VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 02 2009 - 11:48:41 CST

Ondrej,
  No problem, I appreciate the feedback.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Dec 02, 2009 at 06:22:21PM +0100, Ondrej Marsalek wrote:
> 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
> > 

-- 
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