From 3a7d1e60c83664f284907189286dcf64f7d700fa Mon Sep 17 00:00:00 2001
From: "Kurt A. O'Hearn" <ohearnku@msu.edu>
Date: Sun, 27 Jan 2019 17:08:20 -0800
Subject: [PATCH] PuReMD-old: fix issue where nonbonded time was incorrect when
energy_update_freq > 1. Update tools/run_sim.py to include both total
simulation time and mean time per step.
---
PuReMD/src/forces.c | 2 +-
PuReMD/src/io_tools.c | 2 +-
tools/run_sim.py | 28 ++++++++++++++++------------
3 files changed, 18 insertions(+), 14 deletions(-)
diff --git a/PuReMD/src/forces.c b/PuReMD/src/forces.c
index c9d71e82..fbd7acf9 100644
--- a/PuReMD/src/forces.c
+++ b/PuReMD/src/forces.c
@@ -2425,7 +2425,7 @@ void Compute_Forces( reax_system *system, control_params *control,
if ( system->my_rank == MASTER_NODE )
{
t_end = MPI_Wtime( );
- data->timing.nonb += t_end - t_start + data->timing.cm;;
+ data->timing.nonb += t_end - t_start;
t_start = t_end;
}
#endif
diff --git a/PuReMD/src/io_tools.c b/PuReMD/src/io_tools.c
index b86f82a7..1c878f6e 100644
--- a/PuReMD/src/io_tools.c
+++ b/PuReMD/src/io_tools.c
@@ -1128,7 +1128,7 @@ void Output_Results( reax_system *system, control_params *control,
data->timing.init_cm * denom,
data->timing.init_bond * denom,
data->timing.bonded * denom,
- data->timing.nonb * denom,
+ (data->timing.nonb + data->timing.cm) * denom,
data->timing.cm * denom,
data->timing.cm_sort * denom,
(double)(data->timing.cm_solver_iters * denom),
diff --git a/tools/run_sim.py b/tools/run_sim.py
index d18b2fde..d77771ab 100644
--- a/tools/run_sim.py
+++ b/tools/run_sim.py
@@ -431,6 +431,7 @@ restart_freq 0 ! 0: do not output any restart f
step_0_cnt = 0
total_time = 0.0
+ step_time = 0.0
comm = 0.0
neighbors = 0.0
init = 0.0
@@ -461,6 +462,7 @@ restart_freq 0 ! 0: do not output any restart f
for line in fp:
line = line.split()
try:
+ _step_time = float(line[1])
_comm = float(line[2])
_neighbors = float(line[3])
_init = float(line[4])
@@ -483,6 +485,7 @@ restart_freq 0 ! 0: do not output any restart f
(min_step and not max_step and cnt_valid >= min_step) or \
(not min_step and max_step and cnt_valid <= max_step) or \
(cnt_valid >= min_step and cnt_valid <= max_step):
+ step_time = step_time + _step_time
comm = comm + _comm
neighbors = neighbors + _neighbors
init = init + _init
@@ -512,6 +515,7 @@ restart_freq 0 ! 0: do not output any restart f
line_cnt = line_cnt + 1
if cnt > 0:
+ step_time = step_time / cnt
comm = comm / cnt
neighbors = neighbors / cnt
init = init / cnt
@@ -551,7 +555,7 @@ restart_freq 0 ! 0: do not output any restart f
param['cm_solver_q_err'],
param['reneighbor'],
param['cm_solver_pre_comp_sai_thres'],
- total_time, comm, neighbors, init, init_dist, init_cm, init_bond,
+ total_time, step_time, 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:
@@ -952,7 +956,7 @@ if __name__ == '__main__':
if param[0] in control_params_dict:
control_params_dict[param[0]] = param[1].split(',')
else:
- print("ERROR: Invalid parameter {0}. Terminating...".format(param[0]))
+ print("[ERROR] Invalid parameter {0}. Terminating...".format(param[0]))
