VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 02 2009 - 11:16:06 CST

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