From 4c09c5f15211d18887859c78595236eb1d6d5b84 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnku@cse.msu.edu>
Date: Tue, 12 Apr 2016 23:11:37 -0400
Subject: [PATCH] sPuReMD: begin adding OpenMP support to SpMV, Jacobi iter,
and ICHOL_PAR.
---
puremd_rc_1003/sPuReMD/GMRES.c | 109 ++++++++++++++++++++++++++------
puremd_rc_1003/sPuReMD/Makefile | 2 +-
puremd_rc_1003/sPuReMD/QEq.c | 11 ++--
3 files changed, 96 insertions(+), 26 deletions(-)
mode change 100755 => 100644 puremd_rc_1003/sPuReMD/Makefile
diff --git a/puremd_rc_1003/sPuReMD/GMRES.c b/puremd_rc_1003/sPuReMD/GMRES.c
index bbc9fc0e..0bf02708 100644
--- a/puremd_rc_1003/sPuReMD/GMRES.c
+++ b/puremd_rc_1003/sPuReMD/GMRES.c
@@ -35,25 +35,60 @@ static void Sparse_MatVec( const sparse_matrix * const A,
{
int i, j, k, n, si, ei;
real H;
+#ifdef _OPENMP
+ real *b_local;
+#endif
n = A->n;
Vector_MakeZero( b, n );
- for ( i = 0; i < n; ++i )
+ #pragma omp parallel \
+ default(none) shared(n) private(b_local, si, ei, H, i, j, k)
{
- si = A->start[i];
- ei = A->start[i + 1] - 1;
+#ifdef _OPENMP
+ if ( (b_local = (real*) calloc(n, sizeof(real))) == NULL )
+ {
+ exit( INSUFFICIENT_SPACE );
+ }
+#endif
+ #pragma omp for schedule(guided)
+ for ( i = 0; i < n; ++i )
+ {
+ si = A->start[i];
+ ei = A->start[i + 1] - 1;
- for ( k = si; k < ei; ++k )
+ for ( k = si; k < ei; ++k )
+ {
+ j = A->entries[k].j;
+ H = A->entries[k].val;
+#ifdef _OPENMP
+ b_local[j] += H * x[i];
+ b_local[i] += H * x[j];
+#else
+ b[j] += H * x[i];
+ b[i] += H * x[j];
+#endif
+ }
+
+ // the diagonal entry is the last one in
+#ifdef _OPENMP
+ b_local[i] += A->entries[k].val * x[i];
+#else
+ b[i] += A->entries[k].val * x[i];
+#endif
+ }
+
+#ifdef _OPENMP
+ #pragma omp critical(redux)
{
- j = A->entries[k].j;
- H = A->entries[k].val;
- b[j] += H * x[i];
- b[i] += H * x[j];
+ for ( i = 0; i < n; ++i )
+ {
+ b[i] += b_local[i];
+ }
}
- // the diagonal entry is the last one in
- b[i] += A->entries[k].val * x[i];
+ free(b_local);
+#endif
}
}
@@ -70,28 +105,60 @@ static void Sparse_MatVec2( const sparse_matrix * const R,
const real * const x, real * const b)
{
int i, k, si = 0, ei = 0;
+#ifdef _OPENMP
+ real *b_local;
+#endif
Vector_MakeZero( b, R->n );
- for ( i = 0; i < R->n; ++i )
+ #pragma omp parallel default(none) private(b_local, i, k) firstprivate(si, ei)
{
- if (tri == LOWER)
+#ifdef _OPENMP
+ if ( (b_local = (real*) calloc(R->n, sizeof(real))) == NULL )
{
- si = R->start[i];
- ei = R->start[i + 1] - 1;
+ exit( INSUFFICIENT_SPACE );
}
- else if (tri == UPPER)
+#endif
+ #pragma omp for schedule(guided)
+ for ( i = 0; i < R->n; ++i )
{
+ if (tri == LOWER)
+ {
+ si = R->start[i];
+ ei = R->start[i + 1] - 1;
+ }
+ else if (tri == UPPER)
+ {
- si = R->start[i] + 1;
- ei = R->start[i + 1];
- }
+ si = R->start[i] + 1;
+ ei = R->start[i + 1];
+ }
- for ( k = si; k < ei; ++k )
