<div dir="ltr">You could also try setting up miniconda and only install the basic dependencies. We do this for our build bot.<div><br></div><div><a href="https://github.com/mne-tools/mne-python/blob/master/.travis.yml#L16">https://github.com/mne-tools/mne-python/blob/master/.travis.yml#L16</a><br>
</div><div><br></div><div>up to line 20 (but strip away the dashes which are specific to the yaml syntax).</div><div><br></div><div>Best,</div><div>Denis</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Wed, Jul 9, 2014 at 9:16 PM, Alexandre Gramfort <span dir="ltr"><<a href="mailto:alexandre.gramfort@telecom-paristech.fr" target="_blank">alexandre.gramfort@telecom-paristech.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="">> Thanks for responding so quickly.<br>
> 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<br>
<br>
</div>it's shipped with anaconda. So it should work.<br>
<br>
I would see with your sys admin<br>
<br>
Alex<br>
<div class="HOEnZb"><div class="h5"><br>
> I can include this library in my package but I need to alter some environmental variable (?) so that it will be found.<br>
> Any thoughts about this?<br>
><br>
> Regards,<br>
><br>
> Don<br>
><br>
> Don Krieger, Ph.D.<br>
> Department of Neurological Surgery<br>
> University of Pittsburgh<br>
> (412)648-9654 Office<br>
> (412)521-4431 Cell/Text<br>
><br>
><br>
>> -----Original Message-----<br>
>> From: <a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu">mne_analysis-bounces@nmr.mgh.harvard.edu</a> [mailto:<a href="mailto:mne_analysis-">mne_analysis-</a><br>
>> <a href="mailto:bounces@nmr.mgh.harvard.edu">bounces@nmr.mgh.harvard.edu</a>] On Behalf Of Alexandre Gramfort<br>
>> Sent: Wednesday, July 09, 2014 11:16 AM<br>
>> To: Discussion and support forum for the users of MNE Software<br>
>> Subject: Re: [Mne_analysis] mne-python dependence on numpy and scipy<br>
>><br>
>> hi Don,<br>
>><br>
>> mne cannot work without numpy and scipy.<br>
>> we need numpy at the very low level to read files from disk.<br>
>><br>
>> can you use a complete python distribution like anaconda that consists of a<br>
>> simple folder?<br>
>><br>
>> Alex<br>
>><br>
>><br>
>><br>
>> On Wed, Jul 9, 2014 at 3:31 PM, Krieger, Donald N. <<a href="mailto:kriegerd@upmc.edu">kriegerd@upmc.edu</a>><br>
>> wrote:<br>
>> > I am attempting to use mne-python in a grid computing application.<br>
>> ><br>
>> > The only function that I need is read_forward_solution .<br>
>> ><br>
>> > Both mne-python and all the files imported and used by it must be<br>
>> > included in the package which is uploaded to each grid computer in<br>
>> > order to get it to work.<br>
>> ><br>
>> > As a first cut I’m including both numpy and scipy along with<br>
>> > mne-python since it imports modules from them.<br>
>> ><br>
>> > The whole thing is failing because the linear algebra routines in<br>
>> > numpy require a shared compiled library which is not found on the<br>
>> > target machines on the grid.<br>
>> ><br>
>> ><br>
>> ><br>
>> > I’ve fooled around with commenting out the import statements for numpy<br>
>> > and scipy functions but the dependencies are not readily eliminated.<br>
>> ><br>
>> > Perhaps someone has a better idea about how to go about this.<br>
>> ><br>
>> > I would like to get this to work and secondarily to work without<br>
>> > requiring numpy or scipy at all.<br>
>> ><br>
>> > The reason for that is that I am running on average 35,000 jobs per day.<br>
>> ><br>
>> > Each requires uploading the entire package which requires that much<br>
>> > more network bandwidth given the size of the assembled packages.<br>
>> ><br>
>> ><br>
>> ><br>
>> > A somewhat optimal solution would be to “skeletonize” the chain of<br>
>> > dependencies and required files needed to support the limited<br>
>> > functionality required for the application.<br>
>> ><br>
>> > Is there a simple algorithm or even a tool for doing this?<br>
>> ><br>
>> > Your thoughts and direction would be appreciated.<br>
>> ><br>
>> > Thanks.<br>
>> ><br>
>> ><br>
>> ><br>
>> > Regards,<br>
>> ><br>
>> ><br>
>> ><br>
>> > Don<br>
>> ><br>
>> ><br>
>> ><br>
>> > Don Krieger, Ph.D.<br>
>> ><br>
>> > Department of Neurological Surgery<br>
>> ><br>
>> > University of Pittsburgh<br>
>> ><br>
>> > (412)648-9654 Office<br>
>> ><br>
>> > (412)521-4431 Cell/Text<br>
>> ><br>
>> ><br>
>> ><br>
>> ><br>
>> > _______________________________________________<br>
>> > Mne_analysis mailing list<br>
>> > <a href="mailto:Mne_analysis@nmr.mgh.harvard.edu">Mne_analysis@nmr.mgh.harvard.edu</a><br>
>> > <a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
>> ><br>
>> ><br>
>> > The information in this e-mail is intended only for the person to whom<br>
>> > it is addressed. If you believe this e-mail was sent to you in error<br>
>> > and the e-mail contains patient information, please contact the<br>
>> > Partners Compliance HelpLine at <a href="http://www.partners.org/complianceline" target="_blank">http://www.partners.org/complianceline</a><br>
>> > . If the e-mail was sent to you in error but does not contain patient<br>
>> > information, please contact the sender and properly dispose of the<br>
>> > e-mail.<br>
>> ><br>
>><br>
>> _______________________________________________<br>
>> Mne_analysis mailing list<br>
>> <a href="mailto:Mne_analysis@nmr.mgh.harvard.edu">Mne_analysis@nmr.mgh.harvard.edu</a><br>
>> <a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
><br>
> _______________________________________________<br>
> Mne_analysis mailing list<br>
> <a href="mailto:Mne_analysis@nmr.mgh.harvard.edu">Mne_analysis@nmr.mgh.harvard.edu</a><br>
> <a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
<br>
_______________________________________________<br>
Mne_analysis mailing list<br>
<a href="mailto:Mne_analysis@nmr.mgh.harvard.edu">Mne_analysis@nmr.mgh.harvard.edu</a><br>
<a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a></div></div></blockquote></div><br></div>