VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Tue Jun 05 2007 - 17:47:06 CDT

John:
Although, as a practical organic chemist, I find
myself not qualified to give suggestions about
files/packages, a general way of doing with Linux
Debian may be (where # means superuser and $ user):

(1) # apt-file update

which updates the database from the repositories one
has chosen for his system in /etc/apt/sources.list

(2) $ apt-file search libstdc++.so.5

which will tell which package(s) contain(s) this file,
such as from my machine:

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:~$

this tells that the package that should be installed
is libstdc++5, which could be done with command

# apt-get install libstdc++5

In my case the Debian package is libstdc++5
(1:3.3.6-15) The GNU Standard C++ Library v3 (one can
go to learn about to the package section of Debian). I
use the stable version (etch), which was until a few
weeks ago the intermediate version.

If the package had already been installed, though not
working properly, try to use "reinstall" instead of
install. However, I warn against using such commands
(as superuser) without reading first APT HOWTO. That
recipe above may be expected to work cleanly for a
clean system. Otherwise many different situations may
be found.

It depends also from the Debian version in use. It may
happen that the application that requests the library
needs a more recent version of the C++ library than
provided from the repositories one has chosen ( as for
version before etch). In that case one may try to
manually to upload the package from a higher version,
though it is easy to drop into dependency problems. In
general it is safer to upgrade Debian to the higher
version.

Cheers
francesco

--- John Stone <johns_at_ks.uiuc.edu> wrote:

>
> 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?
> > > Check out fitting gifts for grads at Yahoo!
> Search
> > >
> >
>
http://search.yahoo.com/search?fr=oni_on_mail&p=graduation+gifts&cs=bz
> > >
> >
> >
> >
> >
> >
>
____________________________________________________________________________________
> > Moody friends. Drama queens. Your life? Nope! -
> their life, your story. Play Sims Stories at Yahoo!
> Games.
> > http://sims.yahoo.com/
>
> --
> 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
>

       
____________________________________________________________________________________
Choose the right car based on your needs. Check out Yahoo! Autos new Car Finder tool.
http://autos.yahoo.com/carfinder/