+ for ( k = si; k < ei; ++k )
+ {
+#ifdef _OPENMP
+ b_local[i] += R->entries[k].val * x[R->entries[k].j];
+#else
+ b[i] += R->entries[k].val * x[R->entries[k].j];
+#endif
+ }
+#ifdef _OPENMP
+ b_local[i] *= -Dinv[i];
+#else
+ b[i] *= -Dinv[i];
+#endif
+ }
+#ifdef _OPENMP
+ #pragma omp critical(redux)
{
- b[i] += R->entries[k].val * x[R->entries[k].j];
+ for ( i = 0; i < R->n; ++i )
+ {
+ b[i] += b_local[i];
+ }
}
- b[i] *= -Dinv[i];
+
+ free(b_local);
+#endif
}
}
diff --git a/puremd_rc_1003/sPuReMD/Makefile b/puremd_rc_1003/sPuReMD/Makefile
old mode 100755
new mode 100644
index afb0d13a..a403e107
--- a/puremd_rc_1003/sPuReMD/Makefile
+++ b/puremd_rc_1003/sPuReMD/Makefile
@@ -1,7 +1,7 @@
CC = gcc
LIBS = -lm -lz
-CFLAGS = -I. -Wall -O3 -funroll-loops -fstrict-aliasing
+CFLAGS = -I. -Wall -O3 -funroll-loops -fstrict-aliasing -fopenmp
#CFLAGS = -I. -Wall -pg -gstabs
#CFLAGS = -I. -Wall -funroll-loops -fstrict-aliasing
#-finline-functions -finline-limit=15 -g#-DTEST -pg -ldl -rdynamic -g
diff --git a/puremd_rc_1003/sPuReMD/QEq.c b/puremd_rc_1003/sPuReMD/QEq.c
index 25033088..ca8efc67 100644
--- a/puremd_rc_1003/sPuReMD/QEq.c
+++ b/puremd_rc_1003/sPuReMD/QEq.c
@@ -120,7 +120,7 @@ real ICHOLT( sparse_matrix *A, real *droptol,
struct timeval start, stop;
gettimeofday( &start, NULL );
-
+
Utop = (int*) malloc((A->n + 1) * sizeof(int));
// clear variables
@@ -296,6 +296,8 @@ static void ICHOL_PAR( const sparse_matrix * const A, const unsigned int sweeps,
for ( i = 0; i < sweeps; ++i )
{
/* for each nonzero */
+ #pragma omp parallel for schedule(guided) \
+ default(none) private(sum, ei_x, ei_y) firstprivate(x, y)
for ( j = 0; j < A->start[A->n]; ++j )
{
sum = ZERO;
@@ -461,10 +463,11 @@ void Init_MatVec( reax_system *system, control_params *control,
}
data->timing.pre_comp += ICHOLT( workspace->H, workspace->droptol, workspace->L, workspace->U );
+// data->timing.pre_comp += ICHOLT( workspace->H_sp, workspace->droptol, workspace->L, workspace->U );
// TODO: add parameters for sweeps to control file
// ICHOL_PAR( workspace->H, 1, workspace->L, workspace->U );
- fprintf( stderr, "condest = %f\n", condest(workspace->L, workspace->U) );
+// fprintf( stderr, "condest = %f\n", condest(workspace->L, workspace->U) );
#if defined(DEBUG_FOCUS)
sprintf( fname, "%s.L%d.out", control->sim_name, data->step );
@@ -548,8 +551,8 @@ void QEq( reax_system *system, control_params *control, simulation_data *data,
Init_MatVec( system, control, data, workspace, far_nbrs );
- if( data->step == 0 || data->step == 100 )
- Print_Linear_System( system, control, workspace, data->step );
+// if( data->step == 0 || data->step == 100 )
+// Print_Linear_System( system, control, workspace, data->step );
//TODO: add parameters in control file for solver choice and options
// matvecs = GMRES( workspace, workspace->H,
--
GitLab