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.
Thanks in advance for your help
Lorenzo
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