VMD-L Mailing List

From: Grischa Meyer (grischa_at_uq.edu.au)
Date: Wed Apr 12 2006 - 21:57:19 CDT

Hi John,

just for your information: 10.4.6 is the current Mac OS X version.

Cheers,
Grischa

On 4/13/06, John Stone <johns_at_ks.uiuc.edu> 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
> 

--
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