VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 02 2010 - 00:26:18 CDT

Rui,
  Did you compile your Python against the same Tk that VMD was
compiled with?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 01, 2010 at 05:51:06PM +0100, J. Rui Rodrigues wrote:
> Dear all,
>
> I am trying to get ied running in VMD but I am getting the following error:
> RuntimeError: tk.h version (8.4) doesn't match libtk.a version (8.5)
>
> I have compiled VMD 1.8.7 in Ubuntu 8.04.4. Except for libtachyon, all libraries
> and headers were installed with apt-get from Ubuntu repositories. And I do
> not have any tk.h file from tcl8.4:
> sudo find / -name tk.h -print
> /usr/include/tcl8.5/tk.h
> /usr/include/tcl8.5/tk-private/generic/tk.h
> (these two tk.h files are identical).
>
> Similar errors were reported several years ago in this list, but I could
> not find a solution:
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/4210.html
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/4721.html
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/5210.html
>
> Does anybody have any suggestions to get over this error?
> Please find below details of installation and output from VMD.
>
> Thanks for your time,
> Rui Rodrigues
>
>
>
> => VMD plug-ins were compiled with:
> export TCLINC=-I/usr/include/tcl8.5
> export TCLLIB=-L/usr/lib
> cd plugins
> make LINUX
> export PLUGINDIR=/home/jrui/vmd/vmd-1.8.7/plugins
> make distrib
>
> => For compilation of VMD, I changed the following variables in configure:
> $install_bin_dir="/home/jrui/bin";
> $install_library_dir="/home/jrui/lib/$install_name
> $python_dir = "";
> $numpy_dir = "";
> $python_include = "-I/usr/include/python2.5
> -I/usr/lib/python2.5/site-packages/Numeric/Numeric_headers"
> $python_library = "-L/usr/lib";
>
> and then I did
> ./configure LINUX OPENGL TCL TK FLTK NETCDF PTHREADS LIBTACHYON PYTHON NUMPY
> cd src
> make
> make install
>
>
> => Here is the complete output from VMD:
> jrui_at_herbert:~$ vmd
> Info) VMD for LINUX, version 1.8.7 (April 1, 2010)
> 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, 1 CPU detected.
> Info) Free system memory: 304MB (60%)
> Warning) Detected X11 'Composite' extension: if incorrect display occurs
> Warning) try disabling this optional X server feature.
> Info) OpenGL renderer: GeForce4 488 Go/AGP/SSE2
> Info) Features: STENCIL MDE CVA MTX PP PS GLSL(OV)
> Info) GLSL rendering mode is NOT available.
> Info) Textures: 2-D (2048x2048), 3-D (64x64x64), Multitexture (2)
> vmd > gopython ied-2.02/ied.py
> Info) Starting Python...
> Info) Text interpreter now Python
>
> Interactive Essential Dynamics v 2.0 (http://mccammon.ucsd.edu/ied)
> Copyright John Mongan <jmongan_at_mccamon.ucsd.edu>, 2003, 2004
>
> Citation: Interactive Essential Dynamics. John Mongan. Journal of
> Computer-Aided Molecular Design. In press.
>
> This library is provided under the LGPL with ABSOLUTELY NO WARRANTY.
>
> Traceback (most recent call last):
> File "VMD", line 541, in <module>
> File "VMD", line 538, in tkmenu
> File "VMD", line 328, in __init__
> File "VMD", line 331, in launchGUI
> File "/home/jrui/lib/vmd/scripts/python/Tkinter.py", line 1547, in __init__
> % (_tkinter.TK_VERSION, tk_version)
> RuntimeError: tk.h version (8.4) doesn't match libtk.a version (8.5)
> Info) Text interpreter now Tcl
> vmd >
>
>
>
> => and here is the output from ldd:
> jrui_at_herbert:~/lib/vmd$ ldd vmd_LINUX
> linux-gate.so.1 => (0xb7784000)
> libGL.so.1 => /usr/lib/libGL.so.1 (0xb76e9000)
> libGLU.so.1 => /usr/lib/libGLU.so.1 (0xb7666000)
> libpython2.5.so.1.0 => /usr/lib/libpython2.5.so.1.0 (0xb7530000)
> libpthread.so.0 => /lib/tls/i686/cmov/libpthread.so.0 (0xb7518000)
> libtk8.5.so.0 => /usr/lib/libtk8.5.so.0 (0xb7403000)
> libX11.so.6 => /usr/lib/libX11.so.6 (0xb731c000)
> libtcl8.5.so.0 => /usr/lib/libtcl8.5.so.0 (0xb7226000)
> libnetcdf.so.4 => /usr/lib/libnetcdf.so.4 (0xb71f4000)
> libfltk.so.1.1 => /usr/lib/libfltk.so.1.1 (0xb7147000)
> libXft.so.2 => /usr/lib/libXft.so.2 (0xb7135000)
> libdl.so.2 => /lib/tls/i686/cmov/libdl.so.2 (0xb7131000)
> libutil.so.1 => /lib/tls/i686/cmov/libutil.so.1 (0xb712d000)
> libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0xb703a000)
> libm.so.6 => /lib/tls/i686/cmov/libm.so.6 (0xb7015000)
> libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xb7009000)
> libc.so.6 => /lib/tls/i686/cmov/libc.so.6 (0xb6eba000)
> libGLcore.so.1 => /usr/lib/libGLcore.so.1 (0xb6634000)
> libnvidia-tls.so.1 => /usr/lib/tls/libnvidia-tls.so.1 (0xb6632000)
> libXext.so.6 => /usr/lib/libXext.so.6 (0xb6624000)
> /lib/ld-linux.so.2 (0xb7785000)
> libXss.so.1 => /usr/lib/libXss.so.1 (0xb6620000)
> libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0xb65b3000)
> libz.so.1 => /usr/lib/libz.so.1 (0xb659e000)
> libfontconfig.so.1 => /usr/lib/libfontconfig.so.1 (0xb6574000)
> libXrender.so.1 => /usr/lib/libXrender.so.1 (0xb656c000)
> libxcb-xlib.so.0 => /usr/lib/libxcb-xlib.so.0 (0xb6569000)
> libxcb.so.1 => /usr/lib/libxcb.so.1 (0xb6551000)
> libXinerama.so.1 => /usr/lib/libXinerama.so.1 (0xb654e000)
> libXau.so.6 => /usr/lib/libXau.so.6 (0xb654b000)
> libexpat.so.1 => /usr/lib/libexpat.so.1 (0xb652a000)
> libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0xb6524000)
>
>
> --
> Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt) 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078