Prepend container launcher script to pbs command, if it exists#607
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jo-basevi merged 3 commits intopayu-org:masterfrom Jul 21, 2025
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aidanheerdegen
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LGTM. Thanks.
I think you'd said you might add a test, but I'll leave that up to your discretion.
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aidanheerdegen
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Awesome. Thanks!
minghangli-uni
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…org#607) This is support singularity containers that set `ENV_LAUNCHER_SCRIPT_PATH` environment variable in a script that starts a container and then runs the command arguments inside the container.
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Related to ACCESS-NRI/model-release-condaenv#17 which requires running payu from an environment within a singularity container.
This allows a custom launcher script to run at the start of the PBS job which launches a singularity container with a SquashFS overlay for the environment, and then runs the python and payu executable within that environment.
Could use a shorter or other name than
ENV_LAUNCHER_SCRIPT_PATH? Now would be the time to change it if so..I've manually tested that this does not add
ENV_LAUNCHER_SCRIPT_PATHif it isn't set in the environment, and if it is, it then works with an launcher script implementation in the ACCESS-NRI/model-release-condaenv#19 PR.Note: qsub call looks like
qsub <qsub_flags> -- /path/to/env-launcher-scripts/bin/launcher.sh /path/to/envs/payu/bin/python3.10 /path/to/envs/payu/bin/payu-runwhere/path/to/envs/payu/bindirectory is only accessible when running within the singularity container.