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Welcome to the M3 user guide

warning

These are our old docs! Please see our new docs at https://docs.erc.monash.edu/M3/.

These old docs were roughly converted from our old format. As a result, this copy is not identical to our previous docs. You can still find our original old docs at https://old-docs.massive.org.au/.

You may notice some formatting and structural issues with these old docs. We will not resolve these, this is here purely for backwards compatibility to ensure old URLs do not die.

Help and Support​

Using M3​

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
    • Topaz script
    • 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

Advanced​

News and events​

Archive​