def _worker(src, seeds, results, sim_args, sim_kwargs):
# create a rr obj
print("starting worker processes: " + str(os.getpid()))
n = 0;
r = RoadRunner(src);
# remove and apply the selections
# no sense in re-evaluating selection list each time.
if 'sel' in sim_kwargs:
r.selections = sim_kwargs['sel']
del sim_kwargs['sel']
if 'selections' in sim_kwargs:
r.selections = sim_kwargs['selections']
del sim_kwargs['selections']
# might have forgot to reset sim,
# default is to reset sim between each simulation.
if not 'reset' in sim_kwargs:
Logger.log(Logger.LOG_WARNING,
"simulate args missing reset, defaulting to reset between simulations")
sim_kwargs['reset'] = True
# read until None,
# blocks if queue is empty
for seed in iter(seeds.get, None):
sim_kwargs['seed'] = seed
result = r.simulate(*sim_args, **sim_kwargs)
results.put(result)
n += 1
print("process {} finished with {} simulations".format(os.getpid(), n))
def _worker(src, seeds, results, sim_args, sim_kwargs):
# create a rr obj
print("starting worker processes: " + str(os.getpid()))
n = 0
r = RoadRunner(src)
# remove and apply the selections
# no sense in re-evaluating selection list each time.
if 'sel' in sim_kwargs:
r.selections = sim_kwargs['sel']
del sim_kwargs['sel']
if 'selections' in sim_kwargs:
r.selections = sim_kwargs['selections']
del sim_kwargs['selections']
# might have forgot to reset sim,
# default is to reset sim between each simulation.
if not 'reset' in sim_kwargs:
Logger.log(
Logger.LOG_WARNING,
"simulate args missing reset, defaulting to reset between simulations"
)
sim_kwargs['reset'] = True
# read until None,
# blocks if queue is empty
for seed in iter(seeds.get, None):
sim_kwargs['seed'] = seed
result = r.simulate(*sim_args, **sim_kwargs)
results.put(result)
n += 1
print("process {} finished with {} simulations".format(os.getpid(), n))
def runTester (testDir=None):
"""
Run a series of tests from a testing dir.
This enumerates all the files in a directory, and all the files ending with '.rrtest'
are assumed to be testing files.
"""
global fHandle
global gFailedTests
global gPassedTests
import os.path as p
from glob import glob
gFailedTests = 0
gPassedTests = 0
if testDir is None:
testDir = getDefaultTestDir()
if not p.isdir(testDir):
raise Exception("{} is NOT a directory".format(testDir))
files = glob(p.join(testDir, "*.rrtest"))
unknownTests = 0
for file in files:
print("\n\nStarting Test on ", file)
# set the globals, these should be class instance vars...
fHandle = open (file, 'r')
testId = jumpToNextTest()
if testId == '[SBML]':
sbmlStr, testId = getSBMLStr ()
else:
Logger.log(Logger.LOG_WARNING, "rrtest file, \""
+ file + "\" missing SBML section, ignoring test file")
continue
# Load any initialization actions
if testId == '[INITIALIZATION]':
testId = jumpToNextTest ()
while testId != '[END_INITIALIZATION]':
if functions.has_key(testId):
func = functions[testId]
func (rrInstance, testId)
else:
print('No initialization function found for ' + testId)
testId = jumpToNextTest()
testId = jumpToNextTest()
# create a RoadRunner obj with the sbml from the test file
rrInstance = roadrunner.RoadRunner(sbmlStr)
print('Successfully loaded model.\n')
# Now start the tests proper
while testId != '':
if functions.has_key(testId):
func = functions[testId]
func(rrInstance, testId)
else:
#getFloatingSpeciesAmountRates
unknownTests = unknownTests+1
print(string.ljust (testId, rpadding), 'UNKNOWN TEST')
testId = jumpToNextTest()
print("\n\nTotal failed tests:\t", gFailedTests, \
"\nTotal unknown tests:\t", unknownTests, \
"\nTotal passed tests:\t", gPassedTests)
return gFailedTests
# Sabaody
# Copyright 2018 J Kyle Medley
from __future__ import print_function, division, absolute_import
from roadrunner import RoadRunner, Logger
Logger.disableConsoleLogging()
Logger.setLevel(Logger.LOG_FATAL)
from params import getDefaultParamValues, getUpperBound, getLowerBound
from b2problem import B2_UDP
from pygmo import island as pg_island, problem, rosenbrock, simulated_annealing, de, mp_island
from math import sqrt
def benchmark_loading_time():
import arrow
time_start = arrow.utcnow()
r = RoadRunner('../../../../../sbml/b2.xml')
delta_t = arrow.utcnow() - time_start
print('Loading time:', delta_t)
def benchmark_simulated_annealing():
island = pg_island(
algo=simulated_annealing(Ts=1.,Tf=.01),
prob=problem(B2_UDP(getLowerBound(),getUpperBound(),'../../../../../sbml/b2.xml')),
size=10)
N = 10
import arrow
time_start = arrow.utcnow()
from roadrunner import RoadRunner, Logger
#Logger.setLevel(Logger.LOG_DEBUG) # too verbose
Logger.setLevel(Logger.LOG_WARNING)
# Load model
rr = RoadRunner('/tmp/tx.sbml')
#rr = RoadRunner('/tmp/tx-reduced.sbml')
#rr = RoadRunner('/tmp/antsbml.xml')
# Simulate model
results = rr.simulate(0, 10, 30, integrator='gillespie')
print(results)
# Write results to temp file
with open('/tmp/sim_res.csv', 'w') as f:
f.write(str(results))
# Plot
rr.plot()
def runTester(testDir=None):
"""
Run a series of tests from a testing dir.
This enumerates all the files in a directory, and all the files ending with '.rrtest'
are assumed to be testing files.
"""
global fHandle
global gFailedTests
global gPassedTests
import os.path as p
from glob import glob
gFailedTests = 0
gPassedTests = 0
if testDir is None:
testDir = getDefaultTestDir()
if not p.isdir(testDir):
raise Exception("{} is NOT a directory".format(testDir))
files = glob(p.join(testDir, "*.rrtest"))
unknownTests = 0
for file in files:
print("\n\nStarting Test on ", file)
# set the globals, these should be class instance vars...
fHandle = open(file, 'r')
testId = jumpToNextTest()
if testId == '[SBML]':
sbmlStr, testId = getSBMLStr()
else:
Logger.log(
Logger.LOG_WARNING, "rrtest file, \"" + file +
"\" missing SBML section, ignoring test file")
continue
# Load any initialization actions
if testId == '[INITIALIZATION]':
testId = jumpToNextTest()
while testId != '[END_INITIALIZATION]':
if testId in functions:
func = functions[testId]
func(rrInstance, testId)
else:
print('No initialization function found for ' + testId)
testId = jumpToNextTest()
testId = jumpToNextTest()
# create a RoadRunner obj with the sbml from the test file
rrInstance = roadrunner.RoadRunner(sbmlStr)
print('Successfully loaded model.\n')
# Now start the tests proper
while testId != '':
if testId in functions:
func = functions[testId]
func(rrInstance, testId)
else:
#getFloatingSpeciesAmountRates
unknownTests = unknownTests + 1
print((testId).ljust(rpadding), 'UNKNOWN TEST')
testId = jumpToNextTest()
for testFunc in [unitTestIntegratorSettings]:
testFunc(testDir)
print("\n\nTotal failed tests:\t", gFailedTests, \
"\nTotal unknown tests:\t", unknownTests, \
"\nTotal passed tests:\t", gPassedTests)
return gFailedTests