VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Oct 13 2006 - 14:12:10 CDT

Hi,
  What PYTHONHOME do you have set when you're testing the unofficial build?
You should be leaving the python environment variables unset, otherwise
odd things will occur due to mixing the Apple-provided stuff with your own.
You'll also need to install Numeric (should be described in the README
file that comes with the unofficial Mac builds), if you didn't already.

When compiling your own binary, the linkage errors you're getting below are
because you need to uncomment some lines in the configure script in order to
have VMD use the Apple-provided (or your own) Tcl/Tk/Python, and FLTK
libraries, which are needed by VMD.

Let me know if you need more help on this.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Oct 12, 2006 at 06:15:53PM -0400, Michael Lerner wrote:
> Hi,
>
> I tried on of the unofficial builds, but here's what happens when I
> type gopython:
>
> vmd > gopython
> Info) Starting Python...
> Traceback (most recent call last):
> File "<string>", line 1, in ?
> ImportError: No module named VMD
> Info) Text interpreter now Python
> >>>
>
> I tried compiling things myself, but it's a little harder than I
> expected. I got netcdf installed and working via fink after setting
> the appropriate LD_LIBRARY_PATH, and I got all of the plugins compiled
> and installed, but I'm having trouble with FLTK at the moment. I'm
> getting errors like this now:
>
> Linking vmd_MACOSXX86 ...
> /usr/bin/ld: warning -L: directory name (../lib/tcl/lib_MACOSXX86)
> does not exist
> /usr/bin/ld: warning -L: directory name (../lib/tk/lib_MACOSXX86) does not
> exist
> /usr/bin/ld: warning -L: directory name (../lib/netcdf/lib_MACOSXX86)
> does not exist
> /usr/bin/ld: warning -L: directory name (../lib/fltk/MACOSXX86) does not
> exist
> /usr/bin/ld: can't locate file for: -ltk8.4-x11
> collect2: ld returned 1 exit status
>
> So, it may take quite a while for me to figure out how to install things.
>
> Just to check, I went into the plugins directory and typed
>
> make MACOSXX86
>
> then I set an environment variable PLUGINDIR and moved the plugins
> there and did "make distrib" from the plugins directory. In the VMD
> directory, I uncommented the second version of macosx.x86.opengl and
> used it. Is that the right thing to use? It looks like this:
>
> macosx.x86.opengl:
> ./configure MACOSXX86 FLTKOPENGL FLTK IMD TK TCL SILENT SPACEBALL
> PTHREADS LIBTACHYON ACTC NETCDF PYTHON NUMPY
>
> I also tried the tried-and-true method of deleting things I didn't
> understand, and ended up with this:
>
> macosx.x86.opengl:
> ./configure MACOSXX86 OPENGL FLTK IMD TK TCL SILENT PTHREADS NETCDF
> PYTHON NUMPY
>
> But it looks like I still have some things to do before that'll work.
> Does VMD want its *own* versions of tcl, tk, fltk, etc.?
>
> Feel free to reply with "compiling this is hard; good luck" :).
>
> Thanks,
>
> -Michael
>
> On 10/12/06, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> >Hi,
> > The standard builds of VMD 1.8.5 for MacOS X don't have Python compiled
> >in due to stability problems I encountered during testing. The problem
> >wasn't
> >actually Python, but the Python-enabled builds we made use the
> >Apple-provided
> >Tcl, Tk, and Python libraries (all three have to work together...), however
> >the Apple-based-builds exhibited some flaky behavior, so I decided to
> >relegate
> >them as an alternative build (they are posted on the "unofficial builds"
> >link in the download system), since I didn't want the stability issues I
> >saw affecting the entire MacOS X community. So in order to use Python,
> >you can either try using the alternative OSX builds based on the
> >Apple-provided Tcl/Tk/Python, or you can compile VMD from source using your
> >own Python library. I'd suggest trying the unofficial builds I made first,
> >if they are stable enough, you could just use them as-is. If you
> >experience
> >stability problems like I did, then you may want to build from source using
> >your own Python library. For the next version of VMD, I'll try building
> >against either the "MacPython" distribution of Python, or I'll make my
> >own, since the Apple provided library combination wasn't stable enough for
> >my taste. In theory Apple might update their libraries with a system
> >update,
> >and the stability issues could improve, but as far as I know they didn't do
> >this for prior versions of Tcl/Tk/Python included with MacOS X, so for now
> >I assume I'll have to do this for myself.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Thu, Oct 12, 2006 at 02:25:01PM -0400, Michael Lerner wrote:
> >> Hi,
> >>
> >> I've googled around and looked through the mailing list, but I still
> >> haven't quite found the answer, so my appologies in advance if this is
> >> a dumb question.
> >>
> >> I just downloaded VMD 1.8.5 for MacOS X (Intel x86) using native
> >> OpenGL. The release notes say, among other things "MacOS 10.4
> >> versions for PowerPC and Intel processors use the Apple-provided
> >> Tcl/Tk and Python frameworks, ..." However, when I type "gopython"
> >> from the vmd prompt, I get
> >>
> >> vmd > gopython
> >> invalid command name "gopython"
> >> vmd >
> >>
> >> I'm not terribly experienced with OS X, but I also tried running
> >>
> >> /Applications/VMD 1.8.5.app/Contents/vmd/vmd_MACOSXX86 -python
> >>
> >> from a shell and got
> >>
> >> ERROR) Sorry, this version VMD was compiled with Python support disabled
> >> ERROR) Skipping startup script because Python could not be started.
> >>
> >> So ... is there a Python-enabled version available somewhere? Am I
> >> doing something obviously wrong?
> >>
> >> Thanks,
> >>
> >> -Michael Lerner
> >> Graduate Student
> >> Biophysics Research Division
> >> University of Michigan
> >
> >--
> >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