HowTos / Compute

Using the cluster with the Matlab Parallel Toolbox

Cluster machines with matlab9, which has the parallel toolbox:

  • herbie
  • nina
  • mingus
  • ronnie

From these machines, you can use the parallel toolbox to use the Distributed Computing Server (DCS). If your own computer has the parallel toolbox, you can set it up to use the DCS as well, but you must be in the lab, i.e. behind the firewall, in order to use it. There are 3 machines with 2.9GHz dual processors available for use with DCS through the parallel toolbox.

Setting up matlabpool for DCS cluster using gui:

  • start matlab9, go to the Parallel menu and click on Manage Configurations
  • go to File > New > job manager
    • Configuration name and description are just for your use, so just use something convenient
    • Under Scheduler, Job manager hostname is sarah.shadlen.org
    • Job manager name is core
  • click ok (can fill in other stuff as necessary for jobs)
  • click the radio button next to your new job manager to make it the default.
  • click on Start Validation at the bottom right to make sure everything is working fine (won't work from a laptop unless you are in the lab, behind the firewall).

You now have 6 workers on 6 cores at your disposal.

The command matlabpool will start a worker pool using the default configuration with the pool size specified by that configuration. You can also specify the pool size using matlabpool open <poolsize>

Good introductions to DCS and parallel toolbox:

Files given to us in the presentation by Sarah and Angelo from Mathworks: http://www.shadlen.org/matlab/parallel_web_stuff

I ran the PhoneTowerScript.m from the parallelOptim folder from the above directory. I ran it first without matlabpool, and then ran matlabpool (using the DCS cluster as the pool) and ran it again. The process took 52 seconds on nina without the dcs pool, and 20 seconds with the pool.