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

From: Mark Williamson <mjw.sdsc.edu>
Date: Fri, 16 Apr 2010 09:13:26 -0700

Ross Walker wrote:
> Hi All,
>
> I am trying to address the mpich2-1.2.1p1 issue regarding pmemd (and also

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


Highlights:

* Compiles and runs fine with mpich2-1.2.1p1
* All test.parallel.pmemd pass
* Does not require changes to Makefiles/config or passing of extra flags.
* Is MPI-1 Compliant ;)
* Seems not to affect performance, viz:

Benchmarks
==========

Two pmemd.MPI binaries only differing in the above patch were prepared
in an identical fashion. Three repeat run of a modified gb benchmark
were carried out for each binary.

Tested with mpich2-1.0.7 since the old code will fail with the newer mpich2.

Method
------

cd $AMBERHOME/benchmarks/gb_mb

# Modify bench.gb_mb so that nstlim=10000 and
# so that it does not delete bench.gb_mb.out at the end
export TESTsander=../../exe/pmemd.MPI
export DO_PARALLEL="mpirun -np 8"

# Test loop
  for i in `seq 1 3`;
  do
    ./bench.gb_mb && grep "Master Total wall time" bench.gb_mb.out
  done



Results
-------

old
---
|  Master Total wall time:         346    seconds     0.10 hours
|  Master Total wall time:         347    seconds     0.10 hours
|  Master Total wall time:         347    seconds     0.10 hours
new
---
|  Master Total wall time:         345    seconds     0.10 hours
|  Master Total wall time:         347    seconds     0.10 hours
|  Master Total wall time:         346    seconds     0.10 hours
regards,
-- 
Mark Williamson, Post Doc
Walker Molecular Dynamics Group
Room 395E
San Diego Supercomputer Center
9500 Gilman Drive
La Jolla, CA 92093-0505
Email:  mjw at sdsc.edu
Office: 858-246-0827
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Fri Apr 16 2010 - 09:30:05 PDT
Custom Search