Running R in Batch Mode on Linux: Output Issues

Question

I'm running an R program on a linux cluster because it is very demanding on my processor. My program is designed to output multiple (around 15) plots as PDF's into the folder from which the program gathers its input.

I want my program to run in the background, and to continue running when I log out of the cluster.

First, I tried this:

cd /Users/The/Folder/With/My/RScript #changed working directory
nohup ./BatchProgram.R &

However, this didn't work because it appended the output to a file called nohup.out, and did not output any of the PDF's I need.

Next I tried this:

cd /Users/The/Folder/With/My/RScript #changed working directory
R #to run R
source(‘BatchProgram.R’) #to run my program

This gave me the desired output, but didn't run the program in the background (and would stop when I logged out of the cluster).

Could someone enlighten me as to how I might obtain the output of my second block of code, while running the program in the background AND causing it to continue running even after I log off of the linux cluster (like the first block of code)?

Many thanks!

Answer 1

nohup runs a command in the background, makes it ignore signals telling it to stop (e.g., when you log off), and redirects the output to a file. But it has to be an executable command: you probably have error messages in nohup.out telling you that BatchProgram.R could not be run.

The following should work:

nohup Rscript ./BatchProgram.R &

Answer 2

The solution is tested, u can try also making 'nohup' version of it, but what will be presented suits me well. Make bash script as follows (for example run_R.sh):

#!/bin/sh
R CMD BATCH --slave ./_your_R_script_name.R &
exit 0

then, make it runnable

chmod +x run_R.sh

and run file like,

./run_R.sh

sometimes you can get only blinking cursor (depends on what linux distro you're working) but simple press "enter" to continue