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New User Info

 * Obtaining a CRC Account
 * Quick Start Guide
   * Cluster Computing Format
   * Front End Systems
     * Proper Front End Usage
       * Logging in
       * Utilizing Front Ends
   * Available Software
   * File Systems
     * AFS
     * Panasas
   * File Transfers
   * Job Scripts
     * Parallel Environments
     * Queues
     * Host Groups
   * Job Submission and Monitoring
     * Why is my job waiting in the Queue?
       * Parallel Jobs
     * Job Deletion
     * Job Resource Monitoring
     * Job Arrays
 * Connecting to CRC Servers
   * Connecting from Linux
     * X11 Forwarding
   * Connecting from a Mac
     * X11 forwarding for Mac
   * Connecting from Windows
   * Connecting from off campus
 * Basic Linux Guide
   * Navigating File System
     * Paths
     * Viewing Files and Directories
   * Commands
     * Flags, Arguments, Options
     * FS Manipulation
     * Opening Files
     * Editing Files
 * Modules
   * Module Command
     * Searching Modules
     * Module Categories
   * Using Modules
     * Getting information about a module
   * User Created Modules
     * Creating a Private Module
     * What if my Software is a precompiled Binary?
     * Using Private Modules
     * Different Versions of Software
     * Considerations
 * Training Events
   * New User Training
   * Register and Contacts

Help

 * FAQ
   * CRC Accounts
     * How Do I Request a CRC Account?
     * How Do I Find Some Quick Start Information?
     * I Can’t Login (New User / First Time Login)
     * I’ve Forgotten My Password
     * How Do I Request an Account for an External Collaborator?
     * How Can I Maintain My CRC Account After Graduating/Leaving Notre Dame?
     * I am Getting A “Module: Command Not Found” Message When I Log In To My
       CRC Account
   * Remote Access
     * Why Is My Remote Connection So Slow?
     * When I try to login I see the error: “Algorithm Negotiation Failed”, what
       does this mean?
     * When I try to connect CRC through VSCode, why does Remote SSH keep asking
       for password again and again?
   * Training
     * How Do I Receive Training?
   * CRC Software
     * What Software Is Available At The CRC?
     * How Do I Request Help Installing Software?
     * How Do I Request A Software Module To Be Installed/Updated?
     * Notes on sudo/root access
   * AFS Storage
     * How Do I Check My Available AFS Storage?
     * How Do I Request More AFS Storage Space?
     * How Do I Give A Particular User/Group Access To A Directory In My
       Personal AFS Space?
     * I Am Receiving A “Locking Authority File” Error
     * How Do I Add and Remove Users From The Shared Group Space I Administer?
     * I’m Not Seeing My Output When Running From AFS!
     * I Am Getting The Following Message Using Find
   * PANASAS Storage (/scratch365)
     * How Do I Check My Available (/scratch365) Storage?
     * How Do I Request More (/scratch365) Storage Space?
   * Jobs
     * My Job Is Aborted At Runtime Due To Excessive Disk-Swapping
     * Do Different Operating System Versions Affect Performance?
     * Unable to run job: error: no suitable queues’ Message When Submitting Job
       Script
     * How Can I Monitor The Behavior Of My Running Jobs?
     * My Job Has Created Zombies…What Does That Mean?
   * Applications
     * Xquartz gives me a failed request error:
     * I Need To Install ArcGIS On My System
     * I am trying to compile my code with mvapich2 but cannot find
       -lpsm_infinipath
     * I See Incomplete Images In COMSOL v4+
     * My Gaussian Jobs Are Being Aborted Due To /tmp Over-usage
     * Request of ArcGIS Installation and Support
   * Grants/Proposals
     * How Do I Acknowledge the CRC In My Proposals?
     * Does The CRC Provide An Example Of A Data Management Plan?
 * Getting Help
   * Steps to Getting Help
     * Setting up an Appointment
     * User Support Location
   * Training Opportunities

CRC Infrastructure

 * CRC Resources
   * Current Equipment
   * Systems Dashboard
     * Storage and server lookup
 * CRC Software
   * User Requested Software
 * Available Hardware
   * Interactive Front End(s)
   * CRC Owned Compute Clusters
   * Large Memory Systems
   * GPU Systems
 * Storage
   * AFS Storage
     * AFS Limitations and Notes
     * AFS Group Storage
     * AFS Website
     * AFS Permissions / ACLs
   * Panasas (scratch) Storage
     * Panasas Best Practices
   * Local /tmp Space
   * Storage Backups
   * Storage Comparison
 * UGE Environment
   * Queues
   * Parallel Environments
   * Host Groups
   * User Groups
 * Faculty Cluster Partnership Program
   * Purchasing Dedicated Servers
     * Bulk Purchasing
     * Grant Proposals
 * Maintenance
   * Typical Changes
   * Module Changes
   * Reoccuring Maintenance
   * Past Maintenance Periods

