AMBER Archive (2004)

Subject: Re: AMBER: recovering total force array

From: Dave S Walker (dswalker_at_darkwing.uoregon.edu)
Date: Tue Mar 30 2004 - 19:51:41 CST

Hello all,
        Sorry for the vague description of my problem (see below). A few
weeks ago I realized that the values for the force array are distributed
between nodes before they're written over by coordinates in runmd.f. In
my attempt to recover all of these values from the nodes I found myself
stumbling into fdist() in parallel.f, and it was in my poor attempts to
call on fdist() directly that caused all my problems.
        Looking closer at fdist() after getting David's response I
realized that calling on mpi_allreduce() directly would recover all the
values. I declared a "scratch space" variable named 'ftmp' and attempted
to call on mpi_allreduce() from runmd.f:

      call mpi_allreduce(F,ftmp,35,MPI_DOUBLE_PRECISION,MPI_SUM,
     + MPI_COMM_WORLD,ierr)

Sander compiles fine this way but the total force array still isn't
recovered. I hope I have described my actions clearer; any input into how
I can resolve this matter would be greatly appreciated. Thanks again for
your time.

dsw

On Fri, 12 Mar 2004, David A. Case wrote:

> On Thu, Mar 11, 2004, Dave S Walker wrote:
>
> > I've been trying (with no success) to figure out how to output the
> > total force array from runmd.f when running sander parallel. It looks
> > like fdist() in parallel.f would do the trick, but I haven't been able to
> > access it without sander freezing on me when I run it (compiles fine). Is
> > there a simple way to resolve this problem?
>
> I don't think the mailing list is going to be of much help here, given the
> limited amount of information you provide. It sounds like you modified
> the code somehow(?), and then it freezes. This is not much to go on.
>
> To output forces to a disk file, you will probably need an mpi_allreduce
> inside fdist() to make sure that all the forces get to the master processor,
> so that they can be written out. If you have already done that, and it
> doesn't work, you can hone and exercise your debugging skills :-)
>
> ...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ==================================================================
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu