From 2ddfabcd402a690193aa8de06e1810b3a33e7bdf Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnk@msu.edu>
Date: Thu, 1 Feb 2018 16:58:52 -0500
Subject: [PATCH] sPuReMD: multithread SAI computation. Deallocate SAI matrices
upon exit.
---
sPuReMD/src/init_md.c | 5 +
sPuReMD/src/lin_alg.c | 222 ++++++++++++++++++++++--------------------
2 files changed, 120 insertions(+), 107 deletions(-)
diff --git a/sPuReMD/src/init_md.c b/sPuReMD/src/init_md.c
index d392aa3c..c5728825 100644
--- a/sPuReMD/src/init_md.c
+++ b/sPuReMD/src/init_md.c
@@ -1006,6 +1006,11 @@ void Finalize_Workspace( reax_system *system, control_params *control,
Deallocate_Matrix( workspace->L );
Deallocate_Matrix( workspace->U );
}
+ if ( control->cm_solver_pre_comp_type == SAI_PC )
+ {
+ Deallocate_Matrix( workspace->H_spar_patt );
+ Deallocate_Matrix( workspace->H_app_inv );
+ }
for ( i = 0; i < 5; ++i )
{
diff --git a/sPuReMD/src/lin_alg.c b/sPuReMD/src/lin_alg.c
index 30ca4aea..c6f56ed4 100644
--- a/sPuReMD/src/lin_alg.c
+++ b/sPuReMD/src/lin_alg.c
@@ -1620,7 +1620,6 @@ real Sparse_Approx_Inverse( const sparse_matrix * const A,
const sparse_matrix * const A_spar_patt,
sparse_matrix ** A_app_inv )
{
- //trial
int i, k, pj, j_temp, identity_pos;
int N, M, d_i, d_j;
lapack_int m, n, nrhs, lda, ldb, info;
@@ -1632,19 +1631,6 @@ real Sparse_Approx_Inverse( const sparse_matrix * const A,
start = Get_Time( );
- X = (char *) smalloc( sizeof(char) * A->n, "Sparse_Approx_Inverse::X" );
- Y = (char *) smalloc( sizeof(char) * A->n, "Sparse_Approx_Inverse::Y" );
- pos_x = (int *) smalloc( sizeof(int) * A->n, "Sparse_Approx_Inverse::pos_x" );
- pos_y = (int *) smalloc( sizeof(int) * A->n, "Sparse_Approx_Inverse::pos_y" );
-
- for ( i = 0; i < A->n; ++i )
- {
- X[i] = 0;
- Y[i] = 0;
- pos_x[i] = 0;
- pos_y[i] = 0;
- }
-
// Get A and A_spar_patt full matrices
compute_full_sparse_matrix( A, &A_full );
compute_full_sparse_matrix( A_spar_patt, &A_spar_patt_full );
@@ -1658,130 +1644,152 @@ real Sparse_Approx_Inverse( const sparse_matrix * const A,
(*A_app_inv)->start[(*A_app_inv)->n] = A_spar_patt_full->start[A_spar_patt_full->n];
- // For each row of full A_spar_patt
- for ( i = 0; i < A_spar_patt_full->n; ++i )
+#ifdef _OPENMP
+ #pragma omp parallel default(none) \
+ shared(A_full, A_spar_patt_full) private(i, k, pj, j_temp, identity_pos, \
+ N, M, d_i, d_j, m, n, nrhs, lda, ldb, info, X, Y, pos_x, pos_y, e_j, dense_matrix)
+#endif
{
- N = 0;
- M = 0;
+ X = (char *) smalloc( sizeof(char) * A->n, "Sparse_Approx_Inverse::X" );
+ Y = (char *) smalloc( sizeof(char) * A->n, "Sparse_Approx_Inverse::Y" );
+ pos_x = (int *) smalloc( sizeof(int) * A->n, "Sparse_Approx_Inverse::pos_x" );
+ pos_y = (int *) smalloc( sizeof(int) * A->n, "Sparse_Approx_Inverse::pos_y" );
- // find column indices of nonzeros (which will be the columns indices of the dense matrix)
- for ( pj = A_spar_patt_full->start[i]; pj < A_spar_patt_full->start[i + 1]; ++pj )
+ for ( i = 0; i < A->n; ++i )
{
+ X[i] = 0;
+ Y[i] = 0;
+ pos_x[i] = 0;
+ pos_y[i] = 0;
+ }
- j_temp = A_spar_patt_full->j[pj];
-
- Y[j_temp] = 1;
