From f14972a49d808172f8f6be2b7d8acf37b6aa1546 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnk@msu.edu>
Date: Thu, 24 Aug 2017 00:11:41 -0400
Subject: [PATCH] sPuReMD: update SDM with preconditioning methods and OpenMP
support.
---
sPuReMD/src/charges.c | 21 ++++++++-------
sPuReMD/src/init_md.c | 4 ++-
sPuReMD/src/lin_alg.c | 63 +++++++++++++++++++++++--------------------
sPuReMD/src/lin_alg.h | 3 ++-
sPuReMD/src/vector.c | 13 +++------
5 files changed, 54 insertions(+), 50 deletions(-)
diff --git a/sPuReMD/src/charges.c b/sPuReMD/src/charges.c
index d2fddf36..f81fba69 100644
--- a/sPuReMD/src/charges.c
+++ b/sPuReMD/src/charges.c
@@ -2011,7 +2011,7 @@ static void Setup_Preconditioner_QEq( const reax_system * const system,
simulation_data * const data, static_storage * const workspace,
const list * const far_nbrs )
{
- int i, fillin;
+ int fillin;
real time;
sparse_matrix *Hptr;
@@ -2156,7 +2156,7 @@ static void Setup_Preconditioner_EE( const reax_system * const system,
simulation_data * const data, static_storage * const workspace,
const list * const far_nbrs )
{
- int i, fillin;
+ int fillin;
real time;
sparse_matrix *Hptr;
@@ -2305,7 +2305,7 @@ static void Setup_Preconditioner_ACKS2( const reax_system * const system,
simulation_data * const data, static_storage * const workspace,
const list * const far_nbrs )
{
- int i, fillin;
+ int fillin;
real time;
sparse_matrix *Hptr;
@@ -2547,9 +2547,10 @@ static void QEq( reax_system * const system, control_params * const control,
case SDM_S:
iters = SDM( workspace, control, workspace->H, workspace->b_s, control->cm_solver_q_err,
- workspace->s[0] ) + 1;
+ workspace->s[0], (control->cm_solver_pre_comp_refactor > 0 &&
+ (data->step - data->prev_steps) % control->cm_solver_pre_comp_refactor == 0) ? TRUE : FALSE ) + 1;
iters += SDM( workspace,control, workspace->H, workspace->b_t, control->cm_solver_q_err,
- workspace->t[0] ) + 1;
+ workspace->t[0], FALSE ) + 1;
break;
default:
@@ -2628,7 +2629,8 @@ static void EE( reax_system * const system, control_params * const control,
case SDM_S:
iters = SDM( workspace, control, workspace->H, workspace->b_s, control->cm_solver_q_err,
- workspace->s[0] ) + 1;
+ workspace->s[0], (control->cm_solver_pre_comp_refactor > 0 &&
+ (data->step - data->prev_steps) % control->cm_solver_pre_comp_refactor == 0) ? TRUE : FALSE ) + 1;
break;
default:
@@ -2689,8 +2691,8 @@ static void ACKS2( reax_system * const system, control_params * const control,
case GMRES_H_S:
iters = GMRES_HouseHolder( workspace, control, data,workspace->H,
workspace->b_s, control->cm_solver_q_err, workspace->s[0],
- (control->cm_solver_pre_comp_refactor > 0 &&
- data->step - data->prev_steps) % control->cm_solver_pre_comp_refactor == 0 );
+ control->cm_solver_pre_comp_refactor > 0 &&
+ (data->step - data->prev_steps) % control->cm_solver_pre_comp_refactor == 0 );
break;
case CG_S:
@@ -2701,7 +2703,8 @@ static void ACKS2( reax_system * const system, control_params * const control,
case SDM_S:
iters = SDM( workspace, control, workspace->H, workspace->b_s, control->cm_solver_q_err,
- workspace->s[0] ) + 1;
+ workspace->s[0], (control->cm_solver_pre_comp_refactor > 0 &&
+ (data->step - data->prev_steps) % control->cm_solver_pre_comp_refactor == 0) ? TRUE : FALSE ) + 1;
break;
default:
diff --git a/sPuReMD/src/init_md.c b/sPuReMD/src/init_md.c
index 4228f8bd..3cbf575f 100644
--- a/sPuReMD/src/init_md.c
+++ b/sPuReMD/src/init_md.c
@@ -428,7 +428,9 @@ void Init_Workspace( reax_system *system, control_params *control,
break;
case SDM_S:
- //TODO
+ workspace->r = (real *) calloc( system->N_cm, sizeof( real ) );
+ workspace->d = (real *) calloc( system->N_cm, sizeof( real ) );
+ workspace->q = (real *) calloc( system->N_cm, sizeof( real ) );
break;
default:
diff --git a/sPuReMD/src/lin_alg.c b/sPuReMD/src/lin_alg.c
index 631b543a..28b7c956 100644
--- a/sPuReMD/src/lin_alg.c
+++ b/sPuReMD/src/lin_alg.c
@@ -1764,53 +1764,58 @@ int CG( const static_storage * const workspace, const control_params * const con
/* Steepest Descent */
