The UC Berkeley Neuro cluster is designed for scientific research. It provides secure, high-peformance workstations, redundant data storage, high-speed network, and scientific applications. For details, see the technical specifications.

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Our documentation should be current and accurate.

Please email me at support-neuro@berkeley.edu if you have suggestions to improve it.

Neuro Cluster HOWTO

• Unix account
  • open an account
  • change password
• 2-step authentication
  • enable 2-step
  • Install an app for TOTP 2-step authentication
  • troubleshooting
  • 2-step web browser plugin
  • SSH key
• X2Go remote desktop
  • install
  • configure
  • start
  • managing your x2go session
  • performance
  • troubleshooting
• command-line login
  • secure shell (ssh) on Mac and Linux
  • secure shell on Windows
• File transfer
  • sftp
  • secure copy (scp)
  • rsync
• Mount cluster data
  • SSHFS
• Data management
  • data backups
  • disk quotas
  • data compression
• File sharing
  • lab members
  • external collaborators
• Networking
  • request an IP address

Data analysis

Please email support-neuro@berkeley.edu if you want additional software installed/updated on the neuro cluster.

• bash shell
  • using the command line
  • locating software
  • bash shell script
  • bash iteration
  • common commands
• MATLAB
  • Graphics
    • Compatibility with Mac
  • SPM
  • Toolboxes
  • PC Installation
• FSL
  • Installation
  • X2Go display problems
  • Tutorial
  • Documentation
• FreeSurfer
  • Configuration
  • Tutorial
  • Documentation
• Python
  • Conda
  • packages
  • Conda integration with Grid Engine (batch processing)
  • Jupyter Notebook
• R Project
  • rstudio
  • packages
• Grid Engine
  • Scripting Tutorial
    • batch processing
    • defining datasets with numeric_array
    • defining datasets with ‘submit’ qsub wrapper
    • Scripting Example 1: qsub numeric array
    • Scripting Example 2: ‘submit’ qsub wrapper
    • Scripting Example 3: matlab (with memory reservation)
  • command reference
    • qsub
    • qload
    • qdel
    • qstat
    • qacct
  • memory reservation
    • print memory usage
    • print memory availability
    • reserve memory via qsub
    • reserve memory via qsub ‘submit’ wrapper
    • modify memory reservation
  • Why didn’t my job run?
    • troubleshooting with qstat
    • troubleshooting with qquota
    • troubleshooting with qstats
    • using log files