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hpe-mpi: Fix SINGULARITY_CONTAINLIBS env variable #2075

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merged 3 commits into from
Jul 19, 2023

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iomaganaris
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  • In the previous version there was an issue with the way SINGULARITY_CONTAINLIBS was set breaking singularityce module
  • This fixes the issue:
/gpfs/bbp.cscs.ch/data/scratch/proj16/magkanar/spack_modules/linux-rhel7-skylake/hpe-mpi/2.26:

module-whatis    HPE-SGI MPI package
prepend-path     PATH /gpfs/bbp.cscs.ch/data/scratch/proj16/magkanar/spack_packages/software/install_gcc-12.2.0-skylake/hpe-mpi-2.26-zwxxno/bin
prepend-path     MANPATH /gpfs/bbp.cscs.ch/data/scratch/proj16/magkanar/spack_packages/software/install_gcc-12.2.0-skylake/hpe-mpi-2.26-zwxxno/man
prepend-path     CMAKE_PREFIX_PATH /gpfs/bbp.cscs.ch/data/scratch/proj16/magkanar/spack_packages/software/install_gcc-12.2.0-skylake/hpe-mpi-2.26-zwxxno/.
setenv           ROMIO_TUNEGATHER 0
append-path      --delim , SINGULARITY_CONTAINLIBS /gpfs/bbp.cscs.ch/data/scratch/proj16/magkanar/spack_packages/software/install_gcc-12.2.0-skylake/hpe-mpi-2.26-zwxxno/lib/libmpi_panfs.so
append-path      --delim , SINGULARITY_CONTAINLIBS /gpfs/bbp.cscs.ch/data/scratch/proj16/magkanar/spack_packages/software/install_gcc-12.2.0-skylake/hpe-mpi-2.26-zwxxno/lib/libmpi_st.so
append-path      --delim , SINGULARITY_CONTAINLIBS /gpfs/bbp.cscs.ch/data/scratch/proj16/magkanar/spack_packages/software/install_gcc-12.2.0-skylake/hpe-mpi-2.26-zwxxno/lib/libpmi2mpt.so
append-path      --delim , SINGULARITY_CONTAINLIBS /gpfs/bbp.cscs.ch/data/scratch/proj16/magkanar/spack_packages/software/install_gcc-12.2.0-skylake/hpe-mpi-2.26-zwxxno/lib/libsma.so
append-path      --delim , SINGULARITY_CONTAINLIBS /gpfs/bbp.cscs.ch/data/scratch/proj16/magkanar/spack_packages/software/install_gcc-12.2.0-skylake/hpe-mpi-2.26-zwxxno/lib/libmpi_mt.so
append-path      --delim , SINGULARITY_CONTAINLIBS /gpfs/bbp.cscs.ch/data/scratch/proj16/magkanar/spack_packages/software/install_gcc-12.2.0-skylake/hpe-mpi-2.26-zwxxno/lib/libmpi_lustre.so
append-path      --delim , SINGULARITY_CONTAINLIBS /gpfs/bbp.cscs.ch/data/scratch/proj16/magkanar/spack_packages/software/install_gcc-12.2.0-skylake/hpe-mpi-2.26-zwxxno/lib/libmpi_f08_intel.so
append-path      --delim , SINGULARITY_CONTAINLIBS /gpfs/bbp.cscs.ch/data/scratch/proj16/magkanar/spack_packages/software/install_gcc-12.2.0-skylake/hpe-mpi-2.26-zwxxno/lib/libmpi++abi1002.so
append-path      --delim , SINGULARITY_CONTAINLIBS /gpfs/bbp.cscs.ch/data/scratch/proj16/magkanar/spack_packages/software/install_gcc-12.2.0-skylake/hpe-mpi-2.26-zwxxno/lib/libmpi_f08.so
append-path      --delim , SINGULARITY_CONTAINLIBS /gpfs/bbp.cscs.ch/data/scratch/proj16/magkanar/spack_packages/software/install_gcc-12.2.0-skylake/hpe-mpi-2.26-zwxxno/lib/libmpi_bpheap.so
append-path      --delim , SINGULARITY_CONTAINLIBS /gpfs/bbp.cscs.ch/data/scratch/proj16/magkanar/spack_packages/software/install_gcc-12.2.0-skylake/hpe-mpi-2.26-zwxxno/lib/libxmpi.so
append-path      --delim , SINGULARITY_CONTAINLIBS /gpfs/bbp.cscs.ch/data/scratch/proj16/magkanar/spack_packages/software/install_gcc-12.2.0-skylake/hpe-mpi-2.26-zwxxno/lib/libmpi++.so
append-path      --delim , SINGULARITY_CONTAINLIBS /gpfs/bbp.cscs.ch/data/scratch/proj16/magkanar/spack_packages/software/install_gcc-12.2.0-skylake/hpe-mpi-2.26-zwxxno/lib/libmpi.so
append-path      --delim , SINGULARITY_CONTAINLIBS /gpfs/bbp.cscs.ch/data/scratch/proj16/magkanar/spack_packages/software/install_gcc-12.2.0-skylake/hpe-mpi-2.26-zwxxno/lib/libmpi_im.so
prepend-path     --delim , SINGULARITYENV_LD_PRELOAD /.singularity.d/libs/libmpi.so
append-path      --delim , SINGULARITY_CONTAINLIBS /lib64/libpmi2.so

