def rep_bench(func,
n,
initfunc=None,
MAXREPS=10,
MAXTIME=60.0,
profile=False,
profresults="pyutil-benchutil.prof",
UNITS_PER_SECOND=1):
"""
Will run the func up to MAXREPS times, but won't start a new run if MAXTIME
(wall-clock time) has already elapsed (unless MAXTIME is None).
"""
assert isinstance(n, int), (n, type(n))
starttime = time.realtime()
tls = [] # elapsed time in nanoseconds
while ((len(tls) < MAXREPS) or
(MAXREPS is None)) and ((MAXTIME is None) or
((time.realtime() - starttime) < MAXTIME)):
if initfunc:
initfunc(n)
try:
tl = bench_it(func, n, profile=profile, profresults=profresults)
except BadMeasure:
pass
else:
tls.append(tl * UNITS_PER_SECOND)
assert tls
sumtls = reduce(operator.__add__, tls)
mean = sumtls / len(tls)
tls.sort()
worst = tls[-1]
best = tls[0]
m = min(int(math.log(len(tls))) + 1, len(tls))
mthworst = tls[-m]
mthbest = tls[m - 1]
res = {
'worst': worst / n,
'best': best / n,
'm': m,
'mth-best': mthbest / n,
'mth-worst': mthworst / n,
'mean': mean / n,
'num': len(tls),
}
print "best: %(best)#8.03e, %(m)3dth-best: %(mth-best)#8.03e, mean: %(mean)#8.03e, %(m)3dth-worst: %(mth-worst)#8.03e, worst: %(worst)#8.03e (of %(num)6d)" % res
return res
def force_repeatability():
now = 1043659734.0
def faketime():
global tdelta
tdelta += 1
return now + tdelta
time.faketime = faketime
time.time = faketime
from idlib import i2b
def fakeurandom(n):
if n > 64:
raise (
"Can't produce more than 64 bytes of pseudorandomness efficiently."
)
elif n == 0:
return ''
else:
z = i2b(random.getrandbits(n * 8))
x = z + "0" * (n - len(z))
assert len(x) == n
return x
os.fakeurandom = fakeurandom
os.urandom = fakeurandom
global seeded
if not seeded:
SEED = os.environ.get('REPEATABLE_RANDOMNESS_SEED', None)
if SEED is None:
# Generate a seed which is integral and fairly short (to ease cut-and-paste, writing it down, etc.).
t = time.realtime()
subsec = t % 1
t += (subsec * 1000000)
t %= 1000000
SEED = long(t)
import sys
sys.stdout.write("REPEATABLE_RANDOMNESS_SEED: %s\n" % SEED)
sys.stdout.flush()
sys.stdout.write(
"In order to reproduce this run of the code, set the environment variable \"REPEATABLE_RANDOMNESS_SEED\" to %s before executing.\n"
% SEED)
sys.stdout.flush()
random.seed(SEED)
def seed_which_refuses(a):
sys.stdout.write("I refuse to reseed to %s. Go away!\n" % (a, ))
sys.stdout.flush()
return
random.realseed = random.seed
random.seed = seed_which_refuses
seeded = True
import setutil
setutil.RandomSet.DETERMINISTIC = True
def rep_bench(func, n, initfunc=None, MAXREPS=10, MAXTIME=60.0, profile=False, profresults="pyutil-benchutil.prof", UNITS_PER_SECOND=1):
"""
Will run the func up to MAXREPS times, but won't start a new run if MAXTIME
(wall-clock time) has already elapsed (unless MAXTIME is None).
"""
assert isinstance(n, int), (n, type(n))
starttime = time.realtime()
tls = [] # elapsed time in nanoseconds
while ((len(tls) < MAXREPS) or (MAXREPS is None)) and ((MAXTIME is None) or ((time.realtime() - starttime) < MAXTIME)):
if initfunc:
initfunc(n)
try:
tl = bench_it(func, n, profile=profile, profresults=profresults)
except BadMeasure:
pass
else:
tls.append(tl * UNITS_PER_SECOND)
assert tls
sumtls = reduce(operator.__add__, tls)
mean = sumtls / len(tls)
tls.sort()
worst = tls[-1]
best = tls[0]
m = min(int(math.log(len(tls)))+1, len(tls))
mthworst = tls[-m]
mthbest = tls[m-1]
res = {
'worst': worst/n,
'best': best/n,
'm': m,
'mth-best': mthbest/n,
'mth-worst': mthworst/n,
'mean': mean/n,
'num': len(tls),
}
print "best: %(best)#8.03e, %(m)3dth-best: %(mth-best)#8.03e, mean: %(mean)#8.03e, %(m)3dth-worst: %(mth-worst)#8.03e, worst: %(worst)#8.03e (of %(num)6d)" % res
return res
def bench_it(func, n, profile=False, profresults="pyutil-benchutil.prof"):
if profile:
st = time.realtime()
cProfile.run('func(n)', profresults)
sto = time.realtime()
else:
st = time.realtime()
func(n)
sto = time.realtime()
timeelapsed = sto - st
if timeelapsed <= 0:
raise BadMeasure(timeelapsed)
global worstemptymeasure
emsta = time.realtime()
do_nothing(2**32)
emstop = time.realtime()
empty = emstop - emsta
if empty > worstemptymeasure:
worstemptymeasure = empty
_assert(
timeelapsed * MARGINOFERROR > worstemptymeasure,
"Invoking func %s(%s) took only %0.20f seconds, but we cannot accurately measure times much less than %0.20f seconds. Therefore we cannot produce good results here. Try benchmarking a more time-consuming variant."
