NeSI Support Documentation
Troubleshooting on NeSI
Initializing search
GitHub
Contact Support
NeSI Support Documentation
GitHub
Getting Started
Getting Started
Accounts, Projects and Allocations
Accounts, Projects and Allocations
Creating a NeSI Account
Applying for a new NeSI project
Applying to join an existing NeSI project
Allocations
Quarterly allocation periods
Account Requests for non-Tuakiri Members
Adding members to your NeSI project
Project Extensions and New Allocations on Existing Projects
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
Accessing the HPCs
Accessing the HPCs
Setting Up and Resetting Your Password
Setting Up Two Factor Authentication
Connecting via SSH
Connecting via SSH
Recommended SSH config
Git Bash (Windows)
MobaXterm Setup (Windows)
VSCode
WinSCP/PuTTY Setup (Windows)
Windows Subsystem for Linux (WSL)
Connecting via Web
Port Forwarding
X Forwarding on NeSI
Your First Job
Your First Job
File Transfer
Environment Modules
Slurm Scheduler
Finding Job Efficiency
Parallel Computing
Parallel Computing
Hyperthreading
Job Scaling - Ascertaining job dimensions
MPI Scaling Example
Multithreading Scaling Example
Getting Help
Getting Help
NeSI wide area network connectivity
Weekly Online Office Hours
Consultancy
Job efficiency review
System status
Introductory Material
Software
Software
Software Catalogue
Software Catalogue
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
Developing
Developing
Compiling software: Mahuika
Compiling software: Māui
Configuring Dask-MPI jobs
Installing (Third Party) applications
NetCDF / HDF5 file locking
Offloading to GPU with OpenACC
Offloading to GPU with OpenMP
Programming environment differences between Maui and Mahuika
Thread Placement and Thread Affinity
Profiling and Debugging
Profiling and Debugging
Debugging
Profiler: ARM MAP
Profiler: VTune
Slurm Native Profiling
Containers
Containers
Build an Apptainer container on a Milan compute node
NVIDIA GPU Containers
Run an executable under Apptainer in parallel
Running Jobs
Running Jobs
Batch Scheduling
Batch Scheduling
Checking your project's usage using nn_corehour_usage
Fair Share
Job Checkpointing
Job prioritisation
Mahuika Slurm Partitions
Māui Slurm Partitions
OpenMP settings
Per job temporary directories
Slurm Best Practice
Slurm Interactive Sessions
Temporary directories
Interactive computing with Jupyter
Interactive computing with Jupyter
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
Interactive computing with OpenOnDemand
Interactive computing with OpenOnDemand
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
Using GPUs
Using GPUs
Available GPUs on NeSI
GPU use on NeSI
Data Management
Data Management
File Systems and Quotas
File Systems and Quotas
Automatic cleaning of nobackup file system
Data Compression
File Recovery
File permissions and groups
I/O Performance Considerations
Globus Data Transfer
Globus Data Transfer
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
Preparing small files for migration to Nearline storage
Verifying uploads to Nearline storage
Checksums
Contracts and Policy
Contracts and Policy
Access
Access
Acceptable Use Policy
Access Policy
Acknowledgement, Citation and Publication
How we review applications
Password Policy
Privacy Policy
Allocations
Allocations
Allocation classes
Institutional allocations
Merit allocations
Postgraduate allocations
Proposal Development allocations
Service Subscriptions
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
Support
Support
Application Support Model
Licence Policy
Total HPC Resources Available
Troubleshooting on NeSI
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