Help Using the HPC Clusters at UMD

The following is the main table of contents for the usage documentation for the High Performance Computing clusters made available to researchers at the University of Maryland by the Division of Information Technology. Kindly read the documentation before contacting us for help. If you still need assistance, please open a help ticket.

1. FAQ
2. Quick start
   1. Command line quick start
   2. OnDemand Web portal quick start
3. Using the OnDemand Web Portal
   1. Connecting to the OnDemand Web Portal
   2. Using the OnDemand File Manager
   3. OnDemand Interactive Apps
   4. The OnDemand Job Composer and Batch Jobs
   5. Monitoring Jobs in OnDemand
   6. Shell Access from OnDemand
   7. Developing Job Templates
4. The basics
   1. Logging into the system
   2. Graphics
   3. Basic unix commands
   4. Setting up your Environment
   5. Files and Storage
   6. Transferring files to/from the Deepthought clusters and your computer
   7. Compiling codes
5. Submitting Jobs
   1. Basic job submission
   2. Your Job Script
   3. Choosing a Queue
   4. Specifying how long the job will run
   5. Specifying node and core requirements
   6. Specifying memory requirements
   7. Requesting nodes with specific features
   8. Requesting nodes with specific CPU architectures
   9. Using infiniband
   10. Using GPUs
   11. Specifying the amount/type of scratch space needed
   12. Specifying the account to be charged
   13. Specifying email options
   14. Specifying output options
   15. Specifying which shell to run the job in
   16. Specifying which directory to run the job in
   17. Specifying whether or not other jobs can be on the same node
   18. Common env vars set by Slurm
6. Running codes, serial and parallel
   1. Running Serial jobs
   2. Running multithreaded jobs on a single node
   3. Running MPI jobs
      1. OpenMPI jobs
      2. Intel MPI jobs
   4. Running hybrid OpenMP/MPI jobs
   5. Running non-MPI jobs on multiple nodes
7. Examples
   1. Submitting a Sequential job
   2. Submitting an OpenMPI job
   3. Submitting an Intel MPI job
8. Monitoring and Managing Your Jobs
   1. Seeing what jobs are running/queued
   2. When will my job run?
   3. Detailed information about your jobs
   4. Viewing output of jobs in progress
   5. Cancelling your jobs
   6. Monitoring the cluster
9. Allocations and job accounting
   1. Basics of allocations and job accounting
   2. Choosing the account to use
   3. The Replenishing process
   4. Monitoring usage
   5. ColdFront Allocation Management Web GUI
      1. Overview of ColdFront GUI
      2. Accessing ColdFront
      3. Usage for Project PIs
      4. Usage for College/Dept Pool Managers
      5. Adding/removing users from a Project
      6. Adding/removing users from an Allocation
10. Diagnosing and Fixing Problems
    1. Jobs not running/Deferred Jobs
    2. Debug Queues
    3. Interactive Jobs
11. Files, Storage and Securing your data
    1. Your home directory
    2. Data directories
    3. Scratch space
    4. Using lustre
    5. Archival Storage
    6. Securing your data
    7. Policies regarding usage of Disk Space on the Deepthought* HPC Clusters
12. Queues and Partitions
    1. Queues vs. Partitions
    2. Quality of Service (QoS) levels and Walltime Limits
    3. How queued jobs get processed
13. Available Software
    1. The tap and module commands
    2. Available software, not classified by field
    3. Categorized by subject field, etc
    4. Packages/Modules for scripting languages
14. Glossary/Terminology
15. Help for migrating from PBS/Maui/Moab systems

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