Question

I have a script test.R that takes arguments arg1, arg2 and outputs a arg1-arg2.csv file.

I would like to run the test.R in 6 parallel sessions (i am on a 6 core CPU) and in the background. How can I do it?

I am on linux

Answer 1

You did not provide a reproducible example so I am making one up. As you are on Linux, I am also swicthing to littler which was after all writtten for the very purpose of scripting with R.

#!/usr/bin/env r
#
# a simple example to install one or more packages

if (is.null(argv) | length(argv) != 2) {
    cat("Usage: myscript.r arg1 arg2\n")
    q()
}

filename <- sprintf("%s-%s.csv", argv[1], argv[2])
Sys.sleep(60)   # do some real work here instead
write.csv(matrix(rnorm(9), 3, 3), file=filename)

and you can then lauch this either from the command-line as I do here, or from another (shell) script. The key is the & at the end to send it in the background:

edd@max:/tmp/tempdir$ ../myscript.r a b &
[1] 19575
edd@max:/tmp/tempdir$ ../myscript.r c d &
[2] 19590
edd@max:/tmp/tempdir$ ../myscript.r e f &
[3] 19607
edd@max:/tmp/tempdir$

The [$n] indicates how process how been launched in the background, the number that follows is the process id which you can use to monitor or kill. After a little while we get the results:

edd@max:/tmp/tempdir$ 
[1]   Done                    ../myscript.r a b
[2]-  Done                    ../myscript.r c d
[3]+  Done                    ../myscript.r e f
edd@max:/tmp/tempdir$ ls -ltr
total 12
-rw-rw-r-- 1 edd edd 192 Jun 24 09:39 a-b.csv
-rw-rw-r-- 1 edd edd 193 Jun 24 09:40 c-d.csv
-rw-rw-r-- 1 edd edd 193 Jun 24 09:40 e-f.csv
edd@max:/tmp/tempdir$ 

You may want to read up on Unix shells to learn more about &m the fg and bg background s etc.

Lastly, all this can a) also be done with Rscript though picking arguments is slightly different and b) there are CRAN packages getopt and optparse to facilitate working with command-line arguments.