[Mne_analysis] mne-python dependence on numpy and scipy

[Krieger, Donald N.]

Hi Alex,

Thanks for responding so quickly.
I downloaded and installed it and see that it includes the shared library that numpy tries to load and fails to find: libpython2.7.so.1.0

I can include this library in my package but I need to alter some environmental variable (?) so that it will be found.
Any thoughts about this?

Regards,
 
Don
 
Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text


> -----Original Message-----
> From: mne_analysis-bounces at nmr.mgh.harvard.edu [mailto:mne_analysis-
> bounces at nmr.mgh.harvard.edu] On Behalf Of Alexandre Gramfort
> Sent: Wednesday, July 09, 2014 11:16 AM
> To: Discussion and support forum for the users of MNE Software
> Subject: Re: [Mne_analysis] mne-python dependence on numpy and scipy
> 
> hi Don,
> 
> mne cannot work without numpy and scipy.
> we need numpy at the very low level to read files from disk.
> 
> can you use a complete python distribution like anaconda that consists of a
> simple folder?
> 
> Alex
> 
> 
> 
> On Wed, Jul 9, 2014 at 3:31 PM, Krieger, Donald N. <kriegerd at upmc.edu>
> wrote:
> > I am attempting to use mne-python in a grid computing application.
> >
> > The only function that I need is read_forward_solution .
> >
> > Both mne-python and all the files imported and used by it must be
> > included in the package which is uploaded to each grid computer in
> > order to get it to work.
> >
> > As a first cut I’m including both numpy and scipy along with
> > mne-python since it imports modules from them.
> >
> > The whole thing is  failing because the linear algebra routines in
> > numpy require a shared compiled library which is not found on the
> > target machines on the grid.
> >
> >
> >
> > I’ve fooled around with commenting out the import statements for numpy
> > and scipy functions but the dependencies are not readily eliminated.
> >
> > Perhaps someone has a better idea about how to go about this.
> >
> > I would like to get this to work and secondarily to work without
> > requiring numpy or scipy at all.
> >
> > The reason for that is that I am running on average 35,000 jobs per day.
> >
> > Each requires uploading the entire package which requires that much
> > more network bandwidth given the size of the assembled packages.
> >
> >
> >
> > A somewhat optimal solution would be to “skeletonize” the chain of
> > dependencies and required files needed to support  the limited
> > functionality required for the application.
> >
> > Is there a simple algorithm or even a tool for doing this?
> >
> > Your thoughts and direction would be appreciated.
> >
> > Thanks.
> >
> >
> >
> > Regards,
> >
> >
> >
> > Don
> >
> >
> >
> > Don Krieger, Ph.D.
> >
> > Department of Neurological Surgery
> >
> > University of Pittsburgh
> >
> > (412)648-9654 Office
> >
> > (412)521-4431 Cell/Text
> >
> >
> >
> >
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