[Eeglablist] How to make an ICA run in less than a week?

Tue Jul 31 13:34:00 PDT 2012

James -

AMICA (Jason Palmer) runs in parallel on a cluster (Linux, Windows, Mac
OS). It is also the most powerful ICA for EEG (Delorme et al., PLoS One,
2012) and the ICA algorithm we use by default now at SCCN (though extended
infomax ICA in EEGLAB as runica() and binica() is related and 2nd most
powerful of the ~22 linear blind source separation algorithms we compared).

Scott

On Wed, Jul 25, 2012 at 12:41 PM, James Desjardins <jdesjardins at brocku.ca>wrote:

>  Hi Baris,
>
> In order to overcome the time costs of ICA I have been using EEGLab and a
> modified Batch plugin on the Shared Hierarchical Academic Research Computer
> Network (SHARCNet, www.sharcnet.ca, it is on my to-do-list to explore
> similar international HPC resources). While this does not necessarily speed
> up the ICA calculation it allows me to run up to 64 simultaneous Matlab
> workers (shared across users). I am also exploring Octave in this context
> (no licensing limitations).
>
> While presenting this strategy to the HPC community at a recent research
> day I was enthusiastically approached by someone who witnessed a GPU
> optimized ICA implemented in R. I have not had a chance to look into it
> further than finding this site
> http://brainarray.mbni.med.umich.edu/brainarray/rgpgpu/
>
> See alsohttp://sccn.ucsd.edu/wiki/GPU_and_EEGLAB
>
> ___
> Sent from an auto-correcting touch screen device.
> ___
> James A. Desjardins, MA
> Electrophysiology Technologist
> Cognitive and Affective Neuroscience Lab, Psychology Department
> Jack and Nora Centre for Lifespan Development Research
> Brock University
> 500 Glenridge Ave.
> St. Catharine's, ON. Canada L2S 3A1
> 905-688-5550 x4676
> ___
> "'Cause you never can tell What goes on down below!
> "This pool might be bigger Than you or I know!"
>
>  McElligot's Pool
> Dr. Seuss 1947
>
> On Jul 24, 2012, at 2:42 PM, "Baris Demiral" <demiral.007 at googlemail.com>
> wrote:
>
>   Hi James,
>
> 1- For frequency of interest of 200Hz, you can down-sample your data
> down to 512Hz. But before that, low-pass filter your data with cut off
> value of 250Hz or so. Follow Nyquist theorem.
> 2- You can run ICA on continuous data, but make sure you have marked
> AND rejected the bad segments in the EEG data, since bad recording
> WILL influence your ICA analysis A LOT. Pre-processing is still
> important, even though ICA will eventually be used to reject artifacts
> later. SO, observe your data well.
> 3- Xeon processors should have more than 2 cores I think. Run parallel
> MATLABs on the same computer over the different cores for different
> sets of subjects.
>
> Arno, and other eeglab gurus, do you have any plans to
> implement/combine ICA routines with parallel computing toolbox in
> matlab?  Is it possible to create, say, a PARICA? Is this
> theoretically possible? For instance, ICA routine can divide the data
> into 4 or so and then combine them over different cores/machines?
>
> Cheers,
> Baris
>
> On Fri, Jul 13, 2012 at 1:07 PM, James Schaeffer <schaefj3 at gmail.com>
> wrote:
>
> Hi All,
>
>
>
>  Thanks for your help.  I have started using binica and it is going a bit
>
> faster.  We have chosen to use a high sampling rate (2048 Hz) because we
>
> thought it might be needed for cross-frequency coupling analysis with high
>
> gamma up to 200 Hz.  If I downsample, will I still be able to see these
>
> relationships?
>
>
>
>  Thanks again,
>
>
>  James
>
>
>
>  On Thu, Jul 5, 2012 at 6:24 PM, James Schaeffer <schaefj3 at gmail.com>
> wrote:
>
>
>   Dear eeglablist,
>
>
>   I am running ICAs on 10 minutes of Biosemi EEG data, collected from 128
>
>  channels, and sampled at 2048 Hz. However, the ICAs have been running
> for a
>
>  few days without much progress. Two computers have 8G RAM and an Intel(R)
>
>  Xeon(TM) CPU 2.80GHz. One has been running an ICA for 6 days and is on
> step
>
>  33; the other, for 4 days, and is on step 28. Another computer has 12G
> RAM
>
>  and an Intel(R) Xeon(R) CPU 5110 @ 1.60GHz; it has been running for 3
> days
>
>  and is on step 60. All are running openSUSE 12.1 (x86_64), with eeglab
>
>  version 10.2.2.4b. The 'free' command indicates that they are not using
> any
>
>  swap space.  Should it be taking this long?  Is it possible that we have
>
>  more than the one copy of the data in ram or that Matlab or Eeglab has
>
>  placed something else in ram, or is busy with other processes? Is there
>
>  anything I can do to speed up this process? Any help would be greatly
>
>  appreciated.
>
>
>   Thanks in advance,
>
>  James
>
>
>
>
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>
>
> --
> Ş. Barış Demiral, PhD.
> Department of Psychiatry
> Washington University
> School of Medicine
> 660 S. Euclid Avenue
> Box 8134
> Saint Louis, MO 63110
> Phone: +1 (314) 747 1603
>
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-- 
Scott Makeig, Research Scientist and Director, Swartz Center for
Computational Neuroscience, Institute for Neural Computation; Prof. of
Neurosciences (Adj.), University of California San Diego, La Jolla CA
92093-0559, http://sccn.ucsd.edu/~scott
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