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 o...@hpc.ufl.edu wrote:
On Aug 6, 2012, at 1:01 PM, Wood, James, D james.wo...@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_as_the_Real_User.
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
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