Resources

 * GPU
   * Job Submission Example
   * Installing Software on a GPU machine
   * CUDA And cuDNN Modules’ Avalability
   * Available Hardware For General Access
   * Resource and Job Monitoring
   * Other Resources For GPU Jobs
 * HTCondor
   * Visual Status of the ND Condor Pool
   * Online Short Course
   * About Condor
   * Getting Started With Condor at Notre Dame
   * Important note about AFS
   * Submitting Large Numbers of Jobs
   * To Submit Multicore SMP jobs to the ND Condor Pool
   * Example of Submitting 10 Matlab jobs
   * Example of Submitting an Amber job to a GPU node
   * Condor Status
   * More Information
 * Globus
   * What Is Globus?
   * Setting Up Globus at the CRC
   * Transferring Files to/from CRC
     * Prepare Endpoints/Collections
     * Select and Transfer File(s)
     * Sharing Files
     * Quick Guide
 * NDCMS
   * Logging In and Setting up your Software Environment
     * Setting up environment
     * Add your proxy DN and Notre Dame username (your username on
       earth.crc.nd.edu)
     * If You Forgot to Set Your AFS Permissions at First Login
   * PhEDEx
     * Requesting a PhEDEx Transfer to the Notre Dame Tier 3 Site
       (US_T3_NotreDame)
   * Monitoring Tier 3 components and Jobs
     * HTCondor Monitoring
       * HTCondor Job Monitoring
   * Storage
     * Home Area
     * Scratch Space
       * Accessing the scratch space from grid jobs
     * Hadoop Space
     * Lobster Working Storage
     * Storage space for PhEDEx
 * Apptainer/Singularity
   * Why Use Apptainer
   * Downloading Apptainer
   * Getting Started
     * Obtaining Containers
       * Create Your Own Custom Container
       * Using Pre-Built Containers
   * Accessing Containers
   * Using Apptainer in Batch Jobs
     * Apptainer on GPU Nodes
     * Using Apptainer within AFS
     * Using Modules within Apptainer containers
   * Important Notes
     * Helpful Resources
 * CAML
   * Access requirements
   * Resource description
   * Using the resource on campus
   * Jupyterhub service
     * Pre-requisites
     * Instructions
   * HTCondor Submission
     * HTCondor submission file
     * Setting up the tutorial examples
       * Tensorflow example
       * Pytorch example
       * Amber example
       * JAX example:
       * DeepSphere example

Popular Modules

 * Matlab
   * Toolboxes
   * Submitting Single Core Jobs
   * Submitting Multicore Jobs
   * MATLAB and Array Jobs
   * Memory Profiling
   * License Information
   * Tutorials and Training
   * Known issue with parpool and matlabpool
   * Dynare Support
   * Further Information
 * Python
   * Basic Usage
   * Installing Python Packages Locally
     * Adding ${HOME}/.local/bin to your path
   * Python Virtual Environment
   * Job Submission Example
     * Multi-core Jobs
   * Further Information
 * R
   * Sample R Job
   * Installing Local Packages
     * Installing packages within R
     * Installing R packages from source code
   * Profiling R Code
   * Parallel Computing in R
   * Test for Rmpi
   * Related Software
   * Further Information
 * Tensorflow
   * General Description
   * Basic Usage
   * Tensorflow Python
     * Installing Python Packages Locally
 * Conda
   * General Description
   * Initial setup
   * Environment Management
   * Package Management
   * Python Management
   * Channel Management
   * Job Submission Using Conda Environments

CRC User
 * »
 * CRC User Documentation
 * View page source

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CRC USER DOCUMENTATION

The HPC team within The University of Notre Dame’s Center for Research Computing
provides computing resources with the associated support for faculty members,
researchers, and campus users. Within these pages the supporting documentation
and resources for utilizing the CRC’s infrastructure can be found.

For any questions or assistance please contact us: crcsupport@nd.edu


RECENT ANNOUNCEMENTS:

Note

For more information on the May 2024 Biannual System Maintenance, please see
here: May 2024 Maintenance.

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WHAT DOES THE CRC DO?



The CRC provides faculty sponsored research access to HPC and HTC resources for
members of the Notre Dame community. The Center can also facilitate access to
large Nationally sponsored resources and other resources through XSEDE.

If you are a new user, be sure to check the links under “New User Info” on the
left toolbar starting with the Quick Start Guide.

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HOW CAN I GET HELP?

The CRC User Support Team is happy to help facilitate the use of the CRC
infrastructure with day to day operations, general or specific questions,
issues, and training for proper and efficient use of the cluster. To schedule an
appointment or ask a question, send an email to CRCSupport@nd.edu. Be sure to
first view the Getting Help page to see what all you need to gather before
contacting CRCSupport.

 * The CRC User Support offices are located on the 8th floor of Flanner Hall to
   the right after leaving the elevators.

 * For specific documentation you can search in the toolbar to the upper left,
   common and important sections can be found within the toolbar to the left.

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INTERNSHIPS

Interested in a possible internship? Further information can be found on the
Internship with the CRC page.







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© Copyright 2024, University of Notre Dame Center for Research Computing.

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