Hi Tim,
that answers my question. I wondered if that '—runlocal’ option forced running
the program in the cluster's login node or if it would still accept PBS job
options. I’ll change the queuing_command variable then.
As a new user of Pipelines and the cluster this has been the only confusing
issue so far.
Thanks!
Carolina.
On Feb 5, 2015, at 14:02, Timothy B. Brown <tbbr...@wustl.edu> wrote:
> Hi Carolina,
>
> In the example scripts provided with the HCP Pipelines, the --runlocal flag
> is intended to be an indication that you do not want to submit a job to a
> scheduler or grid engine (whether PBS or SGE). If you specify the --runlocal
> command line option when invoking one of the example scripts, then fsl_sub is
> not used as part of the command that invokes the actual pipeline script.
>
> For example, if you would like to run the Pre-FreeSurfer pipeline, you might
> do so by invoking the example batch script (or your modified version thereof)
> in a way similar to the following:
>
> $ cd <your-pipeline-scripts-directory>/Examples/Scripts
> $ ./PreFreeSurferPipelineBatch.sh
>
> When invoked this way, the batch script will use the fsl_sub command to
> submit the actual processing to be done via the PreFreeSurferPipeline.sh
> script to a scheduler.
>
> If instead you want to run the processing "locally", then you might do this
> by invoking the example batch script similar to the following:
>
> $ cd <your-pipeline-scripts-directory>/Examples/Scripts
> $ ./PreFreeSurferPipelineBatch.sh --runlocal
>
> To run "locally" means to not run the processing on a grid engine or cluster,
> but instead to run right on whatever machine you are currently logged in to,
> with your shell showing the output from the processing and your shell not
> returning to the command prompt until the processing is complete.
>
> So, to submit things to a cluster/grid engine/scheduler, you would not want
> to use the --runlocal option.
>
> If it turns out that the fsl_sub command doesn't work for you when submitting
> jobs to the CHPC cluster, you can change the line in the batch script that
> sets the queuing_command.
>
> queuing_command="${FSLDIR}/bin/fsl_sub ${QUEUE}"
>
> to something like:
>
> queuing_command="qsub ${QUEUE}"
>
> You may also have to change the definition of the QUEUE variable to name a
> queue that is available for you to use.
>
> Hope that helps,
> Tim
>
> On Thu, Feb 5, 2015, at 12:14, Malcolm Tobias wrote:
>>
>> 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
>>
>>
>> _______________________________________________
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
> --
> Timothy B. Brown
> Business & Technology Application Analyst III
> Pipeline Developer (Human Connectome Project)
> tbbrown(at)wustl.edu
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