From bfe478fed6eaf8504d81d996b22fb6f794d233c2 Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnku@cse.msu.edu>
Date: Mon, 27 Feb 2017 18:51:20 -0500
Subject: [PATCH] Update data collection scripts.
---
sPuReMD/src/charges.c | 36 ++++++++++++----
sPuReMD/src/vector.c | 7 ++-
tools/run_sim.py | 99 ++++++++++++++++++++++++-------------------
3 files changed, 89 insertions(+), 53 deletions(-)
diff --git a/sPuReMD/src/charges.c b/sPuReMD/src/charges.c
index c2242449..54233396 100644
--- a/sPuReMD/src/charges.c
+++ b/sPuReMD/src/charges.c
@@ -585,7 +585,14 @@ static real diag_pre_comp( const sparse_matrix * const H, real * const Hdia_inv
default(none) private(i)
for ( i = 0; i < H->n; ++i )
{
- Hdia_inv[i] = 1.0 / H->val[H->start[i + 1] - 1];
+ if ( H->val[H->start[i + 1] - 1] != 0.0 )
+ {
+ Hdia_inv[i] = 1.0 / H->val[H->start[i + 1] - 1];
+ }
+ else
+ {
+ Hdia_inv[i] = 1.0;
+ }
}
return Get_Timing_Info( start );
@@ -2606,13 +2613,6 @@ static void ACKS2( reax_system * const system, control_params * const control,
}
// Print_Linear_System( system, control, workspace, data->step );
-// Print_Sparse_Matrix2( workspace->H, "H_0.out" );
-// Print_Sparse_Matrix2( workspace->L, "L_0.out" );
-// Print_Sparse_Matrix2( workspace->U, "U_0.out" );
-// FILE * fp = fopen( "b.out", "w" );
-// Vector_Print( fp, "b.out", workspace->b_s, system->N_cm );
-// fclose( fp );
-// exit(0);
Extrapolate_Charges_EEM( system, control, data, workspace );
@@ -2663,6 +2663,16 @@ void Compute_Charges( reax_system * const system, control_params * const control
const list * const far_nbrs, const output_controls * const out_control )
{
int i;
+// char fname[200];
+// FILE * fp;
+
+// if ( data->step == 10 || data->step == 50 || data->step == 100 )
+// {
+// sprintf( fname, "s_%d_%s.out", data->step, control->sim_name );
+// fp = fopen( fname, "w" );
+// Vector_Print( fp, NULL, workspace->s[0], system->N_cm );
+// fclose( fp );
+// }
switch ( control->charge_method )
{
@@ -2683,4 +2693,14 @@ void Compute_Charges( reax_system * const system, control_params * const control
exit( INVALID_INPUT );
break;
}
+
+// if ( data->step == 0 )
+// {
+// sprintf( fname, "H_%d_%s.out", data->step, control->sim_name );
+// Print_Sparse_Matrix2( workspace->H, fname );
+//
+// sprintf( fname, "b_%d_%s.out", data->step, control->sim_name );
+// fp = fopen( fname, "w" );
+// Vector_Print( fp, NULL, workspace->b_s, system->N_cm );
+// }
}
diff --git a/sPuReMD/src/vector.c b/sPuReMD/src/vector.c
index ba4a5ea3..483ba806 100644
--- a/sPuReMD/src/vector.c
+++ b/sPuReMD/src/vector.c
@@ -118,12 +118,15 @@ void Vector_Print( FILE * const fout, const char * const vname, const real * con
{
unsigned int i;
- fprintf( fout, "%s:\n", vname );
+ if ( vname != NULL )
+ {
+ fprintf( fout, "%s:\n", vname );
+ }
+
for ( i = 0; i < k; ++i )
{
fprintf( fout, "%24.15e\n", v[i] );
}
- fprintf( fout, "\n" );
}
diff --git a/tools/run_sim.py b/tools/run_sim.py
index 3aa4ad51..2ee79c24 100644
--- a/tools/run_sim.py
+++ b/tools/run_sim.py
@@ -32,24 +32,32 @@ class TestCase():
r'(?P<key>nsteps\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'tabulate_long_range': lambda l, x: sub(
r'(?P<key>tabulate_long_range\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
- 'qeq_solver_type': lambda l, x: sub(
- r'(?P<key>qeq_solver_type\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
- 'qeq_solver_q_err': lambda l, x: sub(
- r'(?P<key>qeq_solver_q_err\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
- 'qeq_domain_sparsity': lambda l, x: sub(
- r'(?P<key>qeq_domain_sparsity\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
- 'pre_comp_type': lambda l, x: sub(
