We are using PBS locally and had our cluster admin set this up, but I think the same principle applies across most job runners/mgrs. As Peter mentioned, there should be a way for cluster admin to add your server as an allowed submitting host, the PBS variant is here: http://www.clusterresources.com/torquedocs/2.1jobsubmission.shtml#submitacce... There also may be additional tweaking required due to firewalls, etc. After that, run some simple job submission tests (we ran a simple 'sleep 60') from your server to check whether you can submit jobs, see submitted job status, etc. I found it helped when debugging to log in on both Galaxy server and cluster sides, and if the cluster admin allows it monitor the job manager logs on the cluster side if you run into problems (we found this very handy when debugging local LDAP issues). chris On May 2, 2012, at 4:16 PM, Anne Pajon wrote:
Yes we do have an LSF cluster. Thanks indeed for all the information, Peter. I'll contact our cluster administrator tomorrow and keep you posted on my progress.
Kind regards, Anne.
On 2 May 2012, at 22:07, Peter Cock wrote:
On Wed, May 2, 2012 at 9:58 PM, Anne Pajon <Anne.Pajon@cancer.org.uk> wrote:
Hi Peter,
Thanks for the clarification, it is really helpful.
Would you mind sharing what needs to be done in term of configuration and instalation to transform the galaxy server into a submitting job to the cluster? Thanks.
You said you have an LSF cluster - so I have no idea, sorry :(
We're using SGE here. I'm presuming similar concepts apply - in our case a key step was getting qsub/qstat/qdel to work from the Galaxy server as well as the cluster head node - which required our cluster administrator to setup our Galaxy server as an SGE submit node.
Regards,
Peter
-- Anne Pajon, Ph.D. Cancer Research UK - Cambridge Research Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon@cancer.org.uk | +44 (0)7958 511 353
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