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

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 pmacshpc@med.upenn.edu.  An up to date software installation list can be obtained on our Wiki page, here.  Listed below are software that has been installed on the cluster centrally, as of May, 2014.  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