Laure QUINTRIC wrote:
Hello,
We are facing some difficulties making the link between galaxy webserver and our cluster.
As galaxy jobs are launched interactively with the user connected on galaxy webserver on this webserver, how is it possible to use PBS qsub command installed on the cluster to perform the job ?
Hi Laure,
The Galaxy server will send jobs out as batch jobs when configured to do so.
Does PBS qsub has to be installed on the webserver also ?
The client software for whatever cluster scheduler you're using (Galaxy is known to work with TORQUE PBS, SGE, and LSF, and should work with other DRMAA-compliant schedulers) will need to be installed on the web server, yes.
In Galaxy documentation, there're the lines below : "The underlying method for execution is “pluggable”. Currently jobs can be executed on the same machine where the GALAXY instance is running, or dispatched to a computational cluster using a standard queue manager (portable batch system [PBS] is used at http://main.g2.bx.psu.edu), however other dispatch strategies can be implemented and plugged in easily"
That page is a bit out of date, the documentation is here:
http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster
Prior to configuring a cluster instance, it's strongly recommended that you implement the other Production Server steps:
http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer
--nate
Can you give more information about these other dispatch strategies ?
Thanks for your help.
Laure
-- Laure QUINTRIC Ifremer - IDM/RIC Technopôle Brest-Iroise 29280 Plouzané Tel: 02 98 22 49 11 - Fax : 02 98 22 46 47 E-mail : Laure.Quintric@ifremer.fr _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev