submit R script to grid in form of batch

Question

I wanted to submit a R job to the grid. I have saved the main R code in MGSA_rand.r In the file callmgsa.r I have written

print('here')
source('/home/users/pegah/MGSA_rand.r')
mgsalooprand($SGE_TASK_ID,382)

And I use the file Rscript.sh to call the job (with the -t parameter I send the value corrseponding to $SGE_TASK_ID)

R CMD BATCH --no-save callmgsa.r

I submit the job like this:

qsub -t 1 -cwd -b y -l  vf=1000m /home/users/pegah/Rscript.sh

I neither get an error nor any output. The job terminates just as I submit it, with out any output. Could you please help me?
thanks, Pegah

Have you tried Rscript as a shebang? That's the usual way for creating scripts: http://stackoverflow.com/questions/750786/whats-the-best-way-to-use-r-scripts-on-the-command-line — flodel, Feb 19 '12 at 12:12
If $SGE_TASK_ID is an environment variable, you need to use `Sys.getenv("SGE_TASK_ID")` to access it within your R script. — flodel, Feb 19 '12 at 12:38

score 0 · Answer 1 · answered Feb 19 '12 at 13:21

0

The variable $SGE_TASK_ID is a shelscript variable. Calling it in R with the same syntax is no going to work. What you could do is use Rscript in stead. From the shellscript you call:

Rscript callmgsa.r $SGE_TASK_ID

In the R script you can catch the command line arguments like:

args <- commandArgs(trailingOnly = TRUE)
print('here')
source('/home/users/pegah/MGSA_rand.r')
mgsalooprand(args[1],382)

This should work...

answered Feb 19 '12 at 13:21

Paul Hiemstra

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thanks for your answer. But where should I call the R itself? I have called it in Rscript.sh. – Pegah Feb 19 '12 at 18:32
You call R using Rscript through the shellscript. – Paul Hiemstra Feb 19 '12 at 22:14
... or put a shebang at the top of your callmgsa.r, something like `#!/path_to_R_install/bin/Rscript` and make the file an executable `chmod +x callmgsa.r`. – flodel Feb 19 '12 at 22:33

submit R script to grid in form of batch

1 Answers1