Skip to content
Snippets Groups Projects
Commit 14d17ee9 authored by Alperen, Abdullah's avatar Alperen, Abdullah
Browse files

PuReMD: add conditional allocation to SAI computation arrays

parent ec9a36ce
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
PuReMD/src/linear_solvers.c
+ 125
− 21
View file @ 14d17ee9
......@@ -457,6 +457,8 @@ real setup_sparse_approx_inverse( reax_system *system, simulation_data *data, st
{
fprintf( stdout, " [INFO] \ntotal nnz in all charge matrices = %d\ntotal nnz in all sparsity patterns = %d\nthreshold = %.15lf\n",
n, nnz, threshold );
fprintf( stdout, "SAI SETUP takes %.2f seconds\n", MPI_Wtime() - start );
fflush( stdout );
}
#endif
......@@ -893,6 +895,7 @@ real sparse_approx_inverse( reax_system *system, simulation_data *data,
lapack_int m, n, nrhs, lda, ldb, info;
int *pos_x, *X;
real *e_j, *dense_matrix;
int size_e, size_dense;
int cnt, scale;
reax_atom *atom;
int *row_nnz;
......@@ -906,6 +909,7 @@ real sparse_approx_inverse( reax_system *system, simulation_data *data,
MPI_Status stat1, stat2, stat3, stat4;
const neighbor_proc *nbr1, *nbr2;
int *j_send, *j_recv1, *j_recv2;
int size_send, size_recv1, size_recv2;
real *val_send, *val_recv1, *val_recv2;
real start, t_start, t_comm;
real total_comm;
......@@ -935,6 +939,15 @@ real sparse_approx_inverse( reax_system *system, simulation_data *data,
j_recv2 = NULL;
val_recv1 = NULL;
val_recv2 = NULL;
size_send = 0;
size_recv1 = 0;
size_recv2 = 0;
e_j = NULL;
dense_matrix = NULL;
size_e = 0;
size_dense = 0;
row_nnz = smalloc( sizeof(int) * system->total_cap,
"sparse_approx_inverse::row_nnz", MPI_COMM_WORLD );
......@@ -989,10 +1002,22 @@ real sparse_approx_inverse( reax_system *system, simulation_data *data,
if( cnt )
{
flag1 = 1;
j_recv1 = smalloc( sizeof(int) * cnt,
"sparse_approx_inverse::j_recv1", MPI_COMM_WORLD );
val_recv1 = smalloc( sizeof(real) * cnt,
"sparse_approx_inverse::val_recv1", MPI_COMM_WORLD );
if ( size_recv1 < cnt )
{
if ( size_recv1 )
{
sfree( j_recv1, "sparse_approx_inverse::j_recv1" );
sfree( val_recv1, "sparse_approx_inverse::val_recv1" );
}
size_recv1 = cnt * SAFE_ZONE;
j_recv1 = smalloc( sizeof(int) * size_recv1,
"sparse_approx_inverse::j_recv1", MPI_COMM_WORLD );
val_recv1 = smalloc( sizeof(real) * size_recv1,
"sparse_approx_inverse::val_recv1", MPI_COMM_WORLD );
}
t_start = MPI_Wtime();
MPI_Irecv( j_recv1, cnt, MPI_INT, nbr1->rank, 2 * d + 1, comm, &req1 );
......@@ -1018,10 +1043,22 @@ real sparse_approx_inverse( reax_system *system, simulation_data *data,
if( cnt )
{
flag2 = 1;
j_recv2 = smalloc( sizeof(int) * cnt,
"sparse_approx_inverse::j_recv2", MPI_COMM_WORLD );
val_recv2 = smalloc( sizeof(real) * cnt,
"sparse_approx_inverse::val_recv2", MPI_COMM_WORLD );
if ( size_recv2 < cnt )
{
if ( size_recv2 )
{
sfree( j_recv2, "sparse_approx_inverse::j_recv2" );
sfree( val_recv2, "sparse_approx_inverse::val_recv2" );
}
size_recv2 = cnt * SAFE_ZONE;
j_recv2 = smalloc( sizeof(int) * size_recv2,
"sparse_approx_inverse::j_recv2", MPI_COMM_WORLD );
val_recv2 = smalloc( sizeof(real) * size_recv2,
"sparse_approx_inverse::val_recv2", MPI_COMM_WORLD );
}
t_start = MPI_Wtime();
MPI_Irecv( j_recv2, cnt, MPI_INT, nbr2->rank, 2 * d, comm, &req3 );
......@@ -1041,10 +1078,21 @@ real sparse_approx_inverse( reax_system *system, simulation_data *data,
if ( cnt > 0 )
{
j_send = smalloc( sizeof(int) * cnt,
"sparse_approx_inverse::j_send", MPI_COMM_WORLD );
val_send = smalloc( sizeof(real) * cnt,
"sparse_approx_inverse::j_send", MPI_COMM_WORLD );
if ( size_send < cnt )
{
if ( size_send )
{
sfree( j_send, "sparse_approx_inverse::j_send" );
sfree( val_send, "sparse_approx_inverse::val_send" );
}
size_send = cnt * SAFE_ZONE;
j_send = smalloc( sizeof(int) * size_send,
"sparse_approx_inverse::j_send", MPI_COMM_WORLD );
