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

Minerva HPC Presentations

Minerva User Group – Upcoming Spring Training Sessions

We will be holding 8 training session this Spring.

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 familiarize with the Data Ark Data Sets and environment.

All sessions will be offered in person in the following rooms: Icahn L3-36, Icahn L3-41 and Icahn L14-84. Zoom links are provided following registration.

 

Session 1: Introduction to Minerva – Thursday, February 13th, 1:00PM – 2:00PM

Click here to register for the Introduction to Minerva Session

Click here to register for the in-person session

Location: Icahn School of Medicine building (1425 Madison Ave) Room 14-84

Remote attendance: Zoom link provided following registration.

This session will cover:

  • Minervaresources
  • Account and logging in
  • User software environment
  • Service on file transfers, web server and TSM archive and Posit connect server

 

Session 2: Load Sharing Facility (LSF) Job Scheduler – Thursday, February 20th, 1:00PM-2:00PM

Click here to register for LSF Job Scheduler Session

Click here to register for the in-person session

Location: Icahn School of Medicine building (1425 Madison Ave) Room L3-41

Remote attendance: Zoom link provided following registration.

This session will cover:

  • LSF introduction and basic/helpful LSF commands
  • Dependent job
  • Self-scheduler
  • Parallel jobs (job arrays, parallel processing and GPUs)
  • Things to avoid

 

Session 3: Introduction to GPU/AI resources on Minerva – Thursday, February 27th, 1:00PM-2:00PM

Click here to register for Introduction to GPU/AI resources on Minerva Session

Click here to register for the in-person session

Location: Icahn School of Medicine building (1425 Madison Ave) Room L3-36

Remote attendance: Zoom link provided following registration

This session will cover:

  • What is a GPU
  • GPU resources on Minerva
  • User GPU/AI Software environnement on Minerva
  • Running GPU/AI jobs in LSF

 

Session 4: Accelerating Biomedical Data Science with GPUs: Practical Approaches and Tools – Thursday, March 6th, 1:00PM-2:00PM

Click here to register for Accelerating Biomedical Data Science with GPUs

Click here to register for the in-person session

Location: Icahn School of Medicine building (1425 Madison Ave) Room L3-41

Remote attendance: Zoom link provided following registration

This session will cover:

  • GPU fundamentals
  • Ways to accelerate with GPUs
  • GPU-Accelerated Numerical Computing with CuPy
  • GPU-Accelerated Data Science with RAPIDS

 

Session 5: Leveraging Large Language Models in Biomedical Research – Thursday, March 13th, 1:00PM – 2:00PM

Click here to register for Leveraging Large Language Models in Biomedical Research

Click here to register for the in-person session

Location: Icahn School of Medicine building (1425 Madison Ave) Room L3-36

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 6: Access Minerva via web browser Open OnDemand – Thursday, March 20th, 1:00PM – 2:00PM

Click here to register Access Minerva via web browser Open OnDemand

Click here to register for the in-person session

Location: Icahn School of Medicine building (1425 Madison Ave) Room L3-41

This session will cover:

  • 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: How to Accelerate Genome Analysis Toolkit (GATK) by using Parabricks – Tuesday, March 25th, 1:00PM – 2:00PM

Click here to register for How to Accelerate Genome Analysis Toolkit (GATK) by using Parabricks

Click here to register for the in-person session

Location: Icahn School of Medicine building (1425 Madison Ave) Room L3-36

Remote attendance: Zoom link provided following registration.

This session will cover the following:

  • Singularity/Apptainer access on Minerva
  • Capabilities and Performance of Parabricks
  • Parabricks for secondary analysis

 

Session 8: Introduction to Data Ark – Thursday, March 27th, 1:00PM – 2:00PM

Click here to register for Introduction to Data Ark

Click here to register for the in-person session

Location: Icahn School of Medicine building (1425 Madison Ave) Room L3-36

This session will cover:

  • Introduction to Data Ark
  • Accessing datasets through Data Ark

 

Minerva User Group – Training Sessions

Computational Scientists in the Scientific Computing Facility provide both beginning and advanced training sessions on how to use Minerva effectively and efficiently.  Times and location will be announced in advance in the Weekly Update email and posted on the Home page of this website.  Our computational Scientists are also available by appointment or 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, and provide advice on operational policies and plans.  All scientists and researchers who use Minerva are encouraged to participate; slides from the meetings are posted on the internal Scientific Computing Facility’s website as well as in the Minerva Weekly Update.  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.

 

Past Scientific Computing Conference Information

 

 

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