Tag Archives: linux

Torque batch queue system for mentat

I have installed the torque batch queue system on our 50 node (~300 core) mentat cluster. Here are some useful PBS commands that can be used with Torque.

qsub script
Submit a job script for execution.
qstat
Show status of running and pending jobs.
tracejob
Display historical information about your jobs.
qdel
Kill a job.
qhold
Hold a job.
qstat -Q
qstat -Qf

Show configuration of queues.

Peer-to-peer distributed Matlab computing – update

After discussing in detail with colleagues at the Donders and at the FIL, I have implemented the peer-to-peer distributed computing toolbox for MATLAB. Most of the desired functionality is now in place, and it seems to work robustly and efficiently.

The peer toolbox allows you to do something like this in MATLAB

a = randn(400,400);
tic; cellfun('pinv', {a, a, a, a, a}, 'UniformOutput', false); toc
tic; peercellfun('pinv', {a, a, a, a, a}, 'UniformOutput', false); toc

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Peer-to-peer distributed Matlab computing

In a recent meeting with the SPM developers, we discussed parallel computing using the Matlab distributed computing toolbox, Star-P, Sun Grid Engine, and other batch systems that can be linked to Matlab. These are all limited in their usefulness for the typical neuroimaging research setting in that they are based on a centralized job distribution system. That may work fine on a large cluster with a centralized configuration and system administration, but even then the usefullness is limited because all input and output data (which are typically large) have to be send over the network twice: first to the job manager, then to the compute node (and vice versa for the results).

To resolve some of these problems, I came up with the idea of peer-to-peer distributed computing in Matlab. The full description can be found on http://fieldtrip.fcdonders.nl/development/peer