VMD-L Mailing List

From: Michael Lerner (mglerner_at_gmail.com)
Date: Thu Oct 12 2006 - 17:15:53 CDT

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
>