I've got the following .sh file which can be run on a cluster computer using sbatch:
Shell.sh
#!/bin/bash
#
#SBATCH -p smp # partition (queue)
#SBATCH -N 2 # number of nodes
#SBATCH -n 2 # number of cores
#SBATCH --mem 2000 # memory pool for all cores
#SBATCH -t 5-0:00 # time (D-HH:MM)
#SBATCH -o out.out # STDOUT
#SBATCH -e err.err # STDERR
module load R
srun -N1 -n1 R CMD BATCH ./MyFile.R &
srun -N1 -n1 R CMD BATCH ./MyFile2.R &
wait
My problem is that MyFile.R and MyFile2.R almost look the same:
MyFile.R
source("Experiment.R")
Experiment(args1) # some arguments
MyFile2.R
source("Experiment.R")
Experiment(args2) # some arguments
In fact, I need to do this for about 100 files. Since they all load some R file and then run the experiment with different arguments, I was wondering whether I could do this without creating a new file for each run. I want to run all processes in parallel, so I can't just create one single R file, I think.
My question is: is there some way to run the process directly from the shell, without having an R file for each run? So can I do something like
srun -N1 -n1 R cmd BATCH 'source("Experiment.R"); Experiment(args1)' &
srun -N1 -n1 R cmd BATCH 'source("Experiment.R"); Experiment(args2)' &
wait
instead of the last three lines in shell.sh?
Your batch script should still include 2 lines to start 2 different R processes, but you can pass the arguments on command line using the same file name:
module load R
srun -N1 -n1 Rscript ./MyFile.R args1_1 args1_2 &
srun -N1 -n1 Rscript ./MyFile.R args2_1 args2_2 &
wait
Then within your R file:
source("Experiment.R")
#Get aruments from the command line
argv <- commandArgs(TRUE)
# Check if the command line is not empty and convert values if needed
if (length(argv) > 0){
nSim <- as.numeric( argv[1] )
meanVal <- as.numeric( argv[2] )
} else {
nSim=100 # some default values
meanVal =5
}
Experiment(nSim, meanVal) # some arguments
If you prefer to use R command instead of Rscript, then your batch script should look like:
module load R
srun -N1 -n1 R -q --slave --vanilla --args args1_1 args1_2 < myFile.R &
srun -N1 -n1 R -q --slave --vanilla --args args2_1 args2_2 < myFile.R &
wait
You might need (or not) quotes for "R -q --slave ... < myFile.R" part
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