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
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Received on Fri Apr 16 2010 - 09:30:05 PDT
