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
Contents
Other Pages
Connecting
Currently, secure shell (SSH) is the only supported method of connecting to the cluster. The login machine name is consign.pmacs.upenn.edu You should probably add "ServerKeepAliveInterval 60" to your SSH client's configuration.
After your account is created, you can connect using your PMACS credentials.
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 Cluster Overview
The hardware of the PMACS Cluster comprises of
- 64 Compute nodes (physical servers)
- Each compute node has 256 GB of RAM and 16 physical cores with hyperthreading turned on; 16.3TB RAM and 2048 cores total
- 1 dedicated "Big-Meomory" machine - 64 cores & 1.5TB RAM
- 1 dedicated master node
- 870TB of usable disk storage provided by IBM's SONAS (Scale Out NAS)
- 1.8PB Archival storage
- All compute and storage connected via 10GigE interconnect
- Dedicated 10GigE PennNet link from campus to the datacenter
The PMACS Cluster is physically housed at the Philadelphia Technology Park (PTP) which is a secure facility within the Philadelphia Navy Yard.
Accounts
For Account requests please contact Jason Hughes, Rikki Godshall or Anand Srinivasan
Usage Policies
Penn Acceptable Use Policy:
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' and the documentation linked below.
Common Commands (IBM Platform LSF)
Please also refer the man pages for bsub, bjobs, bkill, bhist, bqueues and bhosts.
- bsub <job script> : submit a job description file for execution
- bsub -Is bash : request a node for interactive use
- bjbos <jobid> : show the status of a job
- bjbos -l <jobid> : show more details about the job
- bkill <jobid> : cancel a job
- bjobs -u <user> : display jobs queued or running for a single user
- bjobs -u all : to see all jobs
Default Submission Constraints
Please note that all submissions, both batch and interactive sessions, on the cluster have a default memory limit of 3GB. To request more memory for a given request, you can use one of the other queues that allow jobs to request and use more than 3GB. For example, to run a batch job that needs 5GB of RAM
bsub -q plus <job_script>
Where -q tells the LSF scheduler that you wish to use the "plus" queue which allows up to 6GB of RAM usage per slot.
To request more than 6GB of RAM use the "-q max_mem64"
