VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Mar 25 2010 - 10:49:09 CDT

2010/3/25 Knut Jørgen Bjuland <knutjorgen_at_gmail.com>:
> 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.

you should *never* compile software as root!

also, there is no way to replace parts of an existing VMD
installation with "native" compiles unless you have the exact
same compile environment.

the VMD compilation instructions are meant for people who
compile *all* of VMD from source. that is the only way to get
native python and tcl/tk (and you need them all or else you'll
be screwed).

i would strongly recommend to first compile and install
that self-compile VMD somewhere in your user directory.
and test it throughly before you mess up the precompiled
installation. you want that to have a reference in case you
mess up or are missing some parts that are contained in
standard distribution.

cheers,
   axel.

> 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.
>
>
>
>
>
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.