def main():
name = 'L2L-FUN-GD'
try:
with open('bin/path.conf') as f:
root_dir_path = f.read().strip()
except FileNotFoundError:
raise FileNotFoundError(
"You have not set the root path to store your results."
" Write the path to a path.conf text file in the bin directory"
" before running the simulation")
paths = Paths(name, dict(run_no='test'), root_dir_path=root_dir_path)
print("All output logs can be found in directory ", paths.logs_path)
traj_file = os.path.join(paths.output_dir_path, 'data.h5')
# Create an environment that handles running our simulation
# This initializes an environment
env = Environment(
trajectory=name,
filename=traj_file,
file_title='{} data'.format(name),
comment='{} data'.format(name),
add_time=True,
freeze_input=True,
multiproc=True,
automatic_storing=True,
log_stdout=False, # Sends stdout to logs
)
create_shared_logger_data(logger_names=['bin', 'optimizers'],
log_levels=['INFO', 'INFO'],
log_to_consoles=[True, True],
sim_name=name,
log_directory=paths.logs_path)
configure_loggers()
# Get the trajectory from the environment
traj = env.trajectory
# Set JUBE params
traj.f_add_parameter_group("JUBE_params", "Contains JUBE parameters")
# Execution command
traj.f_add_parameter_to_group(
"JUBE_params", "exec", "python " +
os.path.join(paths.simulation_path, "run_files/run_optimizee.py"))
# Paths
traj.f_add_parameter_to_group("JUBE_params", "paths", paths)
## Benchmark function
function_id = 4
bench_functs = BenchmarkedFunctions()
(benchmark_name, benchmark_function), benchmark_parameters = \
bench_functs.get_function_by_index(function_id, noise=True)
optimizee_seed = 100
random_state = np.random.RandomState(seed=optimizee_seed)
function_tools.plot(benchmark_function, random_state)
## Innerloop simulator
optimizee = FunctionGeneratorOptimizee(traj,
benchmark_function,
seed=optimizee_seed)
#Prepare optimizee for jube runs
jube.prepare_optimizee(optimizee, paths.simulation_path)
##
## Outerloop optimizer initialization
# parameters = ClassicGDParameters(learning_rate=0.01, exploration_step_size=0.01,
# n_random_steps=5, n_iteration=100,
# stop_criterion=np.Inf)
# parameters = AdamParameters(learning_rate=0.01, exploration_step_size=0.01, n_random_steps=5, first_order_decay=0.8,
# second_order_decay=0.8, n_iteration=100, stop_criterion=np.Inf)
# parameters = StochasticGDParameters(learning_rate=0.01, stochastic_deviation=1, stochastic_decay=0.99,
# exploration_step_size=0.01, n_random_steps=5, n_iteration=100,
# stop_criterion=np.Inf)
parameters = RMSPropParameters(learning_rate=0.01,
exploration_step_size=0.01,
n_random_steps=5,
momentum_decay=0.5,
n_iteration=100,
stop_criterion=np.Inf,
seed=99)
optimizer = GradientDescentOptimizer(
traj,
optimizee_create_individual=optimizee.create_individual,
optimizee_fitness_weights=(0.1, ),
parameters=parameters,
optimizee_bounding_func=optimizee.bounding_func)
# Add post processing
env.add_postprocessing(optimizer.post_process)
# Run the simulation with all parameter combinations
env.run(optimizee.simulate)
## Outerloop optimizer end
optimizer.end(traj)
# Finally disable logging and close all log-files
env.disable_logging()
def main():
name = 'L2L-FunctionGenerator-PT'
try:
with open('bin/path.conf') as f:
root_dir_path = f.read().strip()
except FileNotFoundError:
raise FileNotFoundError(
"You have not set the root path to store your results."
" Write the path to a path.conf text file in the bin directory"
" before running the simulation")
paths = Paths(name, dict(run_no='test'), root_dir_path=root_dir_path)
print("All output logs can be found in directory ", paths.logs_path)
traj_file = os.path.join(paths.output_dir_path, 'data.h5')
# Create an environment that handles running our simulation
# This initializes an environment
env = Environment(
trajectory=name,
filename=traj_file,
file_title='{} data'.format(name),
comment='{} data'.format(name),
add_time=True,
# freeze_input=True,
# multiproc=True,
# use_scoop=True,
# wrap_mode=pypetconstants.WRAP_MODE_LOCAL,
automatic_storing=True,
log_stdout=False, # Sends stdout to logs
)
create_shared_logger_data(logger_names=['bin', 'optimizers'],
log_levels=['INFO', 'INFO'],
log_to_consoles=[True, True],
sim_name=name,
log_directory=paths.logs_path)
configure_loggers()
# Get the trajectory from the environment
traj = env.trajectory
## Benchmark function
function_id = 14
bench_functs = BenchmarkedFunctions()
(benchmark_name, benchmark_function), benchmark_parameters = \
bench_functs.get_function_by_index(function_id, noise=True)
optimizee_seed = 100
random_state = np.random.RandomState(seed=optimizee_seed)
function_tools.plot(benchmark_function, random_state)
## Innerloop simulator
optimizee = FunctionGeneratorOptimizee(traj,
benchmark_function,
seed=optimizee_seed)
#--------------------------------------------------------------------------
# configure settings for parallel tempering:
# for each of the parallel runs chose
# a cooling schedule
# an upper and lower temperature bound
# a decay parameter
#--------------------------------------------------------------------------
# specify the number of parallel running schedules. Each following container
# has to have an entry for each parallel run
n_parallel_runs = 5
# for detailed information on the cooling schedules see either the wiki or
# the documentaition in l2l.optimizers.paralleltempering.optimizer
cooling_schedules = [
AvailableCoolingSchedules.EXPONENTIAL_ADDAPTIVE,
AvailableCoolingSchedules.EXPONENTIAL_ADDAPTIVE,
AvailableCoolingSchedules.EXPONENTIAL_ADDAPTIVE,
AvailableCoolingSchedules.LINEAR_ADDAPTIVE,
AvailableCoolingSchedules.LINEAR_ADDAPTIVE
]
# has to be from 1 to 0, first entry hast to be larger than second
# represents the starting temperature and the ending temperature
temperature_bounds = [[0.8, 0], [0.7, 0], [0.6, 0], [1, 0.1], [0.9, 0.2]]
# decay parameter for each schedule. If needed can be different for each
# schedule
decay_parameters = np.full(n_parallel_runs, 0.99)
#--------------------------------------------------------------------------
# end of configuration
#--------------------------------------------------------------------------
# Check, if the temperature bounds and decay parameters are reasonable.
assert (
((temperature_bounds.all() <= 1) and (temperature_bounds.all() >= 0))
and (temperature_bounds[:, 0].all() > temperature_bounds[:, 1].all())
), print("Warning: Temperature bounds are not within specifications.")
assert ((decay_parameters.all() <= 1) and (decay_parameters.all() >= 0)
), print("Warning: Decay parameter not within specifications.")
## Outerloop optimizer initialization
parameters = ParallelTemperingParameters(
n_parallel_runs=n_parallel_runs,
noisy_step=.03,
n_iteration=1000,
stop_criterion=np.Inf,
seed=np.random.randint(1e5),
cooling_schedules=cooling_schedules,
temperature_bounds=temperature_bounds,
decay_parameters=decay_parameters)
optimizer = ParallelTemperingOptimizer(
traj,
optimizee_create_individual=optimizee.create_individual,
optimizee_fitness_weights=(-1, ),
parameters=parameters,
optimizee_bounding_func=optimizee.bounding_func)
# Add post processing
env.add_postprocessing(optimizer.post_process)
# Run the simulation with all parameter combinations
env.run(optimizee.simulate)
## Outerloop optimizer end
optimizer.end(traj)
# Finally disable logging and close all log-files
env.disable_logging()
def main():
name = 'L2L-FUN-GD'
try:
with open('bin/path.conf') as f:
root_dir_path = f.read().strip()
except FileNotFoundError:
raise FileNotFoundError(
"You have not set the root path to store your results."
