From 9a8bd2d3eae3b5ee57c21a6de60a58430fef4c38 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnk@msu.edu>
Date: Tue, 17 Apr 2018 15:00:03 -0400
Subject: [PATCH] sPuReMD: add BiCGStab solver.
---
sPuReMD/src/charges.c | 20 +++++++
sPuReMD/src/init_md.c | 33 +++++++++--
sPuReMD/src/lin_alg.c | 126 +++++++++++++++++++++++++++++++++++++++---
sPuReMD/src/lin_alg.h | 4 ++
sPuReMD/src/mytypes.h | 4 +-
5 files changed, 174 insertions(+), 13 deletions(-)
diff --git a/sPuReMD/src/charges.c b/sPuReMD/src/charges.c
index 17c013e6..ca98e585 100644
--- a/sPuReMD/src/charges.c
+++ b/sPuReMD/src/charges.c
@@ -1342,6 +1342,14 @@ static void QEq( reax_system * const system, control_params * const control,
workspace->t[0], FALSE ) + 1;
break;
+ case BiCGStab_S:
+ iters = BiCGStab( 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) ? TRUE : FALSE ) + 1;
+ iters += BiCGStab( workspace, control, data, workspace->H, workspace->b_t, control->cm_solver_q_err,
+ workspace->t[0], FALSE ) + 1;
+ break;
+
default:
fprintf( stderr, "Unrecognized QEq solver selection. Terminating...\n" );
exit( INVALID_INPUT );
@@ -1416,6 +1424,12 @@ static void EE( reax_system * const system, control_params * const control,
(data->step - data->prev_steps) % control->cm_solver_pre_comp_refactor == 0) ? TRUE : FALSE ) + 1;
break;
+ case BiCGStab_S:
+ iters = BiCGStab( 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) ? TRUE : FALSE ) + 1;
+ break;
+
default:
fprintf( stderr, "Unrecognized EE solver selection. Terminating...\n" );
exit( INVALID_INPUT );
@@ -1499,6 +1513,12 @@ static void ACKS2( reax_system * const system, control_params * const control,
(data->step - data->prev_steps) % control->cm_solver_pre_comp_refactor == 0) ? TRUE : FALSE ) + 1;
break;
+ case BiCGStab_S:
+ iters = BiCGStab( 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) ? TRUE : FALSE ) + 1;
+ break;
+
default:
fprintf( stderr, "Unrecognized ACKS2 solver selection. Terminating...\n" );
exit( INVALID_INPUT );
diff --git a/sPuReMD/src/init_md.c b/sPuReMD/src/init_md.c
index d098007c..02a45310 100644
--- a/sPuReMD/src/init_md.c
+++ b/sPuReMD/src/init_md.c
@@ -352,7 +352,7 @@ static void Init_Workspace( reax_system *system, control_params *control,
}
//TODO: check if unused
- //workspace->w = (real *) scalloc( cm_lin_sys_size, sizeof( real ),
+ //workspace->w = (real *) scalloc( cm_lin_sys_size, sizeof( real ),
//"Init_Workspace::workspace->droptol" );
//TODO: check if unused
workspace->b = (real *) scalloc( system->N_cm * 2, sizeof( real ),
@@ -433,7 +433,6 @@ static void Init_Workspace( reax_system *system, control_params *control,
switch ( control->cm_solver_type )
{
- /* GMRES storage */
case GMRES_S:
case GMRES_H_S:
workspace->y = (real *) scalloc( control->cm_solver_restart + 1, sizeof( real ),
@@ -473,7 +472,6 @@ static void Init_Workspace( reax_system *system, control_params *control,
"Init_Workspace::workspace->p" );
break;
- /* CG storage */
case CG_S:
workspace->r = (real *) scalloc( system->N_cm, sizeof( real ),
"Init_Workspace::workspace->r" );
@@ -494,6 +492,23 @@ static void Init_Workspace( reax_system *system, control_params *control,
"Init_Workspace::workspace->q" );
break;
+ case BiCGStab_S:
+ workspace->r = (real *) scalloc( system->N_cm, sizeof( real ),
+ "Init_Workspace::workspace->r" );
+ workspace->r_hat = (real *) scalloc( system->N_cm, sizeof( real ),
+ "Init_Workspace::workspace->r_hat" );
+ workspace->d = (real *) scalloc( system->N_cm, sizeof( real ),
