Hi Knut - I modified fsl_sub to work on our own PBS cluster. This modified version is fsl_sub_seychelles. Anything that works with the original fsl_sub should also work with fsl_sub_seychelles. You can modify either of the two to make it work on your cluster. If you do make it more general to work on more clusters, we'll be happy to incorporate the changes but there's no way for us to know what would work on every possible local setup.
Good luck! a.y On Fri, 27 Apr 2012, Knut J Bjuland wrote: > Hi Anastasia > > > I think this hack was also added > > ## Steinar, steinar, commnet out this to fool the program to run under PBS > ## date 20 april 2012 > ## hack > > #if ($?PBS_JOBID) then > # echo "ERROR: Do not submit $ProgName as a job with pbsubmit or qsub." > # echo "ERROR: Run it directly on the command line." > # echo "ERROR: If run on the cluster, $ProgName will submit the jobs > for you." > # echo "ERROR: Each subject listed in your dmrirc will be submitted as a > job." > # exit 1 > #endif > > ## end hack > > Should I revert those changes? I changed to fsl_sub because the cluster I am > using had my modifcation to fsl_sub. Should I change back? > > Knut J > > > > > > > > On 04/27/2012 05:06 PM, Anastasia Yendiki wrote: >> >> Hi Knut - If I understand correctly, your modification was replacing >> "fsl_sub_seychelles" with "fsl_sub"? >> >> a.y >> >> On Fri, 27 Apr 2012, Knut J Bjuland wrote: >> >> > Hi >> > >> > I am trying to run Trac-all on a cluster with PBS/torque. The trac-all >> > scripts was modified to run with qsub, but >> > the second stage in Trac-all crash without getting finished. This is >> > tested with the tutorial data. I am >> > enclosing the modified trac-all script. >> > >> > Best regard >> > >> > Knut J Bjuland >> > NTNU >> > >> > >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
