VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Sep 01 2017 - 14:10:44 CDT

On Fri, Sep 1, 2017 at 2:12 PM, John Stone <johns_at_ks.uiuc.edu> wrote
​:
​

>
> The reason that the standard VMD builds don't include MPI by default
> is because MPI lacks a binary runtime interface, and requires that
> applications be compiled from source code on the actual target
> hardware where they will be run. To make the deployment of VMD
> with MPI easier, I have been considering making the MPI aspects of
> VMD operate using a plugin type interface and shipping the MPI-related
> plugin source code along with VMD so that an existing VMD binary for
> Linux/Windows/MacOS could just load such an MPI plugin at runtime,
> and you wouldn't have to recompile the whole program, which as many
> here already know is quite a task, particularly for beginners.
>

FWIW: there is already an external MPI plugin for Tcl, that can be used to
parallelize VMD using fast message passing networks via MPI.
​https://sites.google.com/site/akohlmey/software/tclmpi

​this​ exists for over 5 years and i have been using it very successfully
to parallelize plain Tcl scripts but also VMD/Tcl script (e.g. where each
VMD instance loads a subset of a trajectory). you compile the plugin
separately, test it with your local Tcl installation and the load it into
VMD without having to recompile VMD.

the main limitation of this plugin is, that it is made for generic Tcl and
thus only supports Tcl data structures (thus it cannot communicate VMD
internal data directly). on the other hand, it is completely independent of
VMD and can be used with any compatible Tcl interpreter.

axel.

> Best regards,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Sep 01, 2017 at 01:34:59PM +0200, Ajasja Ljubeti?? wrote:
> > Hi!
> > You're not giving a whole lot of details, so my advice will be
> generic as
> > well. Usually I split my trajectories into 1 ns chunks and then I use
> > [1]gnu parallelĀ to run analysis scripts in parallel.Ā
> > If you mean the parallel [2]tcl commandĀ you have to compile VMD with
> MPI
> > support and have MPI installed. But I guess this is meant for large
> > clusters of computers not just a four core processor (or two, in case
> of
> > hyper-threading).
> > Best,
> > Ajasja
> > On 1 September 2017 at 12:59, Saikat Pal
> > <[3]saikatpaliitg_at_remove_yahoo.com> wrote:
> >
> > Dear all,
> > I want o install VMD IN parallel to analysis data.What should I do
> ??I
> > have already installed VMD in serial mode .In my computer there are
> 4
> > processors are available.Please help me out .
> > Thanks And Regards,
> > Saikat
> >
> > References
> >
> > Visible links
> > 1. https://www.gnu.org/software/parallel/
> > 2. http://www.ks.uiuc.edu/Research/vmd/current/ug/node144.html
> > 3. mailto:saikatpaliitg_at_remove_yahoo.com
>
> --
> NIH Center 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/
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.