def cross(self, indiv1, indiv2):
"""Perform the crossover (One crossover by default)
Parameters
----------
self : OptiGenNsga2Deap
Optimization solver
indiv1 : individual
first individual to modify
indiv2 : individual
second individual to modify
Returns
-------
is_cross : bool
True if the crossover append
"""
if random.random() < self.p_cross:
if self.crossover == None:
if cxOnePoint == None:
raise ImportError("deap module is needed.")
else:
cxOnePoint(indiv1, indiv2)
else:
self.crossover(indiv1, indiv2)
return True
else:
return False
def makenewinds(inds, select, nb_inds, nb_args):
"""
parameters:
inds: list of individu
select: list of boolean selector
"""
selectioned = [ind for ind,sel in zip(inds,select) if sel == 1]
ind1 = ind[0][0]
print "first individual"
print ind1
ind2 = ind[0][1]
print "second individual"
print ind2
filho = tools.cxOnePoint(ind1,ind2)
print "FILHO"
for f in filho:
print f
arguments = []
selectioned = zip(*selectioned)
print len(selectioned)
for selection in selectioned:
print len(selection)
for i in range(len(selection)):
print selection[i][0]
def mut_suite(individual, indpb):
# shuffle seq
individual, = tools.mutShuffleIndexes(individual, indpb)
# crossover inside the suite
for i in range(1, len(individual), 2):
if random.random() < settings.MUTPB:
if len(individual[i - 1]) <= 2:
print "\n\n### Indi Length =", len(individual[i - 1]), " ith = ", i - 1, individual[i - 1]
continue # sys.exit(1)
if len(individual[i]) <= 2:
print "\n\n### Indi Length =", len(individual[i]), "ith = ", i, individual[i]
continue # sys.exit(1)
individual[i - 1], individual[i] = tools.cxOnePoint(individual[i - 1], individual[i])
# individual[i - 1], individual[i] = tools.cxUniform(individual[i - 1], individual[i], indpb=0.5)
# shuffle events
for i in range(len(individual)):
if random.random() < settings.MUTPB:
if len(individual[i]) <= 2:
print "\n\n### Indi Length =", len(individual[i]), "ith = ", i, individual[i]
continue # sys.exit(1)
individual[i], = tools.mutShuffleIndexes(individual[i], indpb)
return individual,
def shap_point_crossover(ind1, ind2, p=0.25):
"""Apply one--point crossover on pairs of shapelets from the sets"""
new_ind1, new_ind2 = [], []
np.random.shuffle(ind1)
np.random.shuffle(ind2)
for shap1, shap2 in zip(ind1, ind2):
if len(shap1) > 4 and len(shap2) > 4 and np.random.random() < p:
# plt.figure()
# plt.plot(shap1)
# plt.plot(shap2)
# plt.title('Before Point CX')
# plt.show()
shap1, shap2 = tools.cxOnePoint(list(shap1), list(shap2))
# plt.figure()
# plt.plot(shap1)
# plt.plot(shap2)
# plt.title('After Point CX')
# plt.show()
# input()
new_ind1.append(shap1)
new_ind2.append(shap2)
if len(ind1) < len(ind2):
new_ind2 += ind2[len(ind1):]
else:
new_ind1 += ind1[len(ind2):]
return new_ind1, new_ind2
def crossover(ind1, ind2):
i1 = dec2bin_ind(ind1)
i2 = dec2bin_ind(ind2)
i1, i2 = tools.cxOnePoint(i1,i2)
ind1[:] = bin2dec_ind(i1)
ind2[:] = bin2dec_ind(i2)
return ind1, ind2
def mut_suite(individual, indpb): # shuffle seq individual, = tools.mutShuffleIndexes(individual, indpb) # crossover inside the suite for i in range(1, len(individual), 2): if random.random() < settings.MUTPB: if len(individual[i - 1]) <= 2: print "\n\n### Indi Length =", len(individual[i - 1]), " ith = ", i - 1, individual[i - 1] continue # sys.exit(1) if len(individual[i]) <= 2: print "\n\n### Indi Length =", len(individual[i]), "ith = ", i, individual[i] continue # sys.exit(1) individual[i - 1], individual[i] = tools.cxOnePoint(individual[i - 1], individual[i]) # shuffle events for i in range(len(individual)): if random.random() < settings.MUTPB: if len(individual[i]) <= 2: print "\n\n### Indi Length =", len(individual[i]), "ith = ", i, individual[i] continue # sys.exit(1) individual[i], = tools.mutShuffleIndexes(individual[i], indpb) return individual,
def default_config(wf, rm, estimator):
selector = lambda env, pop: tools.selTournament(pop, len(pop), 4)
return {
"interact_individuals_count": 22,
"generations": 5,
"env": Env(wf, rm, estimator),
"species": [Specie(name=MAPPING_SPECIE, pop_size=10,
cxb=0.8, mb=0.5,
mate=lambda env, child1, child2: tools.cxOnePoint(child1, child2),
mutate=mapping_default_mutate,
select=selector,
initialize=mapping_default_initialize
),
Specie(name=ORDERING_SPECIE, pop_size=10,
cxb=0.8, mb=0.5,
mate=ordering_default_crossover,
mutate=ordering_default_mutate,
select=selector,
initialize=ordering_default_initialize,
)
],
"operators": {
# "choose": default_choose,
"build_solutions": default_build_solutions,
"fitness": fitness_mapping_and_ordering,
"assign_credits": default_assign_credits
}
}
def sapienz_mut_suite(self, individual: Individual,
indpb: float) -> Tuple[Individual]:
