I am trying to run a python subprocess inside Singularity container like this:
singularity exec image_name python python_task.py
And within python_task.py it calls this function with cmd:
def run_shell_cmd(cmd):
p = subprocess.Popen(
['/bin/bash', '-o', 'pipefail'], # to catch error in pipe
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
universal_newlines=True,
preexec_fn=os.setsid) # to make a new process with a new PGID
pid = p.pid
pgid = os.getpgid(pid)
log.info('run_shell_cmd: PID={}, PGID={}, CMD={}'.format(pid, pgid, cmd))
t0 = get_ticks()
stdout, stderr = p.communicate(cmd)
rc = p.returncode
t1 = get_ticks()
err_str = (
'PID={pid}, PGID={pgid}, RC={rc}, DURATION_SEC={dur:.1f}\n'
'STDERR={stde}\nSTDOUT={stdo}'
).format(
pid=pid, pgid=pgid, rc=rc, dur=t1 - t0, stde=stderr.strip(), stdo=stdout.strip()
)
if rc:
# kill all child processes
try:
os.killpg(pgid, signal.SIGKILL)
except:
pass
finally:
raise Exception(err_str)
else:
log.info(err_str)
return stdout.strip('\n')
But I am getting this error/exception
Exception: PID=23793, PGID=23793, RC=255, DURATION_SEC=0.1
STDERR=WARNING: Could not lookup the current user's information: user: unknown userid 29931
FATAL: Couldn't determine user account information: user: unknown userid 29931
Any suggestions on how to correct this? I think userid 29931 is not present inside the container which results into this error. But I am not sure how to fix this.