[Mne_analysis] mne-python dependence on numpy and scipy

Thu Jul 10 06:12:07 EDT 2014

You could also try setting up miniconda and only install the basic
dependencies. We do this for our build bot.

https://github.com/mne-tools/mne-python/blob/master/.travis.yml#L16

up to line 20 (but strip away the dashes which are specific to the yaml
syntax).

Best,
Denis

On Wed, Jul 9, 2014 at 9:16 PM, Alexandre Gramfort <
alexandre.gramfort at telecom-paristech.fr> wrote:

> > 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
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140710/a4d9c28b/attachment.html 