Welcome to the M3 user guide

20 August, 2024: M3 Rocky conversion completed

The upgrade of M3 to the new Rocky 9 Operating System is effectively complete. Thank you for your patience and understanding throughout this process.

For details on what this change means, see our M3 Rocky FAQ.

Help and Support

• Help and Support
• Scheduled Maintenance
• Archived System Status and Known Issues
• MASSIVE Terms of Use

Using M3

• About M3
  • System configuration
  • Partitions
• Requesting an account
  • Overview of the process
    • 1. Log in to the HPC ID system
    • 2. Create an M3 account
    • 3. Create or join an M3 project
    • 4. Set your M3 account password
    • 5. Log in to M3
    • Request an M3 account via email
• Requesting help on M3
  • Software issues
  • System issues
  • Contacting us
    • Help Desk
    • Drop-in Sessions
    • General Enquiries
    • Postal Address
• Connecting to M3
  • Connecting to M3 via ssh
    • Linux and OS X Users
    • Windows Users
  • Connecting to M3 via Strudel2
    • Using the Desktop Application in Strudel2
    • Using the JupyterLab Application in Strudel2
    • Using the Terminal Application in Strudel2
    • Using JupyterLab with Custom Minconda Environments in Strudel2
    • Connecting to M3 with Visual Studio Code and Strudel2
  • Troubleshooting Common Issues Using Strudel
    • I can login to Strudel and launch a desktop but cannot connect. I click the connect button and get an error saying “failed to connect to server”
    • Strudel Web fails to connect to the desktop or Strudel2 crashes when trying to connect to desktop
    • I can connect to a Desktop, but the display looks messed up, or I can see the display, but cannot interact with the Desktop!
    • I’m unable to type certain letters in STRUDEL web desktop
• File Systems on M3
  • What to put on each file system?
    • Home directory (~10GB)
    • Project directory (Shared with everyone on your project)
    • Scratch directory (Shared with everyone on your project)
  • Disk Quotas
  • Default Quotas for New Projects
  • Scratch Usage Policies
  • System Backups and File Recovery
    • File Recovery Procedure
  • Information for Desktop Users
    • Thumbnails Generating Too Much Data
    • Remember to empty your trash folder
    • Already over quota?
  • Storage outside of M3
    • Instructions to access Market and Vault shares on M3
    • Instructions to access Vault with SFTP and Rsync
• Copying files to and from M3
  • GUI Tool - Windows, Mac OS, and Linux Users
    • FileZilla
    • WinSCP - Windows
  • Globus
    • Getting Started
    • Personal Globus Endpoint
    • Transferring Data
  • Globus - Command Line Interface
  • Globus - Platform as a Service
    • Globus Juptyer Notebooks
    • Data Portals
  • Command Line Interface - Linux and OS X Users
    • rsync
• Software on M3
  • Modules
    • Requesting an install
  • Containers and Docker on M3
  • Python and conda on M3
  • Software for the Monash Bioinformatics Platform (MBP)
  • Software Deprecation: Java
• Running jobs on M3
  • Partitions on M3
    • Compute partitions
    • GPU partitions
  • Checking the status of M3
    • The STATUS field explained
  • Slurm Accounts
    • Default accounts
    • Setting the account for a job
    • Questions about slurm accounts
  • Getting started with job submission scripts
  • Running Simple Batch Jobs
    • An example Slurm job script
    • Cancelling jobs
  • MPI on M3
  • On CentOS 7
    • Software
    • Load the MPI compiler
    • Compile the software
    • Running the software
  • On Rocky 9
  • UCX_NET_DEVICES
  • Running Multi-threading Jobs
    • An example Slurm Multi-threading job script
  • Running Interactive Jobs
    • Submitting an Interactive Job
    • How long do interactive jobs last for?
    • Reconnecting to/Disconnecting from an Active Interactive Job
  • Running GPU Jobs
    • Running GPU Batch Jobs
    • Compiling your own CUDA or OpenCL codes for use on M3
  • Running Array Jobs
    • An example of Slurm Array job script
  • QoS (Quality of Service)
    • How to run jobs with QoS
    • Explanation
  • Features & Constraints
    • An example of using constraint in the job script
    • Features Available
  • Checking job status
    • Method 1: show_job
    • Method 2: Slurm commands
  • Project Allocation
    • Project Space
    • Questions about allocation
• Lustre File System Quickstart Guide
  • About Lustre
• GPUs on M3
  • Starter Guide: GPUs on M3
    • GPUs on HPC (remote) vs. Laptop/Workstation (local)
    • How do I choose a GPU?
    • Questions to ask yourself when choosing a GPU
  • GPU Look-Up Tables
    • How do I choose a GPU?
    • Look-Up Tables
  • Frequently Asked Questions About GPUs on M3
    • How long will I wait for a GPU?
    • Why am I waiting so long for a GPU?
    • How do I know if my job is using the GPU?
    • I’m in the Machine Learning Community, do you have any specific advice for me?

