On Sat, Jul 21, 2012 at 6:12 AM, Di Pe dipeit@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-ru...
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