VMD-L Mailing List

From: Justin Gullingsrud (justinrocks_at_gmail.com)
Date: Sun Apr 16 2006 - 21:32:48 CDT

John,

I didn't have to do anything unconventional to install Numeric on my
(10.4) system. Just unpack the Numeric source package and run 'python
setup.py build; sudo python setup.py install' as usual. This should
install Numeric into /System/Library/Frameworks/Python.framework.

Cheers,
Justin

On 4/15/06, John Stone <johns_at_ks.uiuc.edu> wrote:
> 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
> 

--
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"