VMD-L Mailing List

From: Ondrej Marsalek (ondrej.marsalek_at_gmail.com)
Date: Wed Dec 02 2009 - 11:22:21 CST

Just to make it clear, I have my own build with my system python, so I
do not need this. I just wanted to provide some feedback.

Ondrej

On Wed, Dec 2, 2009 at 18:16, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
>  Looks like I'll have to dig into this a bit, it appears there are
> a couple of issues there where the Python build picked up local
> libraries it shouldn't have.
>
> This is just another example of why I always tell people that they're
> better off compiling VMD from source and linking it against their
> local Python installation rather than trying to make a Python
> installation that works on any machine and including it in VMD ;-)
>
> I'll see what I can do about this and tkinter.
>
> Cheers,
>  John
>
>
>
> On Wed, Dec 02, 2009 at 06:11:36PM +0100, Ondrej Marsalek wrote:
>> Hi,
>>
>> I have tried it and I get the following:
>>
>> vmd > gopython
>> Info) Starting Python...
>> Traceback (most recent call last):
>>   File "<string>", line 1, in <module>
>> ValueError: vmdnumpy module not available.
>> Info) Text interpreter now Python
>> Traceback (most recent call last):
>>   File "<string>", line 1, in <module>
>>   File "/usr/local/lib/vmd/scripts/python/Tkinter.py", line 59, in <module>
>>     import _tkinter # If this fails your Python may not be configured for Tk
>> ImportError: No module named _tkinter
>>
>> Still, I get the python promopt. When I try importing numpy, I get:
>>
>> >>> import numpy
>> Traceback (most recent call last):
>>   File "VMD", line 1, in <module>
>>   File "/usr/local/lib/vmd/lib_LINUXAMD64/lib/python2.5/site-packages/numpy/__init__.py",
>> line 43, in <module>
>>     import linalg
>>   File "/usr/local/lib/vmd/lib_LINUXAMD64/lib/python2.5/site-packages/numpy/linalg/__init__.py",
>> line 4, in <module>
>>     from linalg import *
>>   File "/usr/local/lib/vmd/lib_LINUXAMD64/lib/python2.5/site-packages/numpy/linalg/linalg.py",
>> line 25, in <module>
>>     from numpy.linalg import lapack_lite
>> ImportError: liblapack.so.3: cannot open shared object file: No such
>> file or directory
>>
>> I have set PYTHONHOME properly (specifically, I do "export
>> PYTHONHOME=/usr/local/lib/vmd/lib_LINUXAMD64" in the vmd script) and
>> it seems that it is getting the stuff from the right directories.
>>
>> Regards,
>> Ondrej
>>
>>
>> On Wed, Dec 2, 2009 at 17:29, John Stone <johns_at_ks.uiuc.edu> wrote:
>> >
>> > Hi,
>> >  I've posted the python libraries for VMD 1.8.7 on 64-bit Linux here:
>> > http://www.ks.uiuc.edu/Research/vmd/plugins/pythonlib/
>> >
>> > Give it a spin and let me know if you have any trouble using it.
>> >
>> > Cheers,
>> >  John Stone
>> >  vmd_at_ks.uiuc.edu
>> >
>> > On Thu, Nov 26, 2009 at 01:20:39AM +0100, Tru Huynh wrote:
>> >> On Mon, Nov 23, 2009 at 05:30:30PM -0600, John Stone wrote:
>> >> >
>> >> > Hi,
>> >> >   I plan to post this for people to try out shortly, but have
>> >> > just returned from travelling briefly before travelling again
>> >> > later this week.  If you can hold out for a few days I will
>> >> > try and get this done.
>> >> Sure, thanks :)
>> >>
>> >> Best regards,
>> >>
>> >> Tru
>> >> --
>> >> Dr Tru Huynh          | http://www.pasteur.fr/recherche/unites/Binfs/
>> >> mailto:tru_at_pasteur.fr | tel/fax +33 1 45 68 87 37/19
>> >> Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France
>> >
>> > --
>> > NIH Resource for Macromolecular Modeling and Bioinformatics
>> > Beckman Institute for Advanced Science and Technology
>> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> > Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
>> >  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078
>> >
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
>  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078
>