[R] submitting R scripts with command_line_arguments to PBS HPC clusters

[Bogdan Tanasa]

Dear Peter, that is very very helpful, many thanks for your suggestions ;) !

On Tue, Jul 11, 2017 at 11:34 PM, Anthoni, Peter (IMK) <
peter.anthoni at kit.edu> wrote:

> Hi,
>
> The problem is most likely, you need to call a R CMD BATCH with your
> arguments and the R-script inside of a shell script that you submit to your
> qsub.
> Unfortunately we don't use qsub anymore so can't test it, but it should be
> as follows:
>
> R-script eg. test.R:
> > ##First read in the arguments listed at the command line
> > args=(commandArgs(TRUE))
> >
> > ##args is now a list of character vectors
> > ## First check to see if arguments are passed.
> > if(length(args)==0){
> >   stop("no args specified")
> > }
> > ## Then cycle through each element of the list and evaluate the
> expressions.
> > for(i in 1:length(args)){
> >   print(args[[i]])
> >   eval(parse(text=args[[i]]))
> > }
> > print(TUMOR)
> > print(GERMLINE)
> > print(CHR)
>
>
> qsub shell script test.sh:
> > #!/bin/bash
> >
> > #Note: the single quote '...' around the --args ... "..." "..." is
> important!
> > R CMD BATCH --no-save --no-restore '--args TUMOR="tumor.bam"
> GERMLINE="germline.bam" CHR="chr22"' test.R test.Rout
>
> then you submit with a qsub with all the options you specified the test.sh
> qsub .... test.sh
>
> cheers
> Peter
>
>
>
> > On 12. Jul 2017, at 03:01, Jeff Newmiller <jdnewmil at dcn.davis.ca.us>
> wrote:
> >
> > This sounds like an operating system specific question, in that "submit
> the R script to a PBS HPC scheduler" would be the kind of action that would
> run R with very different environment variables and possibly different
> access credentials than your usual interactive terminal.  A thorough
> reading of the "Installation and Administration Guide" and some study of
> your HPC documentation are in order.
> > --
> > Sent from my phone. Please excuse my brevity.
> >
> > On July 11, 2017 5:25:20 PM PDT, Bogdan Tanasa <tanasa at gmail.com> wrote:
> >> Dear all,
> >>
> >> please could you advise me on the following : I've written a R script
> >> that
> >> reads 3 arguments from the command line, i.e. :
> >>
> >> " args <- commandArgs(TRUE)
> >> TUMOR <- args[1]
> >> GERMLINE <- args[2]
> >> CHR <- args[3] ".
> >>
> >> when I submit the R script to a PBS HPC scheduler, I do the following
> >> (below), but ... I am getting an error message.
> >> (I am not posting the error message, because the R script I wrote works
> >> fine when it is run from a regular terminal ..)
> >>
> >> Please may I ask, how do you usually submit the R scripts with command
> >> line
> >> arguments to PBS HPC schedulers ?
> >>
> >> qsub -d $PWD -l nodes=1:ppn=4 -l vmem=10gb -m bea -M tanasa at gmail.com \
> >> -v TUMOR="tumor.bam",GERMLINE="germline.bam",CHR="chr22" \
> >> -e script.efile.chr22 \
> >> -o script.ofile.chr22 \
> >> script.R
> >>
> >> Thank you very very much  !
> >>
> >> -- bogdan
> >>
> >>      [[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.
> >
> > ______________________________________________
> > 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.
>
>

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