VMD-L Mailing List

From: Cun Zhang (apzc2529_at_gmail.com)
Date: Wed Aug 18 2010 - 00:36:33 CDT

OK. Thank you!

CHeers
Cun Zhang

On Tue, Aug 17, 2010 at 12:08 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Cun,
> The issue is that the Tachyon code isn't compiled into the shared
> library version of VMD. To get that to work, we would need to teach
> the shared library builds of VMD to link against a shared library
> version of Tachyon, then it should work ok. I'll have to look at this
> and get back to you.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Mon, Aug 16, 2010 at 05:02:55PM +0800, Cun Zhang wrote:
> > Axel,
> > I have solved this problem temporarily by just updating plugins,
> > say, I just update the cvs code of plugins, re-make and re-install
> these
> > plugins.
> > Then Python works fine with vmd shared libraries(VMD for LINUXAMD64,
> > version 1.8.8a7 (August 9, 2010)). lammpstrj works well too.
> >
> > But this is just a temporarily solution. I still have no idea about
> why
> > VMD shared libraries of the newest cvs version can't work within
> Python.
> >
> > Thank you for your help!
> >
> > Cun Zhang
> >
> > On Sun, Aug 15, 2010 at 9:01 PM, Cun Zhang <apzc2529_at_gmail.com>
> wrote:
> >
> > On Sun, Aug 15, 2010 at 5:28 PM, Axel Kohlmeyer <akohlmey_at_gmail.com
> >
> > wrote:
> >
> > On Sun, Aug 15, 2010 at 4:16 AM, Cun Zhang <apzc2529_at_gmail.com>
> wrote:
> > > Axel and John,
> > > Thank you for your help! I have downloaded it. VMD have been
> working
> > now.
> > > Now I'm trying to compile the python shared library of vmd.
> >
> > i don't think anybody has tried this for quite a while.
> >
> > The last version( VMD for LINUXAMD64, version 1.8.8a7 (December 25,
> > 2009)) works well.
> > I just update to the new cvs version( VMD for LINUXAMD64, version
> > 1.8.8a18 (August 15, 2010)), then it failed.
> >
> >
> > > When I try to import vmd module into python, it returns:
> > > ImportError: /usr/local/lib/vmd/scripts/python/vmd.so: undefined
> > symbol:
> > > ompi_mpi_byte
> > >
> > > I compile tachyon with linux-mpi-64 option. The version of
> PYthon is
> >
> > why compile tachyon with mpi??? why not with threading?
> >
> > Compiling linux-64 or linux-64-thr, Python return "Segmentation
> fault"
> > too.
> > Sometimes return "./vmd.so: undefined symbol: rt_tex_transmode"
> >
> >
> > > 2.6.6rc1+
> > > When I compile vmd without LIBTACHYON option, It fails with
> > "Segmentation
> > > fault" when I import vmd module into python.
> >
> > have you used the SHARED option for configure?
> > have all libraries included in vmd.so compiled with -fPIC?
> > it would first try to compile vmd with as few options as possible
> > and take it from there. if you keep getting segfaults, you'll
> > have to use a debugger to track them down.
> >
> >
> > Yes, SHARED is open
> > Here is:
> > root_at_Debian:/home/cunzhang/
> > VMD/vmd# ./configure
> > using configure.options: LINUXAMD64 OPENGL FLTK TK ACTC CUDA IMD
> > LIBSBALL XINPUT LIBTACHYON VRPN NETCDF TCL PYTHON PTHREADS NUMPY
> SILENT
> > SHARED
> >
> > Sorry, I know nothing about program debugging. :(
> > Cun Zhang
> >
> > --
> > Blog: http://www.edwardpku.com/cun
>
> --
> 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
> 

-- 
Blog: http://www.edwardpku.com/cun