We summarize our seven Spring 2024 training sessions for Minerva users below.
- There were two information/training sessions for Minerva. These sessions are intended to familiarize you with the Minerva environment. Basic understanding of the general Unix operating environment and Linux commands is expected.
- There was a training session for Data Ark to familiarize you with the Data Ark – Mount Sinai Data Commons data sets and environment.
- We also held four GPU/AI training sessions for Minerva users, jointly presented by Minerva HPC staff and NVIDIA domain experts.
- Sessions 2 and 6 were offered in person at the Icahn Building as well as remotely through Zoom. Sessions 3, 4, 5 and 7 were held remotely through Zoom.
Session 1: Introduction to Minerva – held on Wednesday, March 27, 2024, 1 pm-2 pm
Training slides and video are available.
This session covered:
- Minerva resources
- Account and logging in
- User software environment
- Service on file transfers, web server, TSM archive and Posit connect server
Session 2: Load Sharing Facility (LSF) Job Scheduler – Wednesday, April 3, 2024, 1 pm-2 pm
Training slides and video are available.
This session covered:
- 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 – Wednesday, April 10, 2024, 1 pm -2 pm
Training slides and video are available.
This session covered:
- What is a GPU
- GPU resources on Minerva
- User GPU/AI Software environment on Minerva
- Running GPU/AI jobs in LSF
Session 4. 5 Ways to Get Started with GPUs – Friday, April 12, 2024, 1 pm-2 pm
Training slides and video are available.
This session covered:
- Some GPU basics
- 5 ways to accelerate with GPUs (Applications, Library, OpenACC Directives, CUDA Programming, Standard Language Parallelism)
Session 5: Accelerated General Data Science in Medicine with RAPIDS, CuPy and Numba – Wednesday, April 17, 1 pm-2 pm
Training slides and video are available.
This session covered:
- Overview of GPU Computing
- GPU-Accelerated Numerical Computing with CuPy
- GPU-Accelerated Data Science with RAPIDS
- Custom GPU Kernels with Numba Frameworks
- Interoperability – Data Conversion Bottleneck
Session 6: Introduction to Data Ark – Mount Sinai Data Commons – Wednesday, April 24, 2024, 1 pm-2 pm
Training slides and video are available.
This session covered:
- Introduction to Data Ark
- Accessing datasets through Data Ark
- Introduction to MarketScan data
- Accessing MarketScan Data via Minerva HPC
Session 7: How to Accelerate Genome Analysis Toolkit (GATK) by using Parabricks – Wednesday, May 1, 2024, 1 pm-2 pm
Training slides and video are available.
This session covered:
- Capabilities and Performance of Parabricks
- Parabricks for secondary analysis
Please send any questions to hpchelp@hpc.mssm.edu
Thank you—
Scientific Computing and Data
Icahn School of Medicine at Mount Sinai