VMD-L Mailing List

From: V�ctor (victor.gil.sepulveda_at_gmail.com)
Date: Tue Jan 17 2012 - 17:19:48 CST

Great info!! Thanks to all!!

On Wed, Jan 18, 2012 at 12:17 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 2012/1/17 Víctor <victor.gil.sepulveda_at_gmail.com>:
> > I want to paralellize a rmsd matrix script... so it's a double loop where
> > the inner loop works with its own data: an embarrasingly parallel problem
> > (and I must add that it would be very difficult to run into a race
> condition
> > in something like this :) )
>
> that has nothing to do with it. but since VMD's internals in general are
> not thread safe, i.e. you must not access any VMD extensions to the
> Tcl interpreter from multiple threads. if you just write something in plain
> Tcl, then there are two cases to consider.
>
> 1) your calculation is not time very consuming:
> then the additional effort is a nice exercise, but doesn't
> result in much improvement anyway.
>
> 2) your calculation *is* time consuming:
> then a much better speedup would be achieved by replacing
> the Tcl script code with a C-code that is added to the Tcl
> interpreter as a plugin. since math in general in Tcl is *very*
> slow and simply porting it to C will give you much more speedup,
> than threading would do in Tcl. on top of that, you can multi-thread
> your plugin as much as you like, for as long as you only access
> the Tcl interpreter from one thread. i've done this a few times
> already using OpenMP directives.
>
> that being said, for the reasons outline above, VMD already offers
> some accelerated vector and matrix primitives programmed in C,
> that you might want to use to speed up your Tcl code.
> in particular, there are:
>
> vecadd, vecsub, vecscale, transmult, vectrans, veclength,
> vecmean, vecsum, transvec, transvecinv, transabout, vecstddev
>
> cheers,
> axel.
>
>
> >
> > Thanks for your tips anyway!
> >
> >
> > 2012/1/17 Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>
> >>>
> >>> As the script I'm coding works with my tcl interpreter (tclsh), What
> can
> >>> I do to be able to use the thread extension within VMD's tcl
> interpreter?
> >>
> >>
> >> Exactly what part would you like to parallelize? You could either invoke
> >> the thread-enabled tclsh from vmd tcl (using exec or some such - but
> passing
> >> data may be problematic) or run multiple instances of VMD (most
> probably in
> >> text mode) from a bash or tcl script.
> >>
> >> Best regards,
> >> Ajasja
> >
> >
> >
> >
> > --
> >
> > Víctor Gil Sepúlveda
> > E. Informatica - FIB - UPC
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
> 

-- 
Víctor Gil Sepúlveda
E. Informatica - FIB - UPC