VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 30 2009 - 12:46:36 CST

Hi,
  I think I know the cause of this problem. I need to make some
changes to the linkage on the VMD plugins so that the C++ plugins don't
cause difficulties in the case that the main application isn't a C++ program,
as appears to be the case in your tests below.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Dec 25, 2009 at 08:03:46PM +0800, Cun Zhang wrote:
> hi,
> I'm trying to use vmd python library in Python. when I run "import VMD" in
> python,
> it returns the following error. Anybody knows what's wrong with it?
>
> Thank you!
>
> Cun Zhang
>
> cunzhang_at_Debian:~$ ipython
> Python 2.5.4 (r254:67916, Nov 19 2009, 22:14:20)
> Type "copyright", "credits" or "license" for more information.
>
> IPython 0.10 -- An enhanced Interactive Python.
> ? -> Introduction and overview of IPython's features.
> %quickref -> Quick reference.
> help -> Python's own help system.
> object? -> Details about 'object'. ?object also works, ?? prints more.
>
> In [1]: import sys
>
> In [2]: sys.path.append("/usr/local/lib/vmd/scripts/python")
>
> In [3]: import VMD
> Info) VMD for LINUXAMD64, version 1.8.8a7 (December 25, 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: 2444MB (61%)
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/pltplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/pltplugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/pltplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/pltplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/stlplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/stlplugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/stlplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/stlplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/gromacsplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/gromacsplugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/gromacsplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/gromacsplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/situsplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/situsplugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/situsplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/situsplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/mapplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/mapplugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/mapplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/mapplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/biomoccaplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/biomoccaplugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/biomoccaplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/biomoccaplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/fs4plugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/fs4plugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/fs4plugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/fs4plugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/pbeqplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/pbeqplugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/pbeqplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/pbeqplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/mol2plugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/mol2plugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/mol2plugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/mol2plugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/phiplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/phiplugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/phiplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/phiplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/dxplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/dxplugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/dxplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/dxplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/msmsplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/msmsplugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/msmsplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/msmsplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/dsn6plugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/dsn6plugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/dsn6plugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/dsn6plugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/xsfplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/xsfplugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/xsfplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/xsfplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/spiderplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/spiderplugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/spiderplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/spiderplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/cubeplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/cubeplugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/cubeplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/cubeplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/dtrplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/dtrplugin.so:
> undefined symbol: _ZTVN10__cxxabiv120__si_class_type_infoE
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/dtrplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/dtrplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/parmplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/parmplugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/parmplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/parmplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/maeffplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/maeffplugin.so:
> undefined symbol: _ZTVN10__cxxabiv120__si_class_type_infoE
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/maeffplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/maeffplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/edmplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/edmplugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/edmplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/edmplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/uhbdplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/uhbdplugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/uhbdplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/uhbdplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/parm7plugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/parm7plugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/parm7plugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/parm7plugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/ccp4plugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/ccp4plugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/ccp4plugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/ccp4plugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/graspplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/graspplugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/graspplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/graspplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/bgfplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/bgfplugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/bgfplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/bgfplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/mdfplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/mdfplugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/mdfplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/mdfplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/grdplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/grdplugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/grdplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/grdplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/brixplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/brixplugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/brixplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/brixplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/raster3dplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/raster3dplugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/raster3dplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/raster3dplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/avsplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/avsplugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/avsplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/avsplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/xbgfplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/xbgfplugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/xbgfplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/xbgfplugin.so
> ERROR) Unable to open dynamic library
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/gridplugin.so'.
> ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/gridplugin.so:
> undefined symbol: __gxx_personality_v0
> Unable to dlopen
> '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/gridplugin.so':
> Unable to dlopen plugin file
> /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/gridplugin.so
>
> In [4]: 

-- 
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