VMD-L Mailing List

From: Michael Zimmermann (michaelz_at_iastate.edu)
Date: Fri Jun 03 2011 - 09:38:46 CDT

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