- pos_y[j_temp] = N;
- ++N;
+#ifdef _OPENMP
+ #pragma omp for schedule(static)
+#endif
+ for ( i = 0; i < A_spar_patt_full->n; ++i )
+ {
+ N = 0;
+ M = 0;
- // for each of those indices
- // search through the row of full A of that index
- for ( k = A_full->start[j_temp]; k < A_full->start[j_temp + 1]; ++k )
+ // find column indices of nonzeros (which will be the columns indices of the dense matrix)
+ for ( pj = A_spar_patt_full->start[i]; pj < A_spar_patt_full->start[i + 1]; ++pj )
{
- // and accumulate the nonzero column indices to serve as the row indices of the dense matrix
- X[A_full->j[k]] = 1;
+
+ j_temp = A_spar_patt_full->j[pj];
+
+ Y[j_temp] = 1;
+ pos_y[j_temp] = N;
+ ++N;
+
+ // for each of those indices
+ // search through the row of full A of that index
+ for ( k = A_full->start[j_temp]; k < A_full->start[j_temp + 1]; ++k )
+ {
+ // and accumulate the nonzero column indices to serve as the row indices of the dense matrix
+ X[A_full->j[k]] = 1;
+ }
}
- }
- // enumerate the row indices from 0 to (# of nonzero rows - 1) for the dense matrix
- identity_pos = M;
- for ( k = 0; k < A_full->n; k++)
- {
- if ( X[k] != 0 )
+ // enumerate the row indices from 0 to (# of nonzero rows - 1) for the dense matrix
+ identity_pos = M;
+ for ( k = 0; k < A_full->n; k++)
{
- pos_x[M] = k;
- if ( k == i )
+ if ( X[k] != 0 )
{
- identity_pos = M;
+ pos_x[M] = k;
+ if ( k == i )
+ {
+ identity_pos = M;
+ }
+ ++M;
}
- ++M;
}
- }
- // allocate memory for NxM dense matrix
- dense_matrix = (real *) smalloc( sizeof(real) * N * M,
- "Sparse_Approx_Inverse::dense_matrix" );
+ // allocate memory for NxM dense matrix
+ dense_matrix = (real *) smalloc( sizeof(real) * N * M,
+ "Sparse_Approx_Inverse::dense_matrix" );
- // fill in the entries of dense matrix
- for ( d_i = 0; d_i < M; ++d_i)
- {
- // all rows are initialized to zero
- for ( d_j = 0; d_j < N; ++d_j )
+ // fill in the entries of dense matrix
+ for ( d_i = 0; d_i < M; ++d_i)
{
- dense_matrix[d_i * N + d_j] = 0.0;
- }
- // change the value if any of the column indices is seen
- for ( d_j = A_full->start[pos_x[d_i]];
- d_j < A_full->start[pos_x[d_i + 1]]; ++d_j )
- {
- if ( Y[A_full->j[d_j]] == 1 )
+ // all rows are initialized to zero
+ for ( d_j = 0; d_j < N; ++d_j )
{
- dense_matrix[d_i * N + pos_y[A_full->j[d_j]]] = A_full->val[d_j];
+ dense_matrix[d_i * N + d_j] = 0.0;
}
+ // change the value if any of the column indices is seen
+ for ( d_j = A_full->start[pos_x[d_i]];
+ d_j < A_full->start[pos_x[d_i + 1]]; ++d_j )
+ {
+ if ( Y[A_full->j[d_j]] == 1 )
+ {
+ dense_matrix[d_i * N + pos_y[A_full->j[d_j]]] = A_full->val[d_j];
+ }
+ }
+
}
- }
+ /* create the right hand side of the linear equation
+ that is the full column of the identity matrix*/
+ e_j = (real *) smalloc( sizeof(real) * M,
+ "Sparse_Approx_Inverse::e_j" );
- /* create the right hand side of the linear equation
- that is the full column of the identity matrix*/
- e_j = (real *) smalloc( sizeof(real) * M,
- "Sparse_Approx_Inverse::e_j" );
+ for ( k = 0; k < M; ++k )
+ {
+ e_j[k] = 0.0;
+ }
+ e_j[identity_pos] = 1.0;
