[R] To submit R jobs via SLURM

[Erin Hodgess]

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/
> posting-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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