drmaa-python wait not playing nice with Condor

[leipzig]

condor_version 
$CondorVersion: 7.8.5 Oct 09 2012 BuildID: 68720 $
$CondorPlatform: x86_64_rhap_6.3 $

using the example3 (example1.py, example1.1.py, example2.py, and example2.1.py all work fine)

./example3.py
Creating job template
DEBUG: Join_files is set
DEBUG: drmaa_join_files: y
DEBUG: drmaa_v_argv: ?:i
DEBUG: drmaa_remote_command: /home/leipzigj/drmaa-python/examples/sleeper.sh
Your job has been submitted with id variome.chop.edu.108921.0
DEBUG: -> wait_job(variome.chop.edu.108921.0)
DEBUG: Sleeping for a momentDEBUG: Sleeping for a momentDEBUG: Sleeping for a momentDEBUG: Sleeping for a momentDEBUG: Resulting stat value is 200
DEBUG: RUsage data: submission_time=1433953498, start_time=1433953499, end_time=1433953502
DEBUG: Unreferencing job variome.chop.edu.108921.0
DEBUG: Not removing job variome.chop.edu.108921.0 yet (ref_count: 1 -> 0)
DEBUG: Marking job variome.chop.edu.108921.0 as DISPOSED
DEBUG: Removing job info for variome.chop.edu.108921.0 (0x26e58c0, 0x26e58c0, (nil), 1)
DEBUG: <- wait_job(variome.chop.edu.108921.0)
Traceback (most recent call last):
  File "./example3.py", line 29, in <module>
    main()
  File "./example3.py", line 21, in main
    retval = s.wait(jobid, drmaa.Session.TIMEOUT_WAIT_FOREVER)
  File "/nas/is1/bin/variome-env/lib/python3.3/site-packages/drmaa/session.py", line 480, in wait
    c(drmaa_wcoredump, byref(coredumped), stat)
  File "/nas/is1/bin/variome-env/lib/python3.3/site-packages/drmaa/helpers.py", line 299, in c
    return f(*(args + (error_buffer, sizeof(error_buffer))))
  File "/nas/is1/bin/variome-env/lib/python3.3/site-packages/drmaa/errors.py", line 151, in error_check
    raise _ERRORS[code - 1](error_string)
drmaa.errors.InvalidArgumentException: code 4: Invalid argument

[pidupuis]

Have you found a solution?

[leipzig]

no sorry haven't thought about this for years. switched to snakemake.

[pidupuis]

I'm using snakemake + HTCondor too but still the same error :/
How did you figure it out?

[leipzig]

well we were just running condor on top of SGE. i think snakemake DRMAA will work fine with SGE. The problem must be condor.

[stverhae]

Same issue here.
problem is, the straight up condor_wait command also returns with an error(1) when you point it to a log file saying "no jobs found". possibly this is deeper routed than python libdrmaa ..

[stverhae]

Alright, found the issue, when doing a wait in drmaa-python it asks for both info on coredump and termsignal, even when the job exited normally without a signal.
The drmaa.h file describes this: Returns the name of the signal that terminated the process if the drmaa_wifsignaled() returned non-zero.
fixed by actually checking if threre was a signal/abort before calling these functions.

On sge and slurm drmaa libs these called would not complain, but the drmaa stat specify we need to check so this is the correct way to go.

I'll be making a PR shortly ...

@pidupuis