" Write the path to a path.conf text file in the bin directory"
" before running the simulation")
paths = Paths(name, dict(run_no='test'), root_dir_path=root_dir_path)
print("All output logs can be found in directory ", paths.logs_path)
traj_file = os.path.join(paths.output_dir_path, 'data.h5')
# Create an environment that handles running our simulation
# This initializes an environment
env = Environment(
trajectory=name,
filename=traj_file,
file_title='{} data'.format(name),
comment='{} data'.format(name),
add_time=True,
freeze_input=True,
multiproc=True,
automatic_storing=True,
log_stdout=False, # Sends stdout to logs
)
create_shared_logger_data(logger_names=['bin', 'optimizers'],
log_levels=['INFO', 'INFO'],
log_to_consoles=[True, True],
sim_name=name,
log_directory=paths.logs_path)
configure_loggers()
# Get the trajectory from the environment
traj = env.trajectory
# Set JUBE params
traj.f_add_parameter_group("JUBE_params", "Contains JUBE parameters")
# Scheduler parameters
# Name of the scheduler
# traj.f_add_parameter_to_group("JUBE_params", "scheduler", "Slurm")
# Command to submit jobs to the schedulers
traj.f_add_parameter_to_group("JUBE_params", "submit_cmd", "sbatch")
# Template file for the particular scheduler
traj.f_add_parameter_to_group("JUBE_params", "job_file", "job.run")
# Number of nodes to request for each run
traj.f_add_parameter_to_group("JUBE_params", "nodes", "1")
# Requested time for the compute resources
traj.f_add_parameter_to_group("JUBE_params", "walltime", "00:01:00")
# MPI Processes per node
traj.f_add_parameter_to_group("JUBE_params", "ppn", "1")
# CPU cores per MPI process
traj.f_add_parameter_to_group("JUBE_params", "cpu_pp", "1")
# Threads per process
traj.f_add_parameter_to_group("JUBE_params", "threads_pp", "1")
# Type of emails to be sent from the scheduler
traj.f_add_parameter_to_group("JUBE_params", "mail_mode", "ALL")
# Email to notify events from the scheduler
traj.f_add_parameter_to_group("JUBE_params", "mail_address",
"*****@*****.**")
# Error file for the job
traj.f_add_parameter_to_group("JUBE_params", "err_file", "stderr")
# Output file for the job
traj.f_add_parameter_to_group("JUBE_params", "out_file", "stdout")
# JUBE parameters for multiprocessing. Relevant even without scheduler.
# MPI Processes per job
traj.f_add_parameter_to_group("JUBE_params", "tasks_per_job", "1")
# The execution command
traj.f_add_parameter_to_group(
"JUBE_params", "exec",
"mpirun python3 " + root_dir_path + "/run_files/run_optimizee.py")
# Ready file for a generation
traj.f_add_parameter_to_group("JUBE_params", "ready_file",
root_dir_path + "/readyfiles/ready_w_")
# Path where the job will be executed
traj.f_add_parameter_to_group("JUBE_params", "work_path", root_dir_path)
## Benchmark function
function_id = 4
bench_functs = BenchmarkedFunctions()
(benchmark_name, benchmark_function), benchmark_parameters = \
bench_functs.get_function_by_index(function_id, noise=True)
optimizee_seed = 100
random_state = np.random.RandomState(seed=optimizee_seed)
function_tools.plot(benchmark_function, random_state)
## Innerloop simulator
optimizee = FunctionGeneratorOptimizee(traj,
benchmark_function,
seed=optimizee_seed)
#Prepare optimizee for jube runs
jube.prepare_optimizee(optimizee, root_dir_path)
##
## Outerloop optimizer initialization
# parameters = ClassicGDParameters(learning_rate=0.01, exploration_step_size=0.01,
# n_random_steps=5, n_iteration=100,
# stop_criterion=np.Inf)
# parameters = AdamParameters(learning_rate=0.01, exploration_step_size=0.01, n_random_steps=5, first_order_decay=0.8,
# second_order_decay=0.8, n_iteration=100, stop_criterion=np.Inf)
# parameters = StochasticGDParameters(learning_rate=0.01, stochastic_deviation=1, stochastic_decay=0.99,
# exploration_step_size=0.01, n_random_steps=5, n_iteration=100,
# stop_criterion=np.Inf)
parameters = RMSPropParameters(learning_rate=0.01,
exploration_step_size=0.01,
n_random_steps=5,
momentum_decay=0.5,
n_iteration=100,
stop_criterion=np.Inf,
seed=99)
optimizer = GradientDescentOptimizer(
traj,
optimizee_create_individual=optimizee.create_individual,
optimizee_fitness_weights=(0.1, ),
parameters=parameters,
optimizee_bounding_func=optimizee.bounding_func)
# Add post processing
env.add_postprocessing(optimizer.post_process)
# Run the simulation with all parameter combinations
env.run(optimizee.simulate)
## Outerloop optimizer end
optimizer.end(traj)
# Finally disable logging and close all log-files
env.disable_logging()
def prepare_experiment(self, **kwargs):
"""
Prepare the experiment by creating the enviroment and
:param kwargs: optional dictionary, contains
- name: str, name of the run, Default: L2L-run
- trajectory_name: str, name of the trajectory, Default: trajectory
- log_stdout: bool, if stdout should be sent to logs, Default:False
- jube_parameter: dict, User specified parameter for jube.
See notes section for default jube parameter
- multiprocessing, bool, enable multiprocessing, Default: False
:return traj, trajectory object
:return all_jube_params, dict, a dictionary with all parameters for jube
given by the user and default ones
:notes
Default JUBE parameters are:
- scheduler: None,
- submit_cmd: sbatch,
- job_file: job.run,
- nodes: 1,
- walltime: 01:00:00,
- ppn: 1,
- cpu_pp: 1,
- threads_pp: 4,
- mail_mode: ALL,
- err_file: stderr,
- out_file: stdout,
- tasks_per_job: 1,
- exec: python3 + self.paths.simulation_path +
"run_files/run_optimizee.py"
- ready_file: self.paths.root_dir_path + "ready_files/ready_w_"
- work_path: self.paths.root_dir_path,
- paths_obj: self.paths
"""
name = kwargs.get('name', 'L2L-run')
if not os.path.isdir(self.root_dir_path):
os.mkdir(os.path.abspath(self.root_dir_path))
print('Created a folder at {}'.format(self.root_dir_path))
trajectory_name = kwargs.get('trajectory_name', 'trajectory')
self.paths = Paths(name, {},
root_dir_path=self.root_dir_path,
suffix="-" + trajectory_name)
print("All output logs can be found in directory ",
self.paths.logs_path)
# Create an environment that handles running our simulation
# This initializes an environment
self.env = Environment(
trajectory=trajectory_name,
filename=self.paths.output_dir_path,
file_title='{} data'.format(name),
comment='{} data'.format(name),
add_time=True,
automatic_storing=True,
log_stdout=kwargs.get('log_stdout', False), # Sends stdout to logs
multiprocessing=kwargs.get('multiprocessing', False))
create_shared_logger_data(logger_names=['bin', 'optimizers'],
log_levels=['INFO', 'INFO'],
log_to_consoles=[True, True],
sim_name=name,
log_directory=self.paths.logs_path)
configure_loggers()
# Get the trajectory from the environment
self.traj = self.env.trajectory
# Set JUBE params
default_jube_params = {
# "scheduler": "None",
"submit_cmd":
"sbatch",
"job_file":
"job.run",
"nodes":
"1",
"walltime":
"01:00:00",
"ppn":
"1",
"cpu_pp":
"1",
"threads_pp":
"4",
"mail_mode":
"ALL",
"err_file":
"stderr",
"out_file":
"stdout",
"tasks_per_job":
"1",
"exec":
"python3 " + os.path.join(self.paths.simulation_path,
"run_files/run_optimizee.py"),
"ready_file":
os.path.join(self.paths.root_dir_path, "ready_files/ready_w_"),
"work_path":
self.paths.root_dir_path,
"paths_obj":
self.paths,
}
# Will contain all jube parameters
all_jube_params = {}
self.traj.f_add_parameter_group("JUBE_params",
"Contains JUBE parameters")
# Go through the parameter dictionary and add to the trajectory
if kwargs.get('jube_parameter'):
for k, v in kwargs['jube_parameter'].items():
if k == "exec":
val = v + " " + os.path.join(self.paths.simulation_path,
"run_files/run_optimizee.py")
self.traj.f_add_parameter_to_group("JUBE_params", k, val)
all_jube_params[k] = val
else:
self.traj.f_add_parameter_to_group("JUBE_params", k, v)
all_jube_params[k] = v
# Default parameter are added if they are not already set by the user
for k, v in default_jube_params.items():
if kwargs.get('jube_parameter'):
if k not in kwargs.get('jube_parameter').keys():
self.traj.f_add_parameter_to_group("JUBE_params", k, v)
else:
self.traj.f_add_parameter_to_group("JUBE_params", k, v)
all_jube_params[k] = v
print('JUBE parameters used: {}'.format(all_jube_params))
return self.traj, all_jube_params
def main():
name = "FIT-TEMPS"
root_dir_path = os.path.dirname(os.path.abspath(sys.argv[0]))
paths = Paths(name, dict(run_num="test"), root_dir_path=root_dir_path)