exit(-1)
test_cases = setup_test_cases(args.data_sets, data_dir, control_params_dict)
@@ -982,7 +986,7 @@ if __name__ == '__main__':
if param[0] in control_params_dict:
control_params_dict[param[0]] = param[1].split(',')
else:
- print("ERROR: Invalid parameter {0}. Terminating...".format(param[0]))
+ print("[ERROR] Invalid parameter {0}. Terminating...".format(param[0]))
exit(-1)
geo_base, geo_ext = path.splitext(args.geo_file[0])
@@ -995,7 +999,7 @@ if __name__ == '__main__':
elif geo_ext.lower() == '.geo':
geo_format = ['0']
else:
- print("ERROR: unrecognized geometry format {0}. Terminating...".format(ext))
+ print("[ERROR] unrecognized geometry format {0}. Terminating...".format(ext))
exit(-1)
test_case = TestCase(geo_base, args.geo_file[0], args.ffield_file[0],
@@ -1006,16 +1010,16 @@ if __name__ == '__main__':
def parse_results(args):
if args.run_type[0] == 'serial' or args.run_type[0] == 'openmp':
header_fmt_str = '{:15}|{:5}|{:5}|{:5}|{:5}|{:5}|{:5}|{:5}|{:5}|{:5}|{:5}|{:5}|{:10}|{:10}|{:10}|{:10}|{:10}|{:3}|{:10}\n'
- header_str = ['Data Set', 'Steps', 'CM', 'Solvr', 'Q Tol', 'QDS', 'PreCT', 'PreCD', 'PreCS', 'PCSAI', 'PreAT', 'PreAJ', 'Pre Comp',
- 'Pre App', 'Iters', 'SpMV', 'CM', 'Thd', 'Time (s)']
+ header_str = ['Data Set', 'Steps', 'CM', 'Solvr', 'Q_Tol', 'QDS', 'PreCT', 'PreCD', 'PreCS', 'PCSAI', 'PreAT', 'PreAJ', 'Pre_Comp',
+ 'Pre_App', 'Iters', 'SpMV', 'CM', 'Thd', 'Time (s)']
body_fmt_str = '{:15} {:5} {:5} {:5} {:5} {:5} {:5} {:5} {:5} {:5} {:5} {:5} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:3} {:10.3f}\n'
elif args.run_type[0] == 'mpi':
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',
+ header_str = ['Data_Set', 'Proc', 'Steps', 'PreCT', 'Q_Tol', 'Ren', 'PCSAI',
+ 'total_time', 'step_time', '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'
+ 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} {:10.3f}\n'
elif args.run_type[0] == 'mpi+gpu':
#TODO
pass
@@ -1035,7 +1039,7 @@ if __name__ == '__main__':
if param[0] in control_params_dict:
control_params_dict[param[0]] = param[1].split(',')
else:
- print("ERROR: Invalid parameter {0}. Terminating...".format(param[0]))
+ print("[ERROR] Invalid parameter {0}. Terminating...".format(param[0]))
exit(-1)
geo_base, geo_ext = path.splitext(args.geo_file[0])
@@ -1048,7 +1052,7 @@ if __name__ == '__main__':
elif geo_ext.lower() == '.geo':
geo_format = ['0']
else:
- print("ERROR: unrecognized geometry format {0}. Terminating...".format(ext))
+ print("[ERROR] unrecognized geometry format {0}. Terminating...".format(ext))
exit(-1)
if args.out_file:
@@ -1095,7 +1099,7 @@ if __name__ == '__main__':
if param[0] in control_params_dict:
control_params_dict[param[0]] = param[1].split(',')
else:
- print("ERROR: Invalid parameter {0}. Terminating...".format(param[0]))
+ print("[ERROR] Invalid parameter {0}. Terminating...".format(param[0]))
exit(-1)
test_cases = setup_test_cases(args.data_sets, data_dir, control_params_dict)
--
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