# shuffle seq
individual, = tools.mutShuffleIndexes(individual, indpb)
# crossover inside the suite
# perform one point crossover between odd and even pair positions of test cases
for i in range(1, len(individual), 2):
if random.random() < settings.MUTPB:
if len(individual[i - 1]) <= 2:
continue
if len(individual[i]) <= 2:
continue
individual[i - 1], individual[i] = tools.cxOnePoint(
individual[i - 1], individual[i])
# shuffle events inside each test case
for i in range(len(individual)):
if random.random() < settings.MUTPB:
if len(individual[i]) <= 2:
continue
individual[i], = tools.mutShuffleIndexes(individual[i], indpb)
return individual,
def point_crossover(ind1, ind2):
"""Apply one- or two-point crossover on the shapelet sets"""
if len(ind1) > 1 and len(ind2) > 1:
if np.random.random() < 0.5:
ind1, ind2 = tools.cxOnePoint(list(ind1), list(ind2))
else:
ind1, ind2 = tools.cxTwoPoint(list(ind1), list(ind2))
return ind1, ind2
def mate(x, y):
x_ = x.terms.copy()
y_ = y.terms.copy()
n, m = x_.shape
nm = n * m
a = x_.reshape((1, nm)).tolist()[0]
b = y_.reshape((1, nm)).tolist()[0]
c = np.array(tools.cxOnePoint(a, b))
a = creator.pt_individual(c[0, :].reshape((n, m)))
b = creator.pt_individual(c[1, :].reshape((n, m)))
return (a, b)
def mate(x, y):
x_ = x.terms.copy()
y_ = y.terms.copy()
n, m = x_.shape
nm = n * m
a = x_.reshape((1, nm)).tolist()[0]
b = y_.reshape((1, nm)).tolist()[0]
c = np.array(tools.cxOnePoint(a, b))
a = creator.pt_individual(c[0, :].reshape((n, m)))
b = creator.pt_individual(c[1, :].reshape((n, m)))
return (a, b)
def crossover_gus(indv1, indv2):
genes1 = indv1.vector_weights
genes2 = indv2.vector_weights
cross1, cross2 = tools.cxOnePoint(genes1, genes2)
indv1.vector_weights = cross1
indv2.vector_weights = cross2
indv1.set_mat_from_vect()
indv2.set_mat_from_vect()
return indv1, indv2
def validCrossover(ind1, ind2, servers, knapSackList):
"""
Objectif : faire un crossover entre deux individus tout en conservant la validité du knapsack
:param ind1:
:param ind2:
:param servers:
:param knapSackList:
:return: offspring Individu
"""
offspring1, offspring2 = tools.cxOnePoint(ind1, ind2)
offspring1 = deleteOverflow(offspring1, servers, knapSackList)
offspring2 = deleteOverflow(offspring2, servers, knapSackList)
return offspring1, offspring2
def main():
# 杂交函数测试
ind1 = [1, 1, 1, 1, 1]
ind2 = [0, 0, 0, 0, 0]
print(ind1, ind2)
"""交换从任意位置开始并且到结尾的一段基因"""
n1, n2 = tools.cxOnePoint(ind1, ind2)
print(n1, n2)
"""交换连续的一段长度随机，位置随机的基因"""
n3, n4 = tools.cxTwoPoint(ind1, ind2)
print(n3, n4)
"""进行min(len(ind1), len(ind2))次杂交，每轮交换前产生一个随机数a，若a小于indpb则交换该轮次位置的两个基因，否则不执行交换"""
n5, n6 = tools.cxUniform(ind1, ind2, indpb=0.5)
print(n5, n6)
def makenewinds(inds, select, nb_inds, nb_args):
"""
parameters:
inds: list of individu
select: list of boolean selector
"""
selectioned = [ind for ind, sel in zip(inds, select) if sel == 1]
newinds = []
for nb_arg in range(nb_args):
args = [sel[nb_arg] for sel in selectioned]
while len(args) < nb_inds:
for father, mother in zip(args[:-1], args[1:]):
print len(father)
args.append(mother)
args.append(father)
son1 = copy.deepcopy(father)
son2 = copy.deepcopy(mother)
tools.cxOnePoint(son1, son2)
print "Father"
print father
print gp.compile(father, pset)
print "Mother"
print mother
print gp.compile(mother, pset)
print son1
print gp.compile(son1, pset)
print son2
print gp.compile(son2, pset)
args.append(son1)
args.append(son2)
args = args[:nb_inds] # select only nb_ind individus
newinds.append(args)
return newinds
def shap_point_crossover(ind1, ind2):
new_ind1, new_ind2 = [], []
np.random.shuffle(ind1)
np.random.shuffle(ind2)
for shap1, shap2 in zip(ind1, ind2):
if len(shap1) > 4 and len(shap2) > 4:
shap1, shap2 = tools.cxOnePoint(list(shap1), list(shap2))
new_ind1.append(shap1)
new_ind2.append(shap2)
if len(ind1) < len(ind2):
new_ind2 += ind2[len(ind1):]
else:
new_ind1 += ind1[len(ind2):]
return new_ind1, new_ind2
def crossOver(ind1, ind2):
child1, child2 = [toolbox.clone(ind) for ind in (ind1, ind2)]
del child1.fitness.values
del child2.fitness.values
l1 = list(split(child1, N_NUM_ACTUATORS))
l2 = list(split(child2, N_NUM_ACTUATORS))
crossedTotalList = []
new1 = toolbox.individual()
new2 = toolbox.individual()
del new1[:]
del new2[:]
for i in range(N_NUM_ACTUATORS):
crossedTotalList.append(tools.cxOnePoint(l1[i], l2[i]))
for sublist in crossedTotalList:
new1.extend(sublist[0])
new2.extend(sublist[1])
return new1, new2,
def get_child_reward_network(
mom: Agent,
dad: Agent,
mut_sigma: float = 0.3,
mut_p: float = 0.05) -> Tuple[List[np.ndarray], List[np.ndarray]]:
"""
Takes as input a pair of agents, and constructs the child's reward network.
