jobName lost when drmaa used with real user use
When I use the real user method for running drmaa jobs as the real user, the jobName value gets lost. It's kind of annoying, but not a show stopper. The other values (outputPath, errorPath, remoteCommand, nativeSpecification, etc.) are all there, but not jobName. This doesn't happen when the drmaa jobs are run using the default Galaxy user. Weird. David Hoover Helix Systems Staff
On Oct 2, 2012, at 3:56 PM, David Hoover wrote:
When I use the real user method for running drmaa jobs as the real user, the jobName value gets lost. It's kind of annoying, but not a show stopper. The other values (outputPath, errorPath, remoteCommand, nativeSpecification, etc.) are all there, but not jobName.
This doesn't happen when the drmaa jobs are run using the default Galaxy user. Weird.
Hi David, This has been fixed in changeset 7823:62fbfc687692. Thanks for letting us know. --nate
David Hoover Helix Systems Staff ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
David, For instances that run jobs under real user ids I think the job_name variable in drmaa.py does not need the username component in this case anymore as the batch system takes care of that and the resulting job name looks cleaner in the qstat output. I use @@ -184,10 +183,12 @@ ofile = "%s.drmout" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) efile = "%s.drmerr" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) ecfile = "%s.drmec" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) - job_name = "g%s_%s_%s" % ( job_wrapper.job_id, job_wrapper.tool.id, job_wrapper.user ) + job_name = "g%s_%s" % ( job_wrapper.job_id, job_wrapper.tool.id ) The above could be made conditional depending on whether the instance runs jobs under real user ids or the galaxy user if Nate decides to put something like this into the upstream codebase. Regards, Alex On Oct 3, 2012, at 11:51 AM, Nate Coraor <nate@bx.psu.edu> wrote:
On Oct 2, 2012, at 3:56 PM, David Hoover wrote:
When I use the real user method for running drmaa jobs as the real user, the jobName value gets lost. It's kind of annoying, but not a show stopper. The other values (outputPath, errorPath, remoteCommand, nativeSpecification, etc.) are all there, but not jobName.
This doesn't happen when the drmaa jobs are run using the default Galaxy user. Weird.
Hi David,
This has been fixed in changeset 7823:62fbfc687692. Thanks for letting us know.
--nate
David Hoover Helix Systems Staff ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
On Oct 3, 2012, at 12:57 PM, Oleksandr Moskalenko wrote:
David,
For instances that run jobs under real user ids I think the job_name variable in drmaa.py does not need the username component in this case anymore as the batch system takes care of that and the resulting job name looks cleaner in the qstat output. I use
@@ -184,10 +183,12 @@ ofile = "%s.drmout" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) efile = "%s.drmerr" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) ecfile = "%s.drmec" % os.path.join(job_wrapper.working_directory, job_wrapper.get_id_tag()) - job_name = "g%s_%s_%s" % ( job_wrapper.job_id, job_wrapper.tool.id, job_wrapper.user ) + job_name = "g%s_%s" % ( job_wrapper.job_id, job_wrapper.tool.id )
The above could be made conditional depending on whether the instance runs jobs under real user ids or the galaxy user if Nate decides to put something like this into the upstream codebase.
Sure. Committed in e4e1c621b025. --nate
Regards,
Alex
On Oct 3, 2012, at 11:51 AM, Nate Coraor <nate@bx.psu.edu> wrote:
On Oct 2, 2012, at 3:56 PM, David Hoover wrote:
When I use the real user method for running drmaa jobs as the real user, the jobName value gets lost. It's kind of annoying, but not a show stopper. The other values (outputPath, errorPath, remoteCommand, nativeSpecification, etc.) are all there, but not jobName.
This doesn't happen when the drmaa jobs are run using the default Galaxy user. Weird.
Hi David,
This has been fixed in changeset 7823:62fbfc687692. Thanks for letting us know.
--nate
David Hoover Helix Systems Staff ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (3)
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David Hoover -
Nate Coraor -
Oleksandr Moskalenko