Welcome to the M3 user guide#
Upcoming maintenance 20 November 2024
Please be advised that M3 will be offline for scheduled maintenance on Wednesday, 20 November 2024 from 8 AM AEDT to 5 PM AEDT. More details to follow.
- About M3
- Requesting an account
- Requesting help on M3
- Connecting to M3
- Connecting to M3 via ssh
- Connecting to M3 via 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
- Copying files to and from M3
- Software on M3
- Modules
- Containers and Docker on M3
- Python and conda on M3
- Software for the Monash Bioinformatics Platform (MBP)
- Related pages
- Installed software modules
- Common software issues
- Running Python on M3
- Running Anaconda on M3
- Python and conda on M3: Frequently Asked Questions (FAQ)
- Running Miniconda on M3
- Using PyCharm with your Virtual environment
- Running Python Virtual Environments on M3
- Running Python and conda on M3
- Conda on M3 (Rocky 9)
- Software Deprecation: Java
- Running jobs on M3
- Partitions on M3
- Checking the status of M3
- Slurm Accounts
- Getting started with job submission scripts
- Running Simple Batch Jobs
- MPI on M3
- On CentOS 7
- On Rocky 9
- UCX_NET_DEVICES
- Running Multi-threading Jobs
- Running Interactive Jobs
- Running GPU Jobs
- Running Array Jobs
- QoS (Quality of Service)
- Features & Constraints
- Checking job status
- Project Allocation
- Diagnosing problems with jobs
- GPUs on M3
- MX2 Eiger
- Machine Learning
- Neuroimaging
- Cryo EM
- Bioinformatics
- The Genomics partition
- DGX
- 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
- Requesting a data collection
- Machine learning
- XNAT
- 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
- About Field of Research (FOR) and Socio-Economic Objective (SEO) codes
- Miscellaneous
- My HOME directory is full!