[FieldTrip] QSUB toolbox on a multi-core computer

Herring, J.D. (Jim) j.herring at fcdonders.ru.nl
Thu Jun 27 12:45:53 CEST 2013

Dear Graham,


As stated in the tutorial the distributed computing functions are intended
to distribute workload over different computers running a Torque or SGE
batch system: "This tutorial covered how to distribute your
computations/workload over multiple computers in a cluster that uses the
Torque or SGE batch queue system". However, what you could do is make use
of Matlab's parallel processing tools. Matlab allows you to open a pool of
so-called 'workers' to distribute processing jobs to allowing you to run
multiple processes in parallel. Please see
http://www.mathworks.nl/help/distcomp/matlabpool.html and


Once you've opened a pool of workers using 'matlabpool', you can use
'parfor' in the same way as you would use 'for' to create a loop that runs
all processes in parallel over all four cores. 




From: fieldtrip-bounces at science.ru.nl
[mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Graham Peyton
Sent: woensdag 26 juni 2013 12:14
To: fieldtrip at science.ru.nl
Subject: [FieldTrip] QSUB toolbox on a multi-core computer


Dear FieldTrip community,

I am trying to carry out an MEG analysis using the qsub distributed
computing toolbox. I'm using a quad-core i7 computer, and was hoping that
I'd be able to distribute the workload over all four cores. 

I have followed the tutorial below exactly:

The problem I am having is this: I managed to run example 1 (with my own
dataset), but I am finding that when I use qsubcellfun, the function
ft_definetrial is executed sequentially (for each condition), not in
parallel. Is there a way I can correct this, so as to parallelize the
analysis? Or is the toolbox not designed for multi-core machines? 


Many thanks,

Graham Peyton

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