Holland Computing Center

HCC-DOCS

  • Introduction to HPC
  • Creating an Account
    • Setting Up and Using Duo
    • Changing Your Password
  • Connecting to HCC Clusters
    • Connecting with Terminal
    • Connecting with PuTTY (Windows)
    • Connecting with MobaXterm
    • Basic Linux commands
    • How to setup X11 forwarding
    • Reusing SSH connections
  • Handling Data
    • Data Storage
      • Using Scratch
      • Linux File Permissions
      • Using Attic
      • Using the /common File System
      • Preventing File Loss
      • Integrating Box with HCC
      • The Nebraska Research Data Storage (NRDStor)
        • MacOS
        • Smbclient
        • Swan
        • Windows
      • Using NU's Gitlab instance
        • Setting up GitLab on HCC Clusters
    • Data Transfer
      • Globus Connect
        • Activating HCC Cluster Collections
        • File Transfers Between Collections
        • File Transfers to and from Personal Workstations
        • File Sharing
        • Creating Globus Groups
        • Globus Command Line Interface
        • Activating UNL OneDrive on Globus
      • File Transfer with scp
      • File Transfer with WinSCP
      • File Transfer with CyberDuck
      • High Speed Data Transfers
      • Using Rclone for File Transfer
      • Connecting to CB3 iRODS
    • Sharing data on Swan
  • Running Applications
    • Using Preinstalled Software
      • Available Software for Swan
    • Using Custom Software
      • Using Anaconda Package Manager
      • Compiling an OpenMP Application
      • Using Apptainer and Docker Containers
      • Installing Perl modules
      • Using R Libraries
    • Application Specific Guides
      • Fortran/C on HCC
      • Bioinformatics Tools
        • Alignment Tools
          • BLAT
          • Bowtie
          • Bowtie2
          • Clustal Omega
          • TopHat/TopHat2
          • BLAST
            • Running BLAST Alignment
            • Create Local BLAST Database
          • BWA
            • Running BWA Commands
        • Biodata Module
        • Data Manipulation Tools
          • SRAtoolkit
          • BamTools
            • Running BamTools Commands
          • SAMtools
            • Running SAMtools Commands
        • De Novo Assembly Tools
          • Oases
          • Ray
          • SOAPdenovo2
          • Trinity
            • Running Trinity in Multiple Steps
          • Velvet
            • Running Velvet with Paired-End Data
            • Running Velvet with Single-End Data
            • Running Velvet with Single-End and Paired-End Data
        • Pre-processing Tools
          • Cutadapt
          • PRINSEQ
          • Scythe
          • Sickle
          • TagCleaner
        • QIIME
        • Reference-Based Assembly Tools
          • Cufflinks
        • Tools for Removing/Detecting Redundant Sequences
          • CAP3
          • CD-HIT
      • MPI Jobs on HCC
      • Allinea Profiling & Debugging Tools
        • Allinea Performance Reports
          • BLAST with Allinea Performance Reports
          • LAMMPS with Allinea Performance Reports
          • Ray with Allinea Performance Reports
        • Using Allinea Forge via Reverse Connect
      • Building LIS
      • Building WRF
      • DMTCP Checkpointing
      • Install and Running Matlab CobraToolbox, Gurobi, and IBM ILOG CPLEX
      • Running Gaussian at HCC
      • Running OLAM at HCC
      • Running Paraview
      • Running PostgreSQL
      • Running SAS on HCC
      • Running Theano
      • Visual Studio Code on HCC resources
    • Running JupyterLab Notebooks with Slurm
  • Submitting Jobs
    • Creating an Interactive Job
    • Submitting a Job Array
    • Submitting GPU Jobs
    • Submitting an MPI Job
    • Submitting an OpenMP Job
    • Job Dependencies
    • Monitoring Jobs
    • GPU Monitoring and Optimizing
    • Available Partitions
      • Available Partitions for Swan
    • HCC Acknowledgment Credit
    • Application Specific Guides
      • Applications Examples
        • Abaqus 2019 Example
        • Abaqus 6.14.2 Example
        • Comsol Example
        • Gamess Example
        • Gaussan-09 Example
        • Gaussan-16 Example
        • R Example
        • R-Advanced Example
        • fluent-19.2 Example
        • gromacs Example
        • jupyter Example
        • ls-dyna Example
        • mathematica Example
        • matlab Example
        • postgresql Example
        • python Example
        • sas Example
        • turbowave Example
      • Submitting ANSYS Jobs
      • Submitting MATLAB Jobs
      • Submitting R Jobs
  • HCC OnDemand
    • Connecting to HCC OnDemand
    • Managing and Transferring Files with HCC OnDemand
    • Job Management and Submission with HCC OnDemand
    • Shell Access with HCC OnDemand
    • Virtual Desktop and Interactive Apps with HCC OnDemand
    • CryoSPARC Interactive App
  • Anvil: HCC's Cloud
    • Adding SSH Key Pairs
    • Anvil Instance Types
    • Available images
    • Connecting to Linux Instances from Mac
    • Connecting to Linux Instances from Windows
    • Connecting to Linux Instances using X2Go
    • Connecting to Windows Instances
    • Connecting to the Anvil VPN
    • Creating SSH key pairs on Mac
    • Creating an Instance
    • Creating and attaching a volume
    • Formatting and mounting a volume in Linux
    • Formatting and mounting a volume in Windows
    • Resizing an instance
    • Using MySQL instances
    • What are the per-group resources limit?
  • The National Research Platform
    • Quick Start
    • Basic Kubernetes
    • GPU Pods
    • Batch Jobs
    • Deployments
    • Storage
    • JupyterHub Service
  • The OSG Consortium
    • Characteristics of an OSG friendly job
  • FAQ
    • Common Retirement
    • HCC Class Info for Instructors
    • HCC Class Info for Students
    • I have an HCC account, now what?
    • SSH host keys
  • Good HCC Practices
    • ATTIC Guidelines and Best Practices
  • Contact Us
  • hcc.unl.edu
    • Clear History
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