Parameters
----------
mom : ``Agent``.
First parent agent.
dad : ``Agent``.
First parent agent.
mut_sigma : ``float``, optional.
Standard deviation of mutation operation on reward vectors.
mut_p : ``float``, optional.
Probability of mutation on reward vectors.
Returns
-------
childs_reward_weights : ``List[np.ndarray]``.
Weights of the new agent's reward network.
childs_reward_biases : ``List[np.ndarray]``.
Biases of the new agent's reward network.
"""
# Get parents' DNA.
moms_dna = reward_to_DNA(mom.reward_weights, mom.reward_biases)
dads_dna = reward_to_DNA(dad.reward_weights, dad.reward_biases)
# Crossover.
childs_dna, _ = cxOnePoint(moms_dna, dads_dna)
# Mutation.
# HARDCODE: ``mu`` and grabbing first and only tuple element.
childs_dna = mutGaussian(childs_dna, 0.0, mut_sigma, mut_p)[0]
# HARDCODE: using ``mom``'s reward hyperparams for child.
childs_reward_weights, childs_reward_biases = DNA_to_reward(
childs_dna, mom.n_layers, mom.input_dim, mom.hidden_dim)
return childs_reward_weights, childs_reward_biases
def do_exp():
config = {
"interact_individuals_count": 500,
"generations": 1000,
"env": Env(_wf, rm, estimator),
"species": [Specie(name=MAPPING_SPECIE, pop_size=500,
cxb=0.9, mb=0.9,
mate=lambda env, child1, child2: tools.cxOnePoint(child1, child2),
# mutate=mapping_default_mutate,
# mutate=lambda ctx, mutant: mapping_k_mutate(ctx, 3, mutant)
mutate=mapping_all_mutate,
# mutate=mapping_improving_mutation,
select=selector,
initialize=mapping_default_initialize,
# initialize=lambda ctx, pop: mapping_heft_based_initialize(ctx, pop, heft_mapping, 3),
stat=lambda pop: {"hamming_distances": hamming_distances([to_seq(p) for p in pop], to_seq(ms_ideal_ind)),
"unique_inds_count": unique_individuals(pop),
"pcm": pcm(pop),
"gdm": gdm(pop)}
),
Specie(name=ORDERING_SPECIE, fixed=True,
representative_individual=ListBasedIndividual(os_representative))
],
"solstat": lambda sols: {"best_components": hamming_for_best_components(sols, ms_ideal_ind, os_ideal_ind),
"best_components_itself": best_components_itself(sols),
"best": -1*Utility.makespan(build_schedule(_wf, estimator, rm, max(sols, key=lambda x: x.fitness)))
},
"operators": {
# "choose": default_choose,
"build_solutions": default_build_solutions,
# "fitness": fitness_mapping_and_ordering,
"fitness": overhead_fitness_mapping_and_ordering,
# "assign_credits": default_assign_credits
# "assign_credits": max_assign_credits
"assign_credits": assign_from_transfer_overhead
}
}
return do_experiment(saver, config, _wf, rm, estimator)
def main():
nb_of_inputs, nb_of_outputs = get_nb_of_inputs_and_outputs_of_env(env_name)
model = tf.keras.Sequential([
tf.keras.layers.Dense(2 ** 8, input_shape=(nb_of_inputs,), activation='tanh', use_bias=True, name='dense_1'),
# tf.keras.layers.Dense(2**8, activation='tanh', name='dense_2', use_bias=True),
tf.keras.layers.Dense(nb_of_outputs, activation='tanh', name='output'),
])
nb_of_weights_per_layer = extract_nb_of_weights_per_layer(model)
brain = Brain(model, nb_of_weights_per_layer)
genome_model = Genome(brain)
crossover = lambda p1, p2: tools.cxOnePoint(p1, p2)
mutations = [
lambda v: mut_scalar_add_uniform(v, 1., 0.2),
lambda v: mut_scalar_add_uniform(v, 1, 0.01),
lambda v: mut_random_value(v, 1, 0.02),
]
mutation_manager = MutationManager(mutations)
population = Population(
env_name=env_name,
genome_model=genome_model,
crossover=crossover,
mutation_manager=mutation_manager,
nb_of_genomes=nb_of_genomes)
with population as population:
population.init_genomes()
population.init_environments()
for i in range(nb_of_generations):
global g_mut_scale
population.evaluate()
population.evolve()
g_mut_scale = (1. / 1.3) ** i
def default_config(wf, rm, estimator):
selector = lambda env, pop: tools.selTournament(pop, len(pop), 4)
return {
"interact_individuals_count":
22,
"generations":
5,
"env":
Env(wf, rm, estimator),
"species": [
Specie(name=MAPPING_SPECIE,
pop_size=10,
cxb=0.8,
mb=0.5,
mate=lambda env, child1, child2: tools.cxOnePoint(
child1, child2),
mutate=mapping_default_mutate,
select=selector,
initialize=mapping_default_initialize),
Specie(
name=ORDERING_SPECIE,
pop_size=10,
cxb=0.8,
mb=0.5,
mate=ordering_default_crossover,
mutate=ordering_default_mutate,
select=selector,
initialize=ordering_default_initialize,
)
],
"operators": {
