VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jun 07 2011 - 15:58:43 CDT

Mike,
  What do you get from this command:
ls -al /bin/tcsh

I would have expected at least some kind of output from the VMD startup
script assuming that your system isn't missing the shell or having some
weird problem there. What happens if you run "tcsh" manually, do you get
a normal csh/tcsh prompt?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jun 03, 2011 at 02:25:31PM -0500, Michael Zimmermann wrote:
> ---------------------------------------
> -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 

-- 
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