Hi Stephan,
I am no expert with PBS but your default_job_runner looks wrong
Instead of default_cluster_job_runner = drmaa://uv100.awi.de/slong/ you should use some PBS specific
paramters for the drmaa:/// part. I am using SGE an specifiy some of the qsub parameters:
default_cluster_job_runner = drmaa://-pe make 16 -q bioinf.q/ this submits the job to our bioinf-cluster
on a node with 16 free slots. So you should check how you submit jobs via commandline with PBS and use
these paramaters for setting drmaa:///
Cheers,
Sascha Kastens
Project Manager
GATC Biotech AG
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D-78467 Konstanz
Phone: +49 (0) 7531-81604110
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Original Message
processed by CONSOLIDATE
Subject:
[galaxy-dev] PBSpro Cluster Server possible?
Sent:
Dienstag, 24. Juli 2012 12:23
From:
Stephan Frickenhaus (Stephan.Frickenhaus@awi.de)
Hello,
I have tried to couple our GALAXY-server (unified, running on a virtual server, ubuntu 12) with our big SGI Cluster-Server uv100 running PBSpro as job system
(pbs_version = PBSPro_11.1.1.112253).
On the GALAXY-server I have installed
ii pbs-drmaa-dev 1.0.10-2 DRMAA for Torque/PBS Pro - devel ii pbs-drmaa1 1.0.10-2 DRMAA for Torque/PBS Pro - runtime
We have the GALAXY-sources installed very recently; job-creation is prepared, but no job is scheduled to our uv100.
Did you ever hear that the libdrmaa.so coming with this package is useful to couple to a PBSpro-server?
The DRMAA_LIBRARY_PATH has been set accordingly to /usr/lib/libdrmaa.so.1.0.10 .
we set default_cluster_job_runner = drmaa://uv100.awi.de/slong/
We also checked that the torque-system on the GALAXY-Server could successfully submit jobs by "qsub" on the PBSpro-server in the slong queue.
Best regards and many thanks in advance, S. Frickenhaus
--
--
Prof. Dr. Stephan Frickenhaus
Hochschule Bremerhaven
An der Karlstadt 8
27568 Bremerhaven
0471-4823-525
0151-1741 1631
Alfred-Wegener-Institut f. Polar- u. Meeresforschung
Am Handelshafen 12
27570 Bremerhaven
stephan.frickenhaus@awi.de
0471-4831-1179 0151-1741 1631
--
Prof. Dr. Stephan Frickenhaus
FB1 - Biotechnologie
Hochschule Bremerhaven
An der Karlstadt 8
27568 Bremerhaven
0471-4823-525
0151-1741 1631
Alfred-Wegener-Institut f. Polar- u. Meeresforschung
Bioinformatik/Rechenzentrum
Am Handelshafen 12
27570 Bremerhaven
stephan.frickenhaus@awi.de
0471-4831-1179
0151-1741 1631