VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 05 2007 - 13:02:26 CDT

Francesco,
  Excellent, I'm glad you were able to solve the problem.
If you have a suggested set of commands for apt-get or similar
to install the right libstdc++.so.5, let me know so I can add
those instructions to the Linux release notes in case other
Debian users encounter the same problem.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jun 05, 2007 at 10:55:05AM -0700, Francesco Pietra wrote:
> Hi John and Axel:
>
> This is a hurried email to avoid bothering you further
> about this installation problem. As you rightly
> expected, it was my fault. I deeply apologize.
>
> By looking into more carefully, it turned out that, as
> far as libstdc++ libraries are concerned,
>
> /usr/lib/libstdc++.so.6
>
> while libstdcc++.so.5 was contained into a statically
> compiled computational program only.
>
> I don't know while by apt-file it was reported in
> /usr/lib, which was conformed by the same search. Must
> be my misuse of apt-file, I did not investigate
> because this is a hurried email.
>
> Briefly, I copied libstdcc++.so.5 into /usr/lib and
> vmd starts at the command
>
> $ /usr/local/bin/vmd
>
> in a beautiful blue window.
>
> Perhaps the installation can be improved for my use as
> single user but I remember vaguely that Axel should
> have already indicated how.
>
> Sorry for the troubles I gave.
>
> francesco
>
>
>
>
>
>
> --- Francesco Pietra <chiendarret_at_yahoo.com> wrote:
>
> > Date: Tue, 5 Jun 2007 09:38:18 -0700 (PDT)
> > From: Francesco Pietra <chiendarret_at_yahoo.com>
> > Subject: vmd installation Linux Debian i386
> > To: johns_at_ks.uiuc.edu
> >
> > Hi John:
> > Thanks for your understanding about the "Subject"
> > problem. Below I try to reconstruct - in Roman
> > sequential numbering, each section separated by a
> > line
> > - what I did.
> >
> > (1) QUERY IF MY COMPUTER WILL BE ABLE TO RUN VMD
> > GRAPHICALLY as I can't install it on the 64bit Linux
> > Debian amd64 parallel machine where namd should be
> > installed once the vmd problem is solved.
> >
> > CPU 32bit Athlon with OpenGL-graphics programs
> > running
> > OK.
> >
> > francesco_at_deb32:~$ awk '/Section
> >
> "(Module|Device|ServerFlags|Extensions)"/,/EndSection/'
> > /etc/X11/xorg.conf
> > Section "Module"
> > Load "i2c"
> > Load "bitmap"
> > Load "ddc"
> > Load "dri"
> > Load "extmod"
> > Load "freetype"
> > Load "glx"
> > Load "int10"
> > Load "vbe"
> > EndSection
> > Section "Device"
> > Identifier "nVidia Corporation NV11DDR
> > [GeForce2 MX 100 DDR/200 DDR]"
> > Driver "nv"
> > BusID "PCI:1:0:0"
> > EndSection
> > francesco_at_deb32:~$
> > (i.e, I don't use nvidia acceleration):
> > francesco_at_deb32:~$ dpkg -l '*nvidia*' | awk
> > '/^ii/{print $2}'
> > No packages found matching *nvidia*.
> > francesco_at_deb32:~$
> > francesco_at_deb32:~$ apt-cache policy
> > nvidia-{kernel-{source,common},glx}
> > nvidia-kernel-source:
> > Installed: (none)
> > Candidate: 1.0.8776-4
> > Version table:
> > 1.0.8776-4 0
> > 500 http://ftp.debian.org etch/non-free
> > Packages
> > nvidia-kernel-common:
> > Installed: (none)
> > Candidate: 20051028+1
> > Version table:
> > 20051028+1 0
> > 500 http://ftp.debian.org etch/contrib
> > Packages
> > nvidia-glx:
> > Installed: (none)
> > Candidate: 1.0.8776-4
> > Version table:
> > 1.0.8776-4 0
> > 500 http://ftp.debian.org etch/non-free
> >
> > VGA controller:
> > francesco_at_deb32:~$ lspci |egrep -i
> > '(video|vga|display)'
> > 01:00.0 VGA compatible controller: nVidia
> > Corporation
> > NV11DDR [GeForce2 MX 100 DDR/200 DDR] (rev b2)
> > francesco_at_deb32:~$
> > ___________________________________________________
> >
> > (2) INSTALLATION
> >
> > Downloaded the Linux OpenGL binary
> >
> > Uncompressesed and untared into my home
> > /home/francesco/vmd-1.8.6
> >
> > cd vmd-1.8.6
> >
> > I did not change the configure script, which read:
> >
> > # Name of shell script used to start program; this
> > is
> > the name used by users
> > $install_name = "vmd";
> >
> > # Directory where VMD startup script is installed,
> > should be in users' paths.
> > $install_bin_dir="/usr/local/bin";
> >
> > # Directory where VMD files and executables are
> > installed
> > $install_library_dir="/usr/local/lib/$install_name";
> >
> >
> > # optionally override hard-coded defaults above with
> > environment variables
> > if ($ENV{VMDINSTALLNAME}) {
> > $install_name = $ENV{VMDINSTALLNAME}
> > }
> > if ($ENV{VMDINSTALLBINDIR}) {
> > $install_bin_dir = $ENV{VMDINSTALLBINDIR}
> > }
> > if ($ENV{VMDINSTALLLIBRARYDIR}) {
> > $install_library_dir = $ENV{VMDINSTALLLIBRARYDIR}
> > }
> >
> > Then,
> >
> > ./configure LINUX
> > (whereby nothing was reported, though,
> > 'configure.options', opened with a text editor,
> > shows
> > 'LINUX')
> >
> > Then:
> > cd src
> >
> > su
> >
> > make install
> >
> > OK installed according to message
> >
> _____________________________________________________
> >
> > (3) LAUNCHING VMD
> >
> > francesco_at_deb32:~$ /usr/local/bin/vmd
> > [1] 5960
> > francesco_at_deb32:~$ /usr/local/bin/vmd -dispdev text
> > /usr/local/lib/vmd/vmd_LINUX: error while loading
> > shared libraries: libstdc++.so.5: cannot open shared
> > object file: No such file or directory
> > francesco_at_deb32:~$
> >
> _____________________________________________________
> >
> > (4) INQUIRING ABOUT FAILURE TO START
> >
> > francesco_at_deb32:~$ ldd /usr/local/lib/vmd/vmd_LINUX
> > linux-gate.so.1 => (0xffffe000)
> > libGL.so.1 => /usr/lib/libGL.so.1
> > (0xb7efb000)
> > libGLU.so.1 => /usr/lib/libGLU.so.1
> > (0xb7e7c000)
> > libpthread.so.0 =>
> > /lib/tls/i686/cmov/libpthread.so.0 (0xb7e6a000)
> > libX11.so.6 => /usr/lib/libX11.so.6
> > (0xb7d7e000)
> > libXft.so.2 => /usr/lib/libXft.so.2
> > (0xb7d6b000)
> > libdl.so.2 => /lib/tls/i686/cmov/libdl.so.2
> > (0xb7d66000)
> > libutil.so.1 =>
> > /lib/tls/i686/cmov/libutil.so.1 (0xb7d62000)
> > libstdc++.so.5 => not found
> > libm.so.6 => /lib/tls/i686/cmov/libm.so.6
> > (0xb7d3d000)
> > libgcc_s.so.1 => /lib/libgcc_s.so.1
> > (0xb7d32000)
> > libc.so.6 => /lib/tls/i686/cmov/libc.so.6
> > (0xb7c01000)
> > libXext.so.6 => /usr/lib/libXext.so.6
> > (0xb7bf2000)
> > libXxf86vm.so.1 => /usr/lib/libXxf86vm.so.1
> > (0xb7bed000)
> > libdrm.so.2 => /usr/lib/libdrm.so.2
> > (0xb7be6000)
> > libstdc++.so.6 => /usr/lib/libstdc++.so.6
> > (0xb7b01000)
> > /lib/ld-linux.so.2 (0xb7f74000)
> > libXau.so.6 => /usr/lib/libXau.so.6
> > (0xb7afe000)
> > libXdmcp.so.6 => /usr/lib/libXdmcp.so.6
> > (0xb7af8000)
> > libfontconfig.so.1 =>
> > /usr/lib/libfontconfig.so.1 (0xb7acd000)
> > libfreetype.so.6 =>
> > /usr/lib/libfreetype.so.6
> > (0xb7a63000)
> > libz.so.1 => /usr/lib/libz.so.1 (0xb7a4f000)
> > libXrender.so.1 => /usr/lib/libXrender.so.1
> > (0xb7a47000)
> > libexpat.so.1 => /usr/lib/libexpat.so.1
> > (0xb7a27000)
> > francesco_at_deb32:~$
> >
> > Then
> >
> > su
> >
> > apt-file update
> >
> > Then
> >
> > francesco_at_deb32:~$ apt-file search libstdc++.so.6
> > lib64stdc++6: usr/lib64/libstdc++.so.6
> > lib64stdc++6: usr/lib64/libstdc++.so.6.0.8
> > lib64stdc++6-4.1-dbg:
> > usr/lib/debug/usr/lib64/libstdc++.so.6.0.8
> > libstdc++6: usr/lib/libstdc++.so.6
> > libstdc++6: usr/lib/libstdc++.so.6.0.8
> > libstdc++6-4.1-dbg: usr/lib/debug/libstdc++.so.6
> > libstdc++6-4.1-dbg: usr/lib/debug/libstdc++.so.6.0.8
> > libstdc++6-4.1-dbg:
> > usr/lib/debug/usr/lib/libstdc++.so.6.0.8
> > libstdc++6-dbg: usr/lib/debug/libstdc++.so.6
> > libstdc++6-dbg: usr/lib/debug/libstdc++.so.6.0.3
> > libstdc++6-dbg: usr/lib64/debug/libstdc++.so.6
> > libstdc++6-dbg: usr/lib64/debug/libstdc++.so.6.0.3
> > francesco_at_deb32:~$
> >
> > Then
> >
> > francesco_at_deb32:~$ apt-file search libstdc++.so.5
> > libstdc++5: usr/lib/libstdc++.so.5
> > libstdc++5: usr/lib/libstdc++.so.5.0.7
> > libstdc++5-3.3-dbg: usr/lib/debug/libstdc++.so.5
> > libstdc++5-3.3-dbg: usr/lib/debug/libstdc++.so.5.0.7
> > francesco_at_deb32:~$
> > ___________________________________________________
> >
> > That is all I did;
> >
> > Thanks
> > francesco
> >
> >
> >
> >
> ____________________________________________________________________________________
> > Luggage? GPS? Comic books?
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> >
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> >
>
>
>
>
> ____________________________________________________________________________________
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-- 
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