Re: [AMBER-Developers] Suggestions for dealing with mpich2-1.2.1p1

From: David A. Case <case.biomaps.rutgers.edu>
Date: Tue, 20 Apr 2010 07:34:20 -0400

On Mon, Apr 19, 2010, Mark Williamson wrote:
>
> Ok, I've got some results. First off, I applied this modification to
> PMEMD 10
> I think my change
> has not had a significantly detrimental effect on the performance. Would
> you agree with this?

First, by "this modification" do you mean the small patch below; second,
should I go ahead and add this to Amber11?

...thx...dave

===============================================================================

With reference to the PMEMD test fails with recent mpich2 versions,
I find the following patch works well for me:

--- a/src/pmemd/src/gb_parallel.fpp
+++ b/src/pmemd/src/gb_parallel.fpp
.@ -305,14 +305,20 @@ subroutine gb_mpi_gathervec(atm_cnt, vec)

    integer :: atm_cnt
    double precision :: vec(3, atm_cnt)
+ double precision :: recv_buf(3, atm_cnt)

  ! Local variables:

    call mpi_gatherv(vec(1, atm_offsets(mytaskid) + 1), &
                     vec_rcvcnts(mytaskid), mpi_double_precision, &
- vec, vec_rcvcnts, vec_offsets, &
+ recv_buf, vec_rcvcnts, vec_offsets, &
                     mpi_double_precision, 0, mpi_comm_world, err_code_mpi)

+ if (mytaskid == 0) then
+ vec = recv_buf
+ end if
+
+
    return



_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Tue Apr 20 2010 - 05:00:02 PDT
Custom Search