On 12.10.2010 00:55, Lorenzo Cattarino wrote:
Hi R-users,
I have a problem running my R code on a Linux cluster. What I did was
write a .pbs file to instruct the cluster on what to do and how:
#!/bin/sh
#PBS -m ae
#PBS -M uqlca...@uq.edu.au
#PBS -A uq-CSER
#PBS -N job1_lollo
#PBS -l select=1:ncpus=1:NodeType=fast:mem=8GB
#PBS -l walltime=999:00:00
cd $PBS_O_WORKDIR
source /usr/share/modules/init/bash
module load R/2.11.1
/home/uqlcatta/script/diag.sh
The .pbs file calls a .sh file, which is located on my home directory on
the cluster, and which contains the R script (enclosed in " ") to run
#!/bin/bash
echo " mat<- matrix(1:12,nrow=3,ncol=4)
diagonal<- diag(mat)
write.csv(diagonal, file = "diagonal.csv")
"> R_tmp
echo 'source("R_tmp")' | R --vanilla --slave
rm R_tmp
However the cluster sends back to me an error message saying:
Error in write.table(diagonal, file = diagonal.csv, col.names = NA, sep
= ",", :
object 'diagonal.csv' not found
Calls: source ... write.csv -> eval.parent -> eval -> eval ->
write.table
Execution halted
The write.csv command worked on the R consol on my computer, so I don't
know what is the problem here.
You use double quotes inside double quotes. You either have to escape
them or use single quotes (if the shell permits the distinction).
Uwe Ligges
Thanks in advance for your help
Lorenzo
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