NeSI Support Documentation

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NeSI Support Documentation

GitHub

Access
Access
- Accounts Projects and Allocations
  Accounts Projects and Allocations
- NeSI Policies
  NeSI Policies
- NeSI Service Subscriptions
  NeSI Service Subscriptions
  - Overview
    Overview
    
    Pricing
    
    Questions?
    
    What is a Subscription?
  - Contracts and billing processes
    Contracts and billing processes
    
    Billing process
    
    Types of contracts
  - Service Governance
    Service Governance
    
    Allocation approvals
    
    Service Governance contact
    
    Subscriber Monthly Usage Reports
- My nesi org nz
  My nesi org nz
High Performance Computing
High Performance Computing
- Mahuika Cluster
  Mahuika Cluster
  - Terminal Setup
    
    Terminal Setup
    
    SSH Config Setup
    
    Git Bash (Windows)
    
    MobaXterm Setup (Windows)
    
    Port Forwarding
    
    VSCode
    
    WinSCP/PuTTY Setup (Windows)
    
    Windows Subsystem for Linux (WSL)
    
    X11 on NeSI
  - Checksums
  - Hyperthreading
  - NetCDF / HDF5 file locking
- Data Management
  Data Management
  - File Systems and Quotas
    
    File Systems and Quotas
    
    Automatic cleaning of nobackup file system
    
    Data Compression
    
    File permissions and groups
    
    I/O Performance Considerations
    
    Moving to the new filesystem
  - Data Recovery
    Data Recovery
    
    File Recovery
  - Nearline long-term storage
    Nearline long-term storage
    
    Nearline Long-Term Storage Service
    
    Preparing small files for migration to Nearline storage
    
    Verifying uploads to Nearline storage
    
    Release Notes Nearline
    Release Notes Nearline
    
    Long-Term Storage - Nearline release notes v1.1.0.14
    
    Long Term Storage - Nearline release notes v1.1.0.21
    
    Long Term Storage - Nearline release notes v1.1.0.22
    
    Long-term Storage - Nearline release notes v1.1.0.18
    
    Long-term Storage - Nearline release notes v1.1.0.19
    
    Long-term Storage - Nearline release notes v1.1.0.20
  - Moving files to and from the cluster
  - Globus Transfer Service
    Globus Transfer Service
    
    Globus Quick Start Guide
    
    Data Transfer using Globus V5
    
    Globus V5 endpoint activation
    
    Globus V5 Paths, Permissions, Storage_Allocation
    
    Initial Globus Sign-Up, and your Globus Identities
    
    Re-creating Shared Collections and Bookmarks in Globus V5
    
    Personal Globus Endpoint Configuration
    
    National Data Transfer Platform
    
    Download and share CMIP6 data (for NIWA researchers)
    
    Data transfer between NeSI and a PC without NeSI two-factor authentication
    
    Sync'ing files between NeSI and another computer with globus-automate
- Software
  Software
  - Software Catalouge
    
    Software Catalouge
    
    ABAQUS
    
    ANSYS
    
    AlphaFold
    
    BLAST
    
    BRAKER
    
    CESM
    
    COMSOL
    
    Clair3
    
    Cylc
    
    Delft3D
    
    Dorado
    
    FDS
    
    FlexiBLAS
    
    GATK
    
    GROMACS
    
    Gaussian
    
    Java
    
    Julia
    
    Keras
    
    Lambda Stack
    
    MAKER
    
    MATLAB
    
    Miniconda3
    
    Molpro
    
    NWChem
    
    ORCA
    
    OpenFOAM
    
    OpenSees
    
    ParaView
    
    Python
    
    R
    
    RAxML
    
    Relion
    
    Singularity
    
    Supernova
    
    Synda
    
    TensorFlow on CPUs
    
    TensorFlow on GPUs
    
    Trinity
    
    TurboVNC
    
    VASP
    
    VTune
    
    VirSorter
    
    WRF
    
    ipyrad
    
    ont-guppy-gpu
    
    snpEff
  - Building Software
    Building Software
    
    Build an Apptainer container on a Milan compute node
    
    Compiling software
    
    Creating Your Own Modules
    
    Building_Software
  - Profiling and Debugging
    Profiling and Debugging
    
    Debugging
    
    Profiler: ARM MAP
    
    Profiler: VTune
    
    Slurm Native Profiling
- Batch Computing
  Batch Computing
  - Finding Job Efficiency
  - GPU use on NeSI
  - Job Checkpointing
  - Milan Compute Nodes
  - Per job temporary directories
  - SLURM: Best Practice
  - Slurm Interactive Sessions
  - Slurm Partitions
  - Submitting your first job
  - Project Accounting
    Project Accounting
    
