def compress_nested_container(u_container):
if isinstance(u_container, dict):
cdict = {}
for key, value in items(u_container):
if isinstance(value, dict) or isinstance(value, list):
cdict[key] = compress_nested_container(value)
else:
if isinstance(value, np.ndarray):
cdict[key] = compress_array(value)
else:
cdict[key] = value
return cdict
elif isinstance(u_container, list):
clist = []
for value in u_container:
if isinstance(value, dict) or isinstance(value, list):
clist.append(compress_nested_container(value))
else:
if isinstance(value, np.ndarray):
clist.append(compress_array(value))
else:
clist.append(value)
return clist
def to_unit(self, V):
if V.shape[0] == 0:
return np.array([])
if V.ndim == 1:
V = V[None, :]
squeeze = True
else:
squeeze = False
U = np.zeros(V.shape)
for name, variable in items(self.variables_meta):
indices = variable['indices']
if variable['type'] == 'int':
vals = V[:, indices]
U[:, indices] = self.int_to_unit(vals, variable['min'],
variable['max'])
elif variable['type'] == 'float':
vals = V[:, indices]
U[:, indices] = self.float_to_unit(vals, variable['min'],
variable['max'])
elif variable['type'] == 'enum':
for ind in indices:
U[:,
ind] = V[:,
ind] # Assumed to already be stored in a 1-hot encoding
else:
raise Exception("Unknown variable type.")
if squeeze:
U = np.squeeze(U)
return U
def paramify_and_print(self,
data_vector,
left_indent=0,
indent_top_row=False):
params = self.paramify(data_vector)
indentation = ' ' * left_indent
if indent_top_row:
sys.stderr.write(indentation)
sys.stderr.write('NAME TYPE VALUE\n')
sys.stderr.write(indentation)
sys.stderr.write('---- ---- -----\n')
for param_name, param in items(params):
if param['type'] == 'float':
format_str = '%s%-12.12s %-9.9s %-12f\n'
elif param['type'] == 'enum':
format_str = '%s%-12.12s %-9.9s %-12s\n'
else:
format_str = '%s%-12.12s %-9.9s %-12d\n'
for i in xrange(len(param['values'])):
if i == 0:
sys.stderr.write(format_str %
(indentation, param_name, param['type'],
param['values'][i]))
else:
sys.stderr.write(format_str %
(indentation, '', param['values'][i]))
def decompress_nested_container(c_container):
if isinstance(c_container, dict):
if 'ctype' in c_container and c_container['ctype'] == COMPRESS_TYPE:
try:
return decompress_array(c_container)
except:
raise Exception(
'Container does not contain a valid array.'
) # TODO, dangerous, very generic exception catch here
else:
udict = {}
for key, value in items(c_container):
if isinstance(value, dict) or isinstance(value, list):
udict[key] = decompress_nested_container(value)
else:
udict[key] = value
return udict
elif isinstance(c_container, list):
ulist = []
for value in c_container:
if isinstance(value, dict) or isinstance(value, list):
ulist.append(decompress_nested_container(value))
else:
ulist.append(value)
return ulist
def tired(db, experiment_name, resources):
"""
return True if no resources are accepting jobs
"""
jobs = load_jobs(db, experiment_name)
for resource_name, resource in items(resources):
if resource.acceptingJobs(jobs):
return False
return True
def print_dict(d, level=1):
if isinstance(d, dict):
if level > 1: print("")
for k, v in items(d):
print(
" " * level,
k,
)
print_dict(v, level=level + 1)
else:
print(d)
def variables_config_to_meta(self, variables_config):
"""
Converts a dict of variable meta-information from a config-file format into
a format that can be more easily used by bayesopt routines.