print("All output logs can be found in directory ", paths.logs_path)
traj_file = os.path.join(paths.output_dir_path, "data.h5")
print(traj_file)
os.makedirs(paths.output_dir_path, exist_ok=True)
print("Trajectory file is: {}".format(traj_file))
trajectories = load_last_trajs(
os.path.join(paths.output_dir_path, 'per_gen_trajectories'))
if len(trajectories):
k = trajectories['generation']
traj = trajectories[k]
else:
traj = name
# Create an environment that handles running our simulation
# This initializes an environment
env = Environment(
trajectory=traj,
filename=traj_file,
file_title="{} data".format(name),
comment="{} data".format(name),
add_time=bool(1),
automatic_storing=bool(1),
log_stdout=bool(0), # Sends stdout to logs
multiprocessing=MULTIPROCESSING,
)
create_shared_logger_data(logger_names=["bin", "optimizers"],
log_levels=["INFO", "INFO"],
log_to_consoles=[True, True],
sim_name=name,
log_directory=paths.logs_path)
configure_loggers()
# trajectories = load_last_trajs(os.path.join(paths.root_dir_path,'trajectories'))
# env.trajectory.individuals[0] = trajectories
# Get the trajectory from the environment
traj = env.trajectory
if len(trajectories) == 0:
# Set JUBE params
traj.f_add_parameter_group("JUBE_params", "Contains JUBE parameters")
# Scheduler parameters
# Name of the scheduler
# traj.f_add_parameter_to_group("JUBE_params", "scheduler", "Slurm")
# Command to submit jobs to the schedulers
# traj.f_add_parameter_to_group("JUBE_params", "submit_cmd", "sbatch")
# Template file for the particular scheduler
traj.f_add_parameter_to_group("JUBE_params", "job_file", "job.run")
# Number of nodes to request for each run
traj.f_add_parameter_to_group("JUBE_params", "nodes", "1")
# Requested time for the compute resources
traj.f_add_parameter_to_group("JUBE_params", "walltime", "00:10:00")
# MPI Processes per node
traj.f_add_parameter_to_group("JUBE_params", "ppn", "1")
# CPU cores per MPI process
traj.f_add_parameter_to_group("JUBE_params", "cpu_pp", "1")
# Threads per process
traj.f_add_parameter_to_group("JUBE_params", "threads_pp", "1")
# Type of emails to be sent from the scheduler
traj.f_add_parameter_to_group("JUBE_params", "mail_mode", "ALL")
# Email to notify events from the scheduler
traj.f_add_parameter_to_group("JUBE_params", "mail_address",
"*****@*****.**")
# Error file for the job
traj.f_add_parameter_to_group("JUBE_params", "err_file", "stderr")
# Output file for the job
traj.f_add_parameter_to_group("JUBE_params", "out_file", "stdout")
# JUBE parameters for multiprocessing. Relevant even without scheduler.
# MPI Processes per job
traj.f_add_parameter_to_group("JUBE_params", "tasks_per_job", "1")
# The execution command
run_filename = os.path.join(paths.root_dir_path,
"run_files/run_optimizee.py")
command = "python3 {}".format(run_filename)
if ON_JEWELS and not USE_MPI:
# -N num nodes
# -t exec time (mins)
# -n num sub-procs
command = "srun -t 15 -N 1 -n 4 -c 1 --gres=gpu:1 {}".format(
command)
elif USE_MPI:
command = "MPIEXEC_TIMEOUT={} mpiexec -bind-to socket -np 1 {}".format(
60, command)
traj.f_add_parameter_to_group("JUBE_params", "exec", command)
# Ready file for a generation
traj.f_add_parameter_to_group(
"JUBE_params", "ready_file",
os.path.join(paths.root_dir_path, "readyfiles/ready_w_"))
# Path where the job will be executed
traj.f_add_parameter_to_group("JUBE_params", "work_path",
paths.root_dir_path)
### Maybe we should pass the Paths object to avoid defining paths here and there
traj.f_add_parameter_to_group("JUBE_params", "paths_obj", paths)
csv = open('./temperature/temperature-anomaly.csv', 'r')
temps = []
years = []
for i, line in enumerate(csv):
sp = line.split(',')
if sp[0] == 'Global':
temps.append(float(sp[3]))
years.append(float(sp[2]))
if sp[0].startswith('Northern'):
break
csv.close()
traj.f_add_parameter_group("simulation", "Contains JUBE parameters")
traj.f_add_parameter_to_group("simulation", 'target', temps) # ms
traj.f_add_parameter_to_group("simulation", 'years', years)
## Innerloop simulator
optimizee = FitOptimizee(traj, 1234)
# Prepare optimizee for jube runs
JUBE_runner.prepare_optimizee(optimizee, paths.root_dir_path)
_, dict_spec = dict_to_list(optimizee.create_individual(),
get_dict_spec=True)
# step_size = np.asarray([config.ATTR_STEPS[k] for (k, spec, length) in dict_spec])
fit_weights = [
1.0,
] # 0.1]
num_generations = 5000
population_size = 200
# population_size = 5
# if len(trajectories):
# traj.individuals = trajectories_to_individuals(
# trajectories, population_size, optimizee)
parameters = GeneticAlgorithmParameters(
seed=None,
popsize=population_size,
CXPB=0.5, # probability of mating 2 individuals
MUTPB=0.8, # probability of individual to mutate
NGEN=num_generations,
indpb=0.1, # probability of "gene" to mutate
tournsize=population_size, # number of best individuals to mate
matepar=0.5, # how much to mix two genes when mating
mutpar=1. #2.0/4.0, #standard deviations for normal distribution
)
optimizer = GeneticAlgorithmOptimizer(
traj,
optimizee_create_individual=optimizee.create_individual,
optimizee_fitness_weights=fit_weights,
parameters=parameters,
optimizee_bounding_func=optimizee.bounding_func,
percent_hall_of_fame=0.05,
percent_elite=0.5,
)
# Add post processing
### guess this is where we want to split results from multiple runs?
env.add_postprocessing(optimizer.post_process)
# Run the simulation with all parameter combinations
env.run(optimizee.simulate)
## Outerloop optimizer end
optimizer.end(traj)
# Finally disable logging and close all log-files
env.disable_logging()
def main():
name = 'L2L-FUN-GS'
try:
with open('bin/path.conf') as f:
root_dir_path = f.read().strip()
except FileNotFoundError:
raise FileNotFoundError(
"You have not set the root path to store your results."
" Write the path to a path.conf text file in the bin directory"
" before running the simulation"
)
paths = Paths(name, dict(run_no='test'), root_dir_path=root_dir_path)
print("All output logs can be found in directory ", paths.logs_path)
traj_file = os.path.join(paths.output_dir_path, 'data.h5')
# Create an environment that handles running our simulation
# This initializes an environment
env = Environment(trajectory=name, filename=traj_file, file_title='{} data'.format(name),
comment='{} data'.format(name),
add_time=True,
automatic_storing=True,
log_stdout=False, # Sends stdout to logs
)
create_shared_logger_data(logger_names=['bin', 'optimizers'],
log_levels=['INFO', 'INFO'],
log_to_consoles=[True, True],
sim_name=name,
log_directory=paths.logs_path)
configure_loggers()
# Get the trajectory from the environment
traj = env.trajectory
# Get the trajectory from the environment
traj = env.trajectory
# Set JUBE params
traj.f_add_parameter_group("JUBE_params", "Contains JUBE parameters")
# Execution command
traj.f_add_parameter_to_group("JUBE_params", "exec", "python " +
os.path.join(paths.simulation_path, "run_files/run_optimizee.py"))
# Paths
traj.f_add_parameter_to_group("JUBE_params", "paths", paths)
## Benchmark function
function_id = 4
bench_functs = BenchmarkedFunctions()
(benchmark_name, benchmark_function), benchmark_parameters = \
bench_functs.get_function_by_index(function_id, noise=True)
optimizee_seed = 100
random_state = np.random.RandomState(seed=optimizee_seed)
function_tools.plot(benchmark_function, random_state)
## Innerloop simulator
optimizee = FunctionGeneratorOptimizee(traj, benchmark_function, seed=optimizee_seed)
# Prepare optimizee for jube runs
jube.prepare_optimizee(optimizee, paths.simulation_path)
## Outerloop optimizer initialization
n_grid_divs_per_axis = 30
parameters = GridSearchParameters(param_grid={
'coords': (optimizee.bound[0], optimizee.bound[1], n_grid_divs_per_axis)
})
optimizer = GridSearchOptimizer(traj, optimizee_create_individual=optimizee.create_individual,
optimizee_fitness_weights=(-0.1,),
parameters=parameters)
# Add post processing
env.add_postprocessing(optimizer.post_process)
# Run the simulation with all parameter combinations
env.run(optimizee.simulate)
## Outerloop optimizer end
optimizer.end(traj)
# Finally disable logging and close all log-files
env.disable_logging()
def run_experiment():
name = 'L2L-MNIST-ES'
try:
with open('bin/path.conf') as f:
root_dir_path = f.read().strip()
except FileNotFoundError:
raise FileNotFoundError(
"You have not set the root path to store your results."