# "choose": default_choose,
"build_solutions": default_build_solutions,
"fitness": fitness_mapping_and_ordering,
"assign_credits": default_assign_credits
}
}
def _mate(self, ind1, ind2):
if np.random.rand() < self.config.cx_prob:
tools.cxOnePoint(ind1, ind2)
del ind1.fitness.values
del ind2.fitness.values
def do_exp():
config = {
"interact_individuals_count":
100,
"generations":
300,
"env":
Env(_wf, rm, estimator),
"species": [
Specie(
name=MAPPING_SPECIE,
pop_size=50,
cxb=0.9,
mb=0.9,
mate=lambda env, child1, child2: tools.cxOnePoint(
child1, child2),
# mutate=mapping_default_mutate,
# mutate=lambda ctx, mutant: mapping_k_mutate(ctx, 3, mutant)
mutate=mapping_all_mutate,
# mutate=OnlyUniqueMutant()(mapping_all_mutate),
select=selector,
# initialize=mapping_default_initialize,
initialize=lambda ctx, pop: mapping_heft_based_initialize(
ctx, pop, heft_mapping, 3),
stat=lambda pop: {
"hamming_distances":
hamming_distances([to_seq(p)
for p in pop], to_seq(ms_ideal_ind)),
"unique_inds_count":
unique_individuals(pop),
"pcm":
pcm(pop),
"gdm":
gdm(pop)
}),
Specie(name=ORDERING_SPECIE,
fixed=True,
representative_individual=ListBasedIndividual(
os_representative))
],
"solstat":
lambda sols: {
"best_components":
hamming_for_best_components(sols, ms_ideal_ind, os_ideal_ind),
"best_components_itself":
best_components_itself(sols),
"best":
-1 * Utility.makespan(
build_schedule(_wf, estimator, rm,
max(sols, key=lambda x: x.fitness)))
},
"operators": {
# "choose": default_choose,
"build_solutions": default_build_solutions,
"fitness": fitness_mapping_and_ordering,
# "fitness": overhead_fitness_mapping_and_ordering,
# "assign_credits": default_assign_credits
# "assign_credits": max_assign_credits
"assign_credits": assign_from_transfer_overhead
}
}
return do_experiment(saver, config, _wf, rm, estimator)
def genetic(rts, cpus):
def func_X(a, b):
""" length of messages transmitted from a towards b or from b towards a """
comm_load = 0
if "p" in a:
for p in a["p"]:
if p["id"] == b["id"]:
comm_load += p["payload"]
# This part consideres incoming msgs from other tasks (so that task is the successor, b->a)
# if "p" in b:
# for p in b["p"]:
# if p["id"] == a["id"]:
# comm_load += p["payload"]
return comm_load
def func_Y(i, rts):
""" load of the communication control network that the task i produces """
comm_load = 0
other_tasks = [t for t in rts if t is not i]
for j in other_tasks:
comm_load += func_X(i, j)
return comm_load
def func_Xc(cpu_h, cpu_k):
""" length of all messages (in bytes) to be transmitted between processors h and k through the network """
summ = 0
for task_h in cpu_h["tasks"]:
for task_j in cpu_k["tasks"]:
summ += func_X(task_h, task_j)
return summ
def func_Vp(cpus):
""" total amount of information to be transferred over the network """
summ = 0
for cpu in cpus.values():
other_cpus = [c for c in cpus.values() if c is not cpu]
for other_cpu in other_cpus:
summ += func_Xc(cpu, other_cpu)
return summ
def func_B(rts):
""" Total amount of data to be transferred between predecessor and successors throught the network """
summ = 0
for task in rts:
summ += func_Y(task, rts)
return summ
def func_cost_p(rts, cpus):
return func_Vp(cpus) / func_B(rts)
# initialization
n_p = 128 # number of generations
n_g = 16 # population
pc = 0.5 # crossover probability
pm = 0.001 # mutation probability
m = len(rts) # tasks
n = len(cpus) # processors
B = func_B(rts) # total of data to be transferred between predecessor and successor
W = 70 # network bandwith in bytes/slot
Dmin = min([t["d"] for t in rts]) # minimum deadline
WDmin = W * Dmin
# generate first chromosome
chromosome1 = []
for task in rts:
g = func_Y(task, rts) * int(random.uniform(0,1) * m)
chromosome1.append(g)
# the dict stores the cpus tasks lists
chromosomes = [(chromosome1, dict())]
# generate remain population
for _ in range(n_g - 1):
new_chromosome = []
nu = max(chromosome1) / 10
for g1 in chromosome1:
g2 = g1 + random.uniform(-nu, nu)
new_chromosome.append(g2)
chromosomes.append((new_chromosome, dict()))
# initialize the dict associated with each chromosome
for _, cpus_alloc in chromosomes:
for cpu_id in cpus.keys():
cpus_alloc[cpu_id] = {"tasks":[], "uf":0} # tasks assigned to this cpu
# aux for reordering and other stuff
chromosomes_stack = []
# do generations
for _ in range(n_p):
chromosomes_stack.clear()