% (
func,
n,
timeelapsed,
worstemptymeasure,
))
return timeelapsed
def setUp(self, repeatable=False):
"""
@param repeatable: install the repeatable_randomness hacks to attempt
to without access to real randomness and real time.time from the
code under test
"""
self.repeatable = repeatable
if self.repeatable:
import repeatable_random
repeatable_random.force_repeatability()
if hasattr(time, 'realtime'):
self.teststarttime = time.realtime()
else:
self.teststarttime = time.time()
def setUp(self, repeatable=False):
"""
@param repeatable: install the repeatable_randomness hacks to attempt
to without access to real randomness and real time.time from the
code under test
"""
self.repeatable = repeatable
if self.repeatable:
import repeatable_random
repeatable_random.force_repeatability()
if hasattr(time, 'realtime'):
self.teststarttime = time.realtime()
else:
self.teststarttime = time.time()
def force_repeatability():
now = 1043659734.0
def faketime():
global tdelta
tdelta += 1
return now + tdelta
time.faketime = faketime
time.time = faketime
from idlib import i2b
def fakeurandom(n):
if n > 64:
raise ("Can't produce more than 64 bytes of pseudorandomness efficiently.")
elif n == 0:
return ''
else:
z = i2b(random.getrandbits(n*8))
x = z + "0" * (n-len(z))
assert len(x) == n
return x
os.fakeurandom = fakeurandom
os.urandom = fakeurandom
global seeded
if not seeded:
SEED = os.environ.get('REPEATABLE_RANDOMNESS_SEED', None)
if SEED is None:
# Generate a seed which is integral and fairly short (to ease cut-and-paste, writing it down, etc.).
t = time.realtime()
subsec = t % 1
t += (subsec * 1000000)
t %= 1000000
SEED = long(t)
import sys
sys.stdout.write("REPEATABLE_RANDOMNESS_SEED: %s\n" % SEED) ; sys.stdout.flush()
sys.stdout.write("In order to reproduce this run of the code, set the environment variable \"REPEATABLE_RANDOMNESS_SEED\" to %s before executing.\n" % SEED) ; sys.stdout.flush()
random.seed(SEED)
def seed_which_refuses(a):
sys.stdout.write("I refuse to reseed to %s. Go away!\n" % (a,)) ; sys.stdout.flush()
return
random.realseed = random.seed
random.seed = seed_which_refuses
seeded = True
import setutil
setutil.RandomSet.DETERMINISTIC = True
def bench_it(func, n, profile=False, profresults="pyutil-benchutil.prof"):
if profile:
st = time.realtime()
cProfile.run('func(n)', profresults)
sto = time.realtime()
else:
st = time.realtime()
func(n)
sto = time.realtime()
timeelapsed = sto - st
if timeelapsed <= 0:
raise BadMeasure(timeelapsed)
global worstemptymeasure
emsta = time.realtime()
do_nothing(2**32)
emstop = time.realtime()
empty = emstop - emsta
if empty > worstemptymeasure:
worstemptymeasure = empty
_assert(timeelapsed*MARGINOFERROR > worstemptymeasure, "Invoking func %s(%s) took only %0.20f seconds, but we cannot accurately measure times much less than %0.20f seconds. Therefore we cannot produce good results here. Try benchmarking a more time-consuming variant." % (func, n, timeelapsed, worstemptymeasure,))
return timeelapsed
import sys
from time import time as realtime
from pytools_uibcdf.Time import formatted_elapsed_time, formatted_local_time
import molmodmt as m3t
import simtk.openmm as mm
import simtk.openmm.app as app
import simtk.unit as unit
from mdtraj.reporters import HDF5Reporter
from openmmtools.integrators import LangevinIntegrator
#### Log file
logfile = open('logfile.txt', 'w')
#logfile = sys.stdout
start_realtime = realtime()
logfile.write("\n")
logfile.write("Start: " + formatted_local_time() + "\n")
logfile.write("\n")
#### Loading PDB
pdb = m3t.convert('system_equilibrated_NVT.pdb', 'openmm.PDBFile')
#### System
topology = m3t.convert(pdb, 'openmm.Topology')
forcefield = app.ForceField('amber99sbildn.xml', 'tip3p.xml')
system = forcefield.createSystem(topology,
nonbondedMethod=app.PME,
nonbondedCutoff=1.2 * unit.nanometers,
def time(): global _time, _lastTime if (_time == None): _time = realtime() _lastTime = realtime() return _time + (_lastTime - _time) * _dialation
