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Scientific Computing and Data / High Performance Computing / Minerva HPC Presentations

Minerva HPC Presentations

Minerva User Group – Fall 2025 Training Sessions

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

All sessions will be offered in person in the following room: Icahn L3-41. In-Person Attendees: Register here
Zoom Attendees: Links are provided following registration (see zoom registration links below for each session).

 

RECORDING NOW AVAILABLE – Session 1: Introduction to Minerva – Tuesday, Sep 16, 2025, 1 pm- 2 pm

SLIDES AVAILABLE HERE.

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 pm- 2 pm
Zoom 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 pm- 2 pm

Zoom 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 pm – 2 pm
Zoom 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 pm- 2 pm
Zoom 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, 1pm-2pm
Zoom 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 pm – 2 pm
Zoom 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 pm-1:30 pm
Zoom 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 pm – 2 pm
Zoom 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

 

Minerva User Group – Training Sessions

Scientific Computing and Data (SCD) computational scientists provide both introductory and advanced training sessions on how to use the Minerva supercomputer effectively and efficiently. The times and locations will be announced on this website and through the Mount Sinai research email list. Our computational scientists are also available to answer questions by appointment or at the weekly Digital Concierge drop-in. Please see below for archived slides from past training sessions:

Find slide presentations from past training sessions here.

Minerva User Group – Town Hall Meetings

The Minerva User Group (MUG) meets quarterly and on an as-needed basis to review computational and data usage statistics, in addition to providing advice on operational policies and plans. All scientists and researchers who use Minerva are encouraged to participate. Please see below for slides from recent meetings:

Find slide presentations from past Minerva User Group Meetings here.

Minerva User Satisfaction Survey

The Minerva User Satisfaction Survey is issued in January each year to collect feedback from users. Previous results can be found below:

Find past survey results here.

 

Minerva User Group – Upcoming Training Sessions

  • The most recent Spring 2025 training sessions have concluded. Further training will be available in Fall 2025, please check back here for updates.

Minerva User Group – Training Sessions

Scientific Computing and Data (SCD) computational scientists provide both introductory and advanced training sessions on how to use the Minerva supercomputer effectively and efficiently. The times and locations will be announced on this website and through the Mount Sinai research email list. Our computational scientists are also available to answer questions by appointment or at the weekly Digital Concierge drop-in. Please see below for archived slides from past training sessions:

Find slide presentations from past training sessions here.

Minerva User Group – Town Hall Meetings

The Minerva User Group (MUG) meets quarterly and on an as-needed basis to review computational and data usage statistics, in addition to providing advice on operational policies and plans. All scientists and researchers who use Minerva are encouraged to participate. Please see below for slides from recent meetings:

Find slide presentations from past Minerva User Group Meetings here.

Minerva User Satisfaction Survey

The Minerva User Satisfaction Survey is issued in Jan annually to collect your feedback.

Find past survey results here.

 

Archives

 

Past Training Sessions

 

Past Minerva User Group Meetings

 

Past Minerva User Surveys

 

Past Scientific Computing Conference Information

 

 

Supported by grant UL1TR004419 from the National Center for Advancing Translational Sciences, National Institutes of Health.