From 45f6d38a513bdd2919de3d1e01d692424d619209 Mon Sep 17 00:00:00 2001 From: Duncan Macleod Date: Fri, 25 Aug 2023 03:16:21 -0700 Subject: [PATCH 1/3] condor: don't use getenv=true there be dragons --- omicron/condor.py | 1 - 1 file changed, 1 deletion(-) diff --git a/omicron/condor.py b/omicron/condor.py index fee975b..a46918f 100644 --- a/omicron/condor.py +++ b/omicron/condor.py @@ -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) From 1bc19c8ac9655b3d8e1e7751aa38d61b5dfac5c3 Mon Sep 17 00:00:00 2001 From: Duncan Macleod Date: Fri, 25 Aug 2023 03:17:07 -0700 Subject: [PATCH 2/3] omicron-process: pass PATH to omicron-merge-with-gaps so that it can find the executables it needs --- omicron/cli/process.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/omicron/cli/process.py b/omicron/cli/process.py index 0ca1735..41bee25 100644 --- a/omicron/cli/process.py +++ b/omicron/cli/process.py @@ -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() From eefed7f61adb0500907bfcfeb4003f3286bdb9ee Mon Sep 17 00:00:00 2001 From: Duncan Macleod Date: Fri, 1 Sep 2023 09:23:54 -0700 Subject: [PATCH 3/3] omicron-process: set --outdir for omicron-archive workflow doesn't see $OMICRON_ARCHIVE or even $HOME, so need to set it explicitly --- omicron/cli/process.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/omicron/cli/process.py b/omicron/cli/process.py index 41bee25..ff297fc 100644 --- a/omicron/cli/process.py +++ b/omicron/cli/process.py @@ -1268,9 +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