VMD-L Mailing List

From: Cun Zhang (apzc2529_at_gmail.com)
Date: Sun Dec 27 2009 - 08:31:04 CST

hi, Thank you for your reply.

I compiled it from cvs code. So your method isn't suitable for me. :)

I googled and now all is fixed when I change the compiler from gcc to g++.
I don't know whether it is a bug.

Cun Zhang

On Sun, Dec 27, 2009 at 1:33 PM, Yerko Escalona <yescalona_at_ug.uchile.cl> wrote:
> Hi
> maybe this is related with the four step:
>
> cd /to/some/directory/where/you/want/it
> gunzip pylib.macosx.tar.gz
> tar -xvf pylib.macosx.tar.gz
> setenv PYTHONHOME /path/to/lib_LINUX (replace with your correct path...)
> vmd
>
> because all the file *.so are libraries
> Bye :)
> i hope this help
>
>
>
>
> 2009/12/25 Cun Zhang <apzc2529_at_gmail.com>
>>
>> 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]:
>
>
>
> --
> Yerko Ignacio Escalona Balboa
> Ingeniero en Biotecnología Molecular
> Universidad de Chile
> http://zeth.ciencias.uchile.cl/~yescalona/
> 

-- 
Blog: http://blog.4message.net