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- Only 1 slurm script to submit.
- Automated VM integrity test.
Issues and solutions
- GMT doesn't run in MPI unless all processes run GMT in unison. Abandoned MPI and chose multiprocess.
- GMT 6.xx "spatial" output was broken. Downgraded to GMT 5.4.3. The bug reported. (http://gmt.soest.hawaii.edu/issues/1245)
- HDF5 on Cray : File locking issue: Needs `$ export HDF5_USE_FILE_LOCKING=FALSE` (https://github.com/ALPSCore/ALPSCore/issues/348)
- gs for psconvert is not available on Kupe compute node. Copying and placing gs binary doesn work as files in `/usr/share/ghostscript/9.15`/ are missing. ImageMagick can be tried instead. For now, we don't produce png.
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#!/bin/bash # script version: slurm # Please modify this file as needed, this is just a sample #SBATCH --job-name=nhm2srf_vm #SBATCH --account=nesi00213 #SBATCH --partition=NeSI #SBATCH --ntasks=1 #SBATCH --time=03:00:00 #SBATCH --output nhm2srf_vm-%j.out #SBATCH --error nhm2srf_vm-%j.err ###SBATCH --mail-type=all ###SBATCH --mail-user=test@test.com ###SBATCH --mem-per-cpu=16G ###SBATCH -C avx #SBATCH --hint=nomultithread ## END HEADER source machine_env.sh # user specific parameters export NUMPROCS=40 export SELECTION_FILE=`pwd`/nhm_selection_geo_si.txt #nhm_selection_sample2.txt # # important paths export SRFGENPATH=/nesi/nobackup/nesi00213/tmp/Pre-processing/SrfGen export QCOREPATH=/nesi/nobackup/nesi00213/tmp/qcore export GMPEMODELSPATH=/nesi/nobackup/nesi00213/tmp/post-processing/im_processing/computations/GMPE_models # leave these alone export PYTHONPATH=$QCOREPATH:$PYTHONPATH:$SRFGENPATH:$GMPEMODELSPATH export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/nesi/nobackup/nesi00213/gmt/gmt-stable/lib64 # to fix HDF5 file locking issue https://github.com/ALPSCore/ALPSCore/issues/348 export HDF5_USE_FILE_LOCKING=FALSE echo "SRF generation starts" date python2 $SRFGENPATH/NHM/nhm2srf.py $SELECTION_FILE -n $NUMPROCS echo "SRF generation completed" date echo "VM generation starts" srun python2 $SRFGENPATH/srfinfo2vm.py "autosrf/*/Srf/*.info" -n $NUMPROCS date echo "VM generation completed" |
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- Technical debts: /nesi/nobackup/qcore /nesi/nobackup/post-processing need to be updated, and other codes that depend on old versions need to be revised
Issues and solutions
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