From 67b2c00d0afe93e5af3f6ecb251f0a9663cd5418 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnku@msu.edu>
Date: Thu, 1 Sep 2016 20:40:00 -0700
Subject: [PATCH] sPuReMD: parameterize trisolve via level sched for better
memory usage.
---
sPuReMD/src/GMRES.c | 27 +++++++++++++++++++--------
sPuReMD/src/forces.c | 11 ++++++++++-
sPuReMD/src/mytypes.h | 7 ++++---
sPuReMD/src/testmd.c | 2 ++
4 files changed, 35 insertions(+), 12 deletions(-)
diff --git a/sPuReMD/src/GMRES.c b/sPuReMD/src/GMRES.c
index ddbd20a0..2cb7c042 100644
--- a/sPuReMD/src/GMRES.c
+++ b/sPuReMD/src/GMRES.c
@@ -306,9 +306,9 @@ static void tri_solve_level_sched( const sparse_matrix * const LU, const real *
if ( row_levels == NULL || level_rows == NULL || level_rows_cnt == NULL )
{
- if ( (row_levels = (unsigned int*) malloc(LU->n * sizeof(unsigned int))) == NULL
- || (level_rows = (unsigned int*) malloc(LU->n * LU->n * sizeof(unsigned int))) == NULL
- || (level_rows_cnt = (unsigned int*) malloc(LU->n * sizeof(unsigned int))) == NULL )
+ if ( (row_levels = (unsigned int*) malloc((size_t)LU->n * sizeof(unsigned int))) == NULL
+ || (level_rows = (unsigned int*) malloc(MAX_ROWS_PER_LEVEL * (size_t)LU->n * sizeof(unsigned int))) == NULL
+ || (level_rows_cnt = (unsigned int*) malloc((size_t)LU->n * sizeof(unsigned int))) == NULL )
{
fprintf( stderr, "Not enough space for triangular solve via level scheduling. Terminating...\n" );
exit( INSUFFICIENT_MEMORY );
@@ -333,8 +333,14 @@ static void tri_solve_level_sched( const sparse_matrix * const LU, const real *
levels = MAX( levels, local_level + 1 );
row_levels[i] = local_level;
- level_rows[local_level * LU->n + level_rows_cnt[local_level]] = i;
+ level_rows[local_level * MAX_ROWS_PER_LEVEL + level_rows_cnt[local_level]] = i;
++level_rows_cnt[local_level];
+ if( level_rows_cnt[local_level] >= MAX_ROWS_PER_LEVEL )
+ {
+ fprintf( stderr, "Not enough space for triangular solve via level scheduling" );
+ fprintf( stderr, " (MAX_ROWS_PER_LEVEL). Terminating...\n" );
+ exit( INSUFFICIENT_MEMORY );
+ }
}
}
else
@@ -349,8 +355,14 @@ static void tri_solve_level_sched( const sparse_matrix * const LU, const real *
levels = MAX( levels, local_level + 1 );
row_levels[i] = local_level;
- level_rows[local_level * LU->n + level_rows_cnt[local_level]] = i;
+ level_rows[local_level * MAX_ROWS_PER_LEVEL + level_rows_cnt[local_level]] = i;
++level_rows_cnt[local_level];
+ if( level_rows_cnt[local_level] >= MAX_ROWS_PER_LEVEL )
+ {
+ fprintf( stderr, "Not enough space for triangular solve via level scheduling" );
+ fprintf( stderr, " (MAX_ROWS_PER_LEVEL). Terminating...\n" );
+ exit( INSUFFICIENT_MEMORY );
+ }
}
}
}
@@ -364,7 +376,7 @@ static void tri_solve_level_sched( const sparse_matrix * const LU, const real *
default(none) private(j, pj, local_row) shared(stderr, i, level_rows_cnt, level_rows)
for ( j = 0; j < level_rows_cnt[i]; ++j )
{
- local_row = level_rows[i * LU->n + j];
