[pymvpa] PyMVPA searchlight command is freezing up

Yaroslav Halchenko debian at onerussian.com
Tue Oct 23 21:41:53 UTC 2012

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
we are hitting
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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