VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Apr 16 2006 - 00:34:52 CDT

Hi,
  Well, it appears that the problem with loading module .so files on
MacOS X with the older revs of Python is not specific to VMD.
I've tried a number of things to make the builds work with the older
Python library, but they didn't pan out. The recommended solution appears
to be to use the framework builds of Python on OSX, as these get around
the .so loading problems that can occur with the plain unixy Python builds.

I could compile the Mac versions of VMD against the Apple-provided
Python frameworks, the main issue with that is that they don't provide
the Numeric module in the system Python, even in 10.4.6.
There are various pages that describe how to add Numeric into the
system Python, though I'm a bit leery of basing VMD builds off of
a hacked version of the Apple frameworks:
  http://starship.python.net/~hinsen/ScientificPython/
  http://www.physics.ucf.edu/~mdj/MacpythonScipyGnuplot.html

What I may end up doing is disabling Python in the default MacOS X build,
and then do a second build that has it turned on, linked against the same
Python framework that MMTK or one of the other popular packages are using.

I'd be interested to hear from Mac Python users as to which Python framework
you want to see VMD binaries linked against, or if you'd prefer to just
build from source for yourselves?

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Apr 12, 2006 at 09:25:37PM -0500, John Stone wrote:
>
> Hi guys,
> The tar error is innocuous in that it's complaining about restoring some
> file state on the the python interpreter binary (which isn't used by VMD
> anyway) and you can run the unpacked binary, so I'm not sure if it's some
> Apple specific modification to tar, but it doesn't seem to matter.
>
> I also get the same errors you guys are getting with an updated 10.3
> machine, but the same Python libs worked fine on this same box previously.
> (the same machine they were compiled on)
> I'm wondering if some change that Apple made since 10.3 came out broke
> these shared libs. Digging deeper, the problem occurs with _all_ of the
> Python modules which are built with .so files in that library.
> (i.e. 'import time', 'import math', 'import dbm', .....)
>
> I'll have to get back to you on this after I do more testing.
>
> John
>
> On Wed, Apr 12, 2006 at 05:02:22PM -0700, Justin Gullingsrud wrote:
> > Same thing happens to me - tar errors on unpack, and errors when I try
> > to import the math module. I verified that I'm indeed loading the
> > correct math shared library from the pylibs package. Here is the
> > output:
> >
> > vmd > gopython
> > Info) Starting Python...
> > Numeric Python module _numpy not found; vmdnumpy module not available.
> > ImportError: Failure linking new module
> > Info) Text interpreter now Python
> > Traceback (most recent call last):
> > File "<string>", line 1, in ?
> > File "/Applications/VMD
> > 1.8.3.app/Contents/vmd/scripts/python/Tkinter.py", line 59, in ?
> > import _tkinter # If this fails your Python may not be configured for Tk
> > ImportError: No module named _tkinter
> > >>> import math
> > Traceback (most recent call last):
> > File "VMD", line 1, in ?
> > File "VMD", line 1, in ?
> > ImportError: Failure linking new module
> > >>> import string
> > >>> string
> > <module 'string' from
> > '/Users/justin/Desktop/lib_MACOSX-numpy/lib/python2.2/string.pyc'>
> > >>>
> >
> > The failure to load the numpy module is probably related to the
> > failure to load the math library.
> >
> > Justin
> >
> >
> > On 4/11/06, Grischa Meyer <grischa_at_uq.edu.au> wrote:
> > > Hi,
> > >
> > > I am using VMD 1.8.3 and 1.8.4b11 on Mac OS X 10.4.6.
> > > I wrote a little python script that needs to do a sqrt, so needs the math
> > > library. How can I fix VMD to make it import it?
> > > I tried various things, including downloading the pylib package from the vmd
> > > site (which, btw, reports errors when untarring), but none was successful.
> > >
> > > Cheers,
> > > Grischa
> > >
> > > --
> > > Grischa Meyer, BSc (Hons)
> > > PhD student, Prof Boris Martinac Group
> > > School of Biomedical Sciences
> > > University of Queensland
> > > Brisbane, Australia
> > > phone: +61 7 3346 1224
> > > fax: +61 7 3365 1766 (attn. to me)
> > > http://www.uq.edu.au/sbms
> >
> >
> > --
> > Studying texts and stiff meditation can make you lose your Original Mind.
> > A solitary tune by a fisherman, though, can be an invaluable treasure.
> > Dusk rain on the river, the moon peeking in and out of the clouds;
> > Elegant beyond words, he chants his songs night after night.
> > -- Ikkyu, "The Fisherman"
>
> --
> 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