- r'(?P<key>pre_comp_type\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
- 'pre_comp_droptol': lambda l, x: sub(
- r'(?P<key>pre_comp_droptol\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
- 'pre_comp_refactor': lambda l, x: sub(
- r'(?P<key>pre_comp_refactor\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
- 'pre_comp_sweeps': lambda l, x: sub(
- r'(?P<key>pre_comp_sweeps\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
- 'pre_app_type': lambda l, x: sub(
- r'(?P<key>pre_app_type\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
- 'pre_app_jacobi_iters': lambda l, x: sub(
- r'(?P<key>pre_app_jacobi_iters\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'charge_method': lambda l, x: sub(
+ r'(?P<key>charge_method\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'cm_q_net': lambda l, x: sub(
+ r'(?P<key>cm_q_net\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'cm_solver_type': lambda l, x: sub(
+ r'(?P<key>cm_solver_type\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'cm_solver_max_iters': lambda l, x: sub(
+ r'(?P<key>cm_solver_max_iters\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'cm_solver_restart': lambda l, x: sub(
+ r'(?P<key>cm_solver_restart\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'cm_solver_q_err': lambda l, x: sub(
+ r'(?P<key>cm_solver_q_err\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'cm_domain_sparsity': lambda l, x: sub(
+ r'(?P<key>cm_domain_sparsity\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'cm_solver_pre_comp_type': lambda l, x: sub(
+ r'(?P<key>cm_solver_pre_comp_type\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'cm_solver_pre_comp_droptol': lambda l, x: sub(
+ r'(?P<key>cm_solver_pre_comp_droptol\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'cm_solver_pre_comp_refactor': lambda l, x: sub(
+ r'(?P<key>cm_solver_pre_comp_refactor\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'cm_solver_pre_comp_sweeps': lambda l, x: sub(
+ r'(?P<key>cm_solver_pre_comp_sweeps\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'cm_solver_pre_app_type': lambda l, x: sub(
+ r'(?P<key>cm_solver_pre_app_type\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
+ 'cm_solver_pre_app_jacobi_iters': lambda l, x: sub(
+ r'(?P<key>cm_solver_pre_app_jacobi_iters\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'geo_format': lambda l, x: sub(
r'(?P<key>geo_format\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
}
@@ -88,15 +96,16 @@ class TestCase():
for p in product(*[self.__params[k] for k in self.__param_names]):
param_dict = dict((k, v) for (k, v) in zip(self.__param_names, p))
param_dict['name'] = path.basename(self.__geo_file).split('.')[0] \
+ + '_cm' + param_dict['charge_method'] \
+ '_s' + param_dict['nsteps'] \
- + '_q' + param_dict['qeq_solver_type'] \
- + '_qtol' + param_dict['qeq_solver_q_err'] \
- + '_qds' + param_dict['qeq_domain_sparsity'] \
- + '_pc' + param_dict['pre_comp_type'] \
- + '_pctol' + param_dict['pre_comp_droptol'] \
- + '_pcs' + param_dict['pre_comp_sweeps'] \
- + '_pa' + param_dict['pre_app_type'] \
- + '_paji' + param_dict['pre_app_jacobi_iters'] \
+ + '_q' + param_dict['cm_solver_type'] \
+ + '_qtol' + param_dict['cm_solver_q_err'] \
+ + '_qds' + param_dict['cm_domain_sparsity'] \
+ + '_pc' + param_dict['cm_solver_pre_comp_type'] \
+ + '_pctol' + param_dict['cm_solver_pre_comp_droptol'] \
+ + '_pcs' + param_dict['cm_solver_pre_comp_sweeps'] \
+ + '_pa' + param_dict['cm_solver_pre_app_type'] \
+ + '_paji' + param_dict['cm_solver_pre_app_jacobi_iters'] \
+ '_t' + param_dict['threads']
@@ -128,7 +137,7 @@ class TestCase():
def _process_result(self, fout, param):
time = 0.
