Bash R on Oracle Grid Engine (JHPCE)

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<PROJECT>_v<NUM>.sh or for a R bash file to run the v1 R script in the 018 project (I explain my project organization in another post).

Bash Stata on Oracle Grid Engine (JHPCE)

Some statistical jobs are either too memory-greedy or computationally intensive to run on a local machine. At the Johns Hopkins Medical Institutes (JHMI), researchers have access to a Linux cluster running a Oracle Grid Enginge (previously called the Sun Grid Engine). Jobs on the Joint HPC Exchange (JHPCE) can be run interactively with the qrsh command or through a qsub bash submission. JHPCE also has Stata-MP installed so that’s another reason why I use it for larger jobs.