Pegasus Software

• Software Modules
• Application Development
  • Compiling Serial Code
  • Compiling Parallel Programs with MPI
• Parallel Computing
  • Sample parallel programs:
  • The LSF script to run parallel jobs
• Installing Software on a Cluster
  • Downloading and extracting files
  • Configuring installation and compilation
  • Updating PATH
  • Persistent PATH
• Allinea
• Amazon Web Services CLI
  • Getting Started
  • Using AWS s3 buckets from the cli
  • AWS s3 Include and Exclude filters
• MATLAB
  • Interactive Mode
  • Batch Processing
  • Parallel Computations
  • Note on Matlab cluster configurations
  • Troubleshooting
• Nextflow
  • Sample User Nextflow LSF Configuration
  • Nextflow Submission Script
  • Submit Job to LSF Cluster
  • Check status of running Job
  • View your Results
• 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
• RStudio
  • Setup your $RSTUDIO_WORK_DIR
  • Edit your rstudio_lsf.job Script
  • Run RSTUDIO on Pegasus Nodes
• SAS
  • Non-Interactive Batch Mode
• Using R through Anaconda
  • Anaconda Installation
  • Configuring Anaconda environment
  • Common R package dependencies
  • Activating conda environment upon login
  • Running jobs
• Jupyterhub
  • Introduction
  • Using JupyterHub on Pegasus
  • Switching between JupyterLab & JupyterHub
  • Using Jupyter Notebook
• SimVascular
  • Forwarding X11
  • Loading the Module
  • Launching Graphical Interactive Jobs