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Prepend container launcher script to pbs command, if it exists #607

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Merged
jo-basevi merged 3 commits into from
Jul 21, 2025
Merged

Prepend container launcher script to pbs command, if it exists #607

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40ce4f5
Prepend container launcher script to pbs command, if it exists
jo-basevi Jul 16, 2025
8bc93d2
Check whether custom launcher script environment variable is executable
jo-basevi Jul 21, 2025
13f30fe
Add test for setting launcher script in qsub command
jo-basevi Jul 21, 2025
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12 changes: 12 additions & 0 deletions payu/schedulers/pbs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@

# Standard library
import os
from pathlib import Path
import re
import sys
import shlex
Expand Down Expand Up @@ -129,6 +130,17 @@ def submit(self, pbs_script, pbs_config, pbs_vars=None, python_exe=None):
envmod.setup()
envmod.module('load', 'pbs')

# Check for custom container launcher script environment variable
launcher_script = os.environ.get('ENV_LAUNCHER_SCRIPT_PATH')
if (
launcher_script
and Path(launcher_script).is_file()
and os.access(launcher_script, os.X_OK)
):
# Prepend the container launcher script to the python command
# so the python executable is accessible in the container
python_exe = f'{launcher_script} {python_exe}'

# Construct job submission command
cmd = 'qsub {flags} -- {python} {script}'.format(
flags=' '.join(pbs_flags),
Expand Down
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