+ "Init_Workspace::workspace->d" );
+ workspace->q = (real *) scalloc( system->N_cm, sizeof( real ),
+ "Init_Workspace::workspace->q" );
+ workspace->p = (real *) scalloc( system->N_cm, sizeof( real ),
+ "Init_Workspace::workspace->p" );
+ workspace->y = (real *) scalloc( system->N_cm, sizeof( real ),
+ "Init_Workspace::workspace->y" );
+ workspace->z = (real *) scalloc( system->N_cm, sizeof( real ),
+ "Init_Workspace::workspace->z" );
+ break;
+
default:
fprintf( stderr, "Unknown charge method linear solver type. Terminating...\n" );
exit( INVALID_INPUT );
@@ -1217,7 +1232,6 @@ static void Finalize_Workspace( reax_system *system, control_params *control,
switch ( control->cm_solver_type )
{
- /* GMRES storage */
case GMRES_S:
case GMRES_H_S:
for ( i = 0; i < control->cm_solver_restart + 1; ++i )
@@ -1242,7 +1256,6 @@ static void Finalize_Workspace( reax_system *system, control_params *control,
sfree( workspace->p, "Finalize_Workspace::workspace->p" );
break;
- /* CG storage */
case CG_S:
sfree( workspace->r, "Finalize_Workspace::workspace->r" );
sfree( workspace->d, "Finalize_Workspace::workspace->d" );
@@ -1256,6 +1269,16 @@ static void Finalize_Workspace( reax_system *system, control_params *control,
sfree( workspace->q, "Finalize_Workspace::workspace->q" );
break;
+ case BiCGStab_S:
+ sfree( workspace->r, "Finalize_Workspace::workspace->r" );
+ sfree( workspace->r_hat, "Finalize_Workspace::workspace->r_hat" );
+ sfree( workspace->d, "Finalize_Workspace::workspace->d" );
+ sfree( workspace->q, "Finalize_Workspace::workspace->q" );
+ sfree( workspace->p, "Finalize_Workspace::workspace->p" );
+ sfree( workspace->y, "Finalize_Workspace::workspace->y" );
+ sfree( workspace->z, "Finalize_Workspace::workspace->z" );
+ break;
+
default:
fprintf( stderr, "Unknown charge method linear solver type. Terminating...\n" );
exit( INVALID_INPUT );
diff --git a/sPuReMD/src/lin_alg.c b/sPuReMD/src/lin_alg.c
index bcf78513..ac3c2166 100644
--- a/sPuReMD/src/lin_alg.c
+++ b/sPuReMD/src/lin_alg.c
@@ -3162,6 +3162,7 @@ int GMRES( const static_storage * const workspace, const control_params * const
if ( g_itr >= control->cm_solver_max_iters )
{
fprintf( stderr, "[WARNING] GMRES convergence failed (%d outer iters)\n", g_itr );
+ fprintf( stderr, " [INFO] Rel. residual error: %f\n", FABS(workspace->g[g_j]) / bnorm );
return g_itr * (control->cm_solver_restart + 1) + g_j + 1;
}
@@ -3403,6 +3404,7 @@ int GMRES_HouseHolder( const static_storage * const workspace,
if ( g_itr >= control->cm_solver_max_iters )
{
fprintf( stderr, "[WARNING] GMRES convergence failed (%d outer iters)\n", g_itr );
+ fprintf( stderr, " [INFO] Rel. residual error: %f\n", FABS(w[g_j]) / bnorm );
return g_itr * (control->cm_solver_restart + 1) + j + 1;
}
@@ -3461,7 +3463,7 @@ int CG( const static_storage * const workspace, const control_params * const con
t_start = Get_Time( );
Vector_Copy( p, z, N );
- sig_new = Dot( r, z, N );
+ sig_new = Dot( r, p, N );
t_vops += Get_Timing_Info( t_start );
for ( i = 0; i < control->cm_solver_max_iters && r_norm / b_norm > tol; ++i )
@@ -3474,7 +3476,7 @@ int CG( const static_storage * const workspace, const control_params * const con
tmp = Dot( d, p, N );
alpha = sig_new / tmp;
Vector_Add( x, alpha, p, N );
- Vector_Add( r, -alpha, d, N );
+ Vector_Add( r, -1.0 * alpha, d, N );
r_norm = Norm( r, N );
t_vops += Get_Timing_Info( t_start );
