fsl_sub should work with our cluster via PBS in almost all cases*
Perhaps the authors of the PreFreeSurferPipelineBatch.sh script could comment
on what the -runlocal flag is intended to do and whether it's been tested on
our cluster?
Malcolm
*it doesn't properly support submitting to the GPU queues.
On Thursday 05 February 2015 12:05:59 Ramirez San Martin, Carolina wrote:
> I contacted Malcolm at the CHPC to ask about this already, and he told me
> that fsl_sub had been somewhat customized. Yet, when I tried to execute the
> scripts without the —runlocal option, I got an error and the job was stopped.
>
> I guess i’m trying to figure out if the —runlocal flag is the best solution
> in this context
>
> Thanks.
>
>
> On Feb 5, 2015, at 11:53, Glasser, Matthew <glass...@wusm.wustl.edu> wrote:
>
> > 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
> >
>
--
Malcolm Tobias
314.362.1594
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