VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_vitae.cmm.upenn.edu)
Date: Thu Feb 09 2006 - 06:16:54 CST

On Wed, 8 Feb 2006, Dan Wright wrote:

DW> It looks like the libstdc++.so.5 dependency was with VMD1.8.3, and 1.8.4
DW> had an unresolvable dependency on libc++.so.6. So it seems likely that
DW> he just doesn't have libstdc++.so.6 installed for some reason, or ld.so
DW> is misconfigured.
DW>
DW> In my experience CENTOS4 is an _exact_ replica of RHEL4. It's close
DW> enough that the 3dlabs Realizm drivers work perfectly on a CENTOS4.2
DW> box, which I honestly did not expect to happen... generally, I haven't
DW> seen any case where a RHEL-certified app won't run on the equivalent
DW> version of CENTOS.

guys,

that is the point here. if you look closer at the report,
he has CENTOS-3. with the messed up library dependencies
and too many compiler runtimes on linux, you need to find
the oldest possible box to compile, so that your binary
will run on as many platforms as possible.

on my last job i used to compile stuff on a redhat 7.1 machine
and you could use it on basically all currently running hardware.
intel still uses redhat 7.3 for their compilers...

cheers,
     axel.
DW>
DW> Dan
DW>
DW> John Stone wrote:
DW> > Hi,
DW> > On our RHEL4 64-bit build box, I don't get a libstdc++5 dependency...
DW> > Any thoughts on why Centos is different?:
DW> >
DW> > % ldd vmd_LINUXAMD64
DW> > libGL.so.1 => /usr/lib64/libGL.so.1 (0x0000003384e00000)
DW> > libGLU.so.1 => /usr/X11R6/lib64/libGLU.so.1 (0x0000003384c00000)
DW> > libX11.so.6 => /usr/X11R6/lib64/libX11.so.6 (0x0000003a05e00000)
DW> > libpthread.so.0 => /lib64/tls/libpthread.so.0 (0x0000003a06400000)
DW> > libdl.so.2 => /lib64/libdl.so.2 (0x0000003a05c00000)
DW> > libutil.so.1 => /lib64/libutil.so.1 (0x0000003a0a300000)
DW> > libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x0000003a08400000)
DW> > libm.so.6 => /lib64/tls/libm.so.6 (0x0000003a05a00000)
DW> > libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003a08600000)
DW> > libc.so.6 => /lib64/tls/libc.so.6 (0x0000003a05700000)
DW> > libGLcore.so.1 => /usr/lib64/libGLcore.so.1 (0x0000003384300000)
DW> > libnvidia-tls.so.1 => /usr/lib64/tls/libnvidia-tls.so.1 (0x0000003384100000)
DW> > libXext.so.6 => /usr/X11R6/lib64/libXext.so.6 (0x0000003a06000000)
DW> > /lib64/ld-linux-x86-64.so.2 (0x0000003a04a00000)
DW> >
DW> >
DW> > John Stone
DW> > vmd_at_ks.uiuc.edu
DW> >
DW> >
DW> >
DW> > On Tue, Feb 07, 2006 at 03:16:05PM +0100, Tru Huynh wrote:
DW> >> Hello,
DW> >>
DW> >> I am trying vmd-1.8.4b10 on CentOS-3 x86_64 and ran into a library issue:
DW> >>
DW> >> [tru_at_sillage bin]$ ldd /Bis/shared/centos-3_x86_64/vmd-1.8.4b10/vmd_LINUXAMD64
DW> >> libGL.so.1 => /usr/lib64/libGL.so.1 (0x0000002a9568e000)
DW> >> libGLU.so.1 => /usr/X11R6/lib64/libGLU.so.1 (0x0000002a95841000)
DW> >> libX11.so.6 => /usr/X11R6/lib64/libX11.so.6 (0x0000002a959c5000)
DW> >> libpthread.so.0 => /lib64/tls/libpthread.so.0 (0x0000002a95bb8000)
DW> >> libdl.so.2 => /lib64/libdl.so.2 (0x0000002a95ccc000)
DW> >> libutil.so.1 => /lib64/libutil.so.1 (0x0000002a95dd0000)
DW> >> libstdc++.so.6 => not found
DW> >> libm.so.6 => /lib64/tls/libm.so.6 (0x0000002a95ed3000)
DW> >> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000002a9605c000)
DW> >> libc.so.6 => /lib64/tls/libc.so.6 (0x0000002a96167000)