- qeq = 0.
+ cm = 0.
iters = 0.
pre_comp = 0.
pre_app = 0.
@@ -143,7 +152,7 @@ class TestCase():
for line in fp:
line = line.split()
try:
- qeq = qeq + float(line[6])
+ cm = cm + float(line[6])
iters = iters + float(line[8])
pre_comp = pre_comp + float(line[9])
pre_app = pre_app + float(line[10])
@@ -159,7 +168,7 @@ class TestCase():
pass
cnt = cnt - 1
if cnt > 0:
- qeq = qeq / cnt
+ cm = cm / cnt
iters = iters / cnt
pre_comp = pre_comp / cnt
pre_app = pre_app / cnt
@@ -167,10 +176,10 @@ class TestCase():
if cnt == int(param['nsteps']):
fout.write(self.__result_body_fmt.format(path.basename(self.__geo_file).split('.')[0],
- param['nsteps'], param['qeq_solver_type'], param['qeq_solver_q_err'], param['qeq_domain_sparsity'],
- param['pre_comp_type'], param['pre_comp_droptol'], param['pre_comp_sweeps'],
- param['pre_app_type'], param['pre_app_jacobi_iters'], pre_comp, pre_app, iters, spmv,
- qeq, param['threads'], time))
+ param['nsteps'], param['cm_solver_type'], param['cm_solver_q_err'], param['cm_domain_sparsity'],
+ param['cm_solver_pre_comp_type'], param['cm_solver_pre_comp_droptol'], param['cm_solver_pre_comp_sweeps'],
+ param['cm_solver_pre_app_type'], param['cm_solver_pre_app_jacobi_iters'], pre_comp, pre_app, iters, spmv,
+ cm, param['threads'], time))
else:
print('**WARNING: nsteps not correct in file {0}...'.format(log_file))
fout.flush()
@@ -205,22 +214,26 @@ if __name__ == '__main__':
header_fmt_str = '{:15}|{:5}|{:5}|{:5}|{:5}|{:5}|{:5}|{:5}|{:5}|{:5}|{:10}|{:10}|{:10}|{:10}|{:10}|{:3}|{:10}\n'
header_str = ['Data Set', 'Steps', 'QType', 'Q Tol', 'QDS', 'PreCT', 'PreCD', 'PreCS', 'PreAT', 'PreAJ', 'Pre Comp',
- 'Pre App', 'Iters', 'SpMV', 'QEq', 'Thd', 'Time (s)']
+ 'Pre App', 'Iters', 'SpMV', 'CM', 'Thd', 'Time (s)']
body_fmt_str = '{:15} {:5} {:5} {:5} {:5} {:5} {:5} {:5} {:5} {:5} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:3} {:10.3f}\n'
params = {
'ensemble_type': ['0'],
'nsteps': ['20'],
'tabulate_long_range': ['0'],
- 'qeq_solver_type': ['0'],
- 'qeq_solver_q_err': ['1e-6'],
- 'qeq_domain_sparsity': ['1.0'],
- 'pre_comp_type': ['2'],
- 'pre_comp_refactor': ['100'],
- 'pre_comp_droptol': ['0.0'],
- 'pre_comp_sweeps': ['3'],
- 'pre_app_type': ['2'],
- 'pre_app_jacobi_iters': ['30'],
+ 'charge_method': ['0'],
+ 'cm_q_net': ['0.0'],
+ 'cm_solver_type': ['0'],
+ 'cm_solver_max_iters': ['20'],
+ 'cm_solver_restart': ['100'],
+ 'cm_solver_q_err': ['1e-6'],
+ 'cm_domain_sparsity': ['1.0'],
+ 'cm_solver_pre_comp_type': ['2'],
+ 'cm_solver_pre_comp_refactor': ['100'],
+ 'cm_solver_pre_comp_droptol': ['0.0'],
+ 'cm_solver_pre_comp_sweeps': ['3'],
+ 'cm_solver_pre_app_type': ['2'],
+ 'cm_solver_pre_app_jacobi_iters': ['30'],
'threads': ['1'],
'geo_format': [],
}
--
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