Note: As of January 2023, the PMACS HPC is generally only used for burst compute in special circumstances. Please contact Yoseph before using this system.

Access HPC

I am working on this page, it is not complete yet but there were a lot of HPC questions coming up so I thought I could at least start the effort. 

Log Into Submit Host


Example MAJIQ Job


Non-Release MAJIQ



E.g. `bsub -N calebsjob -e err -o out -n 7 -M 5000 -q normal -R "span [hosts=1] rusage [mem=5000]" bash caleb.sh`

Static Directory


Transferring Files

Common Queue Commands

Check the LSF documentation for further information.

Questions or Concerns?

Submit a ticket at https://helpdesk.pmacs.upenn.edu under the "Systems"  queue or email PMACS-SYS-SCI@lists.upenn.edu with all your LPC questions. 


A Warning

Storage costs a lot, you should keep 1TB or below data owned by your user account. 

Where to Store Data (AKA The Capitalistic model)

Finding Data


Available Barash Lab Hosts


Useful Commands

To help mitigate issue where users are controlling nodes, we'll have to include the following arguments in every job submission:

bsub -n 7 -R "span[ptile=7]" < job.sh

For example, if you are running STAR with 7 threads, the -n 7 in the bsub command ensures that you get 7 cores for the job and -R "span[ptile=7]" ensures that you get those 7 cores on the same machine, in most cases, for example running STAR or MAJIQ, you do need the cores on the same machine.  General rule is that number of threads required == number of cores requested. Each machine on LPC has 15 cores, so don't request more than 7 cores unless you absolutely need to.

To increase memory you can use the -M option, for example the following option in your bsub command asks the lsf for 10 GB of RAM for the job:

-M 10240

Interactive mode on specific machine:

bsub -Is -m "mamut" -q barash_interactive 'bash'

Don't use the interactive bash if you need to run computationally heavy jobs, use the normal bsub command. The lsf system doesn't keep track of the resources used by the ibash and you can cause the machine to crash or other jobs to fail.

Check hosts statuses:

bhosts barash_exe

Additional Reading