High Performance Computing

• During this maintenance our admin will perform a tape library audit.
• We will lock the library to perform a comprehensive physical inventory for the audit process.
• No other operations are allowed on the system.

• We need to perform this audit to sync the loaded tapes in the tape library with the TSM server database catalog, as we have noticed some discrepancies.
• After this, all tapes in the library should be available for the new data archive.

ALERT: Scheduled Maintenance on Open OnDemand Server: Thursday, OCTOBER 9th from 9:00 AM – 12:00 PM

There is a scheduled maintenance on ondemand.hpc.mssm.edu on Thursday, Oct 9th, from 9:00 AM to 12:00 noon. The server will be unavailable during this timeframe.

What is the plan and benefits?

During this maintenance, we will perform updates and security patching on the ondemand.hpc.mssm.edu server to improve security and stability.

How this maintenance may impact your work:

• No access to ondemand.hpc.mssm.edu portal

• All other services not dependent on ondemand.hpc.mssm.edu are NOT affected

Please plan your work related ahead of time and contact us with any questions at hpchelp@hpc.mssm.edu. Thanks for your patience and understanding while we maintain the system.

NEW: AIR·MS Fall Training

We will be holding 3 AIR·MS training sessions this Fall. These sessions will introduce you to the AIR·MS environment and AI-related tools through live demonstrations you can follow along with. Each session will be offered in a hybrid format, with our team onsite to provide support and answer questions. Material will be provided 1 week prior to each session for registered users.

Further details including registration links and course content can be found here.

NEW: Minerva High Performance Computing Fall Training

Every Tuesday and Friday starting Sep 16 and ending Oct. 14. 

• We will be holding 9 training sessions this Fall. These sessions are intended to familiarize you with the Minerva environment and AI related tools. Basic understanding of the general Unix operating environment and Linux commands is expected. 
• There is also a training session for Data Ark to get you familiarized with the Data Ark Data Sets and environment.  
   
• All sessions will be offered in person in the following room: Icahn L3-41. 
   
• Zoom links for virtual attendees are provided following registration for each session. 
   
  Every Tuesday and Friday starting Sep 16 and ending Oct. 14
    
  RECORDING NOW AVAILABLE (click to view) — Session 1: Introduction to Minerva – Tuesday, Sep 16, 2025, 1-2 pm
  This session covers:
  • Minerva resources
  • Account and logging in
  • User software environment
  • Preview of service on Minerva
   
  Session 2: Essential Services on Minerva – Friday, Sep 19, 2025, 1-2 pm
  Zoom attendees: Register here for Essential Services on Minerva
  In-Person Attendees: Register here
   
  This session will cover the following and focus on a live demonstration:
  • Globus file transfers
  • Web server usage
  • TSM archive service
  • Posit Connect server
   
  Session 3: Load Sharing Facility (LSF) Job Scheduler – Tuesday, Sep 23, 2025, 1-2 pm
  Zoom attendees: Register here for LSF Job Scheduler
  In-Person Attendees: Register here
   
  This session will cover:
  • LSF introduction and basic/helpful LSF commands
  • Job submission and monitoring
  • Parallel jobs (parallel processing and GPUs)
  • Job Arrays and Self-scheduler
  • DOs and DON’Ts
   
  Session 4. Introduction to GPU/AI resources on Minerva – Friday, Sep 26, 2025, 1-2 pm
  Zoom attendees: Register here for Introduction to GPU/AI resources on Minerva
  In-Person Attendees: Register here
   
  This session will cover:
  • What is a GPU
  • GPU resources on Minerva
  • User GPU/AI Software environment on Minerva
  • Running GPU/AI jobs in LSF
   
  Session 5: Accelerating Biomedical Data Science with GPUs: Practical Approaches and Tools – Tuesday, Sep 30, 2025, 1-2 pm
  Zoom attendees: Register here for Accelerating Biomedical Data Science with GPUs
  In-Person Attendees: Register here
   
  This session will cover:
  • GPU fundamentals
  • Ways to accelerate with GPUs
  • GPU-Accelerated Numerical Computing with CuPy
  • GPU-Accelerated Data Science with RAPIDS
   
  Session 6: Access Minerva via web browser Open OnDemand – Friday, Oct. 3, 2025, 1-2 pm
  Zoom attendees: Register here for Access Minerva via web browser Open OnDemand
  In-Person Attendees: Register here
   
  This session will cover the following and focus on live demonstration:
  • Login via Open OnDemand
  • File Access via Open OnDemand
  • Submit jobs via Open OnDemand
  • Access Interactive Apps within Open OnDemand: Desktop, Rstudio, Jupyter, Code Server, Matlab, SAS etc.
   
  Session 7: Leveraging Large Language Models in Biomedical Research – Tuesday, Oct. 7, 2025, 1-2 pm
  Zoom attendees: Register here for Leveraging Large Language Models in Biomedical Research
  In-Person Attendees: Register here
   
  This session will cover:
  • Introduction to Large Language Models (LLMs)
  • Transformer Architecture
  • Key LLM Models
  • Training and Fine-Tuning LLMs
  • Practical Implementation on GPUs
   
  Session 8: Introduction to Data Ark – Mount Sinai Data Commons – Friday Oct. 10, 2025, 1-1:30 pm
  Zoom attendees: Register here for Introduction to Data Ark – Mount Sinai Data Commons
  In-Person Attendees: Register here
   
  This session will cover:
  • Introduction to Data Ark
  • Accessing datasets through Data Ark
  • Digital pathology slides access through Data Ark
    
  Session 9: Using Containers on Minerva and Accelerating Genome Analysis with Parabricks, Tuesday, Oct. 14, 2025, 1-2 pm
  Zoom attendees: Register here for Using Containers on Minerva and Accelerating Genome Analysis with Parabricks
  In-Person Attendees: Register here
   
  This session will cover the following with a live demonstration:
  • Singularity/Apptainer access on Minerva
  • Capabilities and Performance of Parabricks
  • Parabricks for secondary analysis
   
  Please register ahead of time for sessions. Please check our website for additional details and updates. Direct any questions to hpchelp@hpc.mssm.edu 
  Thank you, and we look forward to seeing you.

Minerva High Performance Computing 2025 Charge Rate

The 2025 charge rate for the Minerva High Performance Computing (HPC) service is now $155/TiB/year, effective on September 1, 2025. The new rate will be reflected in the December quarterly charges. For questions, please reach out to ranjini.kottaiyan@mssm.edu.

July 2025 – National Institutes of Health (NIH) S10 Instrumentation Grant Award

Dean Patricia Kovatch, head of Scientific Computing and Data at the Icahn School of Medicine at Mount Sinai, was awarded $2M from the National Institutes of Health (NIH) as part of an S10 Instrumentation Grant (for advanced instrumentation) to provide state-of-the-art GPU capability and capacity.

These funds will support the creation of 48 NVIDIA B200 GPUs in 6 x DGX compute nodes, with the following specifications:

• 8x NVLinked B200 GPUs per node, 192 GB of memory per GPU, for a total of 48 xB200 GPUs and 9 TB of memory available on B200.
• 112 Intel Xeon Platinum 8570 2.1GHz cores, 2 TB memory, 25 TB high-speed NVME local storage per node for a total of 672 cores and 12 terabytes of memory on servers.
• B200 introduced new format FP4 (floating point 4-bit) capability, enabling the Minerva computing infrastructure to provide nearly an exaflop with FP4 for AI inference as shown in the NVIDIA B200 DGX datasheet.

This award was only possible with the support of the many researchers at Mount Sinai, and Icahn School of Medicine leadership.