-
Notifications
You must be signed in to change notification settings - Fork 0
Working on the Cluster
Start with the fundamentals of using the MASSIVE operating system
MASSIVE/HPC clusters | Linux/bash scripting | |
Principles and Philosophy | As computational neuroscientists, the work we do can get computationally demanding. To facilitate this, we (and many other labs) will use what is called a High-Performance Computing (HPC) cluster.
Our cluster is called MASSIVE, and it consists of many interconnected nodes which function similar to your laptop or desktop PC, but at a much larger scale. MASSIVE is a cloud computing solution. This means that we connect to MASSIVE and its desktops remotely, so you won’t need a powerful computer to access MASSIVE and it can be accessed anywhere in the world. You may however need a reliable internet connection in order to access the remote desktop without much latency. Similarly, nothing you save on MASSIVE will be saved on your personal computer, so you may need to transfer relevant files if necessary. |
Your MASSIVE desktop uses an operating system called Linux, which is a Unix-like operating system. It basically works just like the Windows or Macintosh operating systems that you might be more familiar with, but with a greater emphasis on command line usage than menus for navigation.
This means you’ll want to open what is known as a terminal, where you can run text based commands to open and move files or even run different software programs. Bash is a language used in Linux to write these text based commands. When running software on MASSIVE specifically, you’ll often need to load specific modules before you get started in the terminal you’re currently running. |
Introduction | You should read the guidelines and talk to Chao about creating a MASSIVE account.
The Strudel web client (currently in beta) is the simplest method of opening a desktop and what we recommend for beginners. See the section below on >>>>> gd2md-html alert: undefined internal link (link text: "getting started on MASSIVE"). Did you generate a TOC with blue links? |
Before you run any software, you’ll need to be familiar with the basic syntax of bash.
Andy’s Brain Book provides an intro to bash for Linux/Unix with an emphasis on how this can be used to run relevant neuroimaging software you might use. When using the brain book, you’ll need to launch a MASSIVE desktop and then open the terminal (see >>>>> gd2md-html alert: undefined internal link (link text: "here"). Did you generate a TOC with blue links? here). There are a few small modifications you’ll have to make when using the brain book tutorials on MASSIVE - see >>>>> gd2md-html alert: undefined internal link (link text: "here"). Did you generate a TOC with blue links? here.
|
Advanced techniques | ||
Other notes |
|
VirtualGL
|
- 0.0 Home
- 0.1 Neuroscience fundamentals
- 0.2 Reproducible Science
- 0.3 MRI Physics, BIDS, DICOM, and data formats
- 0.4 Introduction to Diffusion MRI
- 0.5 Introduction to Functional MRI
- 0.6 Measuring functional and effective connectivity
- 0.7 Connectomics, graph theory, and complexity
- 0.8 Statistical and Mathematical Tidbits
- 0.9 Introduction to Psychopathology
- 0.10 Introduction to Genetics and Bioinformatics
- 0.11 Introduction to Programming
- 1.0 Working on the Cluster
- 2.0 Programming Languages
- 2.1 Python
- 2.2 MATLAB
- 2.3 R and RStudio
- 2.4 Programming Intro Exercises
- 2.5 git and GitHub
- 2.6 SLURM and Job Submission
- 3.0 Neuroimaging Tools and Packages
- 3.1 BIDS
- 3.2 FreeSurfer
- 3.2.1 Qdec
- 3.3 FSL
- 3.3.1 ICA-FIX
- 3.4 Connectome Workbench/wb_command
- 3.5 fMRIPrep
- 3.6 QSIPrep
- 3.7 HCP Pipeline
- 3.8 tedana
- 4.0 Quality control
- 4.1 MRIQC
- 4.2 Common Artefacts
- 4.3 T1w
- 4.4 rs-fMRI
- 5.0 Specialist Tools
- 6.0 Putting it all together