Pegasus Software Suites

Modules and Languages

• Modules
• Perl
  • Configuring a Local Library
• Python
  • Loading and Switching Python Modules
  • Installing Python Modules with Package Managers
  • Installing Downloaded Python Modules
• Python Virtual environments
  • Creating Virtual Environments
  • Activating Virtual Environments
  • Comparing two Python Virtual Environments
  • Python virtual environment wrapper
• R
  • Batch R
  • Interactive R
  • Installing additional R packages
• Using R through Anaconda
  • Anaconda Installation
  • Configuring Anaconda environment
  • Common R package dependencies
  • Activating conda environment upon login
  • Running jobs

Data Science Tools

• Jupyterhub
  • Pegasus JupyterhubIntroduction
  • Using JupyterHub on Pegasus
  • Switching between JupyterLab and JupyterHub on Pegasus
  • Using Jupyter Notebook on Pegasus
• RStudio
  • Setup your $RSTUDIO_WORK_DIR
  • Edit your rstudio_lsf.job Script
  • Run RSTUDIO on Pegasus Nodes
  • Updating an RStudio Container
• SAS
  • Non-Interactive Batch Mode
• Pytorch-Cuda
  • Pytorch-Cuda Installation
  • Installing additional packages into your environment
  • Running LSF Jobs

Application Development

• Application Development Overview
  • Compiling Serial Code
  • Compiling Parallel Programs with MPI
• Amazon Web Services CLI
  • Getting Started Amazon Web Services CLI on Pegasus
  • Using AWS s3 buckets from the cli
  • AWS s3 Include and Exclude filters

Scientific Computing

• MATLAB
  • Interactive Mode
  • Batch Processing
  • Parallel Computations
• SimVascular
  • Forwarding X11
  • Loading the SimVascular Software Module
  • Launching Graphical Interactive Jobs

Workflow Engines

• Nextflow
  • Load Nextflow module
  • Sample User Nextflow LSF Configuration
  • Nextflow Submission Script
  • Submit Job to LSF Cluster
  • Check status of running Job
  • View your Results
  • Sources