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#!/usr/bin/env python3
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import argparse
from re import sub
from subprocess import Popen, PIPE
from os import getcwd, environ, path, remove, rename, rmdir
from sys import exit
class TestCase():
def __init__(self, geo_file, ffield_file, control_file, params={}, result_header_fmt='',
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result_header='', result_body_fmt='', result_file='results.txt', geo_format='1'):
self.__geo_file = geo_file
self.__ffield_file = ffield_file
self.__control_file = control_file
self.__param_names = sorted(params.keys())
self.__params = params
self.__result_header_fmt = result_header_fmt
self.__result_body_fmt = result_body_fmt
self.__result_file = result_file
self.__control_res = { \
'name': lambda l, x: sub(
r'(?P<key>simulation_name\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'ensemble_type': lambda l, x: sub(
r'(?P<key>ensemble_type\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
'nsteps': lambda l, x: sub(
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), \
'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_comp_sai_thres': lambda l, x: sub(
r'(?P<key>cm_solver_pre_comp_sai_thres\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), \
}
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self.__params['geo_format'] = geo_format
def _setup(self, param, temp_file):
fp = open(self.__control_file, 'r')
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lines = fp.read()
fp.close()
for k in self.__control_res.keys():
try:
lines = self.__control_res[k](lines, param[k])
except KeyError:
pass
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fp_temp = open(temp_file, 'w')
fp_temp.write(lines)
fp_temp.close()
def run(self, bin_file='sPuReMD/bin/spuremd', process_results=False):
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bin_path = path.join(base_dir, bin_file)
env = dict(environ)
write_header = True
if path.exists(self.__result_file):
write_header = False
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fout = open(self.__result_file, 'a')
fout.write(self.__result_header_fmt.format(*self.__result_header))
fout.flush()
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temp_file = path.join(temp_dir, path.basename(self.__control_file))
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['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'] \
+ '_pcsai' + param_dict['cm_solver_pre_comp_sai_thres'] \
+ '_pa' + param_dict['cm_solver_pre_app_type'] \
+ '_paji' + param_dict['cm_solver_pre_app_jacobi_iters'] \
+ '_t' + param_dict['threads']
if not process_results:
self._setup(param_dict, temp_file)
env['OMP_NUM_THREADS'] = param_dict['threads']
start = time()
proc_handle = Popen([bin_path, self.__geo_file, self.__ffield_file, temp_file],
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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))
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else:
print('stdout:')
print(stdout)
print('stderr:')
print(stderr)
else:
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self._process_result(fout, param_dict)
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if path.exists(temp_file):
remove(temp_file)
if path.exists(temp_dir):
rmdir(temp_dir)
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def _process_result(self, fout, param):
time = 0.
iters = 0.
pre_comp = 0.
pre_app = 0.
spmv = 0.
cnt = 0
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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:
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iters = iters + float(line[8])
pre_comp = pre_comp + float(line[9])
pre_app = pre_app + float(line[10])
spmv = spmv + float(line[11])
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pass
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if line[0] == 'total:':
try:
time = float(line[1])
except Exception:
pass
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if cnt > 0:
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iters = iters / cnt
pre_comp = pre_comp / cnt
pre_app = pre_app / cnt
spmv = spmv / cnt
if cnt == 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,
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else:
print('**WARNING: nsteps not correct in file {0}...'.format(log_file))
fout.flush()
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DATA = [ \
'bilayer_56800', 'bilayer_340800', \
'dna_19733', \
'petn_48256', \
'silica_6000', 'silica_72000', 'silica_300000', \
'water_6540', 'water_78480', 'water_327000', \
]
parser = argparse.ArgumentParser(description='Run molecular dynamics simulations on specified data sets.')
parser.add_argument('-f', '--out_file', metavar='out_file', default=None, nargs=1,
help='Output file to write results.')
parser.add_argument('-r', '--process_results', default=False, action='store_true',
help='Process simulation results only (do not perform simulations).')
parser.add_argument('-p', '--params', metavar='params', action='append', default=None, nargs=2,
help='Paramater name and value pairs for the simulation, which multiple values comma delimited.')
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parser.add_argument('data', nargs='+',
choices=DATA, help='Data sets for which to run simulations.')
# parse args and take action
args = parser.parse_args()
base_dir = getcwd()
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}|{:10}|{:10}|{:10}|{:10}|{:10}|{:3}|{:10}\n'
header_str = ['Data Set', 'Steps', 'CM', 'Solvr', 'Q Tol', 'QDS', 'PreCT', 'PreCD', 'PreCS', '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} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:10.3f} {:3} {:10.3f}\n'
params = {
'ensemble_type': ['0'],
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'nsteps': ['20'],
'tabulate_long_range': ['0'],
'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_comp_sai_thres': ['0.1'],
'cm_solver_pre_app_type': ['2'],
'cm_solver_pre_app_jacobi_iters': ['30'],
'threads': ['1'],
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'geo_format': [],
if args.out_file:
result_file = args.out_file[0]
else:
result_file = 'result.txt'
# overwrite default params, if supplied via command line args
if args.params:
for param in args.params:
params[param[0]] = param[1].split(',')
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test_cases = []
if 'water_6540' in args.data:
test_cases.append(
TestCase(path.join(data_dir, 'water/water_6540.pdb'),
path.join(data_dir, 'water/ffield.water'),
path.join(control_dir, 'param.gpu.water'),
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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))
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if 'water_78480' in args.data:
test_cases.append(
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TestCase(path.join(data_dir, 'water/water_78480.geo'),
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path.join(data_dir, 'water/ffield.water'),
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))
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if 'water_327000' in args.data:
test_cases.append(
TestCase(path.join(data_dir, 'water/water_327000.geo'),
path.join(data_dir, 'water/ffield.water'),
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))
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if 'bilayer_56800' in args.data:
test_cases.append(
TestCase(path.join(data_dir, 'bilayer/bilayer_56800.pdb'),
path.join(data_dir, 'bilayer/ffield-bio'),
path.join(control_dir, 'param.gpu.water'),
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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))
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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))
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if 'dna_19733' in args.data:
test_cases.append(
TestCase(path.join(data_dir, 'dna/dna_19733.pdb'),
path.join(data_dir, 'dna/ffield-dna'),
path.join(control_dir, 'param.gpu.water'),
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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))
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if 'silica_6000' in args.data:
test_cases.append(
TestCase(path.join(data_dir, 'silica/silica_6000.pdb'),
path.join(data_dir, 'silica/ffield-bio'),
path.join(control_dir, 'param.gpu.water'),
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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))
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if 'silica_72000' in args.data:
test_cases.append(
TestCase(path.join(data_dir, 'silica/silica_72000.geo'),
path.join(data_dir, 'silica/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))
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if 'silica_300000' in args.data:
test_cases.append(
TestCase(path.join(data_dir, 'silica/silica_300000.geo'),
path.join(data_dir, 'silica/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))
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if 'petn_48256' in args.data:
test_cases.append(
TestCase(path.join(data_dir, 'petn/petn_48256.pdb'),
path.join(data_dir, 'petn/ffield.petn'),
path.join(control_dir, 'param.gpu.water'),
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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))
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test.run(bin_file='sPuReMD/bin/spuremd', process_results=args.process_results)