@@ -3487,7 +3489,7 @@ int CG( const static_storage * const workspace, const control_params * const con
sig_old = sig_new;
sig_new = Dot( r, z, N );
beta = sig_new / sig_old;
- Vector_Sum( p, 1., z, beta, p, N );
+ Vector_Sum( p, 1.0, z, beta, p, N );
t_vops += Get_Timing_Info( t_start );
}
@@ -3504,6 +3506,115 @@ int CG( const static_storage * const workspace, const control_params * const con
if ( g_itr >= control->cm_solver_max_iters )
{
fprintf( stderr, "[WARNING] CG convergence failed (%d iters)\n", g_itr );
+ fprintf( stderr, " [INFO] Rel. residual error: %f\n", r_norm / b_norm );
+ return g_itr;
+ }
+
+ return g_itr;
+}
+
+
+/* Bi-conjugate gradient stabalized method with left preconditioning for
+ * solving nonsymmetric linear systems
+ *
+ * workspace: struct containing storage for workspace for the linear solver
+ * control: struct containing parameters governing the simulation and numeric methods
+ * data: struct containing simulation data (e.g., atom info)
+ * H: sparse, symmetric matrix, lower half stored in CSR format
+ * b: right-hand side of the linear system
+ * tol: tolerence compared against the relative residual for determining convergence
+ * x: inital guess
+ * fresh_pre: flag for determining if preconditioners should be recomputed
+ * */
+int BiCGStab( const static_storage * const workspace, const control_params * const control,
+ simulation_data * const data, const sparse_matrix * const H, const real * const b,
+ const real tol, real * const x, const int fresh_pre )
+{
+ int i, g_itr, N;
+ real tmp, alpha, beta, omega, rho, rho_old, sigma, r_norm, b_norm;
+ real t_start, t_pa, t_spmv, t_vops;
+
+ N = H->n;
+ t_pa = 0.0;
+ t_spmv = 0.0;
+ t_vops = 0.0;
+
+#ifdef _OPENMP
+ #pragma omp parallel default(none) \
+ private(i, tmp, alpha, beta, omega, rho, rho_old, sigma, r_norm, b_norm, t_start) \
+ reduction(+: t_pa, t_spmv, t_vops) \
+ shared(g_itr, N)
+#endif
+ {
+ t_pa = 0.0;
+ t_spmv = 0.0;
+ t_vops = 0.0;
+
+ t_start = Get_Time( );
+ Sparse_MatVec( workspace, H, x, workspace->d );
+ t_spmv += Get_Timing_Info( t_start );
+
+ t_start = Get_Time( );
+ b_norm = Norm( b, N );
+ Vector_Sum( workspace->r, 1.0, b, -1.0, workspace->d, N );
+ t_vops += Get_Timing_Info( t_start );
+
+ t_start = Get_Time( );
+ Vector_Copy( workspace->r_hat, workspace->r, N );
+ r_norm = Norm( workspace->r, N );
+ Vector_Copy( workspace->p, workspace->r, N );
+ rho_old = Dot( workspace->r, workspace->r_hat, N );
+ t_vops += Get_Timing_Info( t_start );
+
+ for ( i = 0; i < control->cm_solver_max_iters && r_norm / b_norm > tol; ++i )
+ {
+ t_start = Get_Time( );
+ Sparse_MatVec( workspace, H, workspace->p, workspace->d );
+ t_spmv += Get_Timing_Info( t_start );
+
+ t_start = Get_Time( );
+ tmp = Dot( workspace->d, workspace->r_hat, N );
+ alpha = rho_old / tmp;
+ Vector_Sum( workspace->q, 1.0, workspace->r, -1.0 * alpha, workspace->d, N );
+ t_vops += Get_Timing_Info( t_start );
+
+ t_start = Get_Time( );
+ Sparse_MatVec( workspace, H, workspace->q, workspace->y );
+ t_spmv += Get_Timing_Info( t_start );
+
+ t_start = Get_Time( );
+ sigma = Dot( workspace->y, workspace->q, N );
+ tmp = Dot( workspace->y, workspace->y, N );
+ omega = sigma / tmp;
+ Vector_Sum( workspace->z, alpha, workspace->p, omega, workspace->q, N );
+ Vector_Add( x, 1.0, workspace->z, N );
+ Vector_Sum( workspace->r, 1.0, workspace->q, -1.0 * omega, workspace->y, N );
+ r_norm = Norm( workspace->r, N );
+ t_vops += Get_Timing_Info( t_start );
+
+ t_start = Get_Time( );
