VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 02 2006 - 17:51:13 CST

Hi,
  If you have trouble building Python 2.2, I'd suggest building 2.3 or 2.4
and compiling VMD from source against your Python build. There have been
a lot of problems with building Python on 64-bit targets in the last two
years, I know because I've reported many of them to the Python developers
and have spent a lot of time helping them fix the major ones. It is these
64-bit build problems that have kept my VMD builds stuck on the specific
Python 2.2 version I'm using here. I finally got Python 2.4 mostly working
on several platforms, so with any luck I'll upgrade VMD to use 2.4 shortly.

For people that are willing to build VMD from source, you can use any Python
version that you can build successfully on your machine, not just 2.2. :-)

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Feb 02, 2006 at 03:50:36PM +0100, Florian Haberl wrote:
> Hi,
>
> i got some serious problems installing python 2.2.2 for amd64 ( i wanto to use
> ied), on 32bit systems theres no problem but now i got a new machine with
> 64bit:
>
> Linux version 2.6.13-15.7-smp (geeko_at_buildhost) (gcc version 4.0.2 20050901
> (prerelease) (SUSE Linux)) #1 SMP Tue Nov 29 14:32:29 UTC 2005
>
> ./configure --prefix=/raid1/haberl/bin/python-2.2.3
> --x-includes=/usr/X11R6/include/ --x-libraries=/usr/X11R6/lib64/
>
> (x includes with explicit path didn`t fix it it still doesn`t find them)
>
>
> [snip]
> building '_tkinter' extension
> skipping /raid1/haberl/Python-2.2.3/Modules/_tkinter.c
> (build/temp.linux-x86_64-2.2/_tkinter.o up-to-date)
> skipping /raid1/haberl/Python-2.2.3/Modules/tkappinit.c
> (build/temp.linux-x86_64-2.2/tkappinit.o up-to-date)
> gcc -shared build/temp.linux-x86_64-2.2/_tkinter.o
> build/temp.linux-x86_64-2.2/tkappinit.o -L/usr/X11R6/lib -L/usr/local/lib
> -ltk8.4 -ltcl8.4 -lX11 -o build/lib.linux-x86_64-2.2/_tkinter.so
> /usr/lib64/gcc/x86_64-suse-linux/4.0.2/../../../../x86_64-suse-linux/bin/ld:
> skipping incompatible /usr/X11R6/lib/libX11.so when searching for -lX11
> /usr/lib64/gcc/x86_64-suse-linux/4.0.2/../../../../x86_64-suse-linux/bin/ld:
> skipping incompatible /usr/X11R6/lib/libX11.a when searching for -lX11
> /usr/lib64/gcc/x86_64-suse-linux/4.0.2/../../../../x86_64-suse-linux/bin/ld:
> cannot find -lX11
> collect2: ld returned 1 exit status
> WARNING: building of extension "_tkinter" failed: command 'gcc' failed with
> exit status 1
> running build_scripts
> not copying /raid1/haberl/Python-2.2.3/Tools/scripts/pydoc (up-to-date)
> [/snip]
>
>
> so vmd don`t work with numpy of course.
>
> also with a version of python compiled on a 32bit machine it doesn`t work:
>
> vmd > gopython
> Info) Starting Python...
> Numeric Python module _numpy not found; vmdnumpy module not available.
> ImportError: /raid1/haberl/bin/vmd-1.8.3/Python-2.2.3/lib/python2.2/site-package
> s/Numeric/_numpy.so: undefined symbol: _Py_NoneStruct
> Info) Text interpreter now Python
> Traceback (most recent call last):
> File "<string>", line 1, in ?
> File "/raid1/haberl/bin/vmd-1.8.3/lib/vmd/scripts/python/Tkinter.py", line
> 59,
> in ?
> import _tkinter # If this fails your Python may not be configured for Tk
> ImportError
>
>
> So has anyone compiled python 2.2.x on amd64/ em64t machines without problems
> (I assume that there are several people who have done it with success),
> perhaps someone can send me fixed source or binary.
>
> Or maybe there`s soon a version of vmd around, which will work with python
> 2.4.
>
>
> vmd > gopython
> Info) Starting Python...
> Numeric Python module _numpy not found; vmdnumpy module not available.
> ImportError: /raid1/haberl/bin/python-2.2.3-32/lib/python2.2/site-packages/Numeric/_numpy.so:
> cannot open shared object file: No such file or directory
> Info) Text interpreter now Python
> Traceback (most recent call last):
> File "<string>", line 1, in ?
> File "/raid1/haberl/b
>
>
>
> Greetings,
>
> Florian
>
> --
> -------------------------------------------------------------------------------
> Florian Haberl
> Computer-Chemie-Centrum
> Universitaet Erlangen/ Nuernberg
> Naegelsbachstr 25
> D-91052 Erlangen
> Mailto: florian.haberl AT chemie.uni-erlangen.de
> ------------------------------------------------------------------------------- 

-- 
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