On Sat, Jul 21, 2012 at 6:12 AM, Di Pe <dip...@gmail.com> wrote:
> may be some other people would find this a useful enhancement:
>
> https://bitbucket.org/galaxy/galaxy-central/issue/778/add-new-slurm-drmaa-runner-to-galaxy
>
Hi Di,
I've been testing several grid scheduling software trying to find the
one best fits my group needs. I'm testing slurm now but quickly ran
into this issue:
galaxy.jobs.runners.slurm ERROR 2012-12-10 15:30:12,006 Uncaught
exception queueing job
Traceback (most recent call last):
File "/local/opt/galaxy/galaxy-dist.slurm/lib/galaxy/jobs/runners/slurm.py",
line 165, in run_next
self.queue_job( obj )
File "/local/opt/galaxy/galaxy-dist.slurm/lib/galaxy/jobs/runners/slurm.py",
line 286, in queue_job
job_id = self.ds.runJob(jt)
File
"/local/opt/galaxy/env.python2.7.precise/lib/python2.7/site-packages/drmaa/__init__.py",
line 331, in runJob
_h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate)
File
"/local/opt/galaxy/env.python2.7.precise/lib/python2.7/site-packages/drmaa/helpers.py",
line 213, in c
return f(*(args + (error_buffer, sizeof(error_buffer))))
File
"/local/opt/galaxy/env.python2.7.precise/lib/python2.7/site-packages/drmaa/errors.py",
line 90, in error_check
raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value))
InvalidAttributeFormatException: code 13: invalid date/time format:
As you can see I made sure I was using the latest version of python
drmaa module by installing in a virtualenv. Not only in this error but
by modifying slurm.py so it looks in the right place, I can see the
virtualenv drmaa code is been used instead of Galaxy provided egg:
galaxy.jobs.runners.slurm DEBUG 2012-12-10 15:31:12,410 **** using
local python-drmaa from path
/local/opt/galaxy/env.python2.7.precise/lib/python2.7/site-packages
******
galaxy.jobs.runners.slurm DEBUG 2012-12-10 15:31:12,420 *********
DRMAA IMPORTED ************
galaxy.jobs.runners.slurm DEBUG 2012-12-10 15:31:12,425 Supported DRM
systems: SLURM 2.5.0
galaxy.jobs.runners.slurm DEBUG 2012-12-10 15:31:12,425 Supported
DRMAA implementations: PSNC DRMAA for SLURM 1.0.6
galaxy.jobs.runners.slurm DEBUG 2012-12-10 15:31:12,425 Version 1.0
galaxy.jobs.runners.slurm DEBUG 2012-12-10 15:31:12,425 *********
DRMAA INITIALIZED ************
galaxy.jobs.runners.slurm DEBUG 2012-12-10 15:31:12,426 3 workers ready
galaxy.jobs.handler DEBUG 2012-12-10 15:31:12,426 Loaded job runner:
galaxy.jobs.runners.slurm:DRMAAJobRunner
galaxy.jobs.handler DEBUG 2012-12-10 15:31:12,426 Job runners: local:lwr:slurm
Could you please help me figure out this issue? I'm using latest
galaxy-dist and the most updated version from
https://github.com/FredHutch/IT/tree/master/galaxy/slurm
Thanks,
Carlos
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