+ local_row = level_rows[i * MAX_ROWS_PER_LEVEL + j];
x[local_row] = y[local_row];
for ( pj = LU->start[local_row]; pj < LU->start[local_row + 1] - 1; ++pj )
{
@@ -383,7 +395,7 @@ static void tri_solve_level_sched( const sparse_matrix * const LU, const real *
default(none) private(j, pj, local_row) shared(i, level_rows_cnt, level_rows)
for ( j = 0; j < level_rows_cnt[i]; ++j )
{
- local_row = level_rows[i * LU->n + j];
+ local_row = level_rows[i * MAX_ROWS_PER_LEVEL + j];
x[local_row] = y[local_row];
for ( pj = LU->start[local_row] + 1; pj < LU->start[local_row + 1]; ++pj )
{
@@ -787,7 +799,6 @@ int GMRES( const static_storage * const workspace, const control_params * const
}
}
-
workspace->h[j + 1][j] = Norm( workspace->v[j + 1], N );
Vector_Scale( workspace->v[j + 1],
1. / workspace->h[j + 1][j], workspace->v[j + 1], N );
diff --git a/sPuReMD/src/forces.c b/sPuReMD/src/forces.c
index 2746ede2..e6e63707 100644
--- a/sPuReMD/src/forces.c
+++ b/sPuReMD/src/forces.c
@@ -133,10 +133,14 @@ void Compute_NonBonded_Forces( reax_system *system, control_params *control,
#endif
if ( control->tabulate == 0)
+ {
vdW_Coulomb_Energy( system, control, data, workspace, lists, out_control );
+ }
else
+ {
Tabulated_vdW_Coulomb_Energy( system, control, data, workspace,
lists, out_control );
+ }
#if defined(DEBUG_FOCUS)
fprintf( stderr, "nonb forces - " );
#endif
@@ -933,8 +937,13 @@ void Compute_Forces( reax_system *system, control_params *control,
t_start = Get_Time( );
if ( !control->tabulate )
+ {
Init_Forces( system, control, data, workspace, lists, out_control );
- else Init_Forces_Tab( system, control, data, workspace, lists, out_control );
+ }
+ else
+ {
+ Init_Forces_Tab( system, control, data, workspace, lists, out_control );
+ }
t_elapsed = Get_Timing_Info( t_start );
data->timing.init_forces += t_elapsed;
#if defined(DEBUG_FOCUS)
diff --git a/sPuReMD/src/mytypes.h b/sPuReMD/src/mytypes.h
index 3202c622..ff89296f 100644
--- a/sPuReMD/src/mytypes.h
+++ b/sPuReMD/src/mytypes.h
@@ -115,6 +115,7 @@
#define MAX_ITR 10
#define RESTART 50
+#define MAX_ROWS_PER_LEVEL 10000 /* triangular solve using level scheduling */
#define ZERO 0.000000000000000e+00
#define ALMOST_ZERO 1e-10
@@ -725,9 +726,9 @@ typedef struct
* */
typedef struct
{
- int n, m;
- int *start;
- int *j;
+ unsigned int n, m;
+ unsigned int *start;
+ unsigned int *j;
real *val;
} sparse_matrix;
diff --git a/sPuReMD/src/testmd.c b/sPuReMD/src/testmd.c
index 5328a5bc..c4c66453 100644
--- a/sPuReMD/src/testmd.c
+++ b/sPuReMD/src/testmd.c
@@ -191,7 +191,9 @@ int main(int argc, char* argv[])
for ( ; data.step <= control.nsteps; data.step++ )
{
if ( control.T_mode )
+ {
Temperature_Control( &control, &data, &out_control );
+ }
Evolve( &system, &control, &data, &workspace, &lists, &out_control );
Post_Evolve( &system, &control, &data, &workspace, &lists, &out_control );
Output_Results(&system, &control, &data, &workspace, &lists, &out_control);
--
GitLab