VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Sep 28 2007 - 14:35:25 CDT

Geoff,
  If your building against Python 2.5, I think you'll have a much
easier time using the current VMD CVS sources rather than the 1.8.6
tree, as we've been specifically updating the code for Python 2.5 and NumPy.
Regarding the other optional components like NetCDF, the Spaceball, and
other features, you can individually turn those on and off in the VMD
configuration flags if you like. This is all described in the
VMD Programmer's guide on the web.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Sep 24, 2007 at 10:05:54PM +0200, Geoff Wood wrote:
> Hello,
>
> I am writing with regards to the problem associated with python as
> outlined by John Stone (see below).
>
> I am wanting to use the IED program and so it looks like I need to go
> for option 1 that you have outlined below. We are running Redhat
> Enterprise on an x86_64 system.
> I have managed to compile Python 2.5.1 and numpy 24.2 but now I am
> have trouble building vmd.
> First of all I couldn't build the plugins. I set the variable
> PLUGINDIR and then tried make LINUXAMD64 but got the error:
>
> /usr/bin/ld cannot find -lnetcdf
>
> So I thought (probably incorrectly) that since I already have this
> precompiled in the binary distrubution of vmd I could use them by
> copying the directory to the appropriate place. So after running ./
> configure LINUXAMD64 PYTHON NUMPY I tried to run make in the src
> directory but now I have the error:
>
> Spaceball.h:33:51: sball.h: No such file or directory
>
> Any help on building vmd against my versions of python and numpy
> would very much be appreciated.
>
> Cheers, Geoff.
>
>
> From: John Stone (johns_at_ks.uiuc.edu)
> Date: Tue Apr 04 2006 - 16:00:09 CDT
>
> * Next message: L. Michel Espinoza-Fonseca: "ied on vmd"
> * Previous message: John Stone: "Re: alternative display mode of
> HBonds"
> * In reply to: Sacerdoti, Federico: "python Numeric library
> problem"
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> [ attachment ]
>
>
>
> 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
>
>
> Geoffrey Wood
> Ecole Polytechnique Fédérale de Lausanne
> SB - ISIC - LCBC
> BCH 4108
> CH - 1015 Lausanne
>
>
>
> 

-- 
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