VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Tue Jun 05 2007 - 12:55:05 CDT

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
>
>
>
>
____________________________________________________________________________________
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