Tags
Index showing all tags.
access¶
- 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 Is A Trusted Device
- What are my bashrc and bash profile for
- What is Multiple Factor Authentication MFA
- 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 Limits
- Job efficiency review
- Job prioritisation
- Logging in to my.nesi.org.nz
- Managing notification preferences
- Navigating the my.nesi.org.nz web interface
- 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
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
- Common questions about the platform refresh
- December holiday support restrictions
- Known Issues HPC3
- Mahuika HPC3 Differences
batch¶
biology¶
- AlphaFold
- BLAST
- BRAKER
- Clair3
- Databases
- Dorado
- GATK
- MAKER
- RAxML
- Relion
- Supernova
- Trinity
- VirSorter
- fastStructure
- ipyrad
- ont-guppy-gpu
- snpEff
checksum¶
chemistry¶
cloud¶
composer¶
consultancy¶
containers¶
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 to Freezer
- Data Transfer using Globus
- File Managers
- FileSender
- Filesystem Mounts using SSHFS
- Globus CLI
- Globus First Time Setup
- Globus Overview
- 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)
flood modelling¶
freezer¶
globus¶
gpu¶
hydraulics¶
hydrodynamics¶
ide¶
interactive¶
- Batch Computing Guide
- Data Transfer Using OnDemand
- First Time Login
- How do I run my Python Notebook through SLURM
- How-to guide
- Jupyter kernels - Manual management
- Jupyter kernels - Tool-assisted management
- JupyterLab interactive sessions
- MATLAB via OnDemand
- Marimo interactive sessions
- Pluto.jl interactive sessions
- Slurm interactive sessions
- Troubleshooting
- Virtual Desktop via OnDemand
intro¶
job script¶
julia¶
machine_learning¶
mathematics¶
mpi¶
multiplexer¶
ondemand¶
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 Scaling - Ascertaining job dimensions
- Job efficiency review
- 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
- Jupyter kernels - Manual management
- Jupyter kernels - Tool-assisted management
- JupyterLab interactive sessions
- Marimo interactive sessions
- Miniforge3
- 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
- Common questions about the platform refresh
- 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 v2.6.0
- 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
releasenote¶
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 Limits
- Job efficiency review
- Job prioritisation
- Resources
- SLURM: Best Practice
- 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
- 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
- Creating an Account
- Parallel
- Resources
- Scaling
- Slurm: Reference Sheet
- Standard Terminal Setup
- Submitting Your First Job
- What is an HPC