VMD-L Mailing List

From: J. Rui Rodrigues (joaquim.rodrigues_at_estg.ipleiria.pt)
Date: Tue Apr 06 2010 - 08:11:00 CDT

Hi John,
I had not done that. I had only installed python via apt-get. I have now compiled python2.5 from source and
managed to compile VMD with PYTHON.
Now, I will try to compile with NUMPY, but I'm confused: I guess I should compile numpy also, will version 1.3.0
be OK? And should I also install Numeric from source?
Thanks,
Rui Rodrigues

On Fri, 2 Apr 2010 00:26:18 -0500, John Stone wrote
> 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 

--
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