diff --git a/tools/run_sim_puremd.py b/tools/run_sim_puremd.py
index cfb2f96c8e74f914f693b21b4554447738120f8e..f119dec564ad7b0deb364cf4ffdcc2db776493cc 100644
--- a/tools/run_sim_puremd.py
+++ b/tools/run_sim_puremd.py
@@ -205,22 +205,25 @@ class TestCase():
from operator import mul
from functools import reduce
- total = 0.
- comm = 0.
- neighbors = 0.
- init = 0.
- bonded = 0.
- nonbonded = 0.
- time = 0.
- cm = 0.
- cm_sort = 0.
- s_iters = 0.
- pre_comp = 0.
- pre_app = 0.
- s_comm = 0.
- s_allr = 0.
- s_spmv = 0.
- s_vec_ops = 0.
+ total = 0.0
+ comm = 0.0
+ neighbors = 0.0
+ init = 0.0
+ init_dist = 0.0
+ init_cm = 0.0
+ init_bond = 0.0
+ bonded = 0.0
+ nonbonded = 0.0
+ time = 0.0
+ cm = 0.0
+ cm_sort = 0.0
+ s_iters = 0.0
+ pre_comp = 0.0
+ pre_app = 0.0
+ s_comm = 0.0
+ s_allr = 0.0
+ s_spmv = 0.0
+ s_vec_ops = 0.0
cnt = 0
cnt_valid = 0
line_cnt = 0
@@ -241,17 +244,20 @@ class TestCase():
comm = comm + float(line[2])
neighbors = neighbors + float(line[3])
init = init + float(line[4])
- bonded = bonded + float(line[5])
- nonbonded = nonbonded + float(line[6])
- cm = cm + float(line[7])
- cm_sort = cm_sort + float(line[8])
- s_iters = s_iters + float(line[9])
- pre_comp = pre_comp + float(line[10])
- pre_app = pre_app + float(line[11])
- s_comm = s_comm + float(line[12])
- s_allr = s_allr + float(line[13])
- s_spmv = s_spmv + float(line[14])
- s_vec_ops = s_vec_ops + float(line[15])
+ init_dist = init_dist + float(line[5])
+ init_cm = init_cm + float(line[6])
+ init_bond = init_bond + float(line[7])
+ bonded = bonded + float(line[8])
+ nonbonded = nonbonded + float(line[9])
+ cm = cm + float(line[10])
+ cm_sort = cm_sort + float(line[11])
+ s_iters = s_iters + float(line[12])
+ pre_comp = pre_comp + float(line[13])
+ pre_app = pre_app + float(line[14])
+ s_comm = s_comm + float(line[15])
+ s_allr = s_allr + float(line[16])
+ s_spmv = s_spmv + float(line[17])
+ s_vec_ops = s_vec_ops + float(line[18])
cnt = cnt + 1
cnt_valid = cnt_valid + 1
except Exception:
@@ -266,6 +272,9 @@ class TestCase():
comm = comm / cnt
neighbors = neighbors / cnt
init = init / cnt
+ init_dist = init_dist / cnt
+ init_cm = init_cm / cnt
+ init_bond = init_bond / cnt
bonded = bonded / cnt
nonbonded = nonbonded / cnt
cm = cm / cnt
@@ -287,7 +296,8 @@ class TestCase():
param['cm_solver_q_err'],
param['reneighbor'],
param['cm_solver_pre_comp_sai_thres'],
- total, comm, neighbors, init, bonded, nonbonded, cm, cm_sort,
+ total, comm, neighbors, init, init_dist, init_cm, init_bond,
+ bonded, nonbonded, cm, cm_sort,
s_iters, pre_comp, pre_app, s_comm, s_allr, s_spmv, s_vec_ops))
else:
fout.write(self.__result_body_fmt.format(path.basename(self.__geo_file).split('.')[0],
@@ -296,8 +306,11 @@ class TestCase():
param['cm_solver_q_err'],
param['reneighbor'],
param['cm_solver_pre_comp_sai_thres'],
- float('nan'), float('nan'), float('nan'), float('nan'), float('nan'), float('nan'), float('nan'), float('nan'),
- float('nan'), float('nan'), float('nan'), float('nan'), float('nan'), float('nan'), float('nan')))
+ float('nan'), float('nan'), float('nan'), float('nan'),
+ float('nan'), float('nan'), float('nan'), float('nan'),
+ float('nan'), float('nan'), float('nan'), float('nan'),
+ float('nan'), float('nan'), float('nan'), float('nan'),
+ float('nan'), float('nan')))
print('**WARNING: nsteps not correct in file {0} (nsteps = {1:d}, counted steps = {2:d}).'.format(
log_file, int(param['nsteps']), max(line_cnt - 3, 0)))
@@ -338,11 +351,12 @@ if __name__ == '__main__':
control_dir = path.join(base_dir, 'environ')
data_dir = path.join(base_dir, 'data/benchmarks')
- header_fmt_str = '{:15} {:5} {:5} {:5} {:5} {:5} {:5} {:10} {:10} {:10} {:10} {:10} {:10} {:10} {:10} {:10} {:10} {:10} {:10} {:10} {:10} {:10}\n'
- header_str = ['Data Set', 'Proc', 'Steps', 'PreCt', 'Q Tol', 'Ren', 'PCSAI',
- 'total', 'comm', 'neighbors', 'init', 'bonded', 'nonbonded', 'CM', 'CM Sort',
- 'S Iters', 'Pre Comm', 'Pre App', 'S Comm', 'S Allr', 'S SpMV', 'S Vec Ops']
- body_fmt_str = '{:15} {:5} {:5} {:5} {:5} {:5} {:5} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f}\n'
+ header_fmt_str = '{:15} {:5} {:5} {:5} {:5} {:5} {:5} {:10} {:10} {:10} {:10} {:10} {:10} {:10} {:10} {:10} {:10} {:10} {:10} {:10} {:10} {:10} {:10} {:10} {:10}\n'
+ header_str = ['Data_Set', 'Proc', 'Steps', 'PreCt', 'Q_Tol', 'Ren', 'PCSAI',
+ 'total', 'comm', 'neighbors', 'init', 'init_dist', 'init_cm', 'init_bond',
+ 'bonded', 'nonbonded', 'cm', 'cm_sort',
+ 's_iters', 'pre_comm', 'pre_app', 's_comm', 's_allr', 's_spmv', 's_vec_ops']
+ body_fmt_str = '{:15} {:5} {:5} {:5} {:5} {:5} {:5} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f}\n'
params = {
'ensemble_type': ['0'],