val_send = smalloc( sizeof(real) * size_send,
"sparse_approx_inverse::j_send", MPI_COMM_WORLD );
}
cnt = 0;
for ( i = 0; i < out_bufs[2 * d].cnt; ++i )
......@@ -1087,10 +1135,22 @@ real sparse_approx_inverse( reax_system *system, simulation_data *data,
if ( cnt > 0 )
{
j_send = smalloc( sizeof(int) * cnt,
"sparse_approx_inverse::j_send", MPI_COMM_WORLD );
val_send = smalloc( sizeof(real) * cnt,
"sparse_approx_inverse::val_send", MPI_COMM_WORLD );
if ( size_send < cnt )
{
if ( size_send )
{
sfree( j_send, "sparse_approx_inverse::j_send" );
sfree( val_send, "sparse_approx_inverse::j_send" );
}
size_send = cnt * SAFE_ZONE;
j_send = smalloc( sizeof(int) * size_send,
"sparse_approx_inverse::j_send", MPI_COMM_WORLD );
val_send = smalloc( sizeof(real) * size_send,
"sparse_approx_inverse::val_send", MPI_COMM_WORLD );
}
cnt = 0;
for ( i = 0; i < out_bufs[2 * d + 1].cnt; ++i )
......@@ -1178,6 +1238,22 @@ real sparse_approx_inverse( reax_system *system, simulation_data *data,
}
}
}
sfree( j_send, "sparse_approx_inverse::j_send" );
sfree( val_send, "sparse_approx_inverse::val_send" );
sfree( j_recv1, "sparse_approx_inverse::j_recv1" );
sfree( j_recv2, "sparse_approx_inverse::j_recv2" );
sfree( val_recv1, "sparse_approx_inverse::val_recv1" );
sfree( val_recv2, "sparse_approx_inverse::val_recv2" );
#if defined(DEBUG)
if ( system->my_rank == MASTER_NODE )
{
fprintf( stdout, "bigN = %d, N = %d, n = %d\n", system->bigN, system->N, system->n );
fprintf( stdout, "SAI COMP initialization and exchanging row info takes %.2f seconds\n", MPI_Wtime() - start );
fflush( stdout );
}
#endif
X = smalloc( sizeof(int) * (system->bigN + 1),
"sparse_approx_inverse::X", MPI_COMM_WORLD );
......@@ -1245,8 +1321,18 @@ real sparse_approx_inverse( reax_system *system, simulation_data *data,
}
/* allocate memory for NxM dense matrix */
dense_matrix = smalloc( sizeof(real) * N * M,
"sparse_approx_inverse::dense_matrix", MPI_COMM_WORLD );
if ( size_dense < N * M )
{
if ( size_dense )
{
sfree( dense_matrix, "sparse_approx_inverse::dense_matrix" );
}
size_dense = N * M * SAFE_ZONE;
dense_matrix = smalloc( sizeof(real) * size_dense,
"sparse_approx_inverse::dense_matrix", MPI_COMM_WORLD );
}
/* fill in the entries of dense matrix */
for ( d_j = 0; d_j < N; ++d_j)
......@@ -1315,7 +1401,17 @@ real sparse_approx_inverse( reax_system *system, simulation_data *data,
/* create the right hand side of the linear equation
* that is the full column of the identity matrix */
e_j = smalloc( sizeof(real) * M, "sparse_approx_inverse::e_j", MPI_COMM_WORLD );
if ( size_e < M )
{
if ( size_e )
{
sfree( e_j, "sparse_approx_inverse::e_j" );
}
size_e = M * SAFE_ZONE;
e_j = smalloc( sizeof(real) * size_e, "sparse_approx_inverse::e_j", MPI_COMM_WORLD );
}
for ( k = 0; k < M; ++k )
{
......@@ -1351,12 +1447,20 @@ real sparse_approx_inverse( reax_system *system, simulation_data *data,
(*A_app_inv)->entries[k].j = A_spar_patt->entries[k].j;
(*A_app_inv)->entries[k].val = e_j[k - A_spar_patt->start[i]];
}
sfree( dense_matrix, "sparse_approx_inverse::dense_matrix" );
sfree( e_j, "sparse_approx_inverse::e_j" );
}
sfree( dense_matrix, "sparse_approx_inverse::dense_matrix" );
sfree( e_j, "sparse_approx_inverse::e_j" );
sfree( pos_x, "sparse_approx_inverse::pox_x" );
sfree( X, "sparse_approx_inverse::X" );
/*for ( i = 0; i < system->N; ++i )
{
sfree( j_list[i], "sparse_approx_inverse::j_list" );
sfree( val_list[i], "sparse_approx_inverse::val_list" );
}
sfree( j_list, "sparse_approx_inverse::j_list" );
sfree( val_list, "sparse_approx_inverse::val_list" );*/
sfree( row_nnz, "sparse_approx_inverse::row_nnz" );
MPI_Reduce( &t_comm, &total_comm, 1, MPI_DOUBLE, MPI_SUM, MASTER_NODE,
mpi_data->world );
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment