NeSI Support Documentation

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Researcher Support
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NeSI Support Documentation

Researcher Support
Researcher Support
- Getting Started
  Getting Started
  - Accounts, Projects and Allocations
    Accounts, Projects and Allocations
    
    Creating a NeSI Account Profile
    
    Applying for a new NeSI project
    
    Applying to join an existing NeSI project
    
    What is an allocation?
    
    Quarterly allocation periods
    
    Adding members to your NeSI project
    
    Project Extensions and New Allocations on Existing Projects
  - Accessing the HPCs
    Accessing the HPCs
    
    Setting Up and Resetting Your Password
    
    Setting Up Two Factor Authentication
    
    Choosing and Configuring Software for Connecting to the Clusters
    
    X-Forwarding using the Ubuntu Terminal on Windows
    
    Port Forwarding
  - Next Steps
    Next Steps
    
    Moving files to and from the cluster
    
    Submitting your first job
    
    Parallel Execution
    
    Finding Job Efficiency
    
    Job Scaling - Ascertaining job dimensions
    
    MPI Scaling Example
    
    Multithreading Scaling Example
    
    The HPC environment
  - Getting Help
    Getting Help
    
    NeSI wide area network connectivity
    
    Weekly Online Office Hours
    
    Consultancy
    
    Job efficiency review
    
    System status
    
    Introductory Material
  - Cheat Sheets
    Cheat Sheets
    
    Bash: Reference Sheet
    
    Git: Reference Sheet
    
    Slurm: Reference Sheet
    
    tmux: Reference sheet
  - my.nesi.org.nz
    my.nesi.org.nz
    
    Logging in to my.nesi.org.nz
    
    Managing notification preferences
    
    Navigating the my.nesi.org.nz web interface
    
    Requesting to renew an allocation via my.nesi.org.nz
    
    The NeSI Project Request Form
    
    Tuakiri Attribute Validator
    
    Release Notes my.nesi.org.nz
    Release Notes my.nesi.org.nz
    
    my.nesi.org.nz release notes v2.29.0
    
    my.nesi.org.nz release notes v2.28.0
    
    my.nesi.org.nz release notes v2.27.0
    
    my.nesi.org.nz release notes v2.26.0
    
    my.nesi.org.nz release notes v2.25.0
    
    my.nesi.org.nz release notes v2.24.0
    
    my.nesi.org.nz release notes v2.23.0
    
    my.nesi.org.nz release notes v2.22.0
    
    my.nesi.org.nz release notes v2.21.0
    
    My nesi org nz release notes v2 20 0
    
    my.nesi.org.nz release notes v2.19.0
    
    my.nesi.org.nz release notes v2.18.0
    
    my.nesi.org.nz release notes v2.17.0
    
    my.nesi.org.nz release notes v2.16.0
    
    my.nesi.org.nz release notes v2.15.0
    
    my.nesi.org.nz release notes v2.14.0
    
    my.nesi.org.nz release notes v2.13.0
    
    my.nesi.org.nz release notes v2.12.0
    
    my.nesi.org.nz release notes v2.11.0
    
    my.nesi.org.nz release notes v2.10.0
    
    my.nesi.org.nz release notes v2.9.0
    
    my.nesi.org.nz release notes v2.8.0
    
    my.nesi.org.nz release notes v2.7.0
    
    my.nesi.org.nz release notes v2.6.0
    
    my.nesi.org.nz release notes v2.5.0
    
    my.nesi.org.nz release notes v2.4.0
    
    my.nesi.org.nz release notes v2.3.0
    
    my.nesi.org.nz release notes v2.2.0
    
    my.nesi.org.nz release notes v2.1.0
    
    my.nesi.org.nz release notes v2.0.3
    
    my.nesi.org.nz release notes v2.0.1
- General
  General
- Scientific Computing
  Scientific Computing
  - Supported Applications
    
