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I am trying to submit a job to be executed on cluster. And this is done by writing an sbatch submission script. The job involves opening R 3.1.3 and running the referenced R script on the server.

Here is the shell script I wrote:

#!/bin/bash
#SBATCH --account=810639
#SBATCH --time=1200
#SBATCH --mem-per-cpu=4096
#SBATCH --ntasks=1
#SBATCH --constraint=normalmem
#SBATCH --output=output_%j.txt
#SBATCH --error=error_output_%j.txt
#SBATCH --job-name=AggrigatePIXEL
#SBATCH --partition=ESG_Std
#SBATCH --mail-type=FAIL
#SBATCH [email protected]
# print date and time
module load R/3.1.3
module load geos/gcc/64/3.4.2
module load netcdf/gcc/64/4.3.3
module load gdal/gcc/64/1.11.1
source('AggrigatePIXEL_Forecast_easyVerfication_SERVERversion.R')

When I try to run the shell script (saved as yate.sh) it gives me the following error message:

./yate.sh: line 20: syntax error near unexpected token
'AggrigatePIXEL_Forecast_easyVerfication_SERVERversion.R'

./yate.sh: line 20: 
source('AggrigatePIXEL_Forecast_easyVerfication_SERVERversion.R')

I know the problem is related to opening and executing the .R script which requires running the R program first. Can anybody help me on how I can instruct this in the shell script?

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1 Answer 1

up vote 1 down vote

I'm not familiar with R, but your script is attempting to run as a bash script, not an R script. Change your first line to #!/usr/bin/Rscript or possibly #!/usr/bin/env Rscript. You may need to alter the path to wherever R is on your system.

According to http://stat.ethz.ch/R-manual/R-devel/library/utils/html/Rscript.html it should start like this example:

#! /path/to/Rscript --vanilla --default-packages=utils
args <- commandArgs(TRUE)
res <- try(install.packages(args))
if(inherits(res, "try-error")) q(status=1) else q()`
share|improve this answer
    
I am not trying to run the R script as the bash script @Mel. The bash script is needed to specify the required conditions to the SLURM scheduler which will later start and excute the R script on the cluster after finding a space for my job according to the requirements. –  live fan Jul 6 at 21:17
    
@livefan then after you have done your bash commands, you can call the R script with R -f filename –  Mel Jul 6 at 21:28
    
Thanks @Mel. That is it! it is now working for me, –  live fan Jul 8 at 8:11

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