DW> >> libGLcore.so.1 => /usr/lib64/libGLcore.so.1 (0x0000002a963ac000)
DW> >> libnvidia-tls.so.1 => /usr/lib64/tls/libnvidia-tls.so.1 (0x0000002a96c2d000)
DW> >> libXext.so.6 => /usr/X11R6/lib64/libXext.so.6 (0x0000002a96d2e000)
DW> >> libstdc++.so.5 => /usr/lib64/libstdc++.so.5 (0x0000002a96e3f000)
DW> >> /lib64/ld-linux-x86-64.so.2 => /lib64/ld-linux-x86-64.so.2 (0x0000002a95556000)
DW> >>
DW> >> The current version does not have this issue:
DW> >> [tru_at_sillage bin]$ ldd /Bis/shared/centos-3_x86_64/vmd-1.8.3/vmd_LINUXAMD64
DW> >> libGL.so.1 => /usr/lib64/libGL.so.1 (0x0000002a9568e000)
DW> >> libGLU.so.1 => /usr/X11R6/lib64/libGLU.so.1 (0x0000002a95841000)
DW> >> libX11.so.6 => /usr/X11R6/lib64/libX11.so.6 (0x0000002a959c5000)
DW> >> libpthread.so.0 => /lib64/tls/libpthread.so.0 (0x0000002a95bb8000)
DW> >> libdl.so.2 => /lib64/libdl.so.2 (0x0000002a95ccc000)
DW> >> libutil.so.1 => /lib64/libutil.so.1 (0x0000002a95dd0000)
DW> >> libstdc++.so.5 => /usr/lib64/libstdc++.so.5 (0x0000002a95ed3000)
DW> >> libm.so.6 => /lib64/tls/libm.so.6 (0x0000002a960a7000)
DW> >> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000002a96230000)
DW> >> libc.so.6 => /lib64/tls/libc.so.6 (0x0000002a9633b000)
DW> >> libGLcore.so.1 => /usr/lib64/libGLcore.so.1 (0x0000002a96580000)
DW> >> libnvidia-tls.so.1 => /usr/lib64/tls/libnvidia-tls.so.1 (0x0000002a96e01000)
DW> >> libXext.so.6 => /usr/X11R6/lib64/libXext.so.6 (0x0000002a96f02000)
DW> >>
DW> >> -> libstdc++.so.5 instead of libstdc++.so.6
DW> >>
DW> >> The linux 32 bits version is also linked against libstdc++.so.5:
DW> >> [tru_at_sillage bin]$ ldd /Bis/shared/centos-3/vmd-1.8.4b10/vmd_LINUX
DW> >> libGL.so.1 => /usr/lib/libGL.so.1 (0x40037000)
DW> >> libGLU.so.1 => /usr/X11R6/lib/libGLU.so.1 (0x400bb000)
DW> >> libpthread.so.0 => /lib/tls/libpthread.so.0 (0x40137000)
DW> >> libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x40147000)
DW> >> libXft.so.2 => /usr/X11R6/lib/libXft.so.2 (0x40226000)
DW> >> libdl.so.2 => /lib/libdl.so.2 (0x40238000)
DW> >> libutil.so.1 => /lib/libutil.so.1 (0x4023b000)
DW> >> libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0x4023f000)
DW> >> libm.so.6 => /lib/tls/libm.so.6 (0x402f2000)
DW> >> libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x40314000)
DW> >> libc.so.6 => /lib/tls/libc.so.6 (0x4031d000)
DW> >> libGLcore.so.1 => /usr/lib/libGLcore.so.1 (0x40456000)
DW> >> libnvidia-tls.so.1 => /usr/lib/tls/libnvidia-tls.so.1 (0x40c14000)
DW> >> libXext.so.6 => /usr/X11R6/lib/libXext.so.6 (0x40c17000)
DW> >> /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x40000000)
DW> >> libXrender.so.1 => /usr/X11R6/lib/libXrender.so.1 (0x40c25000)
DW> >> libfontconfig.so.1 => /usr/lib/libfontconfig.so.1 (0x40c2d000)
DW> >> libexpat.so.0 => /usr/lib/libexpat.so.0 (0x40c54000)
DW> >> libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0x40c74000)
DW> >> libz.so.1 => /usr/lib/libz.so.1 (0x40cc5000)
DW> >>
DW> >> Cheers,
DW> >>
DW> >> Tru
DW> >> --
DW> >> Dr Tru Huynh | http://www.pasteur.fr/recherche/unites/Binfs/
DW> >> mailto:tru_at_pasteur.fr | tel/fax +33 1 45 68 87 37/19
DW> >> Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France
DW> >
DW> 

-- 
=======================================================================
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.