Cluster

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Connect

get a password

  • press the PASS WORD button on your crypto card
  • enter passoword
  • press enter
  • the 7 digit password is given (without the dash)

setup environment

  • put all your customizations into your .bashrc
  • for login shells, .bash_profile is used, which in turn loads .bashrc

ssh to the gateway computer (hadley)

note: please don't use the gateway for computations (e.g. matlab)!

 ssh -Y neuro-calhpc.berkeley.edu (or hadley.berkeley.edu) 

and use your crypto password

Useful commands

Start interactive session on compute node

  • start interactive session: qsub -X -I
  • start interactive session on particular node: qsub -X -I -l nodes=n0001.cortex

Perceus commands

The perceus manual is here

  • listing available cluster nodes:
 wwstats
  • list cluster usage
 wwtop
  • to restrict the scope of these commands to cortex cluster, add the following line to your .bashrc
 export NODES='*cortex'
  • module list
  • module avail
  • module help


Resource Manager PBS

  • Job Scheduler MOAB
  • List running jobs:
 qstat -a
  • List jobs of a given node:
 qstat -n 98
  • sample script
 #!/bin/bash
 
 #PBS -q cortex
 #PBS -l nodes=1:ppn=2:cortex
 #PBS -l walltime=01:00:00
 #PBS -o path-to-output
 #PBS -e path-to-error
 cd /global/home/users/kilian/
 cat $PBS_NODEFILE
 mpirun -np 8 /bin/hostname
 sleep 60
  • submit script
 qsub scriptname
  • interactive session
 qsub -I -q cortex -l nodes=1:ppn=2:cortex -l walltime=00:15:00
  • list nodes that your job is running on
 cat $PBS_NODEFILE

Matlab

note: remember to start an interactive session before starting matlab!

We don't currently have a proper Matlab installation. However, you can run an old version by appending the following to the .bashrc file in your home directory:

 export PATH=$PATH:/global/home/users/jack/matlab74/bin


Support Requests

  • If you have a problem that is not covered on this page, you can send an email to our user list:
 redwood_cluster@lists.berkeley.edu
  • If you need additional help from the LBL group, send an email to their email list. Please always cc our email list as well.
 scs@lbl.gov
  • In urgent cases, you can also email Krishna Muriki (LBL User Services) directly.