def main(number):
random.seed(4)
N_ISLES = number
FREQ = 5
pob = int(500 / number)
islands = [toolbox.population(n=pob) for i in range(N_ISLES)]
toolbox.unregister("indices")
toolbox.unregister("individual")
toolbox.unregister("population")
toolbox.register("alg_scoop",
algorithms.eaSimple,
toolbox=toolbox,
cxpb=0.8,
mutpb=0.2,
ngen=5,
verbose=False)
start_time = time.time()
for i in range(0, 400, FREQ):
results = futures.map(toolbox.alg_scoop, islands)
islands = [pop for pop, logbook in results]
tools.migRing(islands, 15, tools.selBest)
print("--- %s seconds ---" % (time.time() - start_time))
return "finished"
def main():
start = time.time()
random.seed(64)
NISLES = 100
islands = [toolbox.population(n=300) for i in range(NISLES)]
# Unregister unpicklable methods before sending the toolbox.
toolbox.unregister("attr_bool")
toolbox.unregister("individual")
toolbox.unregister("population")
NGEN, FREQ = 40, 5
toolbox.register("algorithm",
algorithms.eaSimple,
toolbox=toolbox,
cxpb=0.5,
mutpb=0.2,
ngen=FREQ,
verbose=False)
registration_time = time.time()
for i in range(0, NGEN, FREQ):
results = toolbox.map(toolbox.algorithm, islands)
islands = [pop for pop, logbook in results]
tools.migRing(islands, 1, tools.selBest)
end = time.time()
#print(islands)
print("start time: ")
print(start)
print("registration_time:")
print(registration_time)
print("end time: ")
print(end)
def parallel_evolution():
print_infos()
islands = [toolbox.population(n=POP_SIZE) for i in range(N_ISLES)]
with Parallel(n_jobs=N_JOBS) as parallel:
hof = tools.ParetoFront()
it = 0
while it == 0 or (it < N_GEN
and not stop_cond(islands, STOP_CONDITION)):
#for i in range(0, generations, migration_interval):
print("\nIteration: " + str(it))
res = parallel(
delayed(single_evolver)
(pop=island, n_gen=MIGRATION_INTERVAL, hof=hof, verbose=True)
for island in islands)
islands = []
for pop, logbook, hofi in res:
hof.update(pop)
islands.append(pop)
tools.migRing(islands, N_MIGRATION,
tools.selBest) if N_ISLES > 1 else 0
it += MIGRATION_INTERVAL
#for island in islands:
# print_output(island, it)
#print_output(hof, it,n_ind=N_ISLES)
return hof
def multi_islands():
random.seed(64)
NISLES = 6
islands = [toolbox.population(n=300) for i in range(NISLES)]
# Unregister unpicklable methods before sending the toolbox.
toolbox.unregister("attr_AP")
toolbox.unregister("individual")
toolbox.unregister("population")
NGEN, FREQ = 50, 5
toolbox.register("algorithm",
algorithms.eaSimple,
toolbox=toolbox,
cxpb=0.5,
mutpb=0.2,
ngen=FREQ,
verbose=False)
for i in range(0, NGEN, FREQ):
results = toolbox.map(toolbox.algorithm, islands)
islands = [pop for pop, logbook in results]
tools.migRing(islands, 15, tools.selBest)
for island in islands:
best_inds = tools.selBest(island, 1)
for best_ind in best_inds:
print("Best individual is:\n\t %s\n\t %s" %
(best_ind, best_ind.fitness.values))
eval = SolutionEvaluer()
eval.plot(best_ind)
print("")
return islands
def main():
population = toolbox.populationCreator(n=POPULATION_SIZE)
random.seed(64)
NISLES = 6
stats = tools.Statistics(lambda ind: ind.fitness.values)
stats.register("min", np.min)
stats.register("avg", np.mean)
logbook = tools.Logbook()
logbook.header = "gen", "evals", "min", "avg"
hof = tools.HallOfFame(HALL_OF_FAME_SIZE)
NGEN, FREQ = 40, 30
toolbox.register("algorithm",
algorithms.eaSimple,
toolbox=toolbox,
cxpb=P_CROSSOVER,
mutpb=P_MUTATION,
ngen=MAX_GENERATIONS,
stats=stats,
halloffame=hof,
verbose=True)
islands = [population for i in range(NISLES)]
for i in range(0, MAX_GENERATIONS, FREQ):
results = toolbox.map(toolbox.algorithm, islands)
islands = [population for population, logbook in results]
tools.migRing(islands, 25, tools.selBest)
record = stats.compile(population)
logbook.record(gen=i, evals=len(population), **record)
hof.update(population)
best = hof.items[0]
print(i)
print("-- Best Ever Individual = ", best)
print("-- Best Ever Fitness = ", best.fitness.values[0])
if i == FREQ:
plt.figure(1)
tsp.plotData(best)
minFitnessValues, meanFitnessValues = logbook.select("min", "avg")
plt.figure(2)
sns.set_style("whitegrid")
plt.plot(minFitnessValues, color='red')
plt.plot(meanFitnessValues, color='green')
plt.xlabel('Generation')
plt.ylabel('Min / Average Fitness')
plt.title('Min and Average fitness over Generations')
plt.show()
return islands
def main():
random.seed(64)
NISLES = 5
islands = [toolbox.population(n=300) for i in range(NISLES)]
# