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 uqlcatta@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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