# A stack is assembled containing the tasks ordered by the value of its allele in decreasing order.
for item in chromosomes:
chromosome, cpus_alloc = item[0], item[1]
task_stack = []
for task_id, allele in enumerate(chromosome):
task_stack.append((allele, rts[task_id]))
task_stack.sort(key=lambda allele: allele[0], reverse=True)
# clear previous task assignation
for cpu in cpus_alloc.values():
cpu["tasks"].clear()
# aux -- for easy sorting
cpu_stack = [cpu for cpu in cpus_alloc.values()]
# partition
for _, max_task in task_stack:
if "cpu" in max_task:
cpu_id = max_task["cpu"]
cpus_alloc[cpu_id]["tasks"].append(max_task)
else:
# create auxiliary stack with all task j that communicate with i
aux_stack = []
# add the succesors
if "p" in max_task:
for p in max_task["p"]:
for task in rts:
if task["id"] == p["id"]:
aux_stack.append((func_Y(task, rts), task))
# add other tasks that communicate with the task (the task will be the succesor)
#for task in [t for t in rts if t is not max_task]:
# if "p" in task:
# for p in task["p"]:
# if p["id"] == max_task["id"]:
# aux_stack.append((func_Y(task, rts), task))
cpu_a = None
# order by func_y
if aux_stack:
aux_stack.sort(key=lambda t: t[0], reverse=True)
aux_max_task = aux_stack[0]
# find the cpu at which the aux_max_task is allocated
for cpu in cpus_alloc.values():
if aux_max_task in cpu["tasks"]:
cpu_a = cpu
#if not aux_stack or cpu_a is None:
if cpu_a is None:
# update uf factors and allocate task to cpu with min uf
for cpu in cpus_alloc.values():
cpu["uf"] = sum([t["uf"] for t in cpu["tasks"]])
cpu_stack.sort(key=lambda c: c["uf"])
cpu_stack[0]["tasks"].append(max_task)
else:
cpu_a["tasks"].append(max_task)
# apply the cost function to the chromosomes
chromosomes_stack.append((func_cost_p(rts, cpus_alloc), chromosome))
# evaluation, cost and fitness
# elistist selection -- for the sake of simplicity, separate the first two chromosomes as the 'best'
chromosomes_stack.sort(key=lambda c: c[0]) # order by ascending value
chromosomes_stack = chromosomes_stack[2:]
# apply roulette selection on the rest -- an apply crossover
sum_fitness = sum([c[0] for c in chromosomes_stack]) # sum of all fitness values (cost function result)
chromosomes_stack = [(c[0] / sum_fitness, c[1]) for c in chromosomes_stack] # normalization
# calculate probabilities
sum_prob = 0
probs = []
for fitness, c in chromosomes_stack:
prob = sum_prob + fitness
probs.append(prob)
sum_prob += fitness
# perform crossover
for _ in range(int(n_g / 2)):
cs = [] # selected chromosomes
for s in range(2):
r = random.uniform(0,1)
for idx, p in enumerate(probs):
if r < p:
cs.append(chromosomes_stack[idx][1])
# uses radint() function for selecting a crossover point
tools.cxOnePoint(cs[0], cs[1])
# mutate
for c in chromosomes_stack:
tools.mutGaussian(c[1], pm, pm, pm)
# memory constraint verification
for idx, chromosome in enumerate(chromosomes):
print("Chromosome {0}".format(idx))
valid_cpu = True
ch_cpus = chromosome[1]
for cpuid, cpu in ch_cpus.items():
if cpus[cpuid]["capacity"] < sum([t["r"] for t in cpu["tasks"]]):
valid_cpu = False
if valid_cpu:
print_results(rts, chromosome[1])
else:
print(" -- Invalid assignation found.")