- for ( k = 0; k < M; ++k )
- {
- e_j[k] = 0.0;
- }
- e_j[identity_pos] = 1.0;
+ /* Solve the overdetermined system AX = B through the least-squares problem:
+ * min ||B - AX||_2 */
+ m = M;
+ n = N;
+ nrhs = 1;
+ lda = N;
+ ldb = nrhs;
+ info = LAPACKE_dgels( LAPACK_ROW_MAJOR, 'N', m, n, nrhs, dense_matrix, lda,
+ e_j, ldb );
- /* Solve the overdetermined system AX = B through the least-squares problem:
- * min ||B - AX||_2 */
- m = M;
- n = N;
- nrhs = 1;
- lda = N;
- ldb = nrhs;
- info = LAPACKE_dgels( LAPACK_ROW_MAJOR, 'N', m, n, nrhs, dense_matrix, lda,
- e_j, ldb );
+ /* Check for the full rank */
+ if ( info > 0 )
+ {
+ fprintf( stderr, "The diagonal element %i of the triangular factor ", info );
+ fprintf( stderr, "of A is zero, so that A does not have full rank;\n" );
+ fprintf( stderr, "the least squares solution could not be computed.\n" );
+ exit( INVALID_INPUT );
+ }
- /* Check for the full rank */
- if ( info > 0 )
- {
- fprintf( stderr, "The diagonal element %i of the triangular factor ", info );
- fprintf( stderr, "of A is zero, so that A does not have full rank;\n" );
- fprintf( stderr, "the least squares solution could not be computed.\n" );
- exit( INVALID_INPUT );
- }
+ /* Print least squares solution */
+ // print_matrix( "Least squares solution", n, nrhs, b, ldb );
- /* Print least squares solution */
- // print_matrix( "Least squares solution", n, nrhs, b, ldb );
+ // accumulate the resulting vector to build A_app_inv
+ (*A_app_inv)->start[i] = A_spar_patt_full->start[i];
+ for ( k = A_spar_patt_full->start[i]; k < A_spar_patt_full->start[i + 1]; ++k)
+ {
+ (*A_app_inv)->j[k] = A_spar_patt_full->j[k];
+ (*A_app_inv)->val[k] = e_j[k - A_spar_patt_full->start[i]];
+ }
- // accumulate the resulting vector to build A_app_inv
- (*A_app_inv)->start[i] = A_spar_patt_full->start[i];
- for ( k = A_spar_patt_full->start[i]; k < A_spar_patt_full->start[i + 1]; ++k)
- {
- (*A_app_inv)->j[k] = A_spar_patt_full->j[k];
- (*A_app_inv)->val[k] = e_j[k - A_spar_patt_full->start[i]];
+ //empty variables that will be used next iteration
+ sfree( dense_matrix, "Sparse_Approx_Inverse::dense_matrix" );
+ sfree( e_j, "Sparse_Approx_Inverse::e_j" );
+ for ( k = 0; k < A->n; ++k )
+ {
+ X[k] = 0;
+ Y[k] = 0;
+ pos_x[k] = 0;
+ pos_y[k] = 0;
+ }
}
- //empty variables that will be used next iteration
- sfree( dense_matrix, "Sparse_Approx_Inverse::dense_matrix" );
- sfree( e_j, "Sparse_Approx_Inverse::e_j" );
- for ( k = 0; k < A->n; ++k )
- {
- X[k] = 0;
- Y[k] = 0;
- pos_x[k] = 0;
- pos_y[k] = 0;
- }
+ sfree( pos_y, "Sparse_Approx_Inverse::pos_y" );
+ sfree( pos_x, "Sparse_Approx_Inverse::pos_x" );
+ sfree( Y, "Sparse_Approx_Inverse::Y" );
+ sfree( X, "Sparse_Approx_Inverse::X" );
}
- // Deallocate
Deallocate_Matrix( A_full );
Deallocate_Matrix( A_spar_patt_full );
- sfree( pos_y, "Sparse_Approx_Inverse::pos_y" );
- sfree( pos_x, "Sparse_Approx_Inverse::pos_x" );
- sfree( Y, "Sparse_Approx_Inverse::Y" );
- sfree( X, "Sparse_Approx_Inverse::X" );
return Get_Timing_Info( start );
}
--
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