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Add environment variables and shell checks for postscripts #467

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merged 2 commits into from
Jul 28, 2024
Merged

Add environment variables and shell checks for postscripts #467

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d1a7473
Export environment variables and check shell requirements for postscr…
blimlim Jul 26, 2024
931785c
PEP8 fixes
blimlim Jul 26, 2024
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9 changes: 7 additions & 2 deletions payu/experiment.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@
from payu.fsops import mkdir_p, make_symlink, read_config, movetree
from payu.fsops import list_archive_dirs
from payu.fsops import run_script_command
from payu.fsops import needs_subprocess_shell
from payu.schedulers.pbs import get_job_info, pbs_env_init, get_job_id
from payu.models import index as model_index
import payu.profilers
Expand Down Expand Up @@ -826,15 +827,19 @@ def profile(self):

def postprocess(self):
"""Submit any postprocessing scripts or remote syncing if enabled"""

# First submit postprocessing script
if self.postscript:
self.set_userscript_env_vars()
envmod.setup()
envmod.module('load', 'pbs')

cmd = 'qsub {script}'.format(script=self.postscript)

cmd = shlex.split(cmd)
sp.check_call(cmd)
if needs_subprocess_shell(cmd):
sp.check_call(cmd, shell=True)
else:
sp.check_call(shlex.split(cmd))

# Submit a sync script if remote syncing is enabled
sync_config = self.config.get('sync', {})
Expand Down
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