"""
# Stores the metadata for the dataset that allows a conversion
# from a config file representation into a matrix representation.
# The main addition that this variable adds is a mapping between
# each variable and associated column indices in the matrix
# representation.
variables_meta = OrderedDict()
cardinality = 0 # The number of distinct variables
num_dims = 0 # The number of dimensions in the matrix representation
for name, variable in items(variables_config):
cardinality += variable['size']
vdict = {
'type': variable['type'].lower(),
'indices': []
} # indices stores a mapping from these variable(s) to their matrix column(s)
if vdict['type'] == 'int':
vdict['min'] = int(variable['min'])
vdict['max'] = int(variable['max'])
elif vdict['type'] == 'float':
vdict['min'] = float(variable['min'])
vdict['max'] = float(variable['max'])
elif vdict['type'] == 'enum':
vdict['options'] = list(variable['options'])
else:
raise Exception("Unknown variable type.")
for i in xrange(variable['size']):
if vdict['type'] == 'int':
vdict['indices'].append(num_dims)
num_dims += 1
elif vdict['type'] == 'float':
vdict['indices'].append(num_dims)
num_dims += 1
elif vdict['type'] == 'enum':
vdict['indices'].append(
list(
np.arange(len(list(variable['options']))) +
num_dims))
num_dims += len(list(variable['options']))
else:
raise Exception("Unknown variable type.")
variables_meta[name] = vdict
return variables_meta, num_dims, cardinality
def __init__(self, tasks_config, variables_config):
self.tasks = {}
for task_name, task_options in items(tasks_config):
self.tasks[task_name] = Task(task_name, task_options,
variables_config)
self.dummy_task = Task('dummy', {'type': 'dummy'}, variables_config)
#TODO: Validate the data
self._inputs = np.zeros((0, self.num_dims)) #np.array([])
self._pending = np.zeros((0, self.num_dims)) #np.array([])
self._values = np.zeros((0, self.num_dims)) #np.array([])
self._costs = np.zeros((0, self.num_dims)) #np.array([])
self.variables_config = copy.copy(variables_config)
def matlab_launcher(job):
# Run it as a Matlab function.
try:
import pymatlab
except:
raise Exception(
"Cannot import pymatlab. pymatlab is required for Matlab jobs. It is installable with pip."
)
sys.stderr.write("Booting up Matlab...\n")
session = pymatlab.session_factory()
# Add directory to the Matlab path.
session.run("cd('%s')" % os.path.realpath(job['expt_dir']))
session.run('params = struct()')
for name, param in items(job['params']):
vals = param['values']
# sys.stderr.write('%s = %s\n' % (param['name'], str(vals)))
# should have dtype=float explicitly, otherwise
# if they are ints it will automatically do int64, which
# matlab will receive, and will tend to break matlab scripts
# because in matlab things tend to always be double type
session.putvalue('params_%s' % name, np.array(vals, dtype=float))
session.run("params.%s = params_%s" % (name, name))
# pymatlab sucks, so I cannot put the value directly into a struct
# instead i do this silly workaround to put it in a variable and then
# copy that over into the struct
# session.run('params_%s'%param['name'])
sys.stderr.write('Running function %s\n' % job['function-name'])
# Execute the function
session.run('result = %s(params)' % job['function-name'])
# Get the result
result = session.getvalue('result')
# TODO: this only works for single-task right now
result = float(result)
sys.stderr.write("Got result %s\n" % (result))
del session
return result
def parse_resources_from_config(config):
"""Parse the config dict and return a dictionary of resource objects keyed by resource name"""
# If the user did not explicitly specify resources
if "resources" not in config:
default_resource_name = 'Main'
task_names = parse_tasks_in_resource_from_config(config, default_resource_name)
return {default_resource_name : resource_factory(default_resource_name, task_names, config)}
# If resources are specified
else:
resources = dict()
for resource_name, resource_opts in items(config["resources"]):
task_names = parse_tasks_in_resource_from_config(config, resource_name)
resources[resource_name] = resource_factory(resource_name, task_names, resource_opts)
return resources
def vectorify(self, params):
v = np.zeros(self.num_dims)
for name, param in items(params):
indices = self.variables_meta[name]['indices']
if param['type'] == 'int' or param['type'] == 'float':
v[indices] = param['values']
elif param['type'] == 'enum':
for i, ind in enumerate(indices):
offset = self.variables_meta[name]['options'].index(
param['values'][i])
v[ind[0] + offset] = 1
else:
raise Exception('Unknown parameter type.')
