def optimize_tolerance(target_label, reactionModel, rmg, reaction_system_index, error, orig_conv):
"""
Increment the trial tolerance from a very low value until the introduced error is greater than the parameter threshold.
"""
start = 1E-20
incr = 10
tolmax = 1
tol = start
trial = start
while True:
logging.info('Trial tolerance: {trial:.2E}'.format(**locals()))
Xred = reduce_compute(trial, target_label, reactionModel, rmg, reaction_system_index)
dev = np.abs((Xred - orig_conv) / orig_conv)
logging.info('Deviation: {dev:.2f}'.format(**locals()))
if dev > error or trial > tolmax:
break
tol = trial
trial = trial * incr
if tol == start:
logging.error('Starting value for tolerance was too high...')
return tol
def optimize_tolerance(target_label, reactionModel, rmg, reaction_system_index,
error, orig_conv):
"""
Increment the trial tolerance from a very low value until the introduced error is greater than the parameter threshold.
"""
start = 1E-20
incr = 10
tolmax = 1
tol = start
trial = start
while True:
logging.info('Trial tolerance: {trial:.2E}'.format(**locals()))
Xred = reduce_compute(trial, target_label, reactionModel, rmg,
reaction_system_index)
dev = np.abs((Xred - orig_conv) / orig_conv)
logging.info('Deviation: {dev:.2f}'.format(**locals()))
if dev > error or trial > tolmax:
break
tol = trial
trial = trial * incr
if tol == start:
logging.error('Starting value for tolerance was too high...')
return tol
def get(key):
"""
Searches for the shared variable to retrieve identified by the
parameter key.
"""
try:
data = shared.getConst(key)
return data
except KeyError, e:
logging.error('An object with the key {} could not be found.'.format(key))
raise e
def get(key):
"""
Searches for the shared variable to retrieve identified by the
parameter key.
"""
try:
data = shared.getConst(key)
return data
except KeyError, e:
logging.error(
'An object with the key {} could not be found.'.format(key))
raise e
def loadReductionInput(reductionFile):
"""
Load an reduction job from the input file located at `reductionFile`
"""
target = None
tolerance = -1
full_path = os.path.abspath(os.path.expandvars(reductionFile))
try:
f = open(full_path)
except IOError, e:
logging.error('The input file "{0}" could not be opened.'.format(full_path))
logging.info('Check that the file exists and that you have read access.')
raise e
def loadReductionInput(reductionFile):
"""
Load an reduction job from the input file located at `reductionFile`
"""
target = None
tolerance = -1
full_path = os.path.abspath(os.path.expandvars(reductionFile))
try:
f = open(full_path)
except IOError, e:
logging.error(
'The input file "{0}" could not be opened.'.format(full_path))
logging.info(
'Check that the file exists and that you have read access.')
raise e
def parallel(hosts_list, num_of_workers):
# Get a list of resources to launch worker(s) on
hosts = utils.getHosts(None, hosts_list)
external_hostname = [utils.externalHostname(hosts)]
# Launch SCOOP
print(sys.executable)
thisScoopApp = ScoopApp(
hosts=hosts,
n=num_of_workers,
b=1,
verbose=4,
python_executable=[sys.executable],
externalHostname=external_hostname[0],
executable="toRun.py",
arguments=None,
tunnel=False,
path="/home/martin/PycharmProjects/fineGrained/main/",
debug=False,
nice=None,
env=utils.getEnv(),
profile=None,
pythonPath=None,
prolog=None,
backend='ZMQ')
rootTaskExitCode = False
interruptPreventer = threading.Thread(target=thisScoopApp.close)
try:
rootTaskExitCode = thisScoopApp.run()
except Exception as e:
logger.error('Error while launching SCOOP subprocesses:' + str(e))
rootTaskExitCode = -1
finally:
# This should not be interrupted (ie. by a KeyboadInterrupt)
# The only cross-platform way to do it I found was by using a thread.
interruptPreventer.start()
interruptPreventer.join()
# Exit with the proper exit code
if rootTaskExitCode:
sys.exit(rootTaskExitCode)
def launch(hosts_list, num_of_workers, path, executable):
# Get a list of resources to launch worker(s) on
hosts = utils.getHosts(None, hosts_list)
external_hostname = [utils.externalHostname(hosts)]
# Launch SCOOP
app = ScoopApp(hosts=hosts,
n=num_of_workers,
b=1,
verbose=4,
python_executable=[sys.executable],
externalHostname=external_hostname[0],
executable=executable,
arguments=None,
tunnel=False,
path=path,
debug=False,
nice=None,
env=utils.getEnv(),
profile=None,
pythonPath=None,
prolog=None,
backend='ZMQ')
interrupt_prevent = threading.Thread(target=app.close)
try:
root_task_exit_code = app.run()
except Exception as e:
logger.error('Error while launching SCOOP subprocesses:' + str(e))
root_task_exit_code = -1
finally:
# This should not be interrupted (ie. by a KeyboadInterrupt)
# The only cross-platform way to do it I found was by using a thread.
interrupt_prevent.start()
interrupt_prevent.join()
# Exit with the proper exit code
print("exit code " + str(root_task_exit_code))
if root_task_exit_code:
sys.exit(root_task_exit_code)
import sys
#local imports
#global variables
reactions = None
try:
from scoop import shared
from scoop.futures import map as map_
from scoop import logger as logging
logging.setLevel(20)#10 : debug, 20: info
except ImportError:
map_ = map
import logging
logging.error('Import Error!')
from rmgpy.chemkin import getSpeciesIdentifier, loadChemkinFile
from rmgpy.rmg.main import RMG
from rmgpy.solver.base import TerminationTime, TerminationConversion
from workerwrapper import WorkerWrapper
"""
Guidelines for input:
- Do not use the annotated chemkin file as input!
-
"""
CLOSE_TO_ZERO = 1E-20
class ReductionReaction(object):
import sys
#local imports
#global variables
reactions = None
try:
from scoop import shared
from scoop.futures import map as map_
from scoop import logger as logging
logging.setLevel(20) #10 : debug, 20: info
except ImportError:
map_ = map
import logging
logging.error('Import Error!')
from rmgpy.chemkin import getSpeciesIdentifier, loadChemkinFile
from rmgpy.rmg.main import RMG
from rmgpy.solver.base import TerminationTime, TerminationConversion
from workerwrapper import WorkerWrapper
"""
Guidelines for input:
- Do not use the annotated chemkin file as input!
-
"""
CLOSE_TO_ZERO = 1E-20