VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jun 01 2010 - 21:55:58 CDT

On Tue, Jun 1, 2010 at 9:31 PM, Philip Peartree
<p.peartree_at_postgrad.manchester.ac.uk> wrote:
>
> Hi All,
>
> Is it possible to compile vmd without graphics, but still retain full tcl
> scripting? I have tried running vmd in text display mode, but it won't load
> on the compute nodes of our cluster, because it still requests graphics
> libraries, which aren't there (for obvious reasons). I'm aware that vmd is
> mainly for visualising data, but I can't load my full trajectory in for
> analysis, as I have limited RAM.

  first off, depending on the kind of analysis you want to do,
   using the bigdcd script might help with he memory issue.

  second, yes you can compile VMD without graphics, but
  if it is just about getting it to run on a cluster node, you can
  just copy the libraries that are missing on the compute node
  into a directory that is readable on that node and then point
  the LD_LIBRARY_PATH environment variable to it.
  you can find out what you need but running the ldd comand
  on the VMD executable (not the vmd script but the real one
  that has the name vmd_<ARCH>. example:
  [akohlmey_at_fermi]$ ldd ~/vmd-test/vmd_LINUXAMD64
        linux-vdso.so.1 => (0x00007ffff7ffb000)
        libGL.so.1 => /usr/lib64/nvidia/libGL.so.1 (0x0000003559c00000)
        libGLU.so.1 => /usr/lib64/libGLU.so.1 (0x0000003557000000)
        libX11.so.6 => /usr/lib64/libX11.so.6 (0x000000354f800000)
        libcudart.so.3 => /home/akohlmey/cuda-3.0/lib64/libcudart.so.3
(0x00007ffff7ba5000)
        libXinerama.so.1 => /usr/lib64/libXinerama.so.1 (0x0000003556400000)
        libXi.so.6 => /usr/lib64/libXi.so.6 (0x0000003553800000)
        libpng12.so.0 => /usr/lib64/libpng12.so.0 (0x0000003552800000)
        libjpeg.so.62 => /usr/lib64/libjpeg.so.62 (0x000000355dc00000)
        libz.so.1 => /lib64/libz.so.1 (0x000000354ec00000)
        libpython2.6.so.1.0 => /usr/lib64/libpython2.6.so.1.0 (0x0000003564200000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00007ffff7989000)
        libcwiid.so.1 => /usr/lib64/libcwiid.so.1 (0x0000003d5d600000)
        libtk8.5.so => /usr/lib64/libtk8.5.so (0x000000354f000000)
        libtcl8.5.so => /usr/lib64/libtcl8.5.so (0x00007ffff765e000)
        libfltk.so.1.1 => /usr/lib64/libfltk.so.1.1 (0x00007ffff73ae000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00007ffff71aa000)
        libutil.so.1 => /lib64/libutil.so.1 (0x00007ffff6fa7000)
        libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x0000003559800000

cheers,
   axel.

>
> Philip Peartree
> University of Manchester
>
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.