[pymvpa] PyMVPA 0.5: feature wishlist

Johan Carlin jdc55 at cam.ac.uk
Wed Sep 30 16:06:34 UTC 2009

A big one for me would be better support for parallel processing in
iPython. Those multi-subject whole-brain searchlight analyses really
depend on this. :)

Currently it doesn't seem to be possible to pass actual PyMVPA objects
directly to the engines (something unpickleable somewhere?), so the
way I've found to do parallel processing involves passing very basic
information (e.g. 4D file path) to the engines, and leaving them to do
all the local processing independently before going on to the
searchlight. So each searchlight runs in serial, I just have multiple
subjects running in parallel. This is rather crude, compared to what
iPython's parallel processing system is supposed to be capable of.

It would be fantastic to be able to split off to parallel at a later
stage, e.g. with a parallelised searchlight function.

At the very least, a documented example of how to get parallel
processing to work with the current PyMVPA would be hugely helpful.
There are a few odd quirks and pitfalls to work through, as I learned.


2009/9/30  <pkg-exppsy-pymvpa-request at lists.alioth.debian.org>:
> Send Pkg-ExpPsy-PyMVPA mailing list submissions to
>        pkg-exppsy-pymvpa at lists.alioth.debian.org
> To subscribe or unsubscribe via the World Wide Web, visit
>        http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-pymvpa
> or, via email, send a message with subject or body 'help' to
>        pkg-exppsy-pymvpa-request at lists.alioth.debian.org
> You can reach the person managing the list at
>        pkg-exppsy-pymvpa-owner at lists.alioth.debian.org
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Pkg-ExpPsy-PyMVPA digest..."
> Today's Topics:
>   1. PyMVPA 0.5: feature wishlist (Michael Hanke)
> ----------------------------------------------------------------------
> Message: 1
> Date: Tue, 29 Sep 2009 12:55:36 -0400
> From: Michael Hanke <michael.hanke at gmail.com>
> Subject: [pymvpa] PyMVPA 0.5: feature wishlist
> To: PyMVPA mailing list <pkg-exppsy-pymvpa at lists.alioth.debian.org>
> Message-ID: <20090929165536.GA11254 at meiner>
> Content-Type: text/plain; charset=us-ascii
> Hi,
> we just started the design phase for PyMVPA 0.5. This is going to be a
> major release with significant changes that will put PyMVPA in shape for
> future developments. While, right now, I do not want to talk about the
> stuff that we are doing for 0.5 already, we would be interested in
> getting feature requests.
> PyMVPA 0.5 will change the API, therefore we are especially interested
> in feature requests that seem to be impossible or at least difficult to
> achieve with the current interface. We want to incorporate as many
> things into this API transition to keep it again stable for as long as
> possible.
> So if you are doing something with PyMVPA that has some pain associated
> with it, let us know about your suggestions...
> Thanks,
> Michael
> --
> GPG key:  1024D/3144BE0F Michael Hanke
> http://mih.voxindeserto.de
> ------------------------------
> _______________________________________________
> Pkg-ExpPsy-PyMVPA mailing list
> Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
> http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-pymvpa
> End of Pkg-ExpPsy-PyMVPA Digest, Vol 19, Issue 14
> *************************************************

Johan Carlin
Graduate Student
MRC Cognition & Brain Sciences Unit
15 Chaucer Road
Cambridge CB2 7EF

johan.carlin at mrc-cbu.cam.ac.uk
+44 (0)1223 355294 ext 593

More information about the Pkg-ExpPsy-PyMVPA mailing list