diff --git a/sPuReMD/src/QEq.c b/sPuReMD/src/QEq.c
index e8b129d918273381df17a86c1517231d42be8cf4..5a757f9ac2008f65d715931c36d0df4c1eb0c947 100644
--- a/sPuReMD/src/QEq.c
+++ b/sPuReMD/src/QEq.c
@@ -159,7 +159,7 @@ static void Calculate_Droptol( const sparse_matrix * const A, real * const dropt
unsigned int tid;
#endif
- #pragma omp parallel default(none) private(i, j, k, val, tid), shared(droptol_local)
+ #pragma omp parallel default(none) private(i, j, k, val, tid), shared(droptol_local, stderr)
{
#ifdef _OPENMP
tid = omp_get_thread_num();
@@ -172,6 +172,7 @@ static void Calculate_Droptol( const sparse_matrix * const A, real * const dropt
{
if ( (droptol_local = (real*) malloc( omp_get_num_threads() * A->n * sizeof(real))) == NULL )
{
+ fprintf( stderr, "Not enough space for droptol. Terminating...\n" );
exit( INSUFFICIENT_MEMORY );
}
}
@@ -597,16 +598,21 @@ static real diag_pre_comp( const reax_system * const system, real * const Hdia_i
static real ICHOLT( const sparse_matrix * const A, const real * const droptol,
sparse_matrix * const L, sparse_matrix * const U )
{
- //TODO: either add compilation parameter or dynamically allocate
- int tmp_j[1000];
- real tmp_val[1000];
+ int *tmp_j;
+ real *tmp_val;
int i, j, pj, k1, k2, tmptop, Ltop;
real val, start;
int *Utop;
start = Get_Time( );
- Utop = (int*) malloc((A->n + 1) * sizeof(int));
+ if( ( Utop = (int*) malloc((A->n + 1) * sizeof(int)) ) == NULL ||
+ ( tmp_j = (int*) malloc(A->n * sizeof(int)) ) == NULL ||
+ ( tmp_val = (real*) malloc(A->n * sizeof(real)) ) == NULL )
+ {
+ fprintf( stderr, "not enough memory for ICHOLT preconditioning matrices. terminating.\n" );
+ exit( INSUFFICIENT_MEMORY );
+ }
// clear variables
Ltop = 0;
@@ -726,7 +732,9 @@ static real ICHOLT( const sparse_matrix * const A, const real * const droptol,
// fprintf( stderr, "nnz(U): %d, max: %d\n", Utop[U->n], U->n * 50 );
- free(Utop);
+ free( tmp_val );
+ free( tmp_j );
+ free( Utop );
return Get_Timing_Info( start );
}
@@ -750,7 +758,7 @@ static real ICHOL_PAR( const sparse_matrix * const A, const unsigned int sweeps,
if ( Allocate_Matrix( &DAD, A->n, A->m ) == 0 )
{
- fprintf( stderr, "not enough memory for preconditioning matrices. terminating.\n" );
+ fprintf( stderr, "not enough memory for ICHOL_PAR preconditioning matrices. terminating.\n" );
exit( INSUFFICIENT_MEMORY );
}
@@ -758,7 +766,7 @@ static real ICHOL_PAR( const sparse_matrix * const A, const unsigned int sweeps,
( D_inv = (real*) malloc(A->n * sizeof(real)) ) == NULL ||
( Utop = (int*) malloc((A->n + 1) * sizeof(int)) ) == NULL )
{
- fprintf( stderr, "not enough memory for preconditioning matrices. terminating.\n" );
+ fprintf( stderr, "not enough memory for ICHOL_PAR preconditioning matrices. terminating.\n" );
exit( INSUFFICIENT_MEMORY );
}
@@ -948,14 +956,14 @@ static real ILU_PAR( const sparse_matrix * const A, const unsigned int sweeps,
if ( Allocate_Matrix( &DAD, A->n, A->m ) == 0 )
{
- fprintf( stderr, "not enough memory for preconditioning matrices. terminating.\n" );
+ fprintf( stderr, "not enough memory for ILU_PAR preconditioning matrices. terminating.\n" );
exit( INSUFFICIENT_MEMORY );
}
if( ( D = (real*) malloc(A->n * sizeof(real)) ) == NULL ||
( D_inv = (real*) malloc(A->n * sizeof(real)) ) == NULL )
{
- fprintf( stderr, "not enough memory for preconditioning matrices. terminating.\n" );
