Tags
Index showing all tags.
access¶
- AI Agent Guidelines
- Access Policy
- Account Requests for Non-Tuakiri Members
- Bash Shell
- Bash: Reference Sheet
- Can I Change My Time Zone to New Zealand Time
- Connecting to the Cluster
- Converting From Windows Style to UNIX Style Line Endings
- File Managers
- Filesystem Mounts Using SSHFS
- First Time Login
- Git Bash (Windows)
- How Can I View Images Generated on the Cluster
- How Do I Fix My Locale and Language Settings
- How Do I Replace My Additional Authentication Credentials
- Identity Changes for Crown Research Institutes
- Logging in to my.nesi.org.nz
- Login Troubleshooting
- MobaXterm Setup (Windows)
- Port Forwarding
- SCP (Secure Copy)
- Security Policy
- Standard Terminal Setup
- Tuakiri Attribute Validator
- VSCode
- What Are My Bashrc and Bash Profile For
- What Is Multiple Factor Authentication MFA
- What Is a Trusted Device
- Why Am I Seeing Account Is Not Ready
- WinSCP/PuTTY Setup (Windows)
- Windows Subsystem for Linux (WSL)
- X11
account¶
- Acceptable Use Policy
- Access Policy
- Account Requests for Non-Tuakiri Members
- Acknowledgement, Citation and Publication
- Adding Members to Your Project
- Allocation Approvals
- Allocation Classes
- Allocations & Extensions
- Applying for a New Project
- Applying to Join a Project
- Billing Process
- Checking Resource Usage
- Creating an Account
- Fair Share
- File Permissions and Groups
- First Time Login
- How Can I Give Read Only Team Members Access to My Files
- How Can I Let My Fellow Project Team Members Read or Write My Files
- How Do I Replace My Additional Authentication Credentials
- How We Review Applications
- Job Efficiency Review
- Job Limits
- Job Prioritisation
- Logging in to my.nesi.org.nz
- Managing Notification Preferences
- Navigating the my.nesi.org.nz Web Interface
- New HPC Portal
- Pricing
- Privacy Policy
- Project Request Form
- Quarterly Allocation Periods
- Requesting to renew an allocation via my nesi org nz
- Service Governance Contact
- Subscriber Monthly Usage Reports
- Tuakiri Attribute Validator
- Types of Contracts
- What Is a Subscription?
- What Is an Allocation?
- Why Am I Seeing Account Is Not Ready
ai_tools¶
announcement¶
- Accessing REANNZ HPC Support During the Easter and ANZAC Holidays
- Adding Members to Your Project
- Administrative Updates to HPC Policies
- Applying for a New Project
- Applying to Join a Project
- Autodeletion of Scratch Filesystem
- Checksums
- December Holiday Support Restrictions
- Known Issues HPC3
- Mahuika HPC3 Differences
biology¶
- AlphaFold
- BLAST
- BRAKER
- Clair3
- Databases
- Dorado
- FreeSurfer
- GATK
- MAKER
- RAxML
- Relion
- Supernova
- Trinity
- VirSorter
- fastStructure
- ipyrad
- ont-guppy-gpu
- snpEff
checksum¶
chemistry¶
cloud¶
consultancy¶
containers¶
data¶
data management¶
data retention¶
database¶
earth_science¶
engineering¶
fairshare¶
file_transfer¶
- Add Your Computer to Globus
- Bookmarks
- Configuring S3cmd
- Data Transfer Between Two Personal Computers
- Data Transfer Overview
- Data Transfer Using Globus
- Data Transfer to Freezer
- Data Transfer to the Research Developer Cloud
- File Managers
- FileSender
- Filesystem Mounts Using SSHFS
- Globus CLI
- Globus Compute
- Globus First Time Setup
- Globus Overview
- Globus Renaming
- Identity Provider System Maintenance
- MobaXterm (Windows)
- RClone
- Rsync
- SCP (Secure Copy)
- Share Collections
- Signing Up to Join a Globus Subscription
- Sync'ing With Globus-Automate
- WinSCP (Windows)
- WinSCP/PuTTY Setup (Windows)
gpu¶
ide¶
interactive¶
- Batch Computing Guide
- Containers as kernels in JupyterLab
- Data Transfer Using OnDemand
- First Time Login
- How Do I Run My Python Notebook Through SLURM
- How-to guide
- Index
- JupyterLab
- JupyterLab Interactive Sessions
- MATLAB
- Marimo Interactive Sessions
- Pluto.jl Interactive Sessions
- Python and R kernels in JupyterLab
- RStudio
- Slurm Composer
- Slurm interactive sessions
- Troubleshooting
- VSCode
- Virtual Desktop
julia¶
machine_learning¶
mathematics¶
mpi¶
multiplexer¶
openmp¶
- ABAQUS
- Multithreading Scaling Example
- OpenMP Settings
- Simultaneous Multithreading
- Thread Placement and Thread Affinity
parallel¶
- Configuring Dask-Mpi Jobs
- FlexiBLAS
- Job Arrays
- Job Arrays
- MPI Scaling Example
- Multithreading Scaling Example
- OpenMP Settings
- Parallel
- Parallel Computing
- Thread Placement and Thread Affinity
profiling¶
- Debugging
- Job Efficiency Review
- Job Scaling - Ascertaining Job Dimensions
- MPI Scaling Example
- Multithreading Scaling Example
- Profiler: VTune
- Scaling
- Slurm Native Profiling
- Tau for MPI Tracing
- VTune
python¶
- How Do I Run My Python Notebook Through SLURM
- JupyterLab Interactive Sessions
- Marimo Interactive Sessions
- Miniforge3
- Python and R kernels in JupyterLab
- ipyrad
- uv
r¶
release_notes¶
- 2025/06/23
- 2025/07/17
- 2025/08/05
- 2025/08/26
- 2025/09/22
- 2025/10/15
- 2025/10/29
- 2025/12/01
- 2026/01/13
- 2026/02/18
- 2026/04/28
- Known Issues HPC3
- Mahuika HPC3 Differences
- My nesi org nz release notes v2 20 0
- Release Notes
- Slurm Job Email
- my.nesi.org.nz Release Notes v2.0.1
- my.nesi.org.nz Release Notes v2.0.3
- my.nesi.org.nz Release Notes v2.1.0
- my.nesi.org.nz Release Notes v2.10.0
- my.nesi.org.nz Release Notes v2.11.0
- my.nesi.org.nz Release Notes v2.12.0
- my.nesi.org.nz Release Notes v2.13.0
- my.nesi.org.nz Release Notes v2.14.0
- my.nesi.org.nz Release Notes v2.15.0
- my.nesi.org.nz Release Notes v2.16.0
- my.nesi.org.nz Release Notes v2.17.0
- my.nesi.org.nz Release Notes v2.18.0
- my.nesi.org.nz Release Notes v2.19.0
- my.nesi.org.nz Release Notes v2.2.0
- my.nesi.org.nz Release Notes v2.21.0
- my.nesi.org.nz Release Notes v2.22.0
- my.nesi.org.nz Release Notes v2.23.0
- my.nesi.org.nz Release Notes v2.24.0
- my.nesi.org.nz Release Notes v2.25.0
- my.nesi.org.nz Release Notes v2.26.0
- my.nesi.org.nz Release Notes v2.27.0
- my.nesi.org.nz Release Notes v2.28.0
- my.nesi.org.nz Release Notes v2.29.0
- my.nesi.org.nz Release Notes v2.3.0
- my.nesi.org.nz Release Notes v2.30.0
- my.nesi.org.nz Release Notes v2.31.0
- my.nesi.org.nz Release Notes v2.33.0
- my.nesi.org.nz Release Notes v2.34.0
- my.nesi.org.nz Release Notes v2.35.0
- my.nesi.org.nz Release Notes v2.36.0
- my.nesi.org.nz Release Notes v2.37.0
- my.nesi.org.nz Release Notes v2.38.0
- my.nesi.org.nz Release Notes v2.39.0
- my.nesi.org.nz Release Notes v2.4.0
- my.nesi.org.nz Release Notes v2.40.0
