## JHPCE

Since most analyses we run involve resources larger than those in our laptops, we typically used a high performance computing environment. Particularly, JHPCE. One of the first things you’ll do is get a JHPCE account. Once you do, you’ll want to get familiarized with many parts of JHPCE. You can see the archive of questions people have asked through bithelp here.

There were a lot of miscellaneous things about using the cluster that might save some confusion if you knew now:

• there’s a 100G storage max on your home directory /users/[yourusername]/, which will likely fill up very quickly. Most of us have directories under the /dcl01 and /dcl02 filesystems, where there is far more space.
• you generally will want to include the -cwd flag in bash scripts. By default, it will default to dumping output files in your home directory, regardless of where you submit the script.
• for scripts/jobs where you are generating large files, you will need to change the max writeable file size. This is the h_fsize flag for bash scripts, which defaults to 10G. See https://jhpce.jhu.edu/knowledge-base/how-to/.

## Windows

• TODO: WinSCP, putty, etc
• git for windows which includes Git Bash. Check rstudio issue 2224 for specifics on how to install Git Bash such that it will work with RStudio terminal.