+ fprintf( stderr, "not enough memory for ILU_PAR preconditioning matrices. terminating.\n" );
exit( INSUFFICIENT_MEMORY );
}
@@ -1158,14 +1166,14 @@ static real ILUT_PAR( const sparse_matrix * const A, const real * droptol,
Allocate_Matrix( &L_temp, A->n, A->m ) == 0 ||
Allocate_Matrix( &U_temp, A->n, A->m ) == 0 )
{
- fprintf( stderr, "not enough memory for preconditioning matrices. terminating.\n" );
+ fprintf( stderr, "not enough memory for ILUT_PAR preconditioning matrices. terminating.\n" );
exit( INSUFFICIENT_MEMORY );
}
if( ( D = (real*) malloc(A->n * sizeof(real)) ) == NULL ||
( D_inv = (real*) malloc(A->n * sizeof(real)) ) == NULL )
{
- fprintf( stderr, "not enough memory for preconditioning matrices. terminating.\n" );
+ fprintf( stderr, "not enough memory for ILUT_PAR preconditioning matrices. terminating.\n" );
exit( INSUFFICIENT_MEMORY );
}
diff --git a/tools/run_sim.py b/tools/run_sim.py
index ac8aa0cdbd7ec25a89b1a6646be6f45a07ef3bc8..842beacfbf08a38c74065d97b0d638f87fcae19e 100644
--- a/tools/run_sim.py
+++ b/tools/run_sim.py
@@ -103,18 +103,28 @@ class TestCase():
env['OMP_NUM_THREADS'] = param_dict['threads']
start = time()
proc_handle = Popen([bin_path, self.__geo_file, self.__ffield_file, temp_file],
- stdout=PIPE, stderr=PIPE, env=env)
+ stdout=PIPE, stderr=PIPE, env=env, universal_newlines=True)
stdout, stderr = proc_handle.communicate()
stop = time()
if proc_handle.returncode < 0:
print("WARNING: process terminated with code {0}".format(proc_handle.returncode))
+ else:
+ print('stdout:')
+ print(stdout)
+ print('stderr:')
+ print(stderr)
else:
+ #TODO: fix
+ start = 0.
+ stop = 0.
self._process_result(fout, stop - start, param_dict)
fout.close()
- remove(temp_file)
- rmdir(temp_dir)
+ if path.exists(temp_file):
+ remove(temp_file)
+ if path.exists(temp_dir):
+ rmdir(temp_dir)
def _process_result(self, fout, time, param):
qeq = 0.
@@ -123,7 +133,12 @@ class TestCase():
pre_app = 0.
spmv = 0.
cnt = 0
- with open(param['name'] + '.log', 'r') as fp:
+ log_file = param['name'] + '.log'
+
+ if not path.exists(log_file):
+ print('***WARNING: {0} does not exist!'.format(log_file))
+ return
+ with open(log_file, 'r') as fp:
for line in fp:
line = line.split()
try:
@@ -219,7 +234,7 @@ if __name__ == '__main__':
geo_format=['1'], result_file=result_file))
if 'water_78480' in args.data:
test_cases.append(
- TestCase(path.join(data_dir, 'water/water_78480.pdb'),
+ TestCase(path.join(data_dir, 'water/water_78480.geo'),
path.join(data_dir, 'water/ffield.water'),
path.join(control_dir, 'param.gpu.water'),
params=params, result_header_fmt=header_fmt_str,
@@ -241,6 +256,14 @@ if __name__ == '__main__':
params=params, result_header_fmt=header_fmt_str,
result_header = header_str, result_body_fmt=body_fmt_str,
geo_format=['1'], result_file=result_file))
+ if 'bilayer_340800' in args.data:
+ test_cases.append(
+ TestCase(path.join(data_dir, 'bilayer/bilayer_340800.geo'),
+ path.join(data_dir, 'bilayer/ffield-bio'),
+ path.join(control_dir, 'param.gpu.water'),
+ params=params, result_header_fmt=header_fmt_str,
+ result_header = header_str, result_body_fmt=body_fmt_str,
+ geo_format=['0'], result_file=result_file))
if 'dna_19733' in args.data:
test_cases.append(
TestCase(path.join(data_dir, 'dna/dna_19733.pdb'),