NeSI Support Documentation
Troubleshooting on NeSI
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GitHub
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NeSI Support Documentation
GitHub
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 v2.31.0
my.nesi.org.nz release notes v2.30.0
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
Announcements
Announcements
Preparing to move data to NeSI long term storage
Preparing your code for use on NeSI's new HPC platform
Accessing NeSI Support during the holiday break
Improved data management & efficient use of NeSI HPC storage
FAQs
FAQs
Common questions about the platform refresh
Can I change my time zone to New Zealand time?
Can I use SSHFS to mount the cluster filesystem on my local machine?
Converting from Windows-style to UNIX-style line endings
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 can I see how busy the cluster is?
How can I view images generated on the cluster?
How do I find out the size of a directory?
How do I fix my locale and language settings?
How do I request memory?
How do I run my Python Notebook through SLURM?
How to replace my 2FA token
I have not scanned the 2FA QR code
I've run out of storage space
Login Troubleshooting
Mahuika - Māui Differences
Password Expiry
Skylake warning message on Māui
Two Factor Authentication FAQ
What are my .bashrc & .bash_profile for?
What does "oom-kill" mean?
What is a '.core' file?
What software environments on NeSI are optimised for Machine Learning and data science?
Where should I store my data on NeSI systems?
Why am I seeing 'Account is not ready'?
Why can't I log in using MobaXTerm?
Why does my program crash?
Why is my job taking a long time to start?
NeSI Policies
NeSI Policies
Acceptable Use Policy
Access Policy
Account Requests for non-Tuakiri Members
Acknowledgement, Citation and Publication
Allocation classes
How we review applications
Institutional allocations
Merit allocations
NeSI Application Support Model
NeSI Licence Policy
NeSI Password Policy
NeSI Privacy Policy
Postgraduate allocations
Proposal Development allocations
Total HPC Resources Available
Release Notes
Release Notes
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 19/12/2024
jupyter.nesi.org.nz release notes 26/11/2024
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
Known Issues
Known Issues
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
Moving to the new filesystem
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
Troubleshooting on NeSI
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