From 3240cfcf4fc0fa81896b4471fbb9391d0ee0de7f Mon Sep 17 00:00:00 2001
From: Abdullah Alperen <alperena@msu.edu>
Date: Fri, 28 Dec 2018 20:32:20 -0500
Subject: [PATCH] PuReMD: optimize atom enumeration for building dense matrix
for SAI
---
PuReMD/src/linear_solvers.c | 25 ++++++++++++++-----------
1 file changed, 14 insertions(+), 11 deletions(-)
diff --git a/PuReMD/src/linear_solvers.c b/PuReMD/src/linear_solvers.c
index 82777345..39d2d427 100644
--- a/PuReMD/src/linear_solvers.c
+++ b/PuReMD/src/linear_solvers.c
@@ -890,10 +890,10 @@ real sparse_approx_inverse( reax_system *system, simulation_data *data,
sparse_matrix **A_app_inv, int nprocs )
{
int N, M, d_i, d_j, mark;
- int i, k, pj, j_temp;
+ int i, k, pj, j_temp, push;
int local_pos, atom_pos, identity_pos;
lapack_int m, n, nrhs, lda, ldb, info;
- int *X;
+ int *X, *q;
real *e_j, *dense_matrix;
int size_e, size_dense;
int cnt, scale;
@@ -1234,16 +1234,20 @@ real sparse_approx_inverse( reax_system *system, simulation_data *data,
sfree( val_recv2, "sparse_approx_inverse::val_recv2" );
X = smalloc( sizeof(int) * (system->bigN + 1),
- "sparse_approx_inverse::X", MPI_COMM_WORLD );
+ "sparse_approx_inverse::X", MPI_COMM_WORLD );
+ q = smalloc( sizeof(int) * system->N * 2,
+ "sparse_approx_inverse::q", MPI_COMM_WORLD );
+
for ( i = 0; i <= system->bigN; ++i )
{
X[i] = -1;
}
-
+
for ( i = 0; i < A_spar_patt->n; ++i )
{
N = 0;
M = 0;
+ push = 0;
mark = i + system->bigN;
/* find column indices of nonzeros (which will be the columns indices of the dense matrix) */
@@ -1264,6 +1268,7 @@ real sparse_approx_inverse( reax_system *system, simulation_data *data,
/* and accumulate the nonzero column indices to serve as the row indices of the dense matrix */
atom = &system->my_atoms[ A->entries[k].j ];
X[atom->orig_id] = mark;
+ q[push++] = atom->orig_id;
}
}
@@ -1274,6 +1279,7 @@ real sparse_approx_inverse( reax_system *system, simulation_data *data,
{
/* and accumulate the nonzero column indices to serve as the row indices of the dense matrix */
X[ j_list[j_temp][k] ] = mark;
+ q[push++] = j_list[j_temp][k];
}
}
}
@@ -1283,18 +1289,15 @@ real sparse_approx_inverse( reax_system *system, simulation_data *data,
atom = &system->my_atoms[ i ];
atom_pos = atom->orig_id;
- for ( k = 0; k <= system->bigN; k++)
+ for ( k = 0; k < push; k++)
{
- if ( X[k] == mark )
+ if ( X[ q[k] ] == mark )
{
- X[k] = M;
- if ( k == atom_pos )
- {
- identity_pos = M;
- }
+ X[ q[k] ] = M;
++M;
}
}
+ identity_pos = X[atom_pos];
/* allocate memory for NxM dense matrix */
if ( size_dense < N * M )
--
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