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"
>
>
>
>
>
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>HCP-Users@humanconnectome.org
>http://lists.humanconnectome.org/mailman/listinfo/hcp-users
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