    Supported Applications
    
    ABAQUS
    
    ANSYS
    
    AlphaFold
    
    BLAST
    
    BRAKER
    
    CESM
    
    COMSOL
    
    Clair3
    
    Cylc
    
    Delft3D
    
    Dorado
    
    FDS
    
    FlexiBLAS
    
    GATK
    
    GROMACS
    
    Gaussian
    
    Java
    
    Julia
    
    JupyterLab
    
    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
  - Training
    Training
    
    Introduction to computing on the NeSI HPC
    
    Introduction to computing on the NeSI HPC (YouTube Recordings)
    
    Webinars
    
    Workshops
  - Interactive computing using Jupyter
    Interactive computing using Jupyter
    
    Jupyter on NeSI
    
    Jupyter kernels - Tool-assisted management
    
    Jupyter kernels - Manual management
    
    MATLAB via Jupyter on NeSI
    
    RStudio via Jupyter on NeSI
    
    Virtual Desktop via Jupyter on NeSI
    
    Release Notes jupyter.nesi.org.nz
    Release Notes jupyter.nesi.org.nz
    
    jupyter.nesi.org.nz release notes 04/10/2024
    
    jupyter.nesi.org.nz release notes 27/08/2024
    
    jupyter.nesi.org.nz release notes 30/07/2024
    
    jupyter.nesi.org.nz release notes 26/03/2024
    
    jupyter.nesi.org.nz release notes 22/11/2023
    
    jupyter.nesi.org.nz release notes 14/11/2023
    
    jupyter.nesi.org.nz release notes 15/06/2023
    
    jupyter.nesi.org.nz release notes 19/05/2023
    
    jupyter.nesi.org.nz release notes 02/02/2023
    
    jupyter.nesi.org.nz release notes 25/08/2022
    
    jupyter.nesi.org.nz release notes 12/07/2022
    
    jupyter.nesi.org.nz release notes 31/03/2022
    
    jupyter.nesi.org.nz release notes 28/06/2022
    
    jupyter.nesi.org.nz release notes 02/06/2022
    
    jupyter.nesi.org.nz release notes 02/11/2021
    
    jupyter.nesi.org.nz release notes 14/10/2021
    
    jupyter.nesi.org.nz release notes 24/09/2021
    
    jupyter.nesi.org.nz release notes 16/09/2021
    
    jupyter.nesi.org.nz release notes 12/05/2021
  - Interactive computing with NeSI OnDemand
    
    Interactive computing with NeSI 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
    
    v0.2.0 Release Notes
  - The NeSI High Performance Computers
    
    The NeSI High Performance Computers
    
    Mahuika
    
    Māui
    
    Māui Ancillary
    
    Available GPUs on NeSI
  - Running Jobs on Māui and Mahuika
    Running Jobs on Māui and Mahuika
    
    Checking your project's usage using nn_corehour_usage
    
    GPU use on NeSI
    
    Job Checkpointing
    
    Slurm Interactive Sessions
    
    Fair Share
    
    Job prioritisation
    
    Mahuika Slurm Partitions
    
    Milan Compute Nodes
    
    Māui Slurm Partitions
    
    SLURM: Best Practice
    
    NetCDF / HDF5 file locking
    
    Checksums
    
    Fair Share -- How jobs get prioritised
    
    Hyperthreading
  - Profiling and Debugging
    Profiling and Debugging
    
    Debugging
    
    Profiler: ARM MAP
    
    Profiler: VTune
    
    Slurm Native Profiling
  - HPC Software Environment
    HPC Software Environment
    
    Build an Apptainer container on a Milan compute node
    
    OpenMP settings
    
    Offloading to GPU with OpenMP
    
    Offloading to GPU with OpenACC
    
    NVIDIA GPU Containers
    
    Configuring Dask-MPI jobs
    
    Software Version Management
    
    Thread Placement and Thread Affinity
    
    NICE DCV Setup
    
    Visualisation software
    
    Finding Software
    
    Installing (Third Party) applications
    
    Compiling software: Mahuika
    
    Compiling software: Māui
    
    Programming environment differences between Maui and Mahuika
    
    Per job temporary directories
    
    Run an executable under Apptainer in parallel
    
    Software Installation Request
    
    Temporary directories
  - Terminal Setup
    Terminal Setup
    
    Standard Terminal Setup
    
    Git Bash (Windows)
    
