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Commit efc02992 authored by Daniel F Kortemeyer's avatar Daniel F Kortemeyer
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Merge branch 'master' of gitlab.msu.edu:SParTA/PuReMD

parents b5fb8230 5276c950
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environ/param.gpu.water
+ 1
− 1
View file @ efc02992
......@@ -35,7 +35,7 @@ compress 0.008134 ! in ps^2 * A / amu ( 4.5X10^(-5
press_mode 0 ! 0: internal + external pressure, 1: ext only, 2: int only
geo_format 1 ! 0: xyz, 1: pdb, 2: bgf
write_freq 1000 ! write trajectory after so many steps
write_freq 0 ! write trajectory after so many steps
traj_compress 0 ! 0: no compression 1: uses zlib to compress trajectory output
traj_format 0 ! 0: our own format (below options apply to this only), 1: xyz, 2: bgf, 3: pdb
traj_title WATER_NVT ! (no white spaces)
......
tools/run_sim.py
+ 188
− 82
View file @ efc02992
#!/usr/bin/env python
from fileinput import input
from itertools import product
from re import sub
from subprocess import Popen, PIPE
from os import getcwd, environ, path, rename
from os import getcwd, environ, path, remove, rename, rmdir
from sys import exit
from tempfile import mkdtemp
from time import time
base_dir = getcwd()
control_dir = path.join(base_dir, 'environ')
data_dir = path.join(base_dir, 'data/benchmarks')
puremd_args = [ \
# (path.join(data_dir, 'water/water_6540.pdb'), path.join(data_dir, 'water/ffield.water'), path.join(control_dir, 'param.gpu.water')), \
# (path.join(data_dir, 'water/water_78480.pdb'), path.join(data_dir, 'water/ffield.water'), path.join(control_dir, 'param.gpu.water')), \
# (path.join(data_dir, 'water/water_327000.geo'), path.join(data_dir, 'water/ffield.water'), path.join(control_dir, 'param.gpu.water')), \
# (path.join(data_dir, 'bilayer/bilayer_56800.pdb'), path.join(data_dir, 'bilayer/ffield-bio'), path.join(control_dir, 'param.gpu.water')), \
(path.join(data_dir, 'dna/dna_19733.pdb'), path.join(data_dir, 'dna/ffield-dna'), path.join(control_dir, 'param.gpu.water')), \
(path.join(data_dir, 'silica/silica_6000.pdb'), path.join(data_dir, 'silica/ffield-bio'), path.join(control_dir, 'param.gpu.water')), \
# (path.join(data_dir, 'silica/silica_72000.geo'), path.join(data_dir, 'silica/ffield-bio'), path.join(control_dir, 'param.gpu.water')), \
# (path.join(data_dir, 'silica/silica_300000.geo'), path.join(data_dir, 'silica/ffield-bio'), path.join(control_dir, 'param.gpu.water')), \
# (path.join(data_dir, 'petn/petn_48256.pdb'), path.join(data_dir, 'petn/ffield.petn'), path.join(control_dir, 'param.gpu.water')), \
]
header_fmt_str = '{:20}|{:5}|{:5}|{:5}|{:10}|{:10}|{:10}|{:10}|{:10}|{:10}'
body_fmt_str = '{:20} {:5} {:5} {:5} {:10.6f} {:10.6f} {:10.6f} {:10.6f} {:10} {:10.6f}'
steps = ['20'] #['100']
qeq_solver_tol = ['1e-6'] #['1e-6', '1e-8', '1e-10', '1e-14']
pre_comp_type = ['2'] #['0', '1', '2']
threads = ['1', '2', '4', '12', '24']
patterns = [ \
lambda l, x: sub(r'(?P<key>simulation_name\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
lambda l, x: sub(r'(?P<key>nsteps\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
lambda l, x: sub(r'(?P<key>qeq_solver_q_err\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
lambda l, x: sub(r'(?P<key>pre_comp_type\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
lambda l, x: sub(r'(?P<key>geo_format\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
]
d = dict(environ)
print header_fmt_str.format('Data Set', 'Steps', 'Q Tol', 'Pre T', 'Pre Comp',
'Pre App', 'Iters', 'SpMV', 'Threads', 'Time (s)')
for i in xrange(len(puremd_args)):
for s in xrange(len(steps)):
for j in xrange(len(qeq_solver_tol)):
for t in xrange(len(pre_comp_type)):
for k in xrange(len(threads)):
for line in input(puremd_args[i][2], inplace=1):
line = line.rstrip()
line = patterns[0](line, path.basename(puremd_args[i][0]).split('.')[0]
+ '_' + 'tol' + qeq_solver_tol[j] + '_precomp' + pre_comp_type[t] + '_thread' + threads[k])
line = patterns[1](line, steps[s])
line = patterns[2](line, qeq_solver_tol[j])
line = patterns[3](line, pre_comp_type[t])
print line
d['OMP_NUM_THREADS'] = threads[k]
start = time()
p = Popen([path.join(base_dir, 'sPuReMD/bin/spuremd')] + list(puremd_args[i]),
stdout=PIPE, stderr=PIPE, env=d)
stdout, stderr = p.communicate()
stop = time()
iters = 0.
pre_comp = 0.
pre_app = 0.
spmv = 0.
