VMD-L Mailing List

From: Knut Jørgen Bjuland (knutjorgen_at_gmail.com)
Date: Thu Mar 25 2010 - 04:26:35 CDT

I have downloaded python bin from vmd and extract it into
/usr/local/python-2.5. furthermore I have set the export
PYTHONHOME=/usr/local/python-2.5 before starting vmd. I think it strange
that vmd is looking in /home/johns/vmd/lib/python/ which I do not have.
Could you please update an howto using bash to install python-2.5 in
/usr/local. It is possible to use the system python version which is in my
case 2.6 in ubuntu 9.10

vmd > Info) VMD for LINUXAMD64, version 1.8.7 (August 1, 2009)
Info) Exiting normally.
Info) Done with Python.
knut_at_Human-Naa50p:~$ vmd
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: 4899MB (81%)
Info) Detected 1 available CUDA accelerator:
Info) [0] GeForce G210 2 SM_1.2 @ 1.40 GHz, 511MB RAM, KTO, OIO,
ZCP
Info) Creating CUDA device pool and initializing hardware...
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this optional X server feature.
Info) OpenGL renderer: GeForce G210/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)
Invalid axes location: on
/home/knut/vmdplugins /usr/local/lib/vmd/scripts/tcl8.5
/usr/local/lib/vmd/scripts /usr/local/lib/lib
/Projects/johns/tcl/8.5.6/lib_LINUXAMD64/lib
/usr/local/lib/vmd/scripts/tk8.5 /usr/local/lib/vmd/scripts/tk8.5/ttk
/usr/local/lib/vmd/scripts/vmd /usr/local/lib/vmd/plugins/LINUXAMD64/tcl
/usr/local/lib/vmd/plugins/noarch/tcl
vmd > gopython
Info) Starting Python...
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 "<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
>>> gopython
Traceback (most recent call last):
  File "VMD", line 1, in <module>
NameError: name 'gopython' is not defined
>>> import vmdnumpy
Traceback (most recent call last):
  File "VMD", line 1, in <module>
ImportError: No module named vmdnumpy
>>> import numpy
Traceback (most recent call last):
  File "VMD", line 1, in <module>
  File
"/home/johns/vmd/lib/python/Python-2.5.1/lib_LINUXAMD64/lib/python2.5/site-packages/numpy/__init__.py",
line 43, in <module>
  File
"/home/johns/vmd/lib/python/Python-2.5.1/lib_LINUXAMD64/lib/python2.5/site-packages/numpy/linalg/__init__.py",
line 4, in <module>
  File
"/home/johns/vmd/lib/python/Python-2.5.1/lib_LINUXAMD64/lib/python2.5/site-packages/numpy/linalg/linalg.py",
line 25, in <module>
ImportError: liblapack.so.3: cannot open shared object file: No such file or
directory
>>> import numpy
Traceback (most recent call last):
  File "VMD", line 1, in <module>
  File
"/home/johns/vmd/lib/python/Python-2.5.1/lib_LINUXAMD64/lib/python2.5/site-packages/numpy/__init__.py",
line 43, in <module>
  File
"/home/johns/vmd/lib/python/Python-2.5.1/lib_LINUXAMD64/lib/python2.5/site-packages/numpy/linalg/__init__.py",
line 4, in <module>
  File
"/home/johns/vmd/lib/python/Python-2.5.1/lib_LINUXAMD64/lib/python2.5/site-packages/numpy/linalg/linalg.py",
line 25, in <module>
ImportError: liblapack.so.3: cannot open shared object file: No such file or
directory
>>> Info) VMD for LINUXAMD64, version 1.8.7 (August 1, 2009)
Info) Exiting normally.
Info) Done with Python.