From 1ac45a4bed2a84a9d3340ae5721d5fdd6e3d5732 Mon Sep 17 00:00:00 2001
From: Abdullah Alperen <alperena@msu.edu>
Date: Mon, 1 Oct 2018 22:46:10 -0400
Subject: [PATCH] PuReMD: fix read option for python script
---
tools/run_sim_puremd.py | 95 ++++++++++++++++++++++++++++-------------
1 file changed, 66 insertions(+), 29 deletions(-)
diff --git a/tools/run_sim_puremd.py b/tools/run_sim_puremd.py
index b7b13774..c6c68500 100644
--- a/tools/run_sim_puremd.py
+++ b/tools/run_sim_puremd.py
@@ -168,12 +168,24 @@ class TestCase():
rmdir(temp_dir)
def _process_result(self, fout, param, min_step, max_step):
- time = 0.
+ from operator import mul
+ from functools import reduce
+
+ total = 0.
+ comm = 0.
+ neighbors = 0.
+ init = 0.
+ bonded = 0.
+ nonbonded = 0.
cm = 0.
- iters = 0.
+ cm_sort = 0.
+ s_iters = 0.
pre_comp = 0.
pre_app = 0.
- spmv = 0.
+ s_comm = 0.
+ s_allr = 0.
+ s_spmv = 0.
+ s_vec_ops = 0.
cnt = 0
line_cnt = 0
log_file = param['name'] + '.log'
@@ -189,39 +201,63 @@ class TestCase():
(min_step and not max_step and cnt >= min_step) or \
(not min_step and max_step and cnt <= max_step) or \
(cnt >= min_step and cnt <= max_step):
- cm = cm + float(line[6])
- iters = iters + float(line[8])
- pre_comp = pre_comp + float(line[9])
- pre_app = pre_app + float(line[10])
- spmv = spmv + float(line[11])
- cnt = cnt + 1
+ if ( int(line[0]) < int(param['nsteps']) ):
+ total = total + float(line[1])
+ 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])
+ cnt = cnt + 1
except Exception:
pass
- if line[0] == 'total:':
- try:
- time = float(line[1])
- except Exception:
- pass
line_cnt = line_cnt + 1
if cnt > 0:
+ comm = comm / cnt
+ neighbors = neighbors / cnt
+ init = init / cnt
+ bonded = bonded / cnt
+ nonbonded = nonbonded / cnt
cm = cm / cnt
- iters = iters / cnt
+ cm_sort = cm_sort / cnt
+ s_iters = s_iters / cnt
pre_comp = pre_comp / cnt
pre_app = pre_app / cnt
- spmv = spmv / cnt
+ s_comm = s_comm / cnt
+ s_allr = s_allr / cnt
+ s_spmv = s_spmv / cnt
+ s_vec_ops = s_vec_ops / cnt
# subtract for header, footer (total time), and extra step
# (e.g., 100 steps means steps 0 through 100, inclusive)
- if (line_cnt - 3) == int(param['nsteps']):
- fout.write(self.__result_body_fmt.format(path.basename(self.__geo_file).split('.')[0],
- param['nsteps'], param['charge_method'], 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_comp_sai_thres'],
- param['cm_solver_pre_app_type'], param['cm_solver_pre_app_jacobi_iters'],
- pre_comp, pre_app, iters, spmv,
- cm, param['threads'], time))
+ if (line_cnt - 1) >= int(param['nsteps']):
+ fout.write(self.__result_body_fmt.format(path.basename(self.__geo_file).split('.')[0],
+ str(reduce(mul, map(int, param['proc_by_dim'].split(':')), 1)),
+ param['nsteps'], param['cm_solver_pre_comp_type'],
+ param['cm_solver_q_err'],
+ param['reneighbor'],
+ param['cm_solver_pre_comp_sai_thres'],
+ total, comm, neighbors, init, 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],
+ str(reduce(mul, map(int, param['proc_by_dim'].split(':')), 1)),
+ param['nsteps'], param['cm_solver_pre_comp_type'],
+ 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')))
+
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)))
fout.flush()
@@ -259,10 +295,11 @@ 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}|{: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)']
- 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'
+ 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'
params = {
'ensemble_type': ['0'],
--
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