CODEWITHSUNDEEP
rargumentsslurm
pedro
pedro

Reputation: 463

How to include an argument into the slurm command line?

I work on a data.frame (1000 rows and 3 columns) . I use an argument on the 3rd column (which corresponds to correlations) to select values upper or lower than my argument.

Df<-get(load("test.RData"))

library(optparse)

args <- commandArgs(TRUE)

#get options 

option_list = list(
        make_option(c("-t", "--threshold"), type="double", default=NULL));

opt_parser= OptionParser(usage = "Usage: %prog -f [FILE]",option_list=option_list, description= "Description:")

opt = parse_args(opt_parser)

library(dplyr)

Df=Df%>%filter(corr>opt$threshold)

save(Df, file="corr.Rda")

Then, I would like to use Slurm to run this code.

test.sh

#!/bin/bash
#SBATCH -o job-%A_%a_task.out
#SBATCH --job-name=cor
#SBATCH --partition=normal
#SBATCH --time=1-00:00:00
#SBATCH --mem=1G  
#SBATCH --cpus-per-task=2


#Set up whatever package we need to run with

module load gcc/8.1.0 openblas/0.3.3 R

export FILENAME=~/test.R

Rscript $FILENAME --threshold $1

My question is this one : do I neccesarily need to put an argument on the sbatch command line? For example, if I run sbatch test.sh 0.7 , it will work and I will get the correlations > 0.7. But if I don't want to put an argument, in the goal to get all correlations, I will run ``sbatch test.sh``` , I get 

  Error in getopt(spec = spec, opt = args) : 
  flag "threshold" requires an argument

Edit : if I run sbatch test.sh -1 , I will get all the correlations , but I just would like to know if it possible to don't put any argument and get all the correlations?

Any idea?

Upvotes: 0

Views: 511

Answers (1)

Poshi
Poshi

Reputation: 5762

You are using

Rscript $FILENAME --threshold $1

When you give a parameter like 0.7, it gets substituted by

Rscript $FILENAME --threshold 0.7

But when you give no parameter, then you get:

Rscript $FILENAME --threshold

And as the message says, --threshold requires an argument.

You can test $1 for its existence and only pass the --threshold argument when required:

threshold_args=()
if [ -n "$1" ]
then
    threshold_args+=("--threshold" "$1")
fi
Rscript $FILENAME "${threshold_args[@]}"

Upvotes: 1

Related Questions