VMD-L Mailing List

From: Knut Jørgen Bjuland (knutjorgen_at_gmail.com)
Date: Thu Mar 25 2010 - 09:49:05 CDT

I tried to compile the vmd plugin after I exported the plugindir with
export

PLUGINDIR=/usr/lib/vmd/plugins. It all went fine but it did not copy any file though I issue make distrib
as root or sudo make distrib.

Knut J

Den 25.03.2010 12:01, skrev Axel Kohlmeyer:
> 2010/3/25 Knut Jørgen Bjuland<knutjorgen_at_gmail.com>:
>
>> 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
>>
> you can only use the system installed python if you compile
> VMD from source by yourself.
>
> in my opinion this is the only reasonable way to sort out
> the "python dependency hell" and lack of backwards
> compatibility for python modules and packages.
>
> cheers,
> axel.
>
>
>>
>>
>>
>> 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.
>>
>>
>>
>
>
>