[Mne_analysis] mne-python dependence on numpy and scipy

[Alexandre Gramfort]

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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