[pymvpa] PyMVPA searchlight command is freezing up

[Sarah Helfinstein]

Sorry, I'm not exactly sure what you mean. Are you saying you were able to
run the script successfully with my data and got output? Or were you unable
to load my data and that's why you couldn't reproduce the error? If the
former, then we'll just try to run it using the same set-up you used &
maybe that will work for us. Also, I didn't receive the attachment you
sent. I only receive your responses through the mailing list e-mails...I'm
not sure if I'm supposed to be getting them another way, as well.

Best,
Sarah

Message: 3
> Date: Tue, 23 Oct 2012 17:41:53 -0400
> From: Yaroslav Halchenko <debian at onerussian.com>
> To: pkg-exppsy-pymvpa at lists.alioth.debian.org
> Subject: Re: [pymvpa] PyMVPA searchlight command is freezing up
> Message-ID: <20121023214153.GE26676 at onerussian.com>
> Content-Type: text/plain; charset="utf-8"
>
> As with any good bug -- I can't reproduce this on my laptop running
> Debian (wheezy/sid/experimental) amd64 with python2.7 .  Tried with the
> copy of libsvm we ship in sources (good old libsvm 2.89) and built
> linking against system wide libsvm 3.12 ... what is your system (may be
> just cut/paste output of mvpa2.wtf()), version of libsvm (not listed in
> wtf() output)?
>
> you could also try enabling LIBSVM verbose output (I am attaching a copy
> of your script with .*SVM.* debug targets enabled) -- may be some output
> before/during stalling would be of help...
>
> also in that script I placed (in comments) for using shogun's SVM
> instead -- you could try that one as well may be?
>
> NB with this script, loading data from kindly provided by you
> /tmp/problemdata.h5
> we are hitting
> https://github.com/nipy/nibabel/issues/144
> which I haven't had a chance yet to troubleshoot either ...
>
>
> On Mon, 22 Oct 2012, Yaroslav Halchenko wrote:
>
> > Hi Sarah,
>
> > Last weeks were quite hectic due to preparation/travel to SfN... finally
> > I am back so expect to hear from me by the end of the week -- otherwise
> > buzz is welcome.
>
> > Cheers
>
> > On Mon, 22 Oct 2012, Sarah Helfinstein wrote:
>
> > >    Hi Yaroslav,
>
> > >    I wrote a few weeks ago about not being able to get a searchlight to
> > >    converge when doing an SVM() classification analysis with PyMVPA.
> At your
> > >    suggestion, I was able to run a successful classification with a
> GNB()
> > >    classifier, but I also passed along my data in the hopes that you
> could
> > >    get it to run successfully with an SVM() classifier. Have you had
> any luck
> > >    with that? Did you receive the data?
>
> > >    Best,
> > >    Sarah
> --
> Yaroslav O. Halchenko
> Postdoctoral Fellow,   Department of Psychological and Brain Sciences
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
> WWW:   http://www.linkedin.com/in/yarik
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> ------------------------------
>

-- 
Sarah Helfinstein, PhD
Postdoctoral Fellow, Imaging Research Center
Departments of Psychology and Neurobiology
The University of Texas at Austin

Email: shelfins at gmail.com
Web: http://www.poldracklab.org/people<http://luci.iordanescu.googlepages.com/homepage>
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