- my.nesi.org.nz Release Notes v2.41.0
- my.nesi.org.nz Release Notes v2.42.0
- my.nesi.org.nz Release Notes v2.43.0
- my.nesi.org.nz Release Notes v2.44.0
- my.nesi.org.nz Release Notes v2.45.0
- my.nesi.org.nz Release Notes v2.46.0
- my.nesi.org.nz Release Notes v2.47.0
- my.nesi.org.nz Release Notes v2.48.0
- my.nesi.org.nz Release Notes v2.49.0
- my.nesi.org.nz Release Notes v2.5.0
- my.nesi.org.nz Release Notes v2.50.0
- my.nesi.org.nz Release Notes v2.51.0
- my.nesi.org.nz Release Notes v2.52.0
- my.nesi.org.nz Release Notes v2.53.0
- my.nesi.org.nz Release Notes v2.55.0
- my.nesi.org.nz Release Notes v2.6.0
- my.nesi.org.nz Release Notes v2.7.0
- my.nesi.org.nz Release Notes v2.8.0
- my.nesi.org.nz Release Notes v2.9.0
slurm¶
- Batch Computing Guide
- Checking Resource Usage
- Fair Share
- Finding Job Efficiency
- How Do I Request Memory
- How Do I Run My Python Notebook Through SLURM
- Identity Changes for Crown Research Institutes
- Job Arrays
- Job Arrays
- Job Checkpointing
- Job Efficiency Review
- Job Limits
- Job Prioritisation
- Resources
- SLURM: Best Practice
- Scron
- Slurm Composer
- Slurm Job Email
- Slurm Native Profiling
- Slurm interactive sessions
- Slurm: Reference Sheet
- Submitting Your First Job
- Using GPUs
- Why Is My Job Taking a Long Time to Start
software¶
- Application Support Model
- Environment & Modules
- FlexiBLAS
- Installing Applications Yourself
- Java
- Lambda Stack
- Licence Policy
- Miniforge3
- Software Installation Request
- Software Version Management
- Supported Applications
- Synda
- fastStructure
- uv
storage¶
- 2025/06/23
- 2025/07/17
- 2025/08/05
- 2025/08/26
- 2025/09/22
- 2025/10/15
- 2025/10/29
- 2025/12/01
- 2026/01/13
- 2026/02/18
- 2026/04/28
- Automatic Cleaning of Nobackup
- Configuring S3cmd
- Data Recovery
- Data Transfer to Freezer
- Data Transfer to the Research Developer Cloud
- File Permissions and Groups
- Filesystems and Quotas
- Freezer Guide
- Freezer Long Term Storage
- Gufi
- How Can I Give Read Only Team Members Access to My Files
- How Can I Let My Fellow Project Team Members Read or Write My Files
- How Do I Find Out the Size of a Directory
- Identity Provider System Maintenance
- Models
- Offsite Storage Options
- Other Useful Commands
- Temporary Directories
- Troubleshooting
- Where Should I Store My Data?
troubleshooting¶
- Can I Change My Time Zone to New Zealand Time
- Converting From Windows Style to UNIX Style Line Endings
- Fair Share
- Getting Help
- How Busy Is the Cluster?
- How Do I Fix My Locale and Language Settings
- How Do I Request Memory
- I've Run Out of Storage Space
- Making a Helpful Support Request
- System Status
- Troubleshooting
- What Does Oom Kill Mean
- What Is a Core File
- Why Does My Program Crash
tutorial¶
- Account Requests for Non-Tuakiri Members
- Bash Shell
- Bash: Reference Sheet
- Contributing
- Creating an Account
- Introductory Session for New Users
- Parallel
- Resources
- Scaling
- Slurm: Reference Sheet
- Standard Terminal Setup
- Submitting Your First Job
- Weekly Online Office Hours
- What Is an HPC
version_control¶
- Connecting to the Cluster
- Contributing
- Git Bash (Windows)
- Git Hosting Platform Setup
- Git: Reference Sheet