Perelman School of Medicine at the University of Pennsylvania
Perelman School of Medicine at the University of Pennsylvania

High Performance Computing Penn Medicine Academic Computing Services

Software & OS

Cluster Operating System is Red Hat Enterprise Linux v. 6.4, and this version is installed on all compute nodes.  Alternate OS installations are available on an as-needed basis, by request only. 

Cluster software is either loaded on the individual node hard drives by HPC staff, providing the best performance, or is run from a client’s share on the SONAS file system, generally not requiring any HPC staff involvement.  Clients needing software installation should place a service request in the PMACS HPC queue, or e-mail to psom-pmacshpc@pennmedicine.upenn.edu.  An up to date software installation list can be obtained on our Wiki page, here.  Below is a partial list of software packages that have been installed on the cluster centrally.  Please click on the links below for more information on the software installation, location, and use.  

BLAST+

Bowtie

Cufflinks

Devtoolset-2

Java

Environment Modules

Mpich2

NAMD-2.9-Linux-x86_64-multicore

openMPI

Perl

Picard-1.96

Python

R

Ruby-1.8.7-p374

Ruby-1.9.3-p448

RUM-2.0.5_05

Samtools-0.1.19

STAR-2.3.0e

TopHat