    MobaXterm Setup (Windows)
    
    VSCode
    
    WinSCP/PuTTY Setup (Windows)
    
    Windows Subsystem for Linux (WSL)
    
    X11 on NeSI
  - Manuals and User Guides
    Manuals and User Guides
    
    Manuals
    
    Troubleshooting on NeSI
    
    XC50 Aries Network Architecture
- Storage
  Storage
  - File Systems and Quotas
    File Systems and Quotas
    
    NeSI File Systems and Quotas
    
    Automatic cleaning of nobackup file system
    
    Data Compression
    
    File permissions and groups
    
    I/O Performance Considerations
  - Data Recovery
    Data Recovery
    
    File Recovery
  - Data Transfer Services
    Data Transfer Services
    
    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
  - 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
- 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
Research Developer Cloud
Research Developer Cloud
- Research developer cloud
  Research developer cloud
  - Summary
  - Release notes
    Release notes
    
    Essential building blocks v0.9 - 20230918 NZRSE23
    
    Research Developer Cloud updates and fixes v0.10 - 20231205
    
    Research Developer Cloud updates v0.11 - 20240205
    
    Summary
  - Security
    
    Security
    
    Security Policy
    
    Shared Responsibility Model
    
    Summary
    
    Terms
    
    Security practices
    
    Security practices
    
    Building Effective and Efficient Research Security Programs
    
    Summary
  - User guides
    
    User guides
    
    Summary
    
    Create and manage identity
    
    Create and manage identity
    
    Creating and Managing Application Credentials via CLI
    
    Create and manage networks via the dashboard
    
    Summary
    
    Create and manage keypairs
    
    Create and manage keypairs
    
    Create and manage keypairs via CLI
    
    Create and manage keypairs via the dashboard
    
    Summary
    
    Create and manage networks
    
    Create and manage networks
    
    Create and manage network ports via CLI
    
    Create and manage network ports with the dashboard
    
    Create and manage network via CLI
    
    Create and manage networks via the dashboard
    
    Manage Floating IPs via CLI
    
    Manage Floating IPs via the Dashboard
    
    Manage Security groups via CLI
    
    Create and manage Security groups with the dashboard
    
    Summary
    
    Create and manage object storage
    
    Create and manage object storage
    
    Create and manage object storage via CLI
    
    Create and manage object storage via the dashboard
    
    Creating and Managing EC2 Credentials via CLI
    
    Summary
    
    Using boto3 to interact with object storage
    
    Using cyberduck to interact with object storage
    
    Create and manage volumes
    
    Create and manage volumes
    
    Create and manage volumes via CLI
    
    Create and manage volumes via the dashboard
    
    Format and Mount volumes
    
    Summary
    
    Launch and mange instances
    
    Launch and mange instances
    
    Connect to your instance by using SSH
    
    Launch and mange instances
    
    Deployment of an instance with Terraform
    
    Launch an Instance from a volume
    
    Launch an Instance from an Image
    
    Launch an Instance via CLI
    
    Launch an Instance via Dashboard
    
    Manage Security Groups of an Instance via CLI
    
    Manage Security Groups of an Instance via the Dashboard
    
    Resizing an Instance via CLI
    
    Resizing an Instance via the Dashboard
    
    Summary
    
    setting up your CLI environment
    
    setting up your CLI environment
    
    uploading and managing Images
    
    uploading and managing Images
    
    Converting Image types
    
    Image Visibility Types
    
    Upload an Image via CLI
    
    Upload an Image via the Dashboard
    
    Summary
    
    Upload an Image via CLI
    
    Upload an Image via the Dashboard

Summary

Security Practices
Building Effective and Efficient Research Security Programs
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October 19, 2024

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