VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Dec 01 2009 - 07:26:44 CST

On Tue, Dec 1, 2009 at 6:00 AM, Thomas Steinbrecher
<cd186_at_ipc.uni-karlsruhe.de> wrote:
> Dear VMD users,
>
> I am trying to get IED to run with vmd on 64bit Fedora Linux.
>
> I checked that python, numerical python and tkinter are installed. When I
> run python this works

this is irrelevant, because VMD is always built with its own
python package. due to the various interdependencies between
python and tcl and the limited backwards compatibility, it is impossible
top build a reasonably portable executable otherwise.

you have to download the matching python package and install
it according to the instructions posted on the VMD homepage
somewhere (i forgot where). please see the question on this topic
that was posted here recently and the response to it.

cheers,
    axel.:
>
> [root_at_tcbpc142 src]# python
> Python 2.6 (r26:66714, Jun  8 2009, 16:07:29) [GCC 4.4.0 20090506 (Red Hat
> 4.4.0-4)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>>
>>>> import _tkinter
>>>>
>
> However, afterwards I installed vmd version 1.8.7 as a binary, downloaded
> ied and when I start it up I get:
>
> [root_at_tcbpc142 src]# vmd
> /usr/bin/which: no rlwrap in [...]
> Info) VMD for LINUXAMD64, version 1.8.7 (August 1, 2009)
> Info) http://www.ks.uiuc.edu/Research/vmd/                         Info)
> Email questions and bug reports to vmd_at_ks.uiuc.edu           Info) Please
> include this reference in published work using VMD:   Info)    Humphrey, W.,
> Dalke, A. and Schulten, K., `VMD - Visual   Info)    Molecular Dynamics', J.
> Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 4 CPUs detected.
> Info) Free system memory: 6680MB (85%)
> Info) Detected 1 available CUDA accelerator:
> Info)   [0] Quadro NVS 290      2 SM_1.1 @ 0.92 GHz,  255MB RAM, KTO, OIO
> Info) Creating CUDA device pool and initializing hardware...
> CUDA error: no CUDA-capable device is available, line 62
> Info) OpenGL renderer: Quadro NVS 290/PCI/SSE2
> Info)   Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVF) Info)
> Full GLSL rendering mode is available.
> Info)   Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (4)
> vmd > gopython /home/steinbrt/Documents/praktikum/ied-2.02/ied.py
> 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>]
> 'import site' failed; use -v for traceback
> Traceback (most recent call last):
>  File "<string>", line 1, in <module>
> ValueError: vmdnumpy module not available.
> Info) Text interpreter now Python
> Traceback (most recent call last):
>  File "VMD", line 19, in <module>
> ImportError: No module named vmdnumpy
> Info) Text interpreter now Tcl
> Traceback (most recent call last):
>  File "<string>", line 1, in <module>
>  File "/usr/local/lib/vmd/scripts/python/Tkinter.py", line 59, in <module>
>   import _tkinter # If this fails your Python may not be configured for Tk
> ImportError: No module named _tkinter
> vmd > which python
> /usr/bin/python
> vmd > gopython
> Info) Text interpreter now Python
>>>>
>>>> import _tkinter
>
> Traceback (most recent call last):
>  File "VMD", line 1, in <module>
> ImportError: No module named _tkinter
>>>>
> Info) Text interpreter now Tcl
>
>
> So somehow, in the vmd console, my python cannot import tkinter anymore. I
> saw several posts similar to this problem on the mailing list, but none
> helped me. I tried installing the pylib.linux.tar.gz files and set
> PYTHONHOME, but that did not solve the problem either.
>
> Kind Regards,
>
> Dr Thomas Steinbrecher
> Universität Karlsruhe
> Inst. f. phys. Chemie Abt Theor. Chem. Biol.
> Vincenz-Prießnitz-Str. 1
> 76131 Karlsruhe, Germany
> phone ++49 721 608 5703
> fax   ++49 721 608 5710
>
>
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.