[gmx-developers] rvec structure

[David van der Spoel]

On Fri, 2005-07-08 at 17:11 -0500, Nathan Moore wrote:
> Dear Berk, David,
> 
> Well, the implementation with collectives is marginally better.  It looks
> from the trace files though that there's still considerable time spent in
> MPI_Wait (often more time in Wait than in the collective).
> 
> Did an alternate version of gmx_sumf using MPI collectives (function
> defined in network.c) ever get written?  Any insight on where else the
> MPI_wait might be occurring?  So far I've only looked at the dpcc and
> villin benchmarks.
gmx_sumf is only used once (from global_stat) and not very important.

The fact that the real time is in MPI_Wait indicates load balancing
issues. The people working on optimization have added MPI_Barrier before
the communication steps, to distinguish communication problems from load
balancing problems.
> 
> regards,
> 
> Nathan Moore
> 
>  > Hi,
> >
> > You don't need a temp array.
> >
> > My test code is in CVS revision 1.8 of mvxvf.c:
> >
> >  >   static int *recvcounts=NULL,*displs;
> >  >   int i;
> >  >
> >  >   if (recvcounts == NULL) {
> >  >     snew(recvcounts,nsb->nprocs);
> >  >     snew(displs,nsb->nprocs);
> >  >     for(i=0; i<nsb->nprocs; i++) {
> >  >       recvcounts[i] = nsb->homenr[i]*sizeof(x[0]);
> >  >       displs[i]     = nsb->index[i]*sizeof(x[0]);
> >  >     }
> >  >   }
> >  >   MPI_Allgatherv(arrayp(x[nsb->index[nsb->pid]],nsb->homenr[nsb->pid]),
> >  >                MPI_BYTE,x,recvcounts,displs,MPI_BYTE,MPI_COMM_WORLD);
> >
> > It also contains the force summing, just one like is enough for this:
> > MPI_Allreduce(f,f,nsb->natoms*DIM,mpi_type,MPI_SUM,MPI_COMM_WORLD);
> >
> > Berk.
> >
> > _______________________________________________
> > gmx-developers mailing list
> > gmx-developers at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-developers
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-developers-request at gromacs.org.
> >
> 
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-developers-request at gromacs.org.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++