" Write the path to a path.conf text file in the bin directory"
" before running the simulation")
trajectory_name = 'small-mnist-full-monty-100-hidden'
paths = Paths(name,
dict(run_num='test'),
root_dir_path=root_dir_path,
suffix="-" + trajectory_name)
print("All output logs can be found in directory ", paths.logs_path)
# Create an environment that handles running our simulation
# This initializes an environment
env = Environment(
trajectory=trajectory_name,
filename=paths.output_dir_path,
file_title='{} data'.format(name),
comment='{} data'.format(name),
add_time=True,
automatic_storing=True,
log_stdout=False, # Sends stdout to logs
)
create_shared_logger_data(logger_names=['bin', 'optimizers'],
log_levels=['INFO', 'INFO'],
log_to_consoles=[True, True],
sim_name=name,
log_directory=paths.logs_path)
configure_loggers()
# Get the trajectory from the environment
traj = env.trajectory
optimizee_seed = 200
optimizee_parameters = MNISTOptimizeeParameters(n_hidden=10,
seed=optimizee_seed,
use_small_mnist=True)
## Innerloop simulator
optimizee = MNISTOptimizee(traj, optimizee_parameters)
logger.info("Optimizee parameters: %s", optimizee_parameters)
## Outerloop optimizer initialization
optimizer_seed = 1234
optimizer_parameters = EvolutionStrategiesParameters(
learning_rate=0.1,
noise_std=0.1,
mirrored_sampling_enabled=True,
fitness_shaping_enabled=True,
pop_size=20,
n_iteration=2000,
stop_criterion=np.Inf,
seed=optimizer_seed)
logger.info("Optimizer parameters: %s", optimizer_parameters)
optimizer = EvolutionStrategiesOptimizer(
traj,
optimizee_create_individual=optimizee.create_individual,
optimizee_fitness_weights=(1., ),
parameters=optimizer_parameters,
optimizee_bounding_func=optimizee.bounding_func)
# Add post processing
env.add_postprocessing(optimizer.post_process)
# Run the simulation with all parameter combinations
env.run(optimizee.simulate)
# Finally disable logging and close all log-files
env.disable_logging()
return traj.v_storage_service.filename, traj.v_name, paths
def main():
name = 'L2L-FUN-CE'
try:
with open('bin/path.conf') as f:
root_dir_path = f.read().strip()
except FileNotFoundError:
raise FileNotFoundError(
"You have not set the root path to store your results."
" Write the path to a path.conf text file in the bin directory"
" before running the simulation")
paths = Paths(name, dict(run_no='test'), root_dir_path=root_dir_path)
print("All output logs can be found in directory ", paths.logs_path)
traj_file = os.path.join(paths.output_dir_path, 'data.h5')
# Create an environment that handles running our simulation
# This initializes an environment
env = Environment(
trajectory=name,
filename=traj_file,
file_title='{} data'.format(name),
comment='{} data'.format(name),
add_time=True,
freeze_input=True,
multiproc=True,
automatic_storing=True,
log_stdout=False, # Sends stdout to logs
)
create_shared_logger_data(logger_names=['bin', 'optimizers'],
log_levels=['INFO', 'INFO'],
log_to_consoles=[True, True],
sim_name=name,
log_directory=paths.logs_path)
configure_loggers()
# Get the trajectory from the environment
traj = env.trajectory
function_id = 14
bench_functs = BenchmarkedFunctions()
(benchmark_name, benchmark_function), benchmark_parameters = \
bench_functs.get_function_by_index(function_id, noise=True)
optimizee_seed = 100
random_state = np.random.RandomState(seed=optimizee_seed)
function_tools.plot(benchmark_function, random_state)
## Innerloop simulator
optimizee = FunctionGeneratorOptimizee(traj,
benchmark_function,
seed=optimizee_seed)
## Outerloop optimizer initialization
parameters = CrossEntropyParameters(
pop_size=50,
rho=0.9,
smoothing=0.0,
temp_decay=0,
n_iteration=160,
distribution=NoisyBayesianGaussianMixture(
n_components=3,
noise_magnitude=1.,
noise_decay=0.9,
weight_concentration_prior=1.5),
stop_criterion=np.inf,
seed=103)
optimizer = CrossEntropyOptimizer(
traj,
optimizee_create_individual=optimizee.create_individual,
optimizee_fitness_weights=(-0.1, ),
parameters=parameters,
optimizee_bounding_func=optimizee.bounding_func)
# Add post processing
env.add_postprocessing(optimizer.post_process)
# Run the simulation with all parameter combinations
env.run(optimizee.simulate)
## Outerloop optimizer end
optimizer.end(traj)
# Finally disable logging and close all log-files
env.disable_logging()
def main():
name = 'L2L-FUNALL'
try:
with open('bin/path.conf') as f:
root_dir_path = f.read().strip()
except FileNotFoundError:
raise FileNotFoundError(
"You have not set the root path to store your results."
" Write the path to a path.conf text file in the bin directory"
" before running the simulation"
)
paths = Paths(name, dict(run_no='test'), root_dir_path=root_dir_path)
print("All output logs can be found in directory ", paths.logs_path)
traj_file = os.path.join(paths.output_dir_path, 'data.h5')
n_iterations = 100
# NOTE: Need to use lambdas here since we want the distributions within CE, FACE etc. optimizers to be reinitialized
# afresh each time since it seems like they are stateful.
optimizers = [
(CrossEntropyOptimizer,
lambda: CrossEntropyParameters(pop_size=50, rho=0.2, smoothing=0.0, temp_decay=0,
n_iteration=n_iterations,
distribution=NoisyGaussian(noise_decay=0.95, noise_bias=0.05))),
(FACEOptimizer,
lambda: FACEParameters(min_pop_size=20, max_pop_size=50, n_elite=10, smoothing=0.2, temp_decay=0,
n_iteration=n_iterations, distribution=Gaussian(), n_expand=5)),
(GradientDescentOptimizer,
lambda: RMSPropParameters(learning_rate=0.01, exploration_rate=0.01, n_random_steps=5, momentum_decay=0.5,
n_iteration=n_iterations, stop_criterion=np.Inf)),
(GradientDescentOptimizer,
lambda: ClassicGDParameters(learning_rate=0.01, exploration_rate=0.01, n_random_steps=5,
n_iteration=n_iterations, stop_criterion=np.Inf)),
(GradientDescentOptimizer,
lambda: AdamParameters(learning_rate=0.01, exploration_rate=0.01, n_random_steps=5, first_order_decay=0.8,
second_order_decay=0.8, n_iteration=n_iterations, stop_criterion=np.Inf)),
(GradientDescentOptimizer,
lambda: StochasticGDParameters(learning_rate=0.01, stochastic_deviation=1, stochastic_decay=0.99,
exploration_rate=0.01, n_random_steps=5, n_iteration=n_iterations,
stop_criterion=np.Inf))
]
# NOTE: Benchmark functions
bench_functs = BenchmarkedFunctions()
function_ids = range(len(bench_functs.function_name_map))
for function_id, (optimizer_class, optimizer_parameters_fn) in itertools.product(function_ids, optimizers):
logger.info("Running benchmark for %s optimizer and function id %d", optimizer_class, function_id)
optimizer_parameters = optimizer_parameters_fn()
# Create an environment that handles running our simulation
# This initializes an environment
env = Environment(trajectory=name, filename=traj_file, file_title='{} data'.format(name),
comment='{} data'.format(name),
# freeze_input=True,
# multiproc=True,
# use_scoop=True,
# wrap_mode=pypetconstants.WRAP_MODE_LOCAL,
add_time=True,
automatic_storing=True,
log_stdout=False, # Sends stdout to logs
)
create_shared_logger_data(logger_names=['bin', 'optimizers'],
log_levels=['INFO', 'INFO'],
log_to_consoles=[True, True],
sim_name=name,
log_directory=paths.logs_path)
configure_loggers()
# Get the trajectory from the environment
traj = env.trajectory
(benchmark_name, benchmark_function), benchmark_parameters = \
bench_functs.get_function_by_index(function_id, noise=True)
optimizee = FunctionGeneratorOptimizee(traj, benchmark_function)
optimizee_fitness_weights = -1.
# Gradient descent does descent!
if optimizer_class == GradientDescentOptimizer:
optimizee_fitness_weights = +1.
