Hi John,
Thanks so much for the reply. After investigating this more today it turns
out, as you might have suspected, SLURM was a red herring. Despite our
attempts to faithfully rsync everything between the two servers it looks
like there was a problem with our workflows in the new database. Strangely
every single workflow that was previously created had a hide action set
for their outputs despite the past and present configuration of the tool
wrappers. Any newly created workflow does not display this behavior. It
happens that the steps with errors were being displayed despite the
workflow weirdness thanks to an error check
in lib/galaxy/jobs/actions/post.py
Thanks again,
Andrew
On Mon, Nov 11, 2013 at 1:39 PM, John Chilton chil...@msi.umn.edu wrote:
This is really odd. I see no code in the job runner stuff at all that
could cause this behavior outside the context of the dataset being
marked hidden as part of a workflow - let alone something DRM specific
that could cause this. Are you rerunning an existing job that has been
marked this way in a workflow. Does this happen if you click new tools
outside the context of workflows or past jobs.
Can you find the corresponding dataset via the history API or in the
database and determine if they indeed are having visible set to False
- this I guess is what should cause a dataset to become hidden?
-John
On Fri, Nov 8, 2013 at 11:40 AM, Andrew Warren anwar...@vbi.vt.edu
wrote:
Hello all,
We are in the process of switching from SGE to SLURM for our galaxy
setup.
We are currently experiencing a problem where jobs that are completely
successful (no text in their stderr file and the proper exit code) are
being
hidden after the job completes. Any job that fails or has some text in
the
stderr file is not hidden (note: hidden not deleted; they can be viewed
by
selecting 'Unhide Hidden Datasets').
Our drmaa.py is at changeset 10961:432999eabbaa
Our drmaa egg is at drmaa = 0.6
And our SLURM version is 2.3.5
And we are currently passing no parameters for
default_cluster_job_runner =
drmaa:///
We have the same code base on both clusters but only observe this
behavior
when using SLURM.
Any pointers or advice would be greatly appreciated.
Thanks,
Andrew
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