@iomaganaris iomaganaris self-assigned this Jul 19, 2023
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Thank you for your pull request!

Should you want to clear the PR build directory after failures, please use this pipeline. Before running the cleanup pipeline, please ensure that any PR building pipelines have been cancelled or finished running.

@iomaganaris iomaganaris enabled auto-merge (squash) July 19, 2023 16:06
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To test your PR, use the following on BlueBrain5:

unset MODULEPATH
. /gpfs/bbp.cscs.ch/ssd/apps/bsd/pulls/2075/config/modules.sh
module load unstable

Please test the following updated modules:

  • brainbuilder/0.18.5
  • brayns/3.1.2
  • brayns/3.2.0
  • brayns/3.2.1
  • brion/3.3.12
  • caliper/2.8.0
  • connectome-tools/0.6.2
  • darshan-runtime/3.3.1
  • emsim/1.0.2
  • gmsh/4.10.3
  • hdf5/1.14.0
  • highfive/2.7.1
  • hpe-mpi/2.25.hmpt
  • morpho-kit/0.3.5
  • neurodamus-hippocampus/1.8-2.15.3-2.8.0
  • neurodamus-mousify/1.6-2.15.3-2.8.0
  • neurodamus-neocortex-multiscale/1.12-2.15.3-2.8.0
  • neurodamus-neocortex-plasticity/1.12-2.15.3-2.8.0
  • neurodamus-neocortex/1.12-2.15.3-2.8.0
  • neurodamus-thalamus/1.6-2.15.3-2.8.0
  • neuron/9.0.a9
  • omega-h/9.34.13
  • parquet-converters/0.8.0
  • petsc/3.18.1
  • placement-algorithm/2.3.1
  • psp-validation/0.5.0
  • py-archngv/3.0.2
  • py-atlannot/0.1.3
  • py-atlas-building-tools/0.1.10
  • py-atlinter/0.2.4
  • py-bbp-analysis-framework/1.6.42
  • py-bbp-workflow/3.1.19
  • py-bglibpy/4.10.1
  • py-bluepy/2.5.1
  • py-bluepyemodel/0.0.11
  • py-bluepymm/0.7.65
  • py-bluepyopt/1.13.86
  • py-bluepyparallel/0.0.5
  • py-bluepysnap/1.0.7
  • py-connectome-manipulator/0.0.4
  • py-currentscape/0.0.10
  • py-cwl-registry/0.3.8
  • py-dask-mpi/2022.4.0
  • py-h5py/3.8.0
  • py-libsonata/0.1.22
  • py-minis-validation/0.0.5
  • py-morph-tool/2.9.0
  • py-morphio/3.3.6
  • py-mpi4py/3.1.4
  • py-neurodamus/2.15.3
  • py-neuror/1.6.4
  • py-petsc4py/3.18.1
  • py-region-grower/0.4.3
  • py-slepc4py/3.18.1
  • python-dev/0.5
  • singularityce/3.11.3
  • slepc/3.18.1
  • spatial-index/2.1.0
  • spykfunc/0.18.1
  • steps/4.1.0
  • steps/5.0.0a
  • synapsetool/0.6.4
  • touchdetector/6.0.1

@iomaganaris iomaganaris merged commit 717f11f into develop Jul 19, 2023
10 checks passed
@iomaganaris iomaganaris deleted the magkanar/fix_hpe_mpi_singularity branch July 19, 2023 20:33
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3 participants