VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 05 2006 - 20:21:52 CDT

Let me know if you guys need any help with the build, I just walked
someone at LLNL through the same process for their custom builds there...

  John

On Wed, Apr 05, 2006 at 09:16:44PM -0400, Sacerdoti, Federico wrote:
> John, thanks for the reply.
>
> I think we are headed for your suggestion 1), it seems easiest and
> cleanest. We will stick with Python 2.3 (not 2.4) since that is the
> native version for RHEL4.
>
> Thanks,
> -Federico
>
> -----Original Message-----
> From: John Stone [mailto:johns_at_ks.uiuc.edu]
> Sent: Tuesday, April 04, 2006 5:00 PM
> To: Sacerdoti, Federico
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: python Numeric library problem
>
>
>
> Hi Federico,
> The VMD binaries we distribute are all compiled against the same
> version of Python, which has been 2.2.2 thus far. Since every linux
> distribution (and indeed, almost every major OS in fact) comes with a
> different version of Python, linking against the system-provided Python
> interpreter won't work for VMD.
>
> Where this leaves those of us wanting to nontrivial stuff that requires
> the full Python library in VMD:
> 1) If you want to use the same Python setup that's on your system
> already,
> it's currently much easier to compile VMD from source code and link
> it
> against your local Python than to try and get around the Python
> library
> version issues. If people need help with this, contact me and I
> can
> help you get past any sticking points in your builds. You can
> either
> build from one of the source distributions, or you can get the
> latest
> VMD source code from CVS.
>
> 2) If you want to use John Mongan's IED plugin, or other things that
> need
> Tkinter, you're probably also headed for 1) above.
> (tkinter is usually dynamically linked against whatever Tcl/Tk
> version is favored by a particular Linux distribution, so unless
> you
> go through great pains in the Python build and are also lucky, the
>
> Python tkinter module built on one system may not work on another)
>
> Regarding upgrading VMD to one of the more recent Python revs:
> Several times I've tried to upgrade to Python 2.3 and 2.4 only to find
>
> serious problems compiling the newer versions on several of the
> 64-bit platforms that VMD supports, and I won't even mention the fun
> involved in building Python from source on Windows if you want to
> add Numeric and Tkinter support, which is something most VMD users
> want so they can run IED and similar tools.
> I've reported these problems in the Python bug tracking system, and
> I've provided the Python developers fixes for the ones I could solve
> for myself, but the problems still continue and I haven't had time
> to go through another attempt since the last one a few months back.
> In the mean time it would seem that I'm going to have to stick with
> 2.2.2
> for the 1.8.4 release, though it pains me greatly.
>
> What I may do to ease the pain for Python hackers is to try and release
> Python 2.4 based VMD 1.8.4 binaries in addition to the normal ones, for
> the few platforms that they'll work fine for. (Linux for starters)
>
> John
>
> On Tue, Apr 04, 2006 at 12:11:16PM -0400, Sacerdoti, Federico wrote:
> > Hi,
> >
> > I have installed vmd 1.8.3 on our Linux x86_64 (Rocks 4.0 - Centos
> > 4.2/RHEL4 based) systems. I notice that vmd has its own compiled in
> > version of python, which is an older version than the RHEL4 standard:
> > vmd:
> >
> > vmd 1.8.3:
> >
> > >>> import sys
> > >>> sys.version
> > '2.2.2 (#1, Jan 31 2005, 10:19:19) \n[GCC 3.3.3 20040412 (Red Hat
> Linux
> > 3.3.3-7)]'
> > >>>
> >
> > native:
> >
> > >>> import sys
> > >>> sys.version
> > '2.3.4 (#1, Feb 17 2005, 21:01:10) \n[GCC 3.4.3 20041212 (Red Hat
> > 3.4.3-9.EL4)]'
> > >>>
> >
> > This of course causes lots of problems. Right off the bat _tkinter
> > cannot be found, although the native python has no problems with it.
> >
> > I have installed your precompiled python libraries from
> >
> > http://www.ks.uiuc.edu/Research/vmd/plugins/pythonlib/
> >
> > But that does not help with _tkinter, since it does not seem to be
> > included. Perhaps that is due to this unanswered thread:
> >
> > http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/5862.html
> >
> > As for Numeric, if I set the PYTHONPATH to something appropriately
> > awful:
> > export
> >
> PYTHONPATH=$PYTHONPATH:[...]/vmd-1.8.3/lib/pylib/lib_LINUXAMD64/lib/pyth
> > on2.2/site-packages/Numeric
> > then vmd can find Numeric, but there is still an error:
> >
> > vmd > gopython
> > Info) Starting Python...
> > Could not find platform independent libraries <prefix>
> > Could not find platform dependent libraries <exec_prefix>
> > Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
> > /usr/lib64/python2.3/os.py:282: Warning: 'yield' will become a
> reserved
> > keyword in the future
> > 'import site' failed; use -v for traceback
> >
> > Numeric Python module _numpy not found; vmdnumpy module not available.
> > ImportError:
> >
> /proj/desrad/opt/Linux-x86_64/vmd-1.8.3/lib/pylib/lib_LINUXAMD64/lib/pyt
> > hon2.2/site-packages/Numeric/_numpy.so: undefined symbol:
> _Py_NoneStruct
> >
> > Info) Text interpreter now Python
> > Traceback (most recent call last):
> > File "<string>", line 1, in ?
> > File
> >
> "/proj/desrad/opt/Linux-x86_64/vmd-1.8.3/lib/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
> > >>>
> >
> > Was the library compiled incorrectly, or did I do something wrong
> during
> > installation?
> >
> > Thanks,
> > Federico
> >
> > D.E. Shaw Research LLC
> > New York
> >
>
> --
> 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