# bandwidth constraint
bw_ok = B <= WDmin
return
def mate(self, individual1, individual2):
individual1.number_centroids, individual2.number_centroids = individual2.number_centroids, individual1.number_centroids,
tools.cxOnePoint(individual1.attribute_flags,
individual2.attribute_flags)
return individual1, individual2
def cxComb(ind1,ind2):
if numpy.random.randint(2)==0:
tools.cxOnePoint(ind1,ind2)
else:
tools.cxBlend(ind1,ind2,0.0)
return ind1,ind2
def crossverAll(first, second):
return tools.cxOnePoint(first, second)
heft_mapping = extract_mapping_from_ga_file("{0}/temp/heft_etalon_tr100_m50.json".format(__root_path__), rm)
ms_ideal_ind = build_ms_ideal_ind(_wf, rm)
os_ideal_ind = build_os_ideal_ind(_wf)
ms_str_repr = [{k: v} for k, v in ms_ideal_ind]
config = {
"interact_individuals_count": 200,
"generations": 10000,
"env": Env(_wf, rm, estimator),
"species": [Specie(name=MAPPING_SPECIE, pop_size=50,
cxb=0.9, mb=0.9,
mate=lambda env, child1, child2: tools.cxOnePoint(child1, child2),
mutate=mapping_all_mutate,
# mutate=mapping_default_mutate,
# mutate=MappingArchiveMutate(),
select=mapping_selector,
# initialize=mapping_default_initialize,
initialize=lambda ctx, pop: mapping_heft_based_initialize(ctx, pop, heft_mapping, 3),
stat=lambda pop: {"hamming_distances": hamming_distances([to_seq(p) for p in pop], to_seq(ms_ideal_ind)),
"unique_inds_count": unique_individuals(pop),
"pcm": pcm(pop),
"gdm": gdm(pop)}
),
Specie(name=ORDERING_SPECIE, pop_size=50,
cxb=0.8, mb=0.5,
mate=ordering_default_crossover,
config = {
"hall_of_fame_size":
0,
"interact_individuals_count":
50,
"generations":
10,
"env":
Env(_wf, rm, estimator),
"species": [
Specie(
name=MAPPING_SPECIE,
pop_size=50,
cxb=0.9,
mb=0.9,
mate=lambda env, child1, child2: tools.cxOnePoint(child1, child2),
# mutate=mapping_all_mutate,
# mutate=mapping_all_mutate_variable,
mutate=mapping_mut_reg(mapping_all_mutate_configurable),
# mutate=mapping_all_mutate_variable2,
# mutate=mapping_improving_mutation,
# mutate=mapping_default_mutate,
# mutate=MappingArchiveMutate(),
select=mapping_selector,
# initialize=mapping_default_initialize,
initialize=lambda ctx, pop: mapping_heft_based_initialize(
ctx, pop, heft_mapping, 3),
stat=lambda pop: {
"hamming_distances":
hamming_distances([to_seq(p)
for p in pop], to_seq(ms_ideal_ind)),
def mate(ind1, ind2):
return tools.cxOnePoint(ind1, ind2)
def crossover_one_point(self, ind1:Individual, ind2:Individual):
ch1, ch2 = tools.cxOnePoint(ind1.mapping, ind2.mapping)
ind1.mapping = ch1
ind2.mapping = ch2
return ind1, ind2
def defaultCx(mother, father):
return tools.cxOnePoint(mother, father)
def crossover(ind1, ind2):
return cxOnePoint(ind1, ind2)
def cxGIMME_Simple(self, ind1, ind2):
# configs
config1 = ind1[0]
config2 = ind2[0]
newConfig1 = []
newConfig2 = []
l1 = len(config1)
l2 = len(config2)
if (l1 > l2):
maxLenConfig = config1
maxLen = l1
minLenConfig = config2
minLen = l2
else:
maxLenConfig = config2
maxLen = l2
minLenConfig = config1
minLen = l1
cxpoints = []
clist1 = []
clist2 = []
remainder1 = []
remainder2 = []
for i in range(minLen):
parent1 = [None, None]
parent2 = [None, None]
parent1[0] = minLenConfig[i]
parent1[1] = ind1[1][i].flattened()
parent2[0] = maxLenConfig[i]
parent2[1] = ind2[1][i].flattened()
clist1.append(parent1)
clist2.append(parent2)
# breakpoint()
for ind,clist in zip([ind1,ind2], [clist1,clist2]):
# print("-----------[Before]-----------")
# print(json.dumps(ind[1], default=lambda o: o.__dict__))
randI1 = random.randint(0, len(clist1) - 1)
randI2 = random.randint(0, len(clist1) - 1)
newProfilesConfig = tools.cxOnePoint(ind1 = clist[randI1][0], ind2 = clist[randI2][0])
newProfilesGIP = tools.cxOnePoint(ind1 = clist[randI1][1], ind2 = clist[randI2][1])
ind[0][randI1] = newProfilesConfig[0]
ind[1][randI1] = self.interactionsProfileTemplate.unflattened(newProfilesGIP[0])
ind[0][randI2] = newProfilesConfig[1]
ind[1][randI2] = self.interactionsProfileTemplate.unflattened(newProfilesGIP[1])
# print("-----------[After]-----------")
# print(json.dumps(ind[1], default=lambda o: o.__dict__))
# breakpoint()
del ind1.fitness.values
del ind2.fitness.values
return (ind1, ind2)
def genetic(rts, cpus):
def func_X(a, b):
""" length of messages transmitted from a towards b or from b towards a """
comm_load = 0
if "p" in a:
for p in a["p"]:
if p["id"] == b["id"]:
comm_load += p["payload"]
# This part consideres incoming msgs from other tasks (so that task is the successor, b->a)
# if "p" in b:
# for p in b["p"]:
# if p["id"] == a["id"]:
# comm_load += p["payload"]
return comm_load
def func_Xc(cpu_h, cpu_k):
""" length of all messages (in bytes) to be transmitted between processors h and k through the network """
summ = 0
for task_h in cpu_h["tasks"]:
for task_j in cpu_k["tasks"]:
summ += func_X(task_h, task_j)
return summ
def func_Y(i, rts):
""" load of the communication control network that the task i produces """
comm_load = 0
other_tasks = [t for t in rts if t is not i]
for j in other_tasks:
comm_load += func_X(i, j)
return comm_load
def func_Vp(cpus):
""" total amount of information to be transferred over the network """
summ = 0
for cpu in cpus.values():
other_cpus = [c for c in cpus.values() if c is not cpu]
for other_cpu in other_cpus:
summ += func_Xc(cpu, other_cpu)
return summ
def func_B(rts):
""" Total amount of data to be transferred between predecessor and successors throught the network """
summ = 0
for task in rts:
summ += func_Y(task, rts)
return summ
def func_cost_p(rts, cpus):
return func_Vp(cpus) / func_B(rts)
def get_cpu_alloc(individual):
cpus_alloc = dict()
for cpu_id in cpus.keys():
