Hi, Jason,
Thanks a lot for your help.
I'll creat another array ext_force(natom*3), and broadcast the whole
information of ext_force(*) to all threads.
And then add ext_force(*) to original f(*) .
Best Wishes,
Chicago JI
2011/10/2 Jason Swails <jason.swails.gmail.com>
> Hello,
>
> On Sat, Oct 1, 2011 at 2:23 PM, Chicago Ji <chicago.ecnu.gmail.com> wrote:
>
> > Dear Amber users,
> >
> > I want to add an extra energy term on part of the system (only few
> > atoms) in Amber11.
> >
> > I need to add extra force to f(*) in runmd.f .
> >
> > But I'm don't know what was stored in f(*) exactly .
> >
>
> f(*) stores all of the forces. All forces are calculated, and this array
> is
> populated, in force.f (subroutine force). This subroutine begins by
> zeroing
> out the entire force array. Each processor then proceeds to calculate the
> force (according to all of the potential terms that are included) on each
> atom that *that processor is responsible for*.
>
>
> > I tried to print out f(*) on each process.
> >
> > It seems that only part of f(*) was right on each process.
> > ( from id "istart3" to "iend3" )
> >
>
> Correct (except for the very first dynamics step if you're not doing a
> restart).
>
>
> >
> > I guess : f(*) calculted from each process wasn't summarized and brocast
> .
> >
>
> Correct. If you want to see what's happening, see the subroutines "fdist"
> and "fsum" in $AMBERHOME/src/sander/parallel.f. (The force distribution
> routine is called in force.f -- just search for the fdist call). The key
> to
> this is that the force distribution is done via a MPI_Reduce_scatter call
> (see around line 550 in parallel.f), rather than a call to MPI_Allreduce().
> The MPI_Reduce_scatter sums up all of the forces on all threads to the
> master thread, then scatters out the relevant parts for each slave
> processor
> so that it can propagate the coordinates of the atoms it owns. An
> MPI_Allreduce() call would have summed up all forces from all threads *to*
> all threads, which is a more costly communication (and this is what's done
> for the very first dynamics step if you're not doing a restart).
>
>
> > So only part information of f(*) on each process was useful, am i right ?
> >
>
> Correct. This is OK, though, since (as you can see in runmd), each
> processor propagates only the atomic positions of the atoms it owns. (From
> runmd.f:
>
> do i3 = istart3, iend3
> f(i3) = x(i3)
> if (i3 >= cphfirst_sol3 - 3) &
> x(i3) = x(i3) + v(i3)*dtx
> end do
>
> where istart3 and iend3 are set based on atom ownership). Then of course
> the positions have to be sent from everyone to everyone (xdist does this
> via
> an MPI_Allgatherv call).
>
> Note, though, that pmemd's parallelization scheme is _completely_ different
> than sander's. For instance, it works via a spatial decomposition scheme
> rather than sequence decomposition (and pmemd's scaling and performance is
> obviously much better than sander's). Thus, any lessons learned about
> sander parallelization must be relearned if you want to start modifying or
> understanding pmemd.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
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>
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Received on Sun Oct 02 2011 - 03:30:02 PDT
