VMD-L Mailing List

From: Michael Zimmermann (michaelz_at_iastate.edu)
Date: Fri Jun 03 2011 - 14:25:31 CDT

---------------------------------------
-bash-3.2$ head -5 ~/bin/vmd
#!/bin/csh
set defaultvmddir="/usr.data/michaelz/lib/vmd"
set vmdbasename=vmd
#!/bin/csh -f
## In case the installation didn't add these (which means you didn't
---------------------------------------
>>> The computer's name was left off since this is publicly accessible
-bash-3.2$ uname -a
Linux XXXXXXXXXXXXXXX 2.6.18-92.el5 #1 SMP Tue Apr 29 13:16:15 EDT 2008
x86_64 x86_64 x86_64 GNU/Linux
---------------------------------------
-bash-3.2$ head /etc/issue
Red Hat Enterprise Linux Server release 5.5 (Tikanga)
Kernel \r on an \m
---------------------------------------
-bash-3.2$ ls -l /bin/sh
lrwxrwxrwx 1 root root 4 Aug 5 2010 /bin/sh -> bash
-bash-3.2$ ls -l /bin/csh
lrwxrwxrwx 1 root root 4 Dec 16 15:28 /bin/csh -> tcsh
---------------------------------------

Mike

On Fri, Jun 3, 2011 at 9:54 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> 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
> 

-- 
Michael Zimmermann
Ph.D. student in Bioinformatics and Computational Biology
Department of Biochemistry, Biophysics and Molecular Biology
Iowa State University