R programming - submitting jobs on a multiple node linux cluster using PBS

Question

I am running R on a multiple node Linux cluster. I would like to run my analysis on R using scripts or batch mode without using parallel computing software such as MPI or sn

Answer 1

This was an answer to a related question - but it's an answer to the comment above (as well).

For most of our work we do run multiple R sessions in parallel using qsub (instead).

If it is for multiple files I normally do:

while read infile rest
do
qsub -v infile=$infile call_r.pbs 
done < list_of_infiles.txt

call_r.pbs:

...
R --vanilla -f analyse_file.R $infile
...

analyse_file.R:

args <- commandArgs()
infile=args[5]
outfile=paste(infile,".out",sep="")...

Then I combine all the output afterwards...