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

[Anthoni, Peter (IMK)]

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]]
>> 
>> ______________________________________________
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>> 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.