HPC:Main Page

High Performance Computing at PennMedicine is supported by the Enterprise Research Applications (ERA) group within Penn Medicine Academic Computing Services (PMACS). Please send requests and report problems to Jason/Rikki/Anand.

Other Pages

• Connecting to the PMACS cluster
• User Guide
• Available Software
• PMACS Archive System

PMACS ERA

The Enterprise Research Applications (ERA) group within Penn Medicine Academic Computing Services (PMACS) is a small and diverse team of individuals who are focused on providing High Performance and Research Computing Support to the faculty and staff at the University of Pennsylvania.

PMACS ERA Team:

• Jason Hughes, Director, Enterprise Research Applications
• Rikki Godshall, Enterprise IT Architect
• Anand Srinivasan, Sr. IT Project Leader

Weekly Office Hours

Have questions about the PMACS HPC? Come see us in person! We will have weekly Office Hours at the following location and time:

• Location : Smilow Center for Translational Research (SCTR, formerly TRC)
• Room : 10-120
• Day/Time : Thursdays / 3-4PM Eastern Time

Note: On Wednesday, September 29th, 2015, we will meet in TRC 10-100; No meeting on Thursday, October 1st, 2015.

About the PMACS Cluster

The PMACS HPC facility opened in April of 2013 to meet the increasing growth in genomics processing and storage, as well as growth in other scientific areas requiring computational capacity such as imaging and bio-statistics/bioinformatics. The cluster is managed by the Enterprise Research Applications (ERA) team within Penn Medicine Academic Computing Services (PMACS), and is located at the Philadelphia Technology Park, a Tier-3, SSAE 16/SAS 70 Type II Audit compliant colocation/data center facility.

The hardware of the PMACS Cluster comprises of:

• 1 dedicated master node
• 144 IBM iDataPlex cluster nodes which serve Compute nodes
• Each compute node has:
  • Two eight-core Intel E5-2665 2.4Ghz Xeon Processors, with hyperthreading turned on (so 32 threads per node)
  • 196-256 GB of RAM each (12-16GB per physical core, depending on the node)
  • 500 GB of internal storage
• 1 dedicated "Big-Memory" machine - 64 cores & 1.5TB RAM
• 1.6 PetaBytes of total usable shared disk storage provided via an eight-node IBM Scale out Network Attached Storage (SONAS) system
• 1.8 PetaBytes Archival storage
• All compute and storage connected via 10GigE interconnect
• Dedicated 10GigE PennNet link from campus to the datacenter

Computational job scheduling/queuing and cluster management is orchestrated by the IBM Platform Computing suite of products.

Costs

The PennHPC baseline cost structure is fee-for-service based around the service-center model. Below are the costs associated with using the PMACS cluster as of 4/30/2014:

• $0.035/computational/vCore slot hour
• $0.055/GB/month for Disk usage
• $0.015/GB/month for Archive storage
• $95/hour for consulting services (excludes account setup)
• No charges to maintain an account; charges are billed on an as-consumed basis only. If data is left behind by a user who longer uses the cluster, charges will be billed for disk usage until the data is deleted from the account.

Accounts

For Account requests please contact Jason Hughes, Rikki Godshall or Anand Srinivasan

Please be sure to include the following information in your account request email:

• User Info:
  • User's Full Name:
  • User's Email:
  • User's PennKey:
  • User's PennID:
  • User's Status: Student/Post-Doctoral Fellow
  • Data stored on the cluster requires HIPPA/other compliance?: Yes/No

• PI Info:
  • PI's Full Name:
  • PI's Email:
  • PI's PennKey (if exists):

• Business Administrator (BA) info:
  • BA's Name:
  • BA's Email:
  • Does BA have access to the Med. School's SAM billing system?: Yes/No
  • SAM account Number/26-digit Budget code:
  • 26-digit code associated with User's SAM account?: Yes/No
  • BA has access to the HPC billing system (an extension of TRC billing system for CO2/Glass washing)?: Yes/No
  • BA associating the 26-digit SAM account with the User’s account in the TRC/HPC billing system?: Yes/No

Note: If the user account is not requested by the BA/PI, we will follow up directly with the BA/PI for authorization.

Usage Policies

Penn Acceptable Use Policy: http://www.upenn.edu/computing/policy/aup.html

Guidelines

Don't run compute-intensive tasks on the cluster head node (consign). Use an interactive node (bsub -Is bash) instead. Please read the man page for 'bsub' or refer the User Guide