cnt = 0
with open(path.basename(puremd_args[i][0]).split('.')[0]
+ '_' + 'tol' + qeq_solver_tol[j] + '_precomp' + pre_comp_type[t] + '_thread'
+ threads[k] + '.log', 'r') as fp:
for line in fp:
line = line.split()
try:
iters = iters + float(line[7])
pre_comp = pre_comp + float(line[8])
pre_app = pre_app + float(line[9])
spmv = spmv + float(line[10])
cnt = cnt + 1
except Exception:
class TestCase():
def __init__(self, geo_file, ffield_file, control_file, params={}, result_header_fmt='',
result_header='', result_body_fmt='', result_file='results.txt'):
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_header = result_header
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), \
'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), \
'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_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), \
'geo_format': lambda l, x: sub(
r'(?P<key>geo_format\s+)\S+(?P<comment>.*)', r'\g<key>%s\g<comment>' % x, l), \
}
def _setup(self, param, temp_file):
fp = open(self.__control_file, 'r')
lines = fp.read()
fp.close()
for k in self.__control_res.keys():
try:
lines = self.__control_res[k](lines, param[k])
except KeyError:
pass
cnt = cnt - 1
iters = iters / cnt
pre_comp = pre_comp / cnt
pre_app = pre_app / cnt
spmv = spmv / cnt
print body_fmt_str.format(path.basename(puremd_args[i][0]).split('.')[0],
steps[s], qeq_solver_tol[j], pre_comp_type[t], pre_comp, pre_app, iters, spmv,
threads[k], stop - start)
fp_temp = open(temp_file, 'w', 0)
fp_temp.write(lines)
fp_temp.close()
def run(self, bin_file='sPuReMD/bin/spuremd'):
base_dir = getcwd()
bin_path = path.join(base_dir, bin_file)
env = dict(environ)
write_header = True
if path.exists(self.__result_file):
write_header = False
fout = open(self.__result_file, 'a', 0)
if write_header:
fout.write(self.__result_header_fmt.format(*self.__result_header))
temp_dir = mkdtemp()
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] \
+ '_step' + param_dict['nsteps'] + '_tol' + param_dict['qeq_solver_q_err'] \
+ '_precomp' + param_dict['pre_comp_type'] + '_thread' + param_dict['threads']
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],
stdout=PIPE, stderr=PIPE, env=env)
#TODO: handle outputs?
stdout, stderr = proc_handle.communicate()
stop = time()
self._process_result(fout, stop - start, param_dict)
fout.close()
remove(temp_file)
rmdir(temp_dir)
def _process_result(self, fout, time, param):
qeq = 0.
iters = 0.
pre_comp = 0.
pre_app = 0.
spmv = 0.
cnt = 0
with open(param['name'] + '.log', 'r') as fp:
for line in fp:
line = line.split()
try:
qeq = qeq + float(line[6])
iters = iters + float(line[7])
pre_comp = pre_comp + float(line[8])
pre_app = pre_app + float(line[9])
spmv = spmv + float(line[10])
cnt = cnt + 1
except Exception:
pass
cnt = cnt - 1
qeq = qeq / cnt
iters = iters / cnt
pre_comp = pre_comp / cnt
pre_app = pre_app / cnt
spmv = spmv / cnt
fout.write(self.__result_body_fmt.format(path.basename(self.__geo_file).split('.')[0],
param['nsteps'], param['qeq_solver_q_err'], param['pre_comp_type'], pre_comp, pre_app, iters, spmv,
qeq, param['threads'], time))
if __name__ == '__main__':
base_dir = getcwd()
control_dir = path.join(base_dir, 'environ')
data_dir = path.join(base_dir, 'data/benchmarks')
header_fmt_str = '{:20}|{:5}|{:5}|{:5}|{:10}|{:10}|{:10}|{:10}|{:10}|{:10}|{:10}\n'
header_str = ['Data Set', 'Steps', 'Q Tol', 'Pre T', 'Pre Comp',
'Pre App', 'Iters', 'SpMV', 'QEq', 'Threads', 'Time (s)']
body_fmt_str = '{:20} {:5} {:5} {:5} {:10.6f} {:10.6f} {:10.6f} {:10.6f} {:10.6f} {:10} {:10.6f}\n'
params = {
'ensemble_type': ['0'],
'nsteps': ['20', '100', '500', '1000'],
'qeq_solver_type': ['0'],
'qeq_solver_q_err': ['1e-6', '1e-10'],
# 'qeq_solver_q_err': ['1e-6', '1e-8', '1e-10', '1e-14'],
'pre_comp_type': ['0'],
# 'pre_comp_type': ['0', '1', '2'],
'pre_comp_refactor': ['1'],
# 'pre_comp_sweeps': ['3'],
# 'pre_app_type': ['0'],
# 'pre_app_jacobi_iters': ['50'],
'threads': ['12'],
# 'threads': ['1', '2', '4', '12', '24'],
'geo_format': ['1'],
}
test_cases = [
TestCase(path.join(data_dir, 'water/water_6540.pdb'),
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),
# TestCase(path.join(data_dir, 'water/water_78480.pdb'),
# 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),
# 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),
TestCase(path.join(data_dir, 'bilayer/bilayer_56800.pdb'),
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),
TestCase(path.join(data_dir, 'dna/dna_19733.pdb'),
path.join(data_dir, 'dna/ffield-dna'),
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),
TestCase(path.join(data_dir, 'silica/silica_6000.pdb'),
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),
# 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),
# 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),
TestCase(path.join(data_dir, 'petn/petn_48256.pdb'),
path.join(data_dir, 'petn/ffield.petn'),
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),
]
for test in test_cases:
test.run(bin_file='sPuReMD/bin/spuremd')
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