int SDM( const static_storage * const workspace, const control_params * const control,
const sparse_matrix * const H, const real * const b, const real tol,
- real * const x )
+ real * const x, const int fresh_pre )
{
- int i, j, N;
- real tmp, alpha, beta, b_norm;
- real sig0, sig;
+ int i, itr, N;
+ real tmp, alpha, b_norm;
+ real sig;
N = H->n;
- b_norm = Norm( b, N );
- Sparse_MatVec( H, x, workspace->q );
- Vector_Sum( workspace->r , 1., b, -1., workspace->q, N );
- for ( j = 0; j < N; ++j )
+ #pragma omp parallel default(none) private(i, tmp, alpha, b_norm, sig) \
+ shared(itr, N)
{
- workspace->d[j] = workspace->r[j] * workspace->Hdia_inv[j];
- }
+ b_norm = Norm( b, N );
- sig = Dot( workspace->r, workspace->d, N );
- sig0 = sig;
+ Sparse_MatVec( H, x, workspace->q );
+ Vector_Sum( workspace->r , 1.0, b, -1.0, workspace->q, N );
- for ( i = 0; i < control->cm_solver_max_iters && SQRT(sig) / b_norm > tol; ++i )
- {
- Sparse_MatVec( H, workspace->d, workspace->q );
+ apply_preconditioner( workspace, control, workspace->r, workspace->d, fresh_pre );
sig = Dot( workspace->r, workspace->d, N );
- tmp = Dot( workspace->d, workspace->q, N );
- alpha = sig / tmp;
- Vector_Add( x, alpha, workspace->d, N );
- Vector_Add( workspace->r, -alpha, workspace->q, N );
- for ( j = 0; j < N; ++j )
+ for ( i = 0; i < control->cm_solver_max_iters && SQRT(sig) / b_norm > tol; ++i )
{
- workspace->d[j] = workspace->r[j] * workspace->Hdia_inv[j];
+ Sparse_MatVec( H, workspace->d, workspace->q );
+
+ sig = Dot( workspace->r, workspace->d, N );
+
+ /* ensure each thread gets a local copy of
+ * the function return value
+ * (which is stored as global inside the function)
+ * before proceeding */
+ #pragma omp barrier
+
+ tmp = Dot( workspace->d, workspace->q, N );
+ alpha = sig / tmp;
+
+ Vector_Add( x, alpha, workspace->d, N );
+ Vector_Add( workspace->r, -alpha, workspace->q, N );
+
+ apply_preconditioner( workspace, control, workspace->r, workspace->d, FALSE );
}
- //fprintf( stderr, "d_norm:%24.15e, q_norm:%24.15e, tmp:%24.15e\n",
- //Norm(workspace->d,N), Norm(workspace->q,N), tmp );
+ #pragma omp single
+ itr = i;
}
- fprintf( stderr, "SDM took %d iterations\n", i );
-
- if ( i >= 300 )
+ if ( itr >= control->cm_solver_max_iters )
{
- fprintf( stderr, "SDM convergence failed!\n" );
- return i;
+ fprintf( stderr, "[WARNING] SDM convergence failed (%d iters)\n", itr );
+ return itr;
}
- return i;
+ return itr;
}
diff --git a/sPuReMD/src/lin_alg.h b/sPuReMD/src/lin_alg.h
index f62742a2..a3148514 100644
--- a/sPuReMD/src/lin_alg.h
+++ b/sPuReMD/src/lin_alg.h
@@ -63,7 +63,8 @@ int CG( const static_storage * const, const control_params * const,
real * const, const int );
int SDM( const static_storage * const, const control_params * const,
- const sparse_matrix * const, const real * const, const real, real * const );
+ const sparse_matrix * const, const real * const, const real,
+ real * const, const int );
real condest( const sparse_matrix * const, const sparse_matrix * const );
diff --git a/sPuReMD/src/vector.c b/sPuReMD/src/vector.c
index 24e05de8..5329aea7 100644
--- a/sPuReMD/src/vector.c
+++ b/sPuReMD/src/vector.c
@@ -32,13 +32,11 @@ inline int Vector_isZero( const real * const v, const unsigned int k )
{
unsigned int i;
- #pragma omp master
+ #pragma omp single
{
ret = TRUE;
}
- #pragma omp barrier
-
#pragma omp for reduction(&&: ret) schedule(static)
for ( i = 0; i < k; ++i )
{
@@ -134,14 +132,11 @@ inline real Dot( const real * const v1, const real * const v2, const unsigned in
{
unsigned int i;
- #pragma omp master
+ #pragma omp single
{
ret2 = ZERO;
}
- #pragma omp barrier
-
-
#pragma omp for reduction(+: ret2) schedule(static)
for ( i = 0; i < k; ++i )
{
@@ -156,13 +151,11 @@ inline real Norm( const real * const v1, const unsigned int k )
{
unsigned int i;
- #pragma omp master
+ #pragma omp single
{
ret2 = ZERO;
}
- #pragma omp barrier
-
#pragma omp for reduction(+: ret2) schedule(static)
for ( i = 0; i < k; ++i )
{
--
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