This might be a better question for the mailing list of this specific cluster, but I believe the version of fsl_sub on the Wash U cluster still works with PBS (I helped modify it to do this some years ago).
Peace, Matt. On 2/5/15, 11:48 AM, "Ramirez San Martin, Carolina" <ramirezsanmart...@wustl.edu> wrote: >Hi, > >I¹m starting to use HCP Pipelines in the WashU CHPC cluster, and got a >bit confused on the way jobs are submitted to it, so I¹d like to confirm >a few details about this. >As far as I could tell, since the cluster takes PBS jobs, and because >fsl_sub works only in Sun Grid Engines(?), the way to run a Pipelines >script >would be creating a PBS script that executes the Pipelines script with >the Œ‹runlocal¹ command line option. >For example, to run the PreFreeSurferPipelineBatch.sh script, the PBS >script command would be '.PreFreeSurferPipelineBatch.sh ‹runlocal' > >>From the code(*) I assume that given this command, the fsl_sub queuing >>is bypassed, and when the job is submitted to the cluster it will use >>the options specified in the PBS script. >Is that correct? > >Thanks, >Carolina. > >______________________ >(*) For example, these lines in PreFreeSurferPipelineBatch.sh: >"if [ -n "${command_line_specified_run_local}" ] ; then > echo "About to run >${HCPPIPEDIR}/PreFreeSurfer/PreFreeSurferPipeline.sh" > queuing_command="" > else > echo "About to use fsl_sub to queue or run >${HCPPIPEDIR}/PreFreeSurfer/PreFreeSurferPipeline.sh" > queuing_command="${FSLDIR}/bin/fsl_sub ${QUEUE}" > fi" > > > > > >_______________________________________________ >HCP-Users mailing list >HCP-Users@humanconnectome.org >http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users