From 5f5fe7dc2895b50714a569d8b644266b12e737e4 Mon Sep 17 00:00:00 2001
From: Abdullah Alperen <alperena@msu.edu>
Date: Fri, 23 Nov 2018 00:23:23 -0500
Subject: [PATCH] PuReMD: fix allocation problem regarding NT buffers
---
PuReMD/src/allocate.c | 6 +++---
PuReMD/src/basic_comm.c | 32 ++------------------------------
PuReMD/src/comm_tools.c | 3 ++-
PuReMD/src/forces.c | 6 ++++--
PuReMD/src/linear_solvers.c | 11 +++--------
5 files changed, 14 insertions(+), 44 deletions(-)
diff --git a/PuReMD/src/allocate.c b/PuReMD/src/allocate.c
index ffdd965b..d638b8da 100644
--- a/PuReMD/src/allocate.c
+++ b/PuReMD/src/allocate.c
@@ -742,15 +742,15 @@ int Allocate_MPI_Buffers( mpi_datatypes *mpi_data, int est_recv,
//TODO: add an exact number
/* in buffers */
mpi_data->in_nt_buffer[i] = (void*)
- scalloc( my_nbrs[i].est_recv, sizeof(real), "mpibuf:in_nt_buffer", comm );
+ scalloc( my_nt_nbrs[i].est_recv, sizeof(real), "mpibuf:in_nt_buffer", comm );
//TODO
mpi_buf = &( mpi_data->out_nt_buffers[i] );
/* allocate storage for the neighbor processor i */
mpi_buf->index = (int*)
- scalloc( my_nbrs[i].est_send, sizeof(int), "mpibuf:nt_index", comm );
+ scalloc( my_nt_nbrs[i].est_send, sizeof(int), "mpibuf:nt_index", comm );
mpi_buf->out_atoms = (void*)
- scalloc( my_nbrs[i].est_send, sizeof(real), "mpibuf:nt_out_atoms",
+ scalloc( my_nt_nbrs[i].est_send, sizeof(real), "mpibuf:nt_out_atoms",
comm );
}
#endif
diff --git a/PuReMD/src/basic_comm.c b/PuReMD/src/basic_comm.c
index 83f01e52..92c834ef 100644
--- a/PuReMD/src/basic_comm.c
+++ b/PuReMD/src/basic_comm.c
@@ -156,22 +156,11 @@ void Dist_NT( reax_system* system, mpi_datatypes *mpi_data,
MPI_Irecv( buf + nbr->atoms_str * scale, nbr->atoms_cnt, type,
nbr->receive_rank, d, comm, &(req[d]) );
}
-
- /*if(d==0)
- {
- fprintf( stdout, "p%d dist: entered and need to receive %d numbers from %d\n", system->my_rank, nbr->atoms_cnt, nbr->receive_rank );
- fflush( stdout );
- }*/
}
for( d = 0; d < 6; ++d)
{
nbr = &(system->my_nt_nbrs[d]);
- if(d==0)
- {
- //fprintf( stdout, "p%d dist: entered and need to send %d numbers to %d\n", system->my_rank, out_bufs[d].cnt, nbr->rank );
- //fflush( stdout );
- }
/* send both messages in dimension d */
if ( out_bufs[d].cnt )
{
@@ -181,16 +170,8 @@ void Dist_NT( reax_system* system, mpi_datatypes *mpi_data,
}
}
- /*
- MPI_Barrier( MPI_COMM_WORLD );
- fprintf( stdout, "p%d dist: MISSION COMPLETED\n", system->my_rank );
- fflush( stdout );
- */
-
for( d = 0; d < 6; ++d )
{
- //fprintf( stdout, "p%d dist: direction %d\n", system->my_rank, d );
- //fflush( stdout );
nbr = &(system->my_nbrs[d]);
if ( nbr->atoms_cnt )
{
@@ -198,20 +179,11 @@ void Dist_NT( reax_system* system, mpi_datatypes *mpi_data,
}
}
-
/*for( d = 0; d < count; ++d )
{
MPI_Waitany( REAX_MAX_NT_NBRS, req, &index, stat);
}*/
-
- /*
- MPI_Barrier( MPI_COMM_WORLD );
- fprintf( stdout, "p%d dist: MPI_Waitany is done\n", system->my_rank );
- fflush( stdout );
- */
-
-
#if defined(DEBUG)
fprintf( stderr, "p%d dist: done\n", system->my_rank );
#endif
@@ -373,8 +345,8 @@ void Coll_NT( reax_system* system, mpi_datatypes *mpi_data,
for( d = 0; d < 6; ++d )
