I am a systems administrator for a cluster, and we use Torque and Moab as the resource manager and scheduler. I read that you can use drmaa to submit jobs as a different user other than the 'galaxy' user using the external scripts, but I haven't yet found a way to do it with torque. Is there a solution that you could suggest? I am guessing that the pbs runner process would have to be forked and use setuid to be able to run under the user. This would be great, because it would make it easier to keep track of user time utilization.
On Aug 6, 2012, at 1:01 PM, "Wood, James, D" james.wood3@topper.wku.edu wrote:
I am a systems administrator for a cluster, and we use Torque and Moab as the resource manager and scheduler. I read that you can use drmaa to submit jobs as a different user other than the 'galaxy' user using the external scripts, but I haven't yet found a way to do it with torque. Is there a solution that you could suggest? I am guessing that the pbs runner process would have to be forked and use setuid to be able to run under the user. This would be great, because it would make it easier to keep track of user time utilization.
Hi James,
I am in the same situation as you are. The basic documentation is at http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster#Submitting_Jobs_a.... However, there could be some site-specific issues with that configuration. For instance the user names in my instance do not correspond to the uid part of the galaxy username (email address), which is what released galaxy-dist code assumes. Fortunately, Nate and Scott from the Core Galaxy Team helped me get through almost all of the issues while we were at the Galaxy Community Conference. I am still working through the single remaining issue of drmaa not passing modified resource requests to Torque, but the rest appears to work stably with Torque 2.5.12.
Regards,
Alex
It looks like the Torque provided libdrmaa.so does not support DRMAA native options. I built a 3rd party library (http://apps.man.poznan.pl/trac/pbs-drmaa/wiki) and was able to successfully run text galaxy jobs under a real user id with a correct resource request specified through the dynamic runner as a native DRMAA option. The only remaining step is to populate the galaxy_user.username from our LDAP. All modified galaxy code has been provided to the core Galaxy Team by the way.
Cheers,
Alex
On Aug 6, 2012, at 1:16 PM, Oleksandr Moskalenko om@hpc.ufl.edu wrote:
On Aug 6, 2012, at 1:01 PM, "Wood, James, D" james.wood3@topper.wku.edu wrote:
I am a systems administrator for a cluster, and we use Torque and Moab as the resource manager and scheduler. I read that you can use drmaa to submit jobs as a different user other than the 'galaxy' user using the external scripts, but I haven't yet found a way to do it with torque. Is there a solution that you could suggest? I am guessing that the pbs runner process would have to be forked and use setuid to be able to run under the user. This would be great, because it would make it easier to keep track of user time utilization.
Hi James,
I am in the same situation as you are. The basic documentation is at http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster#Submitting_Jobs_a.... However, there could be some site-specific issues with that configuration. For instance the user names in my instance do not correspond to the uid part of the galaxy username (email address), which is what released galaxy-dist code assumes. Fortunately, Nate and Scott from the Core Galaxy Team helped me get through almost all of the issues while we were at the Galaxy Community Conference. I am still working through the single remaining issue of drmaa not passing modified resource requests to Torque, but the rest appears to work stably with Torque 2.5.12.
Regards,
Alex ___________________________________________________________ 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:
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Oleksandr Moskalenko -
Wood, James, D