(gcc intel)
cp ${ENVDIR}/spack.yaml ${ENVDIR}/spack.yaml.original

for compiler in "${!compilers[@]}"
do
# Set compiler and MPI
cp ${ENVDIR}/spack.yaml.original ${ENVDIR}/spack.yaml
sed -i "s/\['\%aocc', '\%apple-clang', '\%gcc', '\%intel'\]/\['\%${compiler}'\]/g" ${ENVDIR}/spack.yaml
cat spack.yaml

# Concretize and check for duplicates
spack concretize --force --fresh 2>&1 | tee log.concretize.${ENVNAME}.${compiler}
${SPACK_STACK_DIR}/util/show_duplicate_packages.py -d log.concretize.${ENVNAME}.${compiler} -i fms -i crtm -i esmf -i mapl

# Update spack source cache
spack mirror create -a -d /mnt/experiments-efs/spack-stack/source-cache

# Add binary cache if requested
if [ "$USE_BINARY_CACHE" = true ] ; then
spack mirror add local-binary file:///mnt/experiments-efs/spack-stack/build-cache/
spack buildcache update-index local-binary
echo "Packages in spack binary cache:"
spack buildcache list
fi

# Create/update binary cache
echo "Create/update build cache for environment ${TEMPLATE} and compiler ${compiler}..."
spack install --fail-fast --source --no-check-signature 2>&1 | tee log.install.${TEMPLATE}.${compiler}
spack buildcache create -a -u /mnt/experiments-efs/spack-stack/build-cache/

# Next steps: synchronize source and build cache to a central/combined mirror?
#echo "Next steps ..."

# Remove binary cache for next round of concretization
if [ "$USE_BINARY_CACHE" = true ] ; then
spack mirror rm local-binary
fi
done

spack env deactivate
rm -fr /home/ubuntu/spack-stack/CI/tmp/spack-stack-dev-buildcache
Expand All @@ -113,9 +127,6 @@ jobs:
spack env activate ${ENVDIR}
spack add ${{ inputs.specs || '' }}

# Set compiler and MPI
sed -i "s/\['\%aocc', '\%apple-clang', '\%gcc', '\%intel'\]/\['\%gcc', '\%intel'\]/g" ${ENVDIR}/spack.yaml

# Add additional variants for MET packages, different from config/common/packages.yaml
spack config add "packages:met:variants:+python +grib2 +graphics +lidar2nc +modis"

Expand All @@ -126,26 +137,43 @@ jobs:
spack config add "config:source_cache:/home/ubuntu/spack-stack/CI/tmp/source_cache"
spack config add "config:misc_cache:/home/ubuntu/spack-stack/CI/tmp/misc_cache"

# Concretize and check for duplicates
spack concretize 2>&1 | tee log.concretize.${ENVNAME}
${SPACK_STACK_DIR}/util/show_duplicate_packages.py -c -d log.concretize.${ENVNAME} -i fms -i crtm -i esmf -i mapl
# Loop over compilers
compilers=(gcc intel)
cp ${ENVDIR}/spack.yaml ${ENVDIR}/spack.yaml.original

# Update spack source cache
spack mirror create -a -d /mnt/experiments-efs/spack-stack/source-cache
for compiler in "${!compilers[@]}"
do
# Set compiler and MPI
cp ${ENVDIR}/spack.yaml.original ${ENVDIR}/spack.yaml
sed -i "s/\['\%aocc', '\%apple-clang', '\%gcc', '\%intel'\]/\['\%${compiler}'\]/g" ${ENVDIR}/spack.yaml
cat spack.yaml

# Add binary cache
spack mirror add local-binary file:///mnt/experiments-efs/spack-stack/build-cache/
spack buildcache update-index local-binary
echo "Packages in spack binary cache:"
spack buildcache list
# Concretize and check for duplicates
spack concretize --force --fresh 2>&1 | tee log.concretize.${ENVNAME}.${compiler}
${SPACK_STACK_DIR}/util/show_duplicate_packages.py -d log.concretize.${ENVNAME}.${compiler} -i fms -i crtm -i esmf -i mapl

# Install from binary cache
echo "Install environment ${TEMPLATE} from binary cache ..."
spack install --fail-fast --no-check-signature 2>&1 | tee log.install.${TEMPLATE}
spack clean -a
# Update spack source cache
spack mirror create -a -d /mnt/experiments-efs/spack-stack/source-cache

# Add binary cache
spack mirror add local-binary file:///mnt/experiments-efs/spack-stack/build-cache/
spack buildcache update-index local-binary
echo "Packages in spack binary cache:"
spack buildcache list

# Install from binary cache
echo "Install environment ${TEMPLATE} for compiler ${compiler} from binary cache ..."
spack install --fail-fast --no-check-signature 2>&1 | tee log.install.${TEMPLATE}.${compiler}
spack clean -a

# Create modules
spack module lmod refresh -y
spack stack setup-meta-modules

# Remove binary cache for next round of concretization
spack mirror rm local-binary
done

spack module lmod refresh -y
spack stack setup-meta-modules
spack env deactivate

- name: test-env
Expand All @@ -170,6 +198,17 @@ jobs:
module load soca-env/1.0.0
module list

module purge
module load stack-gcc/9.4.0
module load stack-openmpi/4.1.4
module load stack-python/3.10.13
module available

module load jedi-ufs-env/1.0.0
module load ewok-env/1.0.0
module load soca-env/1.0.0
module list

# Create empty file to signal that this environment is ready for testing
touch /home/ubuntu/spack-stack/CI/unified-env/${TODAY}.ready

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