VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jun 03 2011 - 09:54:39 CDT

Mike,
  You cannot change the configure.options file for a binary distribution
and have any effect (e.g. removing CUDA). I doubt there's actually something
wrong with the VMD binary or its shared library dependencies based on what
you sent, but there must be something going on with the VMD startup script.
What do you get from these commands:
  head ~/bin/vmd
  uname -a
  head /etc/issue
  ls -l /bin/sh
  ls -l /bin/csh
 
Cheers,
  John Stone

On Fri, Jun 03, 2011 at 09:38:46AM -0500, Michael Zimmermann wrote:
> I have checked the other directories in my $PATH to be sure there are no
> other "vmd"s - I did not find any. Also, the following is under bash, but
> I've tried all of these under csh too.
>
> I am not root on the computer I am working on, so I have changed the
> install path to:
>
> $install_bin_dir="/usr.data/michaelz/bin";
> $install_library_dir="/usr.data/michaelz/lib/$install_name";
>
> These are the same as "~/bin" and "~/lib"
>
> Running any of the options you suggest, I get no output whatsoever (except
> ldd). I will be using the text interface most of the time (-dispdev
> text), so that is my main concern (just for reference). Also, I am using
> vmd-1.9.bin.LINUXAMD64.opengl.tar.gz that was decompressed with "tar
> -zxvf"
>
> --------------------------------------------------------------
> -bash-3.2$ ldd ~/lib/vmd/vmd_LINUXAMD64
> /usr/local/lib/preloadable_libiconv.so (0x00002b3dd295c000)
> libGL.so.1 => /usr/lib64/libGL.so.1 (0x00000030c7400000)
> libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x00000030c0a00000)
> libX11.so.6 => /usr/lib64/libX11.so.6 (0x00000030be600000)
> libcudart.so.3 => not found
> libXinerama.so.1 => /usr/lib64/libXinerama.so.1
> (0x00000030c1200000)
> libXi.so.6 => /usr/lib64/libXi.so.6 (0x00000030c5600000)
> libpthread.so.0 => /lib64/libpthread.so.0 (0x00000030bde00000)
> libdl.so.2 => /lib64/libdl.so.2 (0x00000030bda00000)
> libutil.so.1 => /lib64/libutil.so.1 (0x00000030ca400000)
> libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00000030c3600000)
> libm.so.6 => /lib64/libm.so.6 (0x00000030bd600000)
> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00000030c2200000)
> libc.so.6 => /lib64/libc.so.6 (0x00000030bd200000)
> libXext.so.6 => /usr/lib64/libXext.so.6 (0x00000030bf200000)
> libXxf86vm.so.1 => /usr/lib64/libXxf86vm.so.1 (0x00000030ce000000)
> libdrm.so.2 => /usr/lib64/libdrm.so.2 (0x00000030c4200000)
> libXau.so.6 => /usr/lib64/libXau.so.6 (0x00000030bea00000)
> libXdmcp.so.6 => /usr/lib64/libXdmcp.so.6 (0x00000030bee00000)
> /lib64/ld-linux-x86-64.so.2 (0x00000030bce00000)
> --------------------------------------------------------------
>
> If I remove CUDA from configure.options and re-run the installation, then
> re-run ldd, I get the same output as well as the lack of any output from
> running ~/bin/vmd.
>
> Mike
>
> On Thu, Jun 2, 2011 at 11:11 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> If you're not getting any console output at all, that seems to indicate
> that you're not really running the actual VMD startup script, and are
> somehow
> finding something else?
>
> What do you get if you do this:
> vmd -dispdev text
> Or this:
> /usr/local/bin/vmd -dispdev text
>
> Or this:
> ldd /usr/local/lib/vmd/vmd_LINUXAMD64
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
> > On Thu, Jun 02, 2011 at 11:00:40PM -0500, Michael Zimmermann wrote:
> > I have been attempting to install the pre-compiled binaries of on a
> linux
> > computer that is running "Red Hat Enterprise Linux Server release
> 5.5" and
> > has AMD 64-bit processors. I have tried using both the 64 and
> 32-bit
> > linux distributions available (v1.9 and 1.8.7) on the main site. I
> have
> > followed the installation instructions and the files are copied to
> the
> > designated bin and lib directories (I did fully delete the contents
> of
> > these directories between install attempts). Running "make
> install" says
> > that the installation was successful, but when I execute the vmd
> startup
> > script, nothing happens. There are no errors thrown, or output of
> any
> > kind that I can see. I have tried changing the configuration
> options to
> > leave out IMD, CUDA, OpenGL, etc. in case those components are the
> issue,
> > but none of these changes have helped. I am out of ideas at this
> point.
> >
> > Have any of you experienced this behavior, or do you have advice on
> how to
> > continue?
> >
> > Thank you,
> >
> > Michael Z.
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
>
> --
> Michael Zimmermann
> Ph.D. student in Bioinformatics and Computational Biology
> Department of Biochemistry, Biophysics and Molecular Biology
> Iowa State University 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078