{
- fprintf( stderr, "p%d coll: d = %d\n", system->my_rank, d );
- fflush( stdout );
+ //fprintf( stderr, "p%d coll: d = %d\n", system->my_rank, d );
+ //fflush( stdout );
if ( out_bufs[d].cnt )
{
MPI_Wait( &(req[d]), &(stat[d]));
diff --git a/PuReMD/src/comm_tools.c b/PuReMD/src/comm_tools.c
index 2162456c..38315557 100644
--- a/PuReMD/src/comm_tools.c
+++ b/PuReMD/src/comm_tools.c
@@ -163,12 +163,13 @@ void Init_Neutral_Territory( reax_system* system, mpi_datatypes *mpi_data )
if( mpi_data->in_nt_buffer[d] == NULL )
{
//TODO
- mpi_data->in_nt_buffer[d] = (void *) smalloc( 100 * cnt * sizeof(real), "in", comm );
+ mpi_data->in_nt_buffer[d] = (void *) smalloc( SAFER_ZONE * cnt * sizeof(real), "in", comm );
}
nbr = &(system->my_nt_nbrs[d]);
nbr->atoms_str = end;
nbr->atoms_cnt = cnt;
+ nbr->est_recv = MAX( SAFER_ZONE * cnt, MIN_SEND );
end += cnt;
}
}
diff --git a/PuReMD/src/forces.c b/PuReMD/src/forces.c
index 8178856d..93cbe8cf 100644
--- a/PuReMD/src/forces.c
+++ b/PuReMD/src/forces.c
@@ -1161,6 +1161,10 @@ void Estimate_Storages( reax_system *system, control_params *control,
BO_pi2 = exp( C56 );
}
else BO_pi2 = C56 = 0.0;
+
+ /* Initially BO values are the uncorrected ones, page 1 */
+ BO = BO_s + BO_pi + BO_pi2;
+
if ( BO >= control->bo_cut )
{
++bond_top[i];
@@ -1278,8 +1282,6 @@ void Compute_Forces( reax_system *system, control_params *control,
//MPI_Barrier( mpi_data->world );
if ( system->my_rank == MASTER_NODE )
Update_Timing_Info( &t_start, &(data->timing.nonb) );
-#endif
- Update_Timing_Info( &t_start, &(data->timing.nonb) );
#endif
#if defined(DEBUG_FOCUS)
fprintf( stderr, "p%d @ step%d: nonbonded forces completed\n",
diff --git a/PuReMD/src/linear_solvers.c b/PuReMD/src/linear_solvers.c
index 3606d90d..1d1ccc9a 100644
--- a/PuReMD/src/linear_solvers.c
+++ b/PuReMD/src/linear_solvers.c
@@ -1238,12 +1238,7 @@ int CG( reax_system *system, control_params *control, simulation_data *data,
else
{
#if defined(NEUTRAL_TERRITORY)
- fprintf(stdout,"BEFORE COLL\n");
- fflush( stdout );
-
Coll_NT( system, mpi_data, workspace->q, MPI_DOUBLE, scale, real_unpacker );
- fprintf(stdout,"AFTER COLL\n");
- fflush( stdout );
#endif
}
@@ -1288,8 +1283,8 @@ int CG( reax_system *system, control_params *control, simulation_data *data,
for ( i = 0; i < control->cm_solver_max_iters && sqrt(sig_new) / b_norm > tol; ++i )
{
- fprintf( stdout, "p%d, i = %d, res = %.6f\n", system->my_rank, i, sqrt(sig_new) / b_norm );
- fflush( stdout );
+ //fprintf( stdout, "p%d, i = %d, res = %.6f\n", system->my_rank, i, sqrt(sig_new) / b_norm );
+ //fflush( stdout );
t_start = Get_Time( );
#if defined(NEUTRAL_TERRITORY)
Dist_NT( system, mpi_data, workspace->d, MPI_DOUBLE, scale, real_packer );
@@ -1364,7 +1359,7 @@ int CG( reax_system *system, control_params *control, simulation_data *data,
}
t_start = Get_Time( );
- //sig_new = Parallel_Dot(workspace->r, workspace->p, H->NT, mpi_data->world);
+ sig_old = sig_new;
sig_new = Parallel_Dot(workspace->r, workspace->p, system->n, mpi_data->world);
t_allreduce += Get_Timing_Info( t_start );
--
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