# Grid search optimizer input depends on optimizee!
elif optimizer_class == GridSearchOptimizer:
optimizer_parameters = GridSearchParameters(param_grid={
'coords': (optimizee.bound[0], optimizee.bound[1], 30)
})
optimizer = optimizer_class(traj, optimizee_create_individual=optimizee.create_individual,
optimizee_fitness_weights=(optimizee_fitness_weights,),
parameters=optimizer_parameters,
optimizee_bounding_func=optimizee.bounding_func)
# Add post processing
env.add_postprocessing(optimizer.post_process)
# Run the simulation with all parameter combinations
env.run(optimizee.simulate)
# NOTE: Outerloop optimizer end
optimizer.end(traj)
# Finally disable logging and close all log-files
env.disable_logging()
def run_experiment():
name = 'L2L-FUN-ES'
try:
with open('bin/path.conf') as f:
root_dir_path = f.read().strip()
except FileNotFoundError:
raise FileNotFoundError(
"You have not set the root path to store your results."
" Write the path to a path.conf text file in the bin directory"
" before running the simulation")
trajectory_name = 'mirroring-and-fitness-shaping'
paths = Paths(name,
dict(run_num='test'),
root_dir_path=root_dir_path,
suffix="-" + trajectory_name)
print("All output logs can be found in directory ", paths.logs_path)
# Create an environment that handles running our simulation
# This initializes an environment
env = Environment(
trajectory=trajectory_name,
filename=paths.output_dir_path,
file_title='{} data'.format(name),
comment='{} data'.format(name),
add_time=True,
automatic_storing=True,
log_stdout=False, # Sends stdout to logs
)
create_shared_logger_data(logger_names=['bin', 'optimizers'],
log_levels=['INFO', 'INFO'],
log_to_consoles=[True, True],
sim_name=name,
log_directory=paths.logs_path)
configure_loggers()
# Get the trajectory from the environment
traj = env.trajectory
# Set JUBE params
traj.f_add_parameter_group("JUBE_params", "Contains JUBE parameters")
traj.f_add_parameter_to_group(
"JUBE_params", "exec", "python " +
os.path.join(paths.simulation_path, "run_files/run_optimizee.py"))
# Paths
traj.f_add_parameter_to_group("JUBE_params", "paths", paths)
## Benchmark function
function_id = 14
bench_functs = BenchmarkedFunctions()
(benchmark_name, benchmark_function), benchmark_parameters = \
bench_functs.get_function_by_index(function_id, noise=True)
optimizee_seed = 200
random_state = np.random.RandomState(seed=optimizee_seed)
function_tools.plot(benchmark_function, random_state)
## Innerloop simulator
optimizee = FunctionGeneratorOptimizee(traj,
benchmark_function,
seed=optimizee_seed)
# Prepare optimizee for jube runs
jube.prepare_optimizee(optimizee, paths.simulation_path)
## Outerloop optimizer initialization
optimizer_seed = 1234
parameters = EvolutionStrategiesParameters(learning_rate=0.1,
noise_std=1.0,
mirrored_sampling_enabled=True,
fitness_shaping_enabled=True,
pop_size=20,
n_iteration=1000,
stop_criterion=np.Inf,
seed=optimizer_seed)
optimizer = EvolutionStrategiesOptimizer(
traj,
optimizee_create_individual=optimizee.create_individual,
optimizee_fitness_weights=(-1., ),
parameters=parameters,
optimizee_bounding_func=optimizee.bounding_func)
# Add post processing
env.add_postprocessing(optimizer.post_process)
# Run the simulation with all parameter combinations
env.run(optimizee.simulate)
## Outerloop optimizer end
optimizer.end(traj)
# Finally disable logging and close all log-files
env.disable_logging()
return traj.v_storage_service.filename, traj.v_name, paths
def main():
# TODO when using the template: Give some *meaningful* name here
name = 'L2L'
# TODO when using the template: make a path.conf file and write the root path there
try:
with open('bin/path.conf') as f:
root_dir_path = f.read().strip()
except FileNotFoundError:
raise FileNotFoundError(
"You have not set the root path to store your results."
" Write the path to a path.conf text file in the bin directory"
" before running the simulation"
)
paths = Paths(name, dict(run_no='test'), root_dir_path=root_dir_path)
# Load the logging config which tells us where and what to log (loglevel, destination)
print("All output logs can be found in directory ", paths.logs_path)
# Create an environment that handles running our simulation
# This initializes an environment. This environment is based on the Pypet implementation.
# Uncomment 'freeze_input', 'multipproc', 'use_scoop' and 'wrap_mode' lines to disable running the experiment
# across cores and nodes.
env = Environment(trajectory=name, filename=paths.output_dir_path, file_title='{} data'.format(name),
comment='{} data'.format(name),
add_time=True,
freeze_input=False,
multiproc=True,
automatic_storing=True,
log_stdout=False, # Sends stdout to logs
)
create_shared_logger_data(logger_names=['bin', 'optimizers'],
log_levels=['INFO', 'INFO'],
log_to_consoles=[True, True],
sim_name=name,
log_directory=paths.logs_path)
configure_loggers()
# Get the trajectory from the environment.
traj = env.trajectory
# Set JUBE params
traj.f_add_parameter_group("JUBE_params", "Contains JUBE parameters")
# Execution command
traj.f_add_parameter_to_group("JUBE_params", "exec", "python " +
os.path.join(paths.simulation_path, "run_files/run_optimizee.py"))
# Paths
traj.f_add_parameter_to_group("JUBE_params", "paths", paths)
# Scheduler parameters
# Name of the scheduler
traj.f_add_parameter_to_group("JUBE_params", "scheduler", "Slurm")
# Command to submit jobs to the schedulers
traj.f_add_parameter_to_group("JUBE_params", "submit_cmd", "sbatch")
# Template file for the particular scheduler
traj.f_add_parameter_to_group("JUBE_params", "job_file", "job.run")
# Number of nodes to request for each run
traj.f_add_parameter_to_group("JUBE_params", "nodes", "1")
# Requested time for the compute resources
traj.f_add_parameter_to_group("JUBE_params", "walltime", "00:01:00")
# Threads per process
traj.f_add_parameter_to_group("JUBE_params", "threads_pp", "1")
# Type of emails to be sent from the scheduler
traj.f_add_parameter_to_group("JUBE_params", "mail_mode", "ALL")
# Email to notify events from the scheduler
traj.f_add_parameter_to_group("JUBE_params", "mail_address", "*****@*****.**")
# Error file for the job
traj.f_add_parameter_to_group("JUBE_params", "err_file", "stderr")
# Output file for the job
traj.f_add_parameter_to_group("JUBE_params", "out_file", "stdout")
# JUBE parameters for multiprocessing.
# MPI Processes per job
traj.f_add_parameter_to_group("JUBE_params", "tasks_per_job", "1")
# MPI Processes per node
traj.f_add_parameter_to_group("JUBE_params", "ppn", "1")
# CPU cores per MPI process
traj.f_add_parameter_to_group("JUBE_params", "cpu_pp", "1")
## Innerloop simulator
# TODO when using the template: Change the optimizee to the appropriate Optimizee class
optimizee = Optimizee(traj)
# Prepare optimizee for jube runs
jube.prepare_optimizee(optimizee, paths.simulation_path)
## Outerloop optimizer initialization
# TODO when using the template: Change the optimizer to the appropriate Optimizer class
# and use the right value for optimizee_fitness_weights. Length is the number of dimensions of fitness, and
# negative value implies minimization and vice versa
optimizer_parameters = OptimizerParameters()
optimizer = Optimizer(traj, optimizee.create_individual, (1.0,), optimizer_parameters)
# Add post processing
env.add_postprocessing(optimizer.post_process)
# Run the simulation with all parameter combinations
env.run(optimizee.simulate)
## Outerloop optimizer end
optimizer.end(traj)
# Finally disable logging and close all log-files
env.disable_logging()
def run_experiment():
name = 'L2L-MNIST-CE'
try:
with open('bin/path.conf') as f:
root_dir_path = f.read().strip()
except FileNotFoundError:
raise FileNotFoundError("You have not set the root path to store your results."
