I recently link posted on submitting Stata jobs to a Linux computing cluster running the Oracle Grid Engine. Here’s a quick post on how to submit a R job.
I usually submit a
qsub job by writing
qsub Scripts/NAME_OF_SCRIPT into terminal. My R scripts use the following naming convention:
R_018v1.sh for a R bash file to run the v1 R script in the 018 project (I explain my project organization in another post). The command
qsub Scripts/R018v1.sh will read the follow script.
#!/bin/bash -l #$ -pe local 1 #$ -l mem_free=20G #$ -l h_vmem=22G #$ -m e #$ -M email@example.com #$ -o ofiles #$ -e efiles R CMD BATCH ~/ERGOT/000_workspace/018_pump/try_med.R \ ~/ERGOT/000_workspace/018_pump/01_logs/output.txt
Please refer to my previous post to learn more about the
qsub options in the lines that start with
Now the the single R line. I usually submit from my work root file so here I write out the full paths to the R file and then provide R with where I want the log file output. Note that the
\ could be removed and the two lines combined. That’s it!
Here’s a gist.comments powered by Disqus