What is JHPCE? JHPCE or the Joint High-Performance Computing Exchange is a computation resource available to members at the Johns Hopkins Medicial Institute (JHMI). Several research groups across the School of Public Health and School of Medicine tap into the power of JHPCE to run computationally expensive analyses - our transplant epidemiology group included. The JHPCE introduction to new users describes some use cases. This blog will be a brief introduction to getting your system ready to log onto the JHPCE cluster to use Stata-MP.
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 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).
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.