From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Sep 06 2007 - 12:50:08 CDT

On Thu, 6 Sep 2007, John Stone wrote:

hi guys,

this is probably not as obvious at it seems, but it may actually
be, that there is a libstdc++.so.6 which is _not_ compatible with
the one that VMD was compiled against, because of a non satisfied
dependency on the shared linker or libc or ...
this is one of the really, really stupid things that can happen
on linux machines. particularly when the machine a code was compiled
on has a newer set of libraries than the one it is run on.

hu, can you please post _exactly_ what version of red hat you have,
and whether it has been only set up and installed via rpm. if somebody
has manually added or moved libraries that rpm does not know about,
you will have problems with other pacakges, too. this ssa directory,
i only remember seeing on debian-like installations...

try doing: "rpm -qa | grep release"
(and "rpm -qa | grep glibc" and "rpm -qa | grep stdc++" while you are
at it) or: "cat /etc/issue"
and let us know what you got.

cheers,
   axel.
>
> Hi,
> If you have a libstdc++.so.6 already, you shouldn't need to move it, you
> can just add the directory where it is located to your personal
> LD_LIBRARY_PATH environment variable, and linux should find it.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Sep 06, 2007 at 12:31:54PM -0500, Hu Zhonghan wrote:
> > thanks, John.
> > I read the release notes and run the following
> > vmd -dispdev text
> >
> > it shows:
> > /homes/zhonghan/install/lib/vmd/vmd_LINUXAMD64: error while loading
> > shared libraries: libstdc++.so.6: cannot open shared object file: No
> > such file or directory
> >
> > then I search the file system and get the location of libstdc++.so.6 :
> > /lib64/ssa/libstdc++.so
> > /lib64/ssa/libstdc++.so.6
> > /lib64/ssa/libstdc++.so.6.0.0
> >
> > I tried to modify the generated Makefile but it still fails. Is there
> > a simple way to solve this problem instead of installing a new library
> > in the default directory with root permission ?
> >
> > >
> > >Hi,
> > > Please see the VMD Linux release notes, you undoubtably have one
> > >of the distributions that needs adjustment in terms of installing
> > >a missing libstdc++.so.5 library or something similar:
> > > http://www.ks.uiuc.edu/Research/vmd/current/linuxrelnotes.html
> > >
> > >Cheers,
> > > John Stone
> > > vmd_at_ks.uiuc.edu
> > >
> > >On Thu, Sep 06, 2007 at 10:05:15AM -0500, Hu Zhonghan wrote:
> > >>Hi,
> > >> I just installed vmd.1.8.6 following the README file. The
> > >>installation was complete. But vmd does not actually work now. When I
> > >>type the command vmd, the console window starts but then it
> > >>immediately closes by itself without giving any error messages ( or
> > >>the error messages are too fast to be seen ). Can some one help me
> > >>figure out the problem ?
> > >>
> > >>the sourcecode I downloaded is
> > >>vmd-1.8.6.bin.LINUXAMD64.opengl.tar
> > >>
> > >>and here is part of the hardware information:
> > >>
> > >>============================================
> > >>processor : 0
> > >>vendor_id : AuthenticAMD
> > >>model name : AMD Opteron(tm) Processor 250
> > >>clflush size : 64
> > >>address sizes : 40 bits physical, 48 bits virtual
> > >>power management: ts fid vid ttp
> > >>============================================
> > >>
> > >>the operation system is LINUX redhat
> > >>
> > >>thanks,
> > >>Zhonghan
> > >>
> > >>
> > >>
> > >
> > >--
> > >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
> > >
> >
> >
> >
> > --
> > Hu Zhonghan
> > Ph.D. Candidate
> > Department of Chemistry
> > University of Iowa
> > Iowa City, IA 52242
> > Phone: 319-335-1872
> >
>
>

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.