+ rho = Dot( workspace->r, workspace->r_hat, N );
+ beta = (rho / rho_old) * (alpha / omega);
+ Vector_Sum( workspace->z, 1.0, workspace->p, -1.0 * omega, workspace->d, N );
+ Vector_Sum( workspace->p, 1.0, workspace->r, beta, workspace->z, N );
+ rho_old = rho;
+ t_vops += Get_Timing_Info( t_start );
+ }
+
+#ifdef _OPENMP
+ #pragma omp single
+#endif
+ g_itr = i;
+ }
+
+ data->timing.cm_solver_pre_app += t_pa / control->num_threads;
+ data->timing.cm_solver_spmv += t_spmv / control->num_threads;
+ data->timing.cm_solver_vector_ops += t_vops / control->num_threads;
+
+ if ( g_itr >= control->cm_solver_max_iters )
+ {
+ fprintf( stderr, "[WARNING] BiCGStab convergence failed (%d iters)\n", g_itr );
+ fprintf( stderr, " [INFO] Rel. residual error: %f\n", r_norm / b_norm );
return g_itr;
}
@@ -3550,8 +3661,8 @@ int SDM( const static_storage * const workspace, const control_params * const co
t_vops += Get_Timing_Info( t_start );
t_start = Get_Time( );
- apply_preconditioner( workspace, control, workspace->r, workspace->d, fresh_pre, LEFT );
- apply_preconditioner( workspace, control, workspace->r, workspace->d, fresh_pre, RIGHT );
+ apply_preconditioner( workspace, control, workspace->r, workspace->q, fresh_pre, LEFT );
+ apply_preconditioner( workspace, control, workspace->q, workspace->d, fresh_pre, RIGHT );
t_pa += Get_Timing_Info( t_start );
t_start = Get_Time( );
@@ -3583,8 +3694,8 @@ int SDM( const static_storage * const workspace, const control_params * const co
t_vops += Get_Timing_Info( t_start );
t_start = Get_Time( );
- apply_preconditioner( workspace, control, workspace->r, workspace->d, FALSE, LEFT );
- apply_preconditioner( workspace, control, workspace->r, workspace->d, FALSE, RIGHT );
+ apply_preconditioner( workspace, control, workspace->r, workspace->q, FALSE, LEFT );
+ apply_preconditioner( workspace, control, workspace->q, workspace->d, FALSE, RIGHT );
t_pa += Get_Timing_Info( t_start );
}
@@ -3601,6 +3712,7 @@ int SDM( const static_storage * const workspace, const control_params * const co
if ( g_itr >= control->cm_solver_max_iters )
{
fprintf( stderr, "[WARNING] SDM convergence failed (%d iters)\n", g_itr );
+ fprintf( stderr, " [INFO] Rel. residual error: %f\n", SQRT(sig) / b_norm );
return g_itr;
}
diff --git a/sPuReMD/src/lin_alg.h b/sPuReMD/src/lin_alg.h
index ab0237c1..696fdc9b 100644
--- a/sPuReMD/src/lin_alg.h
+++ b/sPuReMD/src/lin_alg.h
@@ -101,6 +101,10 @@ int CG( const static_storage * const, const control_params * const,
simulation_data * const, const sparse_matrix * const, const real * const,
const real, real * const, const int );
+int BiCGStab( const static_storage * const, const control_params * const,
+ simulation_data * const, const sparse_matrix * const, const real * const,
+ const real, real * const, const int );
+
int SDM( const static_storage * const, const control_params * const,
simulation_data * const, const sparse_matrix * const, const real * const, const real,
real * const, const int );
diff --git a/sPuReMD/src/mytypes.h b/sPuReMD/src/mytypes.h
index 0abe07f2..c2712e83 100644
--- a/sPuReMD/src/mytypes.h
+++ b/sPuReMD/src/mytypes.h
@@ -219,6 +219,7 @@ enum solver
GMRES_H_S = 1,
CG_S = 2,
SDM_S = 3,
+ BiCGStab_S = 4,
};
enum pre_comp
@@ -980,8 +981,9 @@ typedef struct
real **rn;
real **v;
- /* CG related storage */
+ /* CG, SDM, BiCGStab related storage */
real *r;
+ real *r_hat;
real *d;
real *q;
real *p;
--
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