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Don't use getenv=true with HTCondor workflows #164

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Don't use getenv=true with HTCondor workflows #164

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45f6d38
condor: don't use getenv=true
duncanmmacleod Aug 25, 2023
1bc19c8
omicron-process: pass PATH to omicron-merge-with-gaps
duncanmmacleod Aug 25, 2023
eefed7f
omicron-process: set --outdir for omicron-archive
duncanmmacleod Sep 1, 2023
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16 changes: 14 additions & 2 deletions omicron/cli/process.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1043,7 +1043,13 @@ def main(args=None):

ppjob.add_condor_cmd('periodic_remove', '(JobStatus == 1) && MemoryUsage >= 7G')

ppjob.add_condor_cmd('environment', '"HDF5_USE_FILE_LOCKING=FALSE"')
ppjob.add_condor_cmd('environment', "\"{}\"".format(" ".join((
# disable file locking over NFS
"HDF5_USE_FILE_LOCKING=FALSE",
# provide the PATH so that omicron-merge-with-gaps can find the
# executables it needs
f"PATH='{os.getenv('PATH', sys.prefix)}'",
))))
ppjob.add_short_opt('e', '')
ppnodes = []
prog_path = dict()
Expand Down Expand Up @@ -1262,9 +1268,15 @@ def main(args=None):
if newdag:
# write shell script to seed archive
with open(archivejob.get_executable(), 'w') as f:
cmd = [
prog_path["omicron_archive"],
"--indir", mergedir.absolute(),
"--outdir", os.getenv("OMICRON_ARCHIVE", const.OMICRON_ARCHIVE),
"-vv",
]
print('#!/bin/bash -e\n', file=f)
print('# Archive all trigger files saved in the merge directory ', file=f)
print(f'{prog_path["omicron_archive"]} --indir {str(mergedir.absolute())} -vv', file=f)
print(" ".join(map(str, cmd)), file=f)

os.chmod(archivejob.get_executable(), 0o755)
# write caches to disk
Expand Down
1 change: 0 additions & 1 deletion omicron/condor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -560,7 +560,6 @@ def __init__(self, universe, executable, tag=None, subdir=None,
logdir, '%s-%s.err' % (tag, self.logtag)))
self.set_stdout_file(os.path.join(
logdir, '%s-%s.out' % (tag, self.logtag)))
cmds.setdefault('getenv', 'True')
for key, val in cmds.items():
if hasattr(self, 'set_%s' % key.lower()):
getattr(self, 'set_%s' % key.lower())(val)
Expand Down