[R] To submit R jobs via SLURM

Sema Atasever s.atasever at gmail.com
Tue Oct 4 11:49:21 CEST 2016


Thank you very much for your help.

On Mon, Oct 3, 2016 at 10:35 PM, Erin Hodgess <erinm.hodgess at gmail.com>
wrote:

> Get a SLURM batch file from someone there and make the appropriate changes
> to it.  Best way to learn.
>
>
>
> On Mon, Oct 3, 2016 at 2:10 PM, Dominik Schneider <dosc3612 at colorado.edu>
> wrote:
>
>> I typically call Rscript inside an sbatch file.
>>
>> *batch_r.sh*
>> #! /bin/bash
>>
>> cd /home/<myusername>/aso_regression_project #make sure you change to
>> your
>> correct working directory
>> Rscript scripts/run_splitsample-modeling.R
>>
>>
>> and on the commandline of the login node:
>> sbatch batch_r.sh
>>
>>
>> There are lots of slurm configurations you can specify. Google for them.
>> Just add these under the first line and modify as needed:
>> #SBATCH --qos=
>> #SBATCH --mem=
>> #SBATCH --mail-type=begin,end,abort
>> #SBATCH --mail-user=userid at email.com
>> #SBATCH --time=
>> #SBATCH --nodes=
>> #SBATCH --job-name=myjob
>> #SBATCH --output=/home/<username>/run-%A_%a.Sout #special output filename
>>
>>
>> Dominik
>>
>>
>> On Mon, Oct 3, 2016 at 3:03 AM, Sema Atasever <s.atasever at gmail.com>
>> wrote:
>>
>> > Dear Authorized Sir / Madam,
>> >
>> > I have an R script file in which it includes this lines:
>> >
>> > How can i to submit this R jobs via SLURM? Thanks in advance.
>> >
>> > *testscript.R*
>> > data=read.table("seqDist.50", header=FALSE)[-1]
>> > attach(data)
>> > d=as.matrix(data)
>> > library(cluster)
>> > cluster.pam = pam(d,6)
>> > table(cluster.pam$clustering)
>> >
>> > filenameclu = paste("outputfile", ".txt")
>> > write.table(cluster.pam$clustering, file=outputfile,sep=",")
>> >
>> >         [[alternative HTML version deleted]]
>> >
>> > ______________________________________________
>> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide http://www.R-project.org/
>> > posting-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.
>> >
>>
>>         [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posti
>> ng-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
>
> --
> Erin Hodgess
> Associate Professor
> Department of Mathematical and Statistics
> University of Houston - Downtown
> mailto: erinm.hodgess at gmail.com
>

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