    Checking your project's usage using nn_corehour_usage
    
    Fair Share
    
    Fair Share -- How jobs get prioritised
    
    Job prioritisation
- Open OnDemand
  Open OnDemand
  - Interactive apps
    Interactive apps
    
    JupyterLab
    
    JupyterLab
    
    Jupyter kernels - Tool-assisted management
    
    Jupyter kernels - Manual management
    
    RStudio
    
    MATLAB
    
    Code server
    
    Virtual desktop
  - How-to guide
  - Changes from Jupyter on NeSI
  - Release Notes
    
    Release Notes
  - Known Issues
    
    Known Issues
- Parallel Computing
  Parallel Computing
Researcher Developer Cloud
Researcher Developer Cloud
- User guides
  User guides
  - Launch and manage instances
    
    Launch and manage instances
    
    With the dashboard
    With the dashboard
    
    Launch an Instance via Dashboard
    
    Resizing an Instance via the Dashboard
    
    Manage Security Groups of an Instance via the Dashboard
    
    with the CLI
    with the CLI
    
    Launch an Instance via CLI
    
    Launch an Instance from an Image
    
    Launch an Instance from a volume
    
    Resizing an Instance via CLI
    
    Manage Security Groups of an Instance via CLI
    
    Other tools
    Other tools
    
    Deployment of an instance with Terraform
    
    Connect to your instance by using SSH
    
    Launch and mange instances
  - uploading and managing Images
    
    uploading and managing Images
    
    With the dashboard
    With the dashboard
    
    Upload Image
    
    Managing Images
    
    Upload an Image via the Dashboard
    
    Upload an Image via the Dashboard
    
    With the cli
    With the cli
    
    Upload Image
    
    Managing Images
    
    Upload an Image via CLI
    
    Upload an Image via CLI
    
    Converting Image types
    
    Image Visibility Types
  - Create and manage volumes
    
    Create and manage volumes
    
    With the dashboard
    With the dashboard
    
    Create and manage volumes via the dashboard
    
    With the cli
    With the cli
    
    Create and manage volumes via CLI
    
    Format and Mount volumes
  - Create and manage networks
    
    Create and manage networks
    
    with the CLI
    with the CLI
    
    Create and manage network ports via CLI
    
    Create and manage network via CLI
    
    Manage Floating IPs via CLI
    
    Manage Security groups via CLI
    
    With the dashboard
    With the dashboard
    
    Create and manage networks via the dashboard
    
    Create and manage Security groups with the dashboard
    
    Create and manage network ports with the dashboard
    
    Manage Floating IPs via the Dashboard
  - Create and manage identity
    
    Create and manage identity
    
    Creating and Managing Application Credentials via CLI
    
    Create and manage networks via the dashboard
  - Create and manage keypairs
    
    Create and manage keypairs
    
    Create and manage keypairs via CLI
    
    Create and manage keypairs via the dashboard
  - Create and manage object storage
    
    Create and manage object storage
    
    With the dashboard
    With the dashboard
    
    Create and manage object storage via the dashboard
    
    with the CLI
    with the CLI
    
    Create and manage object storage via CLI
    
    Creating and Managing EC2 Credentials via CLI
    
    Using boto3 to interact with object storage
    
    Using cyberduck to interact with object storage
  - setting up your CLI environment
    
    setting up your CLI environment
- Security
  Security
  - Security Policy
  - Shared Responsibility Model
  - Terms
  - Security practices
    
    Security practices
    
    Building Effective and Efficient Research Security Programs
- Release notes
  Release notes
Capability & Skills
Capability & Skills

Index

March 3, 2025