On Jan 30, 2012, at 7:37 AM, Louise-Amélie Schmitt wrote:
> Hi Nate,
> Thanks for the info!
> I'm trying to understand how the URL for DRMAA works but I don't understand
> how we can set it so it uses a different machine.
> Our Galaxy runner runs on machine A and the cluster is on machine B, where do
> I put B in the URL?
> In the wiki there is this example:
> I'm a bit confused, I would have expected something like:
> like for TORQUE. Did I miss something?
Hrm, I've only used it with SGE, which uses an environment variable to define
the cell location, and LSF, which I don't remember, but I assume it used the
default. I think if you configure the PBS Pro client on the submission host
and point DRMAA_LIBRARY_PATH at the correct libdrmaa, it will use your client
configuration. There are other PBS Pro users on the list who can hopefully
chime in with more details.
> Le 19/01/2012 19:43, Nate Coraor a écrit :
>> On Jan 16, 2012, at 5:22 AM, Louise-Amélie Schmitt wrote:
>>> We want to move Galaxy's jobs from our small TORQUE local install to a big
>>> cluster running PBS Pro.
>>> In the universe_wsgi.ini, I changed the cluster address as follows:
>>> default_cluster_job_runner = pbs:///
>>> default_cluster_job_runner = pbs://sub-master/clng_new/
>>> where sub-master is the name of the machine and clng_new is the queue.
>>> However, I get an error when trying to run any job:
>>> galaxy.jobs.runners.pbs ERROR 2012-01-16 11:10:00,894 Connection to PBS
>>> server for submit failed: 111: Could not find a text for this error, uhhh
>>> This corresponds to the qsub error 111 (Cannot connect to specified server
>>> host) which is, for some reason, caught by pbs_python as an error of its
>>> own (111 not corresponding to any pbs_python error code, hence the
>>> Our guess is that we might need to re-scramble the pbs_python egg with PBS
>>> pro's libraries, is that correct?
>>> If it's the case, what do we have to set as LIBTORQUE_DIR?
>> Hi L-A,
>> pbs_python is only designed for TORQUE, I don't think it is compatible with
>> the PBS Pro API. For that, you need to use the drmaa runner, which uses the
>> FedStage libdrmaa for PBS Pro.
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