R help - Jul 2017 - submitting R scripts with command_line_arguments to PBS HPC clusters

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]]

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.

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.