return v
def create_task():
task_name = "mytask"
task_type = "OBJECTIVE"
variables_config = OrderedDict([('X', {
"type": "INT",
"size": 2,
"min": -1,
"max": 10
}), ('Y', {
"type": "FLOAT",
"size": 3,
"min": -0.003,
"max": 1e-1
}), ('Z', {
"type": "ENUM",
"size": 2,
"options": ["one", "two", "three"]
})])
variables_meta, num_dims, cardinality = Task.variables_config_to_meta(
variables_config)
# Create a set of inputs that satisfies the constraints of each variable
X = np.zeros((10, num_dims))
for i in xrange(10):
for name, variable in items(variables_meta):
indices = variable['indices']
if variable['type'] == 'int':
X[i, indices] = np.random.randint(variable['min'],
variable['max'] + 1,
len(indices))
elif variable['type'] == 'float':
X[i, indices] = np.random.rand(len(indices)) * (
variable['max'] - variable['min']) + variable['min']
elif variable['type'] == 'enum':
for ind in indices:
cat = np.random.randint(len(ind))
X[i, ind[cat]] = 1
y = np.random.randn(10)
t = Task(task_name, task_type, variables_config, data=X, values=y)
return t
def from_unit(self, U):
if U.shape[0] == 0:
return np.array([])
if U.ndim == 1:
U = U[None, :]
squeeze = True
else:
squeeze = False
V = np.zeros(U.shape)
for name, variable in items(self.variables_meta):
indices = variable['indices']
if variable['type'] == 'int':
vals = U[:, indices]
assert (
variable['max'] - variable['min'] > 0.0
), 'Your specified min (%f) for the variable %s must be less than the max (%f)' % (
variable['min'], name, variable['max'])
V[:, indices] = self.unit_to_int(vals, variable['min'],
variable['max'])
elif variable['type'] == 'float':
vals = U[:, indices]
assert (
variable['max'] - variable['min'] > 0.0
), 'Your specified min (%f) for the variable %s must be less than the max (%f)' % (
variable['min'], name, variable['max'])
V[:, indices] = self.unit_to_float(vals, variable['min'],
variable['max'])
elif variable['type'] == 'enum':
for ind in indices:
# This is a bit more complicated than to_unit because
# the values might come from the unit hypercube, meaning
# that U might not have a 1-hot encoding.
v = np.zeros(V[:, ind].shape)
v[np.arange(v.shape[0]), U[:, ind].argmax(1)] = 1
V[:, ind] = v
else:
raise Exception("Unknown variable type: %s" % variable['type'])
if squeeze:
V = np.squeeze(V)
return V
def python_launcher(job):
# Run a Python function
sys.stderr.write("Running python job.\n")
# Add directory to the system path.
sys.path.append(os.path.realpath(job['expt_dir']))
# Change into the directory.
os.chdir(job['expt_dir'])
sys.stderr.write("Changed into dir %s\n" % (os.getcwd()))
# Convert the JSON object into useful parameters.
params = {}
for name, param in items(job['params']):
vals = param['values']
if param['type'].lower() == 'float':
params[name] = np.array(vals)
elif param['type'].lower() == 'int':
params[name] = np.array(vals, dtype=int)
elif param['type'].lower() == 'enum':
params[name] = vals
else:
raise Exception("Unknown parameter type.")