cpus_alloc[cpu_id] = {"tasks": [], "uf": 0} # tasks assigned to this cpu
# A stack is assembled containing the tasks ordered by the value of the gene in decreasing order.
task_stack = []
for task_id, gene in enumerate(individual):
task_stack.append((gene, rts[task_id]))
task_stack.sort(key=lambda t: t[0], reverse=True) # sort by gene value
# clear previous task assignation
#for cpu in cpus_alloc.values():
# cpu["tasks"].clear()
# aux list -- for easy sorting
cpu_stack = [cpu for cpu in cpus_alloc.values()]
# partition
for _, max_task in task_stack:
if "cpu" in max_task:
cpu_id = max_task["cpu"]
cpus_alloc[cpu_id]["tasks"].append(max_task)
else:
# create auxiliary stack with all task j that communicate with i
aux_stack = []
# add the succesors
if "p" in max_task:
for p in max_task["p"]:
for task in rts:
if task["id"] == p["id"]:
aux_stack.append((func_Y(task, rts), task))
# add other tasks that communicate with the task (the task will be the succesor)
# for task in [t for t in rts if t is not max_task]:
# if "p" in task:
# for p in task["p"]:
# if p["id"] == max_task["id"]:
# aux_stack.append((func_Y(task, rts), task))
cpu_a = None
# order by func_y
if aux_stack:
aux_stack.sort(key=lambda t: t[0], reverse=True)
aux_max_task = aux_stack[0]
# find the cpu at which the aux_max_task is allocated
for cpu in cpus_alloc.values():
if aux_max_task in cpu["tasks"]:
cpu_a = cpu
# if not aux_stack or cpu_a is None:
if cpu_a is None:
# update uf factors and allocate task to cpu with min uf
for cpu in cpus_alloc.values():
cpu["uf"] = sum([t["uf"] for t in cpu["tasks"]])
cpu_stack.sort(key=lambda c: c["uf"])
cpu_stack[0]["tasks"].append(max_task)
else:
cpu_a["tasks"].append(max_task)
# return the task allocation performed using the chromosome
return cpus_alloc
def cost(individual):
# apply the cost function to the chromosome based in the cpu allocation produced
return func_cost_p(rts, get_cpu_alloc(individual))
def init_population(individual, rts, n):
# generate initial population
p_list = []
# generate first chromosome
chromosome = []
for task in rts:
g = func_Y(task, rts) * int(random.uniform(0, 1) * len(rts))
chromosome.append(g)
p_list.append(chromosome)
# remaining chromosomes
for _ in range(n - 1):
new_chromosome = []
nu = max(chromosome) / 10
for g1 in chromosome:
g2 = abs(g1 + int(random.uniform(-nu, nu)))
new_chromosome.append(g2)
p_list.append(new_chromosome)
return [individual(c) for c in p_list]
creator.create("FitnessMin", base.Fitness, weights=(-1.0,))
# Defines each individual as a list
creator.create("Individual", list, fitness=creator.FitnessMin)
toolbox = base.Toolbox()
# Initialize the population
toolbox.register("population", init_population, creator.Individual, rts)
# Applies a gaussian mutation of mean mu and standard deviation sigma on the input individual. The indpb argument
# is the probability of each attribute to be mutated.
toolbox.register("mutate", tools.mutGaussian, mu=0, sigma=1, indpb=0.01)
# Use map to pass values
toolbox.register("evaluate", cost)
# Generate the initial population (first generation)
population = toolbox.population(n=6)
# Evaluate the first generation
fitnesses = map(toolbox.evaluate, population)
for ind, fit in zip(population, fitnesses):
ind.fitness.values = (fit,)