" Write the path to a path.conf text file in the bin directory"
" before running the simulation")
trajectory_name = 'small-mnist-full-monty'
paths = Paths(name, dict(run_num='test'), root_dir_path=root_dir_path, suffix="-" + trajectory_name)
print("All output logs can be found in directory ", paths.logs_path)
# Create an environment that handles running our simulation
# This initializes an environment
env = Environment(
trajectory=trajectory_name,
filename=paths.output_dir_path,
file_title='{} data'.format(name),
comment='{} data'.format(name),
add_time=True,
automatic_storing=True,
log_stdout=False, # Sends stdout to logs
)
create_shared_logger_data(
logger_names=['bin', 'optimizers'],
log_levels=['INFO', 'INFO'],
log_to_consoles=[True, True],
sim_name=name,
log_directory=paths.logs_path)
configure_loggers()
# Get the trajectory from the environment
traj = env.trajectory
# Set JUBE params
traj.f_add_parameter_group("JUBE_params", "Contains JUBE parameters")
# Scheduler parameters
# Name of the scheduler
# traj.f_add_parameter_to_group("JUBE_params", "scheduler", "Slurm")
# Command to submit jobs to the schedulers
traj.f_add_parameter_to_group("JUBE_params", "submit_cmd", "sbatch")
# Template file for the particular scheduler
traj.f_add_parameter_to_group("JUBE_params", "job_file", "job.run")
# Number of nodes to request for each run
traj.f_add_parameter_to_group("JUBE_params", "nodes", "1")
# Requested time for the compute resources
traj.f_add_parameter_to_group("JUBE_params", "walltime", "00:01:00")
# MPI Processes per node
traj.f_add_parameter_to_group("JUBE_params", "ppn", "1")
# CPU cores per MPI process
traj.f_add_parameter_to_group("JUBE_params", "cpu_pp", "1")
# Threads per process
traj.f_add_parameter_to_group("JUBE_params", "threads_pp", "1")
# Type of emails to be sent from the scheduler
traj.f_add_parameter_to_group("JUBE_params", "mail_mode", "ALL")
# Email to notify events from the scheduler
traj.f_add_parameter_to_group("JUBE_params", "mail_address", "*****@*****.**")
# Error file for the job
traj.f_add_parameter_to_group("JUBE_params", "err_file", "stderr")
# Output file for the job
traj.f_add_parameter_to_group("JUBE_params", "out_file", "stdout")
# JUBE parameters for multiprocessing. Relevant even without scheduler.
# MPI Processes per job
traj.f_add_parameter_to_group("JUBE_params", "tasks_per_job", "1")
# The execution command
traj.f_add_parameter_to_group("JUBE_params", "exec", "mpirun python3 " + root_dir_path +
"/run_files/run_optimizee.py")
# Ready file for a generation
traj.f_add_parameter_to_group("JUBE_params", "ready_file", root_dir_path + "/readyfiles/ready_w_")
# Path where the job will be executed
traj.f_add_parameter_to_group("JUBE_params", "work_path", root_dir_path)
optimizee_seed = 200
optimizee_parameters = MNISTOptimizeeParameters(n_hidden=10, seed=optimizee_seed, use_small_mnist=True)
## Innerloop simulator
optimizee = MNISTOptimizee(traj, optimizee_parameters)
# Prepare optimizee for jube runs
jube.prepare_optimizee(optimizee, root_dir_path)
logger.info("Optimizee parameters: %s", optimizee_parameters)
## Outerloop optimizer initialization
optimizer_seed = 1234
optimizer_parameters = CrossEntropyParameters(pop_size=40, rho=0.9, smoothing=0.0, temp_decay=0, n_iteration=5000,
distribution=NoisyGaussian(noise_magnitude=1., noise_decay=0.99),
stop_criterion=np.inf, seed=optimizer_seed)
logger.info("Optimizer parameters: %s", optimizer_parameters)
optimizer = CrossEntropyOptimizer(traj, optimizee_create_individual=optimizee.create_individual,
optimizee_fitness_weights=(1.,),
parameters=optimizer_parameters,
optimizee_bounding_func=optimizee.bounding_func)
# Add post processing
env.add_postprocessing(optimizer.post_process)
# Run the simulation with all parameter combinations
env.run(optimizee.simulate)
## Outerloop optimizer end
optimizer.end(traj)
# Finally disable logging and close all log-files
env.disable_logging()
return traj.v_storage_service.filename, traj.v_name, paths
def main():
name = 'L2L-FunctionGenerator-SA'
try:
with open('bin/path.conf') as f:
root_dir_path = f.read().strip()
except FileNotFoundError:
raise FileNotFoundError(
"You have not set the root path to store your results."
" Write the path to a path.conf text file in the bin directory"
" before running the simulation")
paths = Paths(name, dict(run_no='test'), root_dir_path=root_dir_path)
print("All output logs can be found in directory ", paths.logs_path)
traj_file = os.path.join(paths.output_dir_path, 'data.h5')
# Create an environment that handles running our simulation
# This initializes an environment
env = Environment(
trajectory=name,
filename=traj_file,
file_title='{} data'.format(name),
comment='{} data'.format(name),
add_time=True,
# freeze_input=True,
# multiproc=True,
# use_scoop=True,
# wrap_mode=pypetconstants.WRAP_MODE_LOCAL,
automatic_storing=True,
log_stdout=False, # Sends stdout to logs
)
create_shared_logger_data(logger_names=['bin', 'optimizers'],
log_levels=['INFO', 'INFO'],
log_to_consoles=[True, True],
sim_name=name,
log_directory=paths.logs_path)
configure_loggers()
# Get the trajectory from the environment
traj = env.trajectory
# Set JUBE params
traj.f_add_parameter_group("JUBE_params", "Contains JUBE parameters")
# Execution command
traj.f_add_parameter_to_group(
"JUBE_params", "exec", "python " +
os.path.join(paths.simulation_path, "run_files/run_optimizee.py"))
# Paths
traj.f_add_parameter_to_group("JUBE_params", "paths", paths)
## Benchmark function
function_id = 14
bench_functs = BenchmarkedFunctions()
(benchmark_name, benchmark_function), benchmark_parameters = \
bench_functs.get_function_by_index(function_id, noise=True)
optimizee_seed = 100
random_state = np.random.RandomState(seed=optimizee_seed)
function_tools.plot(benchmark_function, random_state)
## Innerloop simulator
optimizee = FunctionGeneratorOptimizee(traj,
benchmark_function,
seed=optimizee_seed)
#Prepare optimizee for jube runs
jube.prepare_optimizee(optimizee, paths.simulation_path)
## Outerloop optimizer initialization
parameters = SimulatedAnnealingParameters(
n_parallel_runs=50,
noisy_step=.03,
temp_decay=.99,
n_iteration=100,
stop_criterion=np.Inf,
seed=np.random.randint(1e5),
cooling_schedule=AvailableCoolingSchedules.QUADRATIC_ADDAPTIVE)
optimizer = SimulatedAnnealingOptimizer(
traj,
optimizee_create_individual=optimizee.create_individual,
optimizee_fitness_weights=(-1, ),
parameters=parameters,
optimizee_bounding_func=optimizee.bounding_func)
# Add post processing
env.add_postprocessing(optimizer.post_process)
# Run the simulation with all parameter combinations
env.run(optimizee.simulate)
## Outerloop optimizer end
optimizer.end(traj)
# Finally disable logging and close all log-files
env.disable_logging()
def run_experiment():
name = 'L2L-FUN-ES'
try:
with open('bin/path.conf') as f:
root_dir_path = f.read().strip()
except FileNotFoundError:
raise FileNotFoundError(
"You have not set the root path to store your results."
" Write the path to a path.conf text file in the bin directory"
" before running the simulation")
trajectory_name = 'mirroring-and-fitness-shaping'
paths = Paths(name,
dict(run_num='test'),
root_dir_path=root_dir_path,
suffix="-" + trajectory_name)
print("All output logs can be found in directory ", paths.logs_path)
# Create an environment that handles running our simulation
# This initializes an environment
env = Environment(
trajectory=trajectory_name,
filename=paths.output_dir_path,
file_title='{} data'.format(name),
comment='{} data'.format(name),
add_time=True,
automatic_storing=True,
log_stdout=False, # Sends stdout to logs
)
create_shared_logger_data(logger_names=['bin', 'optimizers'],
log_levels=['INFO', 'INFO'],
log_to_consoles=[True, True],
sim_name=name,
log_directory=paths.logs_path)
configure_loggers()
# Get the trajectory from the environment
traj = env.trajectory
# Set JUBE params
traj.f_add_parameter_group("JUBE_params", "Contains JUBE parameters")
# Scheduler parameters
# Name of the scheduler
# traj.f_add_parameter_to_group("JUBE_params", "scheduler", "Slurm")
# Command to submit jobs to the schedulers
traj.f_add_parameter_to_group("JUBE_params", "submit_cmd", "sbatch")
# Template file for the particular scheduler
traj.f_add_parameter_to_group("JUBE_params", "job_file", "job.run")
# Number of nodes to request for each run
traj.f_add_parameter_to_group("JUBE_params", "nodes", "1")
# Requested time for the compute resources
traj.f_add_parameter_to_group("JUBE_params", "walltime", "00:01:00")
# MPI Processes per node
traj.f_add_parameter_to_group("JUBE_params", "ppn", "1")
# CPU cores per MPI process
traj.f_add_parameter_to_group("JUBE_params", "cpu_pp", "1")
# Threads per process
traj.f_add_parameter_to_group("JUBE_params", "threads_pp", "1")
# Type of emails to be sent from the scheduler
traj.f_add_parameter_to_group("JUBE_params", "mail_mode", "ALL")
# Email to notify events from the scheduler
traj.f_add_parameter_to_group("JUBE_params", "mail_address",
"*****@*****.**")
# Error file for the job
traj.f_add_parameter_to_group("JUBE_params", "err_file", "stderr")
# Output file for the job
traj.f_add_parameter_to_group("JUBE_params", "out_file", "stdout")
