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

Jakob-Stadler-Platz 7

D-78467 Konstanz

Phone: +49 (0) 7531-81604110

Fax:     +49 (0) 7531-816081

Email:  s.kastens@gatc-biotech.com

http://www.gatc-biotech.com

http://www.twitter.com/gatcbiotech

http://www.facebook.com/gatcbiotech

http://www.xing.com/companies/gatcbiotechag

GATC Biotech AG
Chairman Supervisory Board: Fritz Pohl
Board of Directors: Peter Pohl, Thomas Pohl, Dr. Marcus Benz
UID: DE 142 315 733 | Registration: Konstanz, HRB 1757 | Registered Office: Konstanz

The information contained in this email is intended solely for the addressee. Access to this email by anyone else unauthorized. If you are not the intended recipient, any form of disclosure, reproduction, distribution or any action taken or refrained from in reliance on it, is prohibited and may be unlawful. Please notify the sender immediately. The content of this email is not legally binding unless confirmed by letter.

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