for _ in range(120): # generations
# Select the k worst individuals among the input individuals.
population_worst = tools.selWorst(population, int(len(population) / 2))
# Perform a roulette selection and apply a crossover to the selected individuals
for _ in range(len(population_worst)):
pair = tools.selRoulette(population_worst, 2) # roulette
tools.cxOnePoint(pair[0], pair[1]) # one point crossover
# Mutate
for c in population_worst:
toolbox.mutate(c)
del c.fitness.values # delete the fitness value
# Evaluate again the entire population
fitnesses = map(toolbox.evaluate, population)
for ind, fit in zip(population, fitnesses):
ind.fitness.values = (fit,)
# print the final population
print_population(population)
# memory constraint verification
for i, ind in enumerate(population):
valid_cpu = True
ch_cpus = get_cpu_alloc(ind)
for cpuid, cpu in ch_cpus.items():
if cpus[cpuid]["capacity"] < sum([t["r"] for t in cpu["tasks"]]):
valid_cpu = False
if valid_cpu:
print_results(i, rts, ch_cpus)
else:
print("Chromosome {0} -- Invalid assignation found.".format(i))
def solve(self):
"""Method to perform NSGA-II using DEAP tools
Parameters
----------
self : OptiGenAlgNsga2Deap
Solver to perform NSGA-II
Returns
-------
multi_output : OutputMultiOpti
class containing the results
"""
if self.problem == None:
raise MissingProblem(
"The problem has not been defined, please add a problem to OptiGenAlgNsga2Deap"
)
# Create the toolbox
self.create_toolbox()
# Add the design variable names
self.multi_output.design_var_names = list(self.problem.design_var.keys())
self.multi_output.design_var_names.sort()
# Add the fitness names
self.multi_output.fitness_names = list(self.problem.obj_func.keys())
self.multi_output.fitness_names.sort()
# Add the reference output to multi_output
self.multi_output.output_ref = self.problem.output
# Create the first population
pop = self.toolbox.population(self.size_pop)
# Start of the evaluation of the generation
time_start_gen = datetime.now().strftime("%H:%M:%S")
# Evaluate the population
nb_error = 0
for i in range(0, self.size_pop):
nb_error += evaluate(self, pop[i])
print(
"\r{} gen {:>5}: {:>5.2f}%, {:>4} errors.".format(
time_start_gen, 0, (i + 1) * 100 / self.size_pop, nb_error),
end="",
)
# Check the constraints violation
nb_infeasible = 0
if len(self.problem.constraint) > 0:
for indiv in pop:
nb_infeasible += check_cstr(self, indiv)
print("\r{} gen {:>5}: 100%, {:>4} errors,{:>4} infeasible.".format(
time_start_gen, 0, nb_error, nb_infeasible - nb_error))
# Add pop to OutputMultiOpt
for indiv in pop:
# Check that at every fitness values is different from inf
is_valid = indiv.fitness.valid and indiv.is_simu_valid and indiv.cstr_viol == 0
# Add the indiv to the multi_output
self.multi_output.add_evaluation(indiv.output, is_valid, list(indiv),
indiv.fitness.values, 0)
if self.selector == None:
pop = selNSGA2(pop, self.size_pop)
else:
parents = self.selector(pop, self.size_pop)
############################
# LOOP FOR EACH GENERATION #
############################
for ngen in range(1, self.nb_gen):
time_start_gen = datetime.now().strftime("%H:%M:%S")
# Extracting parents using
parents = tournamentDCD(pop, self.size_pop)
# Copy new indivuals
children = []
for indiv in parents:
child = self.toolbox.individual()
for i in range(len(indiv)):
child[i] = deepcopy(indiv[i])
child.output = Output(init_dict=indiv.output.as_dict())
child.fitness = deepcopy(indiv.fitness)
children.append(child)
for indiv1, indiv2 in zip(children[::2], children[::-2]):
# Crossover
is_cross = False
if random.random() < self.p_cross:
is_cross = True
if self.crossover == None:
cxOnePoint(indiv1, indiv2)
# Mutation
is_mutation = self.mutate(indiv1)
if is_cross or is_mutation:
update(indiv1)
is_mutation = self.mutate(indiv2)
if is_cross or is_mutation:
update(indiv2)
# Evaluate the children
to_eval = []
for indiv in children:
if indiv.fitness.valid == False:
to_eval.append(indiv)
nb_error = 0
for i in range(len(to_eval)):
nb_error += evaluate(self, to_eval[i])
print(
"\r{} gen {:>5}: {:>5.2f}%, {:>4} errors.".format(
time_start_gen, ngen, (i + 1) * 100 / len(to_eval),
nb_error),
end="",
)
# Check the constraints violation
nb_infeasible = 0
if len(self.problem.constraint) > 0:
for indiv in to_eval:
nb_infeasible += check_cstr(self, indiv)
print("\r{} gen {:>5}: 100%, {:>4} errors,{:>4} infeasible.".format(
time_start_gen, ngen, nb_error, nb_infeasible - nb_error))
# Add children to OutputMultiOpti
for indiv in children:
# Check that at every fitness values is different from inf
is_valid = (indiv.fitness.valid and indiv.is_simu_valid
and indiv.cstr_viol == 0)
# Add the indiv to the multi_output
self.multi_output.add_evaluation(
indiv.output,
is_valid,
list(indiv),
indiv.fitness.values,
ngen,
)
# Sorting the population according to NSGA2
if self.selector == None:
pop = selNSGA2(pop + children, self.size_pop)
else:
pop = self.selector(pop, self.size_pop)
return self.multi_output
