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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