VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 09 2006 - 09:38:08 CST

Hi Axel,
  The 32-bit builds of VMD are done on a Redhat 9 box, which is as old as
I can go (and even this, I had to beg our sysadmin not to upgrade it even
with the obvious security issues that RH9 has). As it stands now, I'm getting
reports of the RH9 binaries doing weird things on the bleeding edge linux
distributions (no linking probs, but unusual runtime failures). I may have
to distribute two different 32-bit builds of VMD 1.8.4, one build on RH9,
and one built on RHEL4. For 64-bit, I only plan to build on RHEL4.
Any suggestions, or do you think this is sufficient?

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Feb 09, 2006 at 07:16:54AM -0500, Axel Kohlmeyer 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.
>
> 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. 

-- 
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