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Cluster Documentation

eResearch Support

Cluster Documentation

Research HPC Cluster (Aoraki) Documentation
Getting Started
Getting Started
- Access
  Access
  - Access Overview
  - Getting an Account
  - Account and Allocation Management
    
    Account and Allocation Management
    
    Allocation Management
    
    Viewing Current Status
  - Accessing the login node (ssh)
  - OnDemand Web portal
- Data transfer
  Data transfer
- Software
  Software
  - onDemand
    onDemand
    
    Open OnDemand
    
    Using the Open OnDemand File Manager
    
    OnDemand HPC Desktop
    
    Accessing the Shell through Open OnDemand
    
    Available Apps
  - Applications
    
    Applications
    
    4ti2
    
    AFNI (Analysis of Functional NeuroImages)
    
    AlphaFold
    
    Alphafold3
    
    Ansys Fluent
    
    Bohra
    
    CCP4
    
    Circlator
    
    GLOBEClaritas
    
    ColabFold
    
    Connectome Workbench
    
    Crystal
    
    DeepLabCut
    
    DeepPoseKit
    
    Dorado
    
    fMRIPrep (Containerised)
    
    FSL
    
    Gaussian
    
    Gubbins
    
    Guppy (GPU)
    
    HUMAnN 3.0
    
    Macaulay2
    
    Mathematica
    
    MATLAB
    
    Ollama
    
    Openprose
    
    ORCA
    
    PyTorch via module
    
    Samtools
    
    Space Ranger
    
    TBProfiler
    
    Whisper (speech-to-text)
    
    xdsguI
  - Software environments
    
    Software environments
    
    Apptainer (Singularity)
    
    Conda/Mamba
    
    Using Modules (LMOD)
    
    Renv (R package environments)
    
    SBGrid
    
    Shells (bash, zsh, fish, tcsh)
    
    Spack
    
    Python virtual environments
- Running Jobs
  Running Jobs
  - Running Jobs Overview
  - Interactive
    Interactive
    
    Interactive Jobs
    
    Interactive job efficiency
    
    Launch desktop
  - Batch
    Batch
    
    Slurm Quickstart Outline
    
    Using slurm
    Using slurm
    
    Define job
    
    Slurm Overview
    
    Submit job
    
    Slurm examples
    Slurm examples
    
    Array Jobs
    
    Dependent Jobs
    
    Using a GPU with Slurm
    
    Heterogeneous Jobs
    
    Interactive Jobs
    
    Using Python with Slurm
    
    Using R with Slurm
    
    Job Efficiency
  - Current utilisation
- Workflows
  Workflows
  - Nextflow
  - Project setup
    Project setup
    
    Project setup
    
    Bioinformatics software
    
    Rstudio
General
General
- Research HPC Cluster (Aoraki)
- Announcements
  Announcements
  - April 2025 Maintenance
  - November 2024 Maintenance
- Guidelines
  Guidelines
- Changelogs
  Changelogs
- FAQ
  FAQ
- Support
Storage
Storage
- Storage Overview
- File permissions
- Data Locations
  Data Locations

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