Upcoming Outages




Minerva introductory tutorial schedules

We will be holding 2 information/training sessions on Minerva basics. These sessions are intended to familiarize you with the Minerva environment. Basic understanding of the general Unix operating environment is expected. Both in room Icahn L3-82.


Session 1: Wednesday, 11 March 2020 2:00-3:00PM – Introduction to Minerva

  • Minerva resources
  • Account and Logging in
  • Software Environment Management
  • File Transfers and data archive
  • Basic job submission


Session 2: Wednesday, 18 March 2020 2:00-3:00PM – LSF job scheduler

  • Basic job submission and LSF command
  • Self-scheduler
  • Parallel jobs (job arrays, parallel processing and GPUs)
  • Debugging
  • Things to avoid




New GPFS file system for storage – Arion from BODE2

The new file system Arion is from the awarded BODE2, i.e., 11 petabytes of usable storage (14 PB raw, 1,008 total drives).

  • We are integrating the flash into Arion for better performance on metadata processing.
  • We will do an IO performance test/benchmark on Arion.
  • Start file transfer from Orga/Hydra to Arion with AFM technology.
  • It will be available to users in March.


BODE2 compute nodes are open to all NIH funded projects since Dec 2019

All NIH funded projects reported are eligible to run jobs on those extra 78 BODE2 compute nodes. If you are running jobs under NIH funded projects, please make sure you use the correct project name in LSF to access the resources (i.e.,  #BSUB -P acc_xxx). To check the eligibility of your project on BODE nodes, you can run “mybalance”.


FYI: The BODE2 is consist of:

  • 3,840 24-core 2.9 GHz Cascade Lake 8268 processors in 80 nodes
  • 192 GB of memory per node
  • 240 GB of SSDs per node
  • 15 TB memory (collectively)
  • 11 petabytes of usable storage (14 PB raw, 1,008 total drives)


New home for Scientific Computing website

The home of Scientific Computing at Mount Sinai has a new face!  You will now be forwarded to https://labs.icahn.mssm.edu/minervalab/ to find an organized  look and revised information. Please bookmark this link for future use.

Please also ensure to subscribe to our calendar for all upcoming events, trainings and updates.



TSM files expiring in 2020

The TSM files that were archived in 2014 will expire in 2020. Please check the expiration date of your archived files. There is no simple command to extend the file expiration date. If you would like to keep these files, you will need to retrieve them to disk and archive again. If you would like to query other users’ archived files, please send in a ticket.





We do not backup any data so please begin taking precautions and archive any data that you cannot afford to lose (see https://labs.icahn.mssm.edu/minervalab/archiving-data/).


Acknowledge Scientific Computing at Mount Sinai: An acknowledgment of support from the Icahn School of Medicine at Mount Sinai should appear in the publication of any material, whether copyrighted or not, based on or developed with Mount Sinai-supported computing resources.


Please use the following statement:  “This work was supported in part through the computational resources and staff expertise provided by  Scientific Computing at the Icahn School of Medicine at Mount Sinai.”


NIH requires acknowledgment of the S10 BODE award in publications as follows:  “Research reported in this paper was supported by the Office of Research Infrastructure of the National Institutes of Health under award number S10OD018522. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.”


Minerva on Twitter: Please follow us on Twitter @mssmhpc for notification of Minerva status and problems.


For a complete listing of important recent Announcements & Reminders, please check our Scientific Computing website: https://labs.icahn.mssm.edu/minervalab




Minerva documentation: https://labs.icahn.mssm.edu/minervalab/documentation/

Send in a ticket by email to hpchelp@hpc.mssm.edu