EOS 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
  • 3.5. Slurm Queues and Priorities
• 4. EOS Storage
  • 4.1. Storage Configuration
  • 4.2. Large files and common resources
  • 4.3. Genomic references
• 5. Backup important files
  • 5.1. Software
  • 5.2. Configuration
  • 5.3. Test the software
  • 5.4. Copying files from EOS to your remote
• 6. Installing and using software
  • 6.1. Why Conda?
  • 6.2. Using Conda in your work
  • 6.3. Configuring Conda Environments
  • 6.4. Searching for packages
  • 6.5. Using environments
  • 6.6. Command reference
  • 6.7. I don’t think I can use Conda because…
  • 6.8. Using graphical interfaces
  • 6.9. Available Modules on the Cluster
• 7. Code Version Control
  • 7.1. Configuring Git SSH
  • 7.2. Cloning a Repository
• 8. Best practices
  • 8.1. Structure and document your projects
  • 8.2. Multi-user project
  • 8.3. Use project-specific environments
• 9. Using Nextflow on HPC
  • 9.1. Launching a Nextflow pipeline