# Load up this module and run
main_file = job['main-file']
if main_file[-3:] == '.py':
main_file = main_file[:-3]
sys.stderr.write('Importing %s.py\n' % main_file)
module = __import__(main_file)
sys.stderr.write('Running %s.main()\n' % main_file)
result = module.main(job['id'], params)
# Change back out.
os.chdir('..')
# TODO: add dict capability
sys.stderr.write("Got result %s\n" % (result))
return result
def parse_tasks_in_resource_from_config(config, resource_name):
"""parse the config dict and return a list of task names that use the given resource name"""
# If the user did not explicitly specify tasks, then we have to assume
# the single task runs on all resources
# TODO: THIS IS VERY DANGEROUS, BECAUSE THE TASK MIGHT NOT NAMED MAIN
# NEED TO HAVE A CONFIG PARSING SECTION OF THE CODE!!!
if "tasks" not in config:
return ['main']
else:
tasks = list()
for task_name, task_config in items(config["tasks"]):
# If the user specified tasks but not specific resources for those tasks,
# We have to assume the tasks run on all resources...
if "resources" not in task_config:
tasks.append(task_name)
else:
if resource_name in task_config["resources"]:
tasks.append(task_name)
return tasks
def paramify(self, data_vector):
if data_vector.ndim != 1:
raise Exception('Input to paramify must be a 1-D array.')
params = {}
for name, vdict in items(self.variables_meta):
indices = vdict['indices']
params[name] = {}
params[name]['type'] = vdict['type']
if vdict['type'] == 'int' or vdict['type'] == 'float':
params[name]['values'] = data_vector[indices]
elif vdict['type'] == 'enum':
params[name]['values'] = []
for ind in indices:
params[name]['values'].append(
vdict['options'][data_vector[ind].argmax(0)])
else:
raise Exception('Unknown parameter type.')
return params
def main():
options, expt_dir = get_options()
resources = parse_resources_from_config(options)
# Load up the chooser.
chooser_module = importlib.import_module('spearmint.choosers.' + options['chooser'])
chooser = chooser_module.init(options)
experiment_name = options.get("experiment-name", 'unnamed-experiment')
# Connect to the database
db_address = options['database']['address']
sys.stderr.write('Using database at %s.\n' % db_address)
db = MongoDB(database_address=db_address)
while True:
for resource_name, resource in items(resources):
jobs = load_jobs(db, experiment_name)
# resource.printStatus(jobs)
# If the resource is currently accepting more jobs
# TODO: here cost will eventually also be considered: even if the
# resource is not full, we might wait because of cost incurred
# Note: I chose to fill up one resource and them move on to the next
# You could also do it the other way, by changing "while" to "if" here
while resource.acceptingJobs(jobs):
# Load jobs from DB
# (move out of one or both loops?) would need to pass into load_tasks
jobs = load_jobs(db, experiment_name)
# Remove any broken jobs from pending.
remove_broken_jobs(db, jobs, experiment_name, resources)
# Get a suggestion for the next job
suggested_job = get_suggestion(chooser, resource.tasks, db, expt_dir, options, resource_name)
# Submit the job to the appropriate resource
process_id = resource.attemptDispatch(experiment_name, suggested_job, db_address, expt_dir)
# Set the status of the job appropriately (successfully submitted or not)
if process_id is None:
suggested_job['status'] = 'broken'
save_job(suggested_job, db, experiment_name)
else:
suggested_job['status'] = 'pending'
suggested_job['proc_id'] = process_id
save_job(suggested_job, db, experiment_name)
jobs = load_jobs(db, experiment_name)
# Print out the status of the resources
# resource.printStatus(jobs)
print_resources_status(list(resources.values()), jobs)
# If no resources are accepting jobs, sleep
# (they might be accepting if suggest takes a while and so some jobs already finished by the time this point is reached)
if tired(db, experiment_name, resources):
time.sleep(options.get('polling-time', 5))
def values(self):
"""return a dictionary of the task values keyed by task name"""
return {
task_name: task.values
for task_name, task in items(self.tasks)
}