...
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export R_LIBS=/scratch/$USER/rlibs
> R
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-suse-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(readxl)
> readxl
readxl_example readxl_progress readxl::
> readxl_example()
[1] "clippy.xls" "clippy.xlsx" "datasets.xls" "datasets.xlsx"
[5] "deaths.xls" "deaths.xlsx" "geometry.xls" "geometry.xlsx"
[9] "type-me.xls" "type-me.xlsx"
> readxl_example('clippy.xlsx')
[1] "/lustre/scratch/shaima0d/rlibs/readxl/extdata/clippy.xlsx" |
You can achieve the same goal using the command line invocation of the R installer:
R batch job on compute node
To run a batch job using R script, simple prepare the script and simply prepare the script are use Rscript in your SLURM jobscript to launch it. The following jobscript demonstrates a hello world example run as a batch job:
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simulation = function(long){
c = rep(0,long)
numberIn = 0
for(i in 1:long){
x = runif(2,-1,1)
if(sqrt(x[1]*x[1] + x[2]*x[2]) <= 1){
numberIn = numberIn + 1
}
prop = numberIn / i
piHat = prop *4
c[i] = piHat
}
return(c)
}
size = 1000
res = simulation(size)
sprintf('calculated Pi value= %f',res[size]) |
The SLURM jobscript to execute the above script will look as follows:
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#!/bin/bash
#SBATCH -n 1
#SBATCH -c 32
#SBATCH --hint=nomultithread
#SBATCH -t 00:10:00
module load cray-R
srun -n 1 --hint=nomultithread Rscript pi.R |