VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 12 2006 - 22:09:14 CDT

Grischa,
  Well, it's the newest version, but many VMD users are still running
10.3, so I have to continue to support those users for while yet.
Even as it is, I occasionally get emails from Mac owners that are still
running 10.2 still, but I have to draw the line somewhere.
I'll probably switch to building new versions of VMD on 10.4 later
this year as that will greatly simplify keeping the MacOS X builds
for PowerPC and Intel in sync with each other.
I currently build the MacOS X Intel builds on a 10.4 machine of course.

  John

On Thu, Apr 13, 2006 at 12:57:19PM +1000, Grischa Meyer wrote:
> 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 

-- 
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