Overview of my Workshops

Contents:

• Parabricks Workshop
  • Course objectives
  • Requirements
  • Data Used
  • Introduction to Clara Parabricks
  • DNA alignment with fq2bam
  • Calling Variants with haplotypeCaller
  • Genotyping sample
  • Next Steps
• Parabricks on BCP Workshop
  • Course objectives
  • Requirements
  • Introduction to Clara Parabricks
  • Data Used
  • DNA alignment with fq2bam
  • Calling Variants with haplotypeCaller
  • Genotyping sample
  • Next Steps
• Multi-Node on BCP
  • Objectives
  • Requirements
  • Introduction to distributed environments
  • MPI
  • PyTorch DDP
  • PyTorch Lightning
  • Pytorch + Ray Train
  • Next Steps
• Containers on BCP
  • Objectives
  • Requirements
  • Building and testing your first GPU container
  • Best practices for building python-based containers
  • Developing python scripts inside a running container on BCP
  • Next Steps
• GPU Containers on Slurm
  • Introduction to containers
  • Quickstart: Running your first GPU container
  • Building and testing your first GPU container
  • Best practices for building python-based containers
  • Developing python scripts inside a running container
  • Running multi-node containers
  • Next Steps
• GROMACS and MPS
  • Objectives
  • Requirements
  • Introduction to Gromacs benchmark
  • NVIDIA MPS and benefits
  • FOR and MPS
  • XARGS and MPS
  • Summary
  • Next Steps
• IndeX on Slurm
  • Introduction to IndeX
  • Launching the IndeX viewer on a remote system
  • Exploring IndeX viewer interface
  • Exploring different data formats
  • Exporting visuals and creating animations
  • Launching multi-node rendering jobs

Indices and tables

• Index

• Module Index

• Search Page