Communities

• MX2 Eiger
  • The Big Picture
  • Authorising MASSIVE to download your data (CAP Leaders only)
  • Creating research projects (research lab leaders only)
  • Requesting access to M3
  • Getting started on M3
  • Connecting to M3
  • Accessing your MX data
  • Reprocessing your MX data
  • Recommended Settings
  • Known Issues
    • Cannot open or read filename.tmp error
  • Need help?
• Machine Learning
  • Software
  • Reference datasets
  • GPUs on M3
  • Training
  • Community Engagement
  • Quick guide for checkpointing
    • Why checkpointing?
• Neuroimaging
  • Using SLURM to submit a simple FSL job
    • Background
    • Data and scripts
• Cryo EM
  • Relion
    • The Graphical Interface
    • Using the Queue
    • Motion Correction
    • 2d/3d Classification & Refinement
    • Particle Polishing
  • Access to CryoSPARC on M3
  • Cryo EM Pre-Processing Tool
  • Cryo EM Benchmarking and Optimisation
    • Cryo EM Benchmarking and Optimisation
• Bioinformatics
  • Requesting an account on M3
• The Genomics partition
  • Getting started with the Bioinformatics module
    • Importing the Bioinformatics module environment
    • Installing additional software with Bioconda
  • Pipelines and workflow managers on M3
    • Running NextFlow on M3
  • FAQ
• DGX
  • Hardware
  • How to access the DGX hardware
  • What jobs are suitable?
    • How do you demonstrate a suitable project/job?
• Data Collections
  • Machine learning
    • ImageNet 2012 (ILSVRC2012)
    • ImageNet 2015 Object Detection Data (ILSVRC2015 DET)
    • International Skin Imaging Collaboration 2019 (ISIC 2019)
    • NIH Chest X-ray Dataset (NIH CXR-14)
    • Stanford Natural Language Inference (SNLI) Corpus
    • COCO (Common Objects in Context) 2017
    • AlphaFold
    • AlphaFold v2 - AlphaFold-Multimer release
  • Neuroimaging
    • Human Connectome Project Dataset (HCP): HCP-1200
    • Lifespan Human Connectome Project Development
    • Lifespan Human Connectome Project Aging
    • Baby Connectome Project
    • Human Connectome Project for Early Psychosis
    • Developing Human Connectome Project (dHCP)
    • Brain Genomics Superstruct Project (GSP)
    • Nathan Kline Institute Rockland Sample (NKI-RS): Neuroimaging Release
  • Genomes
    • BlastDB
  • Requesting a data collection
• XNAT
  • Create an account at Monash-XNAT
  • Request to create a project at Monash-XNAT
  • Mirroring data from Alfred-XNAT to Monash-XNAT
  • Pulling Data from Monash-XNAT to MASSIVE M3

FAQs

• MASSIVE M3 on Rocky Linux 2024
  • What is the plan?
  • What has not changed
  • Important Considerations with Strudel2
  • How to access the Rocky Linux front-facing nodes?
  • How do I submit batch jobs to Rocky Linux nodes?
  • What modules are available?
  • Avizo/Amira on Rocky
  • How do I request software to be installed on Rocky Linux?
  • Very long JupyterLab queue times
  • sbatch: error: Batch job submission failed: Requested node configuration is not available
• Frequently asked questions
  • Accounts
  • Jobs
  • M3, desktops and Strudel
• About Field of Research (FOR) and Socio-Economic Objective (SEO) codes
• Miscellaneous
• My HOME directory is full!
  • How to connect to M3 if I can’t use a STRUDEL desktop?
  • The user_info command
  • The ncdu command
  • Common causes of your disk filling up
    • Large Log Files: ~/.vnc/
    • Conda environments and packages: ~/.conda/
    • Cache Folders:
    • Large data files
  • Other disk quota issues