VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 04 2005 - 09:30:05 CST

Olivier,
  You need to make sure that VMD is finding the library in /usr/lib64.
This means that you either need to make your 'ldconfig' set it up correctly,
or you need to change your library search path so it is found when running
VMD.

What happens if you do:
  setenv LD_LIBRARY_PATH /usr/lib64:${LD_LIBRARY_PATH}

and then re-test?
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Mar 04, 2005 at 04:10:15PM +0100, olivier Walker wrote:
> Hi all,
>
>
> Sorry to bother your again with such a question, I currently running VMD
> for AMD64. I was reading the previous post concerning this subject and I
> found a part of the answer.
> I've basically the same problem that Dr Daniel James and some other
> encountered. When launching VMD, a small window appears and the vanishes
> immediately.
> As Axel Kohlmeyer recomended, If I type "ldd ./vmd_LINUXAMD64", I've the
> following information
>
>
> [olivier_at_sanyo vmd]$ ldd ./vmd_LINUXAMD64
> libGL.so.1 => /usr/lib64/libGL.so.1 (0x0000003bf4000000)
> libGLU.so.1 => /usr/X11R6/lib64/libGLU.so.1 (0x0000003bf4200000)
> libX11.so.6 => /usr/X11R6/lib64/libX11.so.6 (0x000000350e500000)
> libpthread.so.0 => /lib64/tls/libpthread.so.0 (0x000000350eb00000)
> libdl.so.2 => /lib64/libdl.so.2 (0x000000350e300000)
> libutil.so.1 => /lib64/libutil.so.1 (0x0000003513a00000)
> libstdc++.so.5 => not found
> libm.so.6 => /lib64/tls/libm.so.6 (0x000000350e100000)
> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003510b00000)
> libc.so.6 => /lib64/tls/libc.so.6 (0x000000350de00000)
> libGLcore.so.1 => /usr/lib64/libGLcore.so.1 (0x0000003bf3800000)
> libnvidia-tls.so.1 => /usr/lib64/tls/libnvidia-tls.so.1
> (0x0000003bf3600000)
> libXext.so.6 => /usr/X11R6/lib64/libXext.so.6 (0x000000350e700000)
> libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x0000003510d00000)
> /lib64/ld-linux-x86-64.so.2 (0x000000350dc00000)
>
>
> In this case I was thinking there was a problem with libstdc++.so.5.
> Right, because I forgot to install the package "compat-libstdc++" to
> ensure compatibility with old libraries. This time if I type "ll
> /usr/lib64/libstdc++*" I obtain:
>
>
> lrwxrwxrwx 1 root root 18 mar 4 15:39 /usr/lib64/libstdc++.so.5 ->
> libstdc++.so.5.0.7
> -rwxr-xr-x 1 root root 739700 mar 4 15:16 /usr/lib64/libstdc++.so.5.0.7
> lrwxrwxrwx 1 root root 18 fév 21 16:00 /usr/lib64/libstdc++.so.6 ->
> libstdc++.so.6.0.3
> -rwxr-xr-x 1 root root 917752 oct 26 10:53 /usr/lib64/libstdc++.so.6.0.3
>
> or "ll /usr/lib/libstdc++*"
>
> -rwxr-xr-x 1 root root 258296 aoû 18 2004
> /usr/lib/libstdc++-2-libc6.1-1-2.9.0.so
> -rwxr-xr-x 1 root root 261960 aoû 18 2004
> /usr/lib/libstdc++-3-libc6.2-2-2.10.0.so
> lrwxrwxrwx 1 root root 30 mar 4 15:06
> /usr/lib/libstdc++-libc6.1-1.so.2 -> libstdc++-2-libc6.1-1-2.9.0.so
> lrwxrwxrwx 1 root root 31 mar 4 15:06
> /usr/lib/libstdc++-libc6.2-2.so.3 -> libstdc++-3-libc6.2-2-2.10.0.so
> lrwxrwxrwx 1 root root 20 mar 4 15:06 /usr/lib/libstdc++.so.2.7.2
> -> libstdc++.so.2.7.2.8
> -rwxr-xr-x 1 root root 222800 aoû 18 2004 /usr/lib/libstdc++.so.2.7.2.8
> lrwxrwxrwx 1 root root 18 mar 4 15:06 /usr/lib/libstdc++.so.2.8 ->
> libstdc++.so.2.8.0
> -rwxr-xr-x 1 root root 251480 aoû 18 2004 /usr/lib/libstdc++.so.2.8.0
> lrwxrwxrwx 1 root root 22 mar 4 15:06 /usr/lib/libstdc++.so.2.9 ->
> libstdc++.so.2.9.dummy
> -rwxr-xr-x 1 root root 3444 aoû 18 2004 /usr/lib/libstdc++.so.2.9.dummy
> lrwxrwxrwx 1 root root 18 mar 4 15:06 /usr/lib/libstdc++.so.5 ->
> libstdc++.so.5.0.7
> -rwxr-xr-x 1 root root 739700 aoû 18 2004 /usr/lib/libstdc++.so.5.0.7
> lrwxrwxrwx 1 root root 18 fév 21 16:00 /usr/lib/libstdc++.so.6 ->
> libstdc++.so.6.0.3
> -rwxr-xr-x 1 root root 811744 oct 26 10:48 /usr/lib/libstdc++.so.6.0.3
>
>
>
> Then I type again "ldd ./vmd_LINUXAMD64", I've the same answer as
> previously, even if the libstdc++.so.5 is now installed.
> I really don't know what is wrong, I would appreciate any help or hints.
>
> Olivier
>
> --
> ++++++++++++++++++++++++++++++++++++++++++++++++++
> Dr. Olivier WALKER
> Laboratoire de RMN Biomoleculaire Université Claude Bernard - Lyon 1
> CNRS UMR 5180 Sciences Analytiques
> ESCPE-Lyon,bâtiment 308G
> 69622 Villeurbanne, France
> Phone : +33 4 72 43 18 27
> Fax : +33 4 72 43 13 95
> mailto: olivier_at_hikari.cpe.fr
> http://sakura.cpe.fr
> +++++++++++++++++++++++++++++++++++++++++++++++++ 

-- 
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              
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