VMD-L Mailing List

From: Thomas Steinbrecher (cd186_at_ipc.uni-karlsruhe.de)
Date: Tue Dec 01 2009 - 05:00:15 CST

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:

[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