# JUBE parameters for multiprocessing. Relevant even without scheduler.
# MPI Processes per job
traj.f_add_parameter_to_group("JUBE_params", "tasks_per_job", "1")
# The execution command
traj.f_add_parameter_to_group(
"JUBE_params", "exec", "python " +
os.path.join(paths.root_dir_path, "run_files/run_optimizee.py"))
# Ready file for a generation
traj.f_add_parameter_to_group(
"JUBE_params", "ready_file",
os.path.join(paths.root_dir_path, "ready_files/ready_w_"))
# Path where the job will be executed
traj.f_add_parameter_to_group("JUBE_params", "work_path",
paths.root_dir_path)
### Maybe we should pass the Paths object to avoid defining paths here and there
traj.f_add_parameter_to_group("JUBE_params", "paths_obj", paths)
## Benchmark function
function_id = 14
bench_functs = BenchmarkedFunctions()
(benchmark_name, benchmark_function), benchmark_parameters = \
bench_functs.get_function_by_index(function_id, noise=True)
optimizee_seed = 200
random_state = np.random.RandomState(seed=optimizee_seed)
function_tools.plot(benchmark_function, random_state)
## Innerloop simulator
optimizee = FunctionGeneratorOptimizee(traj,
benchmark_function,
seed=optimizee_seed)
# Prepare optimizee for jube runs
jube.prepare_optimizee(optimizee, paths.root_dir_path)
## Outerloop optimizer initialization
optimizer_seed = 1234
parameters = EvolutionStrategiesParameters(learning_rate=0.1,
noise_std=1.0,
mirrored_sampling_enabled=True,
fitness_shaping_enabled=True,
pop_size=20,
n_iteration=1000,
stop_criterion=np.Inf,
seed=optimizer_seed)
optimizer = EvolutionStrategiesOptimizer(
traj,
optimizee_create_individual=optimizee.create_individual,
optimizee_fitness_weights=(-1., ),
parameters=parameters,
optimizee_bounding_func=optimizee.bounding_func)
# Add post processing
env.add_postprocessing(optimizer.post_process)
# Run the simulation with all parameter combinations
env.run(optimizee.simulate)
## Outerloop optimizer end
optimizer.end(traj)
# Finally disable logging and close all log-files
env.disable_logging()
return traj.v_storage_service.filename, traj.v_name, paths
def main():
name = "L2L-OMNIGLOT"
root_dir_path = os.path.dirname(os.path.abspath(sys.argv[0]))
paths = Paths(name, dict(run_num="test"), root_dir_path=root_dir_path)
print("All output logs can be found in directory ", paths.logs_path)
traj_file = os.path.join(paths.output_dir_path, "data.h5")
os.makedirs(paths.output_dir_path, exist_ok=True)
print("Trajectory file is: {}".format(traj_file))
trajectories = load_last_trajs(
os.path.join(paths.output_dir_path, 'per_gen_trajectories'))
if len(trajectories):
k = trajectories['generation']
traj = trajectories[k]
else:
traj = name
# Create an environment that handles running our simulation
# This initializes an environment
env = Environment(
trajectory=traj,
filename=traj_file,
file_title="{} data".format(name),
comment="{} data".format(name),
add_time=bool(1),
automatic_storing=bool(1),
log_stdout=bool(0), # Sends stdout to logs
multiprocessing=MULTIPROCESSING,
)
create_shared_logger_data(logger_names=["bin", "optimizers"],
log_levels=["INFO", "INFO"],
log_to_consoles=[True, True],
sim_name=name,
log_directory=paths.logs_path)
configure_loggers()
# Get the trajectory from the environment
traj = env.trajectory
# Set JUBE params
traj.f_add_parameter_group("JUBE_params", "Contains JUBE parameters")
# Scheduler parameters
# Name of the scheduler
# traj.f_add_parameter_to_group("JUBE_params", "scheduler", "Slurm")
# Command to submit jobs to the schedulers
# traj.f_add_parameter_to_group("JUBE_params", "submit_cmd", "sbatch")
# Template file for the particular scheduler
traj.f_add_parameter_to_group("JUBE_params", "job_file", "job.run")
# Number of nodes to request for each run
traj.f_add_parameter_to_group("JUBE_params", "nodes", "1")
# Requested time for the compute resources
traj.f_add_parameter_to_group("JUBE_params", "walltime", "00:01:00")
# MPI Processes per node
traj.f_add_parameter_to_group("JUBE_params", "ppn", "1")
# CPU cores per MPI process
traj.f_add_parameter_to_group("JUBE_params", "cpu_pp", "1")
# Threads per process
traj.f_add_parameter_to_group("JUBE_params", "threads_pp", "1")
# Type of emails to be sent from the scheduler
traj.f_add_parameter_to_group("JUBE_params", "mail_mode", "ALL")
# Email to notify events from the scheduler
traj.f_add_parameter_to_group("JUBE_params", "mail_address",
"*****@*****.**")
# Error file for the job
traj.f_add_parameter_to_group("JUBE_params", "err_file", "stderr")
# Output file for the job
traj.f_add_parameter_to_group("JUBE_params", "out_file", "stdout")
# JUBE parameters for multiprocessing. Relevant even without scheduler.
# MPI Processes per job
traj.f_add_parameter_to_group("JUBE_params", "tasks_per_job", "1")
# The execution command
run_filename = os.path.join(paths.root_dir_path, "run_files",
"run_optimizee.py")
command = "python3 {}".format(run_filename)
if ON_JEWELS and not USE_MPI:
# -N num nodes
# -t exec time (mins)
# -n num sub-procs
command = "srun -n 1 -c {} --gres=gpu:1 {}".format(NUM_SIMS, command)
elif USE_MPI:
# -timeout <seconds>
# command = "MPIEXEC_TIMEOUT={} "
# "mpiexec -bind-to socket -np 1 {}".format(60*240, command)
command = "mpiexec -bind-to socket -np 1 {}".format(command)
traj.f_add_parameter_to_group("JUBE_params", "exec", command)
# Ready file for a generation
traj.f_add_parameter_to_group(
"JUBE_params", "ready_file",
os.path.join(paths.root_dir_path, "readyfiles/ready_w_"))
# Path where the job will be executed
traj.f_add_parameter_to_group("JUBE_params", "work_path",
paths.root_dir_path)
# Maybe we should pass the Paths object to avoid
# defining paths here and there
traj.f_add_parameter_to_group("JUBE_params", "paths_obj", paths)
traj.f_add_parameter_group("simulation", "Contains JUBE parameters")
traj.f_add_parameter_to_group("simulation", 'num_sims', NUM_SIMS) # ms
traj.f_add_parameter_to_group("simulation", 'on_juwels', ON_JEWELS)
traj.f_add_parameter_to_group("simulation", 'steps', config.STEPS) # ms
traj.f_add_parameter_to_group("simulation", 'duration',
config.DURATION) # ms
traj.f_add_parameter_to_group("simulation", 'sample_dt',
config.SAMPLE_DT) # ms
traj.f_add_parameter_to_group(
"simulation", # rows, cols
'input_shape',
config.INPUT_SHAPE)
traj.f_add_parameter_to_group(
"simulation", # rows, cols
'input_divs',
config.INPUT_DIVS)
traj.f_add_parameter_to_group("simulation", 'input_layers',
config.N_INPUT_LAYERS)
traj.f_add_parameter_to_group("simulation", 'num_classes',
config.N_CLASSES)
traj.f_add_parameter_to_group("simulation", 'samples_per_class',
config.N_SAMPLES)
traj.f_add_parameter_to_group("simulation", 'test_per_class',
config.N_TEST)
traj.f_add_parameter_to_group("simulation", 'num_epochs', config.N_EPOCHS)
traj.f_add_parameter_to_group("simulation", 'total_per_class',
config.TOTAL_SAMPLES)
traj.f_add_parameter_to_group("simulation", 'kernel_width',
config.KERNEL_W)
traj.f_add_parameter_to_group("simulation", 'kernel_pad', config.PAD)
traj.f_add_parameter_to_group("simulation", 'output_size',
config.OUTPUT_SIZE)
traj.f_add_parameter_to_group("simulation", 'use_gabor',
config.USE_GABOR_LAYER)
# traj.f_add_parameter_to_group("simulation",
# 'expand', config.EXPANSION_RANGE[0])
# traj.f_add_parameter_to_group("simulation",
# 'conn_dist', config.CONN_DIST)
traj.f_add_parameter_to_group("simulation", 'prob_noise',
config.PROB_NOISE_SAMPLE)
traj.f_add_parameter_to_group("simulation", 'noisy_spikes_path',
paths.root_dir_path)
# db_path = '/home/gp283/brainscales-recognition/codebase/images_to_spikes/omniglot/spikes'
db_path = os.path.abspath('../omniglot_output_%d' % config.INPUT_SHAPE[0])
traj.f_add_parameter_to_group("simulation", 'spikes_path', db_path)
# dbs = [ name for name in os.listdir(db_path)
# if os.path.isdir(os.path.join(db_path, name)) ]
# print(dbs)
dbs = [
'Mkhedruli_-Georgian-', 'Tagalog',
'Ojibwe_-Canadian_Aboriginal_Syllabics-', 'Asomtavruli_-Georgian-',
'Balinese', 'Japanese_-katakana-', 'Malay_-Jawi_-_Arabic-', 'Armenian',
'Burmese_-Myanmar-', 'Arcadian', 'Futurama', 'Cyrillic',
'Alphabet_of_the_Magi', 'Sanskrit', 'Braille', 'Bengali',
'Inuktitut_-Canadian_Aboriginal_Syllabics-', 'Syriac_-Estrangelo-',
'Gujarati', 'Korean', 'Early_Aramaic', 'Japanese_-hiragana-',
'Anglo-Saxon_Futhorc', 'N_Ko', 'Grantha', 'Tifinagh',
'Blackfoot_-Canadian_Aboriginal_Syllabics-', 'Greek', 'Hebrew', 'Latin'
]
# dbs = ['Alphabet_of_the_Magi']
# dbs = ['Futurama']
# dbs = ['Latin']
# dbs = ['Braille']
# dbs = ['Blackfoot_-Canadian_Aboriginal_Syllabics-', 'Gujarati', 'Syriac_-Estrangelo-']
dbs = ['Futurama'] #, 'Braille']
# dbs = ['Cyrillic', 'Futurama', 'Braille']
if config.DEBUG:
dbs = ['Braille']
#dbs = ['Braille']
traj.f_add_parameter_to_group("simulation", 'database', dbs)
# Innerloop simulator
grad_desc = OPTIMIZER == GRADDESC
optimizee = OmniglotOptimizee(traj, 1234, grad_desc)
# Prepare optimizee for jube runs
JUBE_runner.prepare_optimizee(optimizee, paths.root_dir_path)
_, dict_spec = dict_to_list(optimizee.create_individual(),
get_dict_spec=True)
# step_size = np.asarray(
# [config.ATTR_STEPS[k] for (k, spec, length) in dict_spec])
step_size = tuple(
[config.ATTR_STEPS[k] for (k, spec, length) in dict_spec])
fit_weights = [
1.0,
] # 0.1]
optimizer_seed = config.SEED
if OPTIMIZER == GRADDESC:
n_random_steps = 100
n_iteration = 1000
parameters = RMSPropParameters(learning_rate=0.0001,
exploration_step_size=step_size,
n_random_steps=n_random_steps,
momentum_decay=0.5,
n_iteration=n_iteration,
stop_criterion=np.inf,
seed=optimizer_seed)
optimizer = GradientDescentOptimizer(
traj,
optimizee_create_individual=optimizee.create_individual,
optimizee_fitness_weights=fit_weights,
parameters=parameters,
optimizee_bounding_func=optimizee.bounding_func)
elif OPTIMIZER == EVOSTRAT:
parameters = EvolutionStrategiesParameters(
learning_rate=0.0001,
noise_std=step_size,
mirrored_sampling_enabled=True,
fitness_shaping_enabled=True,
pop_size=50, # couples
n_iteration=1000,
stop_criterion=np.inf,
seed=optimizer_seed)
optimizer = EvolutionStrategiesOptimizer(
traj,
optimizee_create_individual=optimizee.create_individual,
optimizee_fitness_weights=fit_weights,
parameters=parameters,
optimizee_bounding_func=optimizee.bounding_func)
else:
num_generations = 1000
if ON_JEWELS:
nodes = 12
gpus_per_node = 4
population_size = gpus_per_node * nodes
else:
population_size = 20
#population_size = 5
# population_size = 5
p_hof = 0.2 if population_size < 50 else 0.1
p_bob = 0.2
# last_trajs = load_last_trajs(os.path.join(
# paths.output_dir_path, 'per_gen_trajectories'))
# last_trajs = load_last_trajs(os.path.join(
# paths.root_dir_path, 'trajectories'))
# if len(last_trajs):
# traj.individuals = trajectories_to_individuals(
# last_trajs, population_size, optimizee)
attr_steps = [config.ATTR_STEPS[k[0]] for k in dict_spec]
parameters = GeneticAlgorithmParameters(
seed=optimizer_seed,
popsize=population_size,
CXPB=0.5, # probability of mating 2 individuals
# note: moved from 0.8 to 0.6 mutpb to see if it removes bouncing
MUTPB=0.7, # probability of individual to mutate
NGEN=num_generations,
indpb=0.1, # probability of "gene" to mutate
# number of best individuals to mate
tournsize=population_size,
matepar=0.5, # how much to mix two genes when mating
# standard deviations for normal distribution
mutpar=attr_steps,
)
optimizer = GeneticAlgorithmOptimizer(
traj,
optimizee_create_individual=optimizee.create_individual,
optimizee_fitness_weights=fit_weights,
parameters=parameters,
optimizee_bounding_func=optimizee.bounding_func,
percent_hall_of_fame=p_hof,
percent_elite=p_bob,
)
# Add post processing
env.add_postprocessing(optimizer.post_process)
# Run the simulation with all parameter combinations
env.run(optimizee.simulate)
# Outerloop optimizer end
optimizer.end(traj)
# Finally disable logging and close all log-files
env.disable_logging()
def run_experiment():
name = 'L2L-MNIST-CE'
try:
with open('bin/path.conf') as f:
root_dir_path = f.read().strip()
except FileNotFoundError:
raise FileNotFoundError(
"You have not set the root path to store your results."
" Write the path to a path.conf text file in the bin directory"
" before running the simulation")
trajectory_name = 'small-mnist-full-monty'
paths = Paths(name,
dict(run_num='test'),
root_dir_path=root_dir_path,
suffix="-" + trajectory_name)
print("All output logs can be found in directory ", paths.logs_path)
# Create an environment that handles running our simulation
# This initializes an environment
env = Environment(
trajectory=trajectory_name,
filename=paths.output_dir_path,
file_title='{} data'.format(name),
comment='{} data'.format(name),
add_time=True,
automatic_storing=True,
log_stdout=False, # Sends stdout to logs
)
create_shared_logger_data(logger_names=['bin', 'optimizers'],
log_levels=['INFO', 'INFO'],
log_to_consoles=[True, True],
sim_name=name,
log_directory=paths.logs_path)
configure_loggers()
# Get the trajectory from the environment
traj = env.trajectory
# Set JUBE params
traj.f_add_parameter_group("JUBE_params", "Contains JUBE parameters")
# Execution command
traj.f_add_parameter_to_group(
"JUBE_params", "exec", "python " +
os.path.join(paths.simulation_path, "run_files/run_optimizee.py"))
# Paths
traj.f_add_parameter_to_group("JUBE_params", "paths", paths)
optimizee_seed = 200
optimizee_parameters = MNISTOptimizeeParameters(n_hidden=10,
seed=optimizee_seed,
use_small_mnist=True)
## Innerloop simulator
optimizee = MNISTOptimizee(traj, optimizee_parameters)
# Prepare optimizee for jube runs
jube.prepare_optimizee(optimizee, paths.simulation_path)
logger.info("Optimizee parameters: %s", optimizee_parameters)
## Outerloop optimizer initialization
optimizer_seed = 1234
optimizer_parameters = CrossEntropyParameters(pop_size=40,
rho=0.9,
smoothing=0.0,
temp_decay=0,
n_iteration=5000,
distribution=NoisyGaussian(
noise_magnitude=1.,
noise_decay=0.99),
stop_criterion=np.inf,
seed=optimizer_seed)
logger.info("Optimizer parameters: %s", optimizer_parameters)
optimizer = CrossEntropyOptimizer(
traj,
optimizee_create_individual=optimizee.create_individual,
optimizee_fitness_weights=(1., ),
parameters=optimizer_parameters,
optimizee_bounding_func=optimizee.bounding_func)
# Add post processing
env.add_postprocessing(optimizer.post_process)
# Run the simulation with all parameter combinations
env.run(optimizee.simulate)
## Outerloop optimizer end
optimizer.end(traj)
# Finally disable logging and close all log-files
env.disable_logging()
return traj.v_storage_service.filename, traj.v_name, paths
