HPC User Guide

Contents

  • 1. What is a cluster?
  • 2. Connecting to the cluster
  • 3. Running Jobs on the HPC
  • 4. Installing and using software
  • 5. Code Version Control
  • 6. Best practices
  • 7. Using Nextflow on HPC
HPC User Guide
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  • HPC User Guide documentation

HPC User Guide documentation¶

Contents

  • 1. What is a cluster?
    • 1.1. Network
    • 1.2. Storage
    • 1.3. Queue manager
    • 1.4. Things to remember…
    • 1.5. Learning to use the shell
  • 2. Connecting to the cluster
    • 2.1. Terminal
    • 2.2. Generate your ssh key
    • 2.3. Request an account
    • 2.4. Connect to the cluster
  • 3. Running Jobs on the HPC
    • 3.1. Interactive jobs
    • 3.2. Batch jobs
    • 3.3. Checking job status
    • 3.4. Cancelling a job
  • 4. Installing and using software
    • 4.1. Why Conda?
    • 4.2. Using Conda in your work
    • 4.3. Configuring Conda Environments
    • 4.4. Searching for packages
    • 4.5. Using environments
    • 4.6. Command reference
    • 4.7. I don’t think I can use Conda because…
    • 4.8. Using graphical interfaces
    • 4.9. Available Modules on the Cluster
  • 5. Code Version Control
    • 5.1. Configuring Git SSH
    • 5.2. Cloning a Repository
  • 6. Best practices
    • 6.1. Structure and document your projects
    • 6.2. Multi-user project
    • 6.3. Use project-specific environments
  • 7. Using Nextflow on HPC
    • 7.1. Launching a Nextflow pipeline
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