SUMMARY.md

Table of contents

• Overview
• Quickstart
• Getting Started
• System Hardware
• Account Information
• Short "How to" Videos
• Quick Reference
  • Common Acronyms and Terms
  • Managing Modules
  • Common Linux Commands
• Getting Help
  • ❓ FAQ
• Citing CCV
• CCV Account Information
• Offboarding

Connecting to Oscar

• SSH (Terminal)
  • SSH Key Login (Passwordless SSH)
    • Mac/Linux/Windows(PowerShell)
    • Windows(PuTTY)
  • SSH Configuration File
  • X-Forwarding
  • SSH Agent Forwarding
    • Mac/Linux
    • Windows (PuTTY)
  • Arbiter2
• Open OnDemand
  • Using File Explorer on OOD
  • Web-based Terminal App
  • Interactive Apps on OOD
  • Using Python or Conda environments in the Jupyter App
  • Using RStudio
  • Desktop App (VNC)
• SMB (Local Mount)
• Remote IDE (VSCode)
  • From Non-compliant Networks (2-FA)
  • Setup virtual environment and debugger

Managing files

• Oscar's Filesystem
• Transferring Files to and from Oscar
• Transferring Files between Oscar and Campus File Storage (Replicated and Non-Replicated)
• Inspecting Disk Usage (Ncdu)
• Restoring Deleted Files
• Best Practices for I/O
• Version Control

Submitting jobs

• Running Jobs
• Slurm Partitions
• Interactive Jobs
• Batch Jobs
• Managing Jobs
• Job Arrays
• MPI Jobs
• Condo/Priority Jobs
• Dependent Jobs
• Associations & Quality of Service (QOS)

GPU Computing

• GPUs on Oscar
  • Grace Hopper GH200 GPUs
  • H100 NVL Tensor Core GPUs
  • Ampere Architecture GPUs
• Submitting GPU Jobs
• Intro to CUDA
• Compiling CUDA
• Installing Frameworks (PyTorch, TensorFlow, Jax)
  • Installing JAX
  • Installing TensorFlow
• Mixing MPI and CUDA

Large Memory Computing

• Large Memory Nodes on Oscar

Software

• Software on Oscar
• Using Modules
• Migration of MPI Apps to Slurm 22.05.7
• Python on Oscar
• Python in batch jobs
• Installing Python Packages
• Installing R Packages
• Using CCMake
• Intro to Parallel Programming
• Anaconda
• Conda and Mamba
• DMTCP
• Screen
• VASP
• Gaussian
• IDL
• MPI4PY

Jupyter Notebooks/Labs

• Jupyter Notebooks on Oscar
• Jupyter Labs on Oscar
• Tunneling into Jupyter with Windows

Debugging

• Arm Forge
  • Configuring Remote Launch
  • Setting Job Submission Settings

MATLAB

• Matlab GUI
• Matlab Batch Jobs
• Improving Performance and Memory Management
• Parallel Matlab

Visualization 🕶

• ParaView Remote Rendering

Singularity Containers

• Intro to Apptainer
• Building Images
• Running Images
• Accessing Oscar Filesystem
  • Example Container (TensorFlow)
• Singularity Tips and Tricks

Installing Software Packages Locally

• Using a CESM module
• Installing your own version of CESM
• Installing your own version of Quantum Espresso
• Installing your own version of Qmcpack

dbGaP

• dbGaP Architecture
• dbGaP Data Transfers
• dbGaP Job Submission

RHEL9 Migration

• RHEL-9 Migration
• LMOD - New Module System
• Module Changes
• Testing Jupyter Notebooks on RHEL9 mini-cluster

Large Language Models

• Ollama