AMBER Archive (2004)

Subject: Re: AMBER: recovering total force array

From: Dave S Walker (dswalker_at_darkwing.uoregon.edu)
Date: Wed Mar 31 2004 - 15:29:13 CST

Carlos,
        My apologies for not catching that 35. I still don't know exactly
what all the components mean to the call statement (besides 'f' and
'forcetmp', which are described in parallel.f), but this was the most
recent form I used for mpi_allreduce which didn't work:

      call mpi_allreduce(F,ftmp,3*natom,MPI_DOUBLE_PRECISION,
     + MPI_SUM,MPI_COMM_WORLD,ierr)

Not knowing the size of ftmp I set it to have 3*natom elements (a guess,
along with 3*natom+40 which I tried once from looking at locmem.f). I
also have the call statement standing alone, which I thought would be okay
seeming as it adds all values from all nodes and sends the results out to
all nodes. I'm running AMBER7 (should have pointed that out earlier). Is
there a difference between MPI_COMM_WORLD and commsander that could cause
my problem? The latter isn't recognized upon compilation and I would only
try to make it as close to the former as possible if I kept it in! Thanks
again for your time.

dsw

On Tue, 30 Mar 2004, Carlos Simmerling wrote:

> Dave,
> I've done collection of all forces using this:
> call mpi_allreduce(f, forcetmp, 3*natom, &
> MPI_DOUBLE_PRECISION,mpi_sum,commsander,ierr)
> it seems to work ok, have you tried it?
>
> why did you use 35 in your allreduce?
>
> Carlos
>
> ----- Original Message -----
> From: "Dave S Walker" <dswalker_at_darkwing.uoregon.edu>
> To: <amber_at_scripps.edu>
> Sent: Tuesday, March 30, 2004 8:51 PM
> Subject: Re: AMBER: recovering total force array
>
>
> > 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
> > > ==================================================================
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