run GW using container with spack-stack 1.9.2 #3964
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This still doesn't address a lot of the concerns about containing the containerization code. Please consider if this can all be done modifying only things run up-front before the j-job is called (*.env script, modulefiles), without using alternate scripts or altering the main flow of scripts.
scripts/exgfs_wave_init.sh
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| # | ||
| ############################################################################### | ||
| # | ||
| source "${HOMEgfs}/dev/ush/load_gw_run_modules.sh" |
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You should not be loading modules in the middle of a job here or in the ush scripts like you have added in many places. All modules need to be loaded up front before the j-job begins.
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So far, I have not think of a better way to handle this.
So, there are quite few scripts are doing this.
I was thinking add this to preamble.sh, what do you think?
| # overwrite MACHINE_ID if in container | ||
| if [[ -v SINGULARITY_CONTAINER ]]; then | ||
| # We are in a container | ||
| MACHINE_ID=container |
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I still think you are going to be more successful if container is just a separate setting and not a MACHINE_ID. There are times we will still need to know what hardware we are on when running from container.
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I need more time to think about this. Please update if you have something to share.
| echo "${nm} ${line}" >> "${mpmd_cmdfile}" | ||
| ((nm=nm+1)) | ||
| done < "${cmdfile}" | ||
| # Redirect output from each process to its own stdout |
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Why are there such drastic changes here? It is designed to detect the scheduler type so it can form the MPMD script properly. This removes all that.
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run_mpmd.sh is little complicated. Need more time to think and re-check.
jobs/JGLOBAL_ARCHIVE_VRFY
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| if [[ "${RUN_WITH_CONTAINER}" == "YES" ]]; then | ||
| "${HOMEgfs}/exec/run_python.sh" "${GLOBALARCHIVESH:-${SCRgfs}/exglobal_archive_vrfy.py}" -c -v | ||
| else | ||
| ${GLOBALARCHIVESH:-${SCRgfs}/exglobal_archive_vrfy.py} | ||
| fi |
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Really do not want to add blocks like this all over the code.
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Tried a different way. Please check and comment.
| chmod +x "${exec_python_script}" | ||
| chmod +x "${run_python_script}" | ||
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| for item in JGLOBAL_WAVE_INIT |
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3 participants
Description
Make GW be able to run with container has spack-stack 1.9.2 inside.
change includes:
Add new module files, make detect-machine, module-setup can detect and setup for container.
Add new scripts to shell-in container compiling GW,
Add new scripts to generate run cases using container.
Add wrapper and other scripts to run GW with container.
Resolves #3963
Type of change
Change characteristics
How has this been tested?
Checklist