• Introduction
  1. Preamble
  2. Access to the Cluster
  3. Using the Cluster
  4. Software Overview
  5. Support 
• Hardware
  1. Introduction
  2. Nodes
  3. Disk Space
  4. InfiniBand Fabric
• Software
  
  1. Introduction
  2. The Command module
     
  3. Compilers
  4. How to build and run MPI programs
  5. How to build and run multi-threaded programs
  6. Libraries
  7. Packages/Tools
  8. BioInformatics/Genomics Software  
• Submitting Jobs
  1. Introduction
  2. Conceptual Examples
  3. Serial Jobs
  4. Job Arrays
  5. Parallel Jobs
     
     1.  MPI Jobs
     2.  Multi-Threaded Jobs
  6. Available Queues
     1.  Serial and High-CPUs Queues
     2. High-Memory Queues
     3.  Restricted Queues
  7. Resource Limits
  8. Help me Choose a Queue and Write a Job Script
     1. QSubGen: a job script generator
     2. What Queue Should I Use?
     3. Why Can't I Queue that Job?
     4. Why Is my Job Queued but not Running?
• Monitoring your Jobs
  
  1. Introduction
  2. How to Check on Jobs
  3. How to Delete/Kill a Job or Jobs
  4. Modifying Queued Jobs
  5. Checking on a Completed Job
  6. Additional Tools
  7. Zombies  
• Monitoring the Cluster
  
  1. Cluster Status
  2. Compute Nodes Status
  3. Query the Cluster Configuration
  4. Ganglia Web Page
  5. Cluster Status Web Page
• Disk Space and Disk Use Policy
  1. What Disks to Use
  2. How to Copy Files to/from Hydra
  3. Disk Quotas
  4. Disk Configuration
  5. Disk Usage Monitoring
  6. NetApp Snapshots: How to Recover Old or Deleted Files
  7. Public Disks Scrubber
     
  8. SSD and Local Disk Space
• Glossary
•  Citing/Acknowledging Hydra
• Hydra Policies
  1. Existing General Policies
  2. User Accounts
  3. Hydra Use
  4. Communication

Last updated 23 Aug 2016 SGK