[Mne_analysis] mne-python dependence on numpy and scipy

[Alexandre Gramfort]

> 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

it's shipped with anaconda. So it should work.

I would see with your sys admin

Alex

> 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
>> >
>> >
>> >
>> >
>> > _______________________________________________
>> > Mne_analysis mailing list
>> > Mne_analysis at nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> > it is addressed. If you believe this e-mail was sent to you in error
>> > and the e-mail contains patient information, please contact the
>> > Partners Compliance HelpLine at http://www.partners.org/complianceline
>> > . If the e-mail was sent to you in error but does not contain patient
>> > information, please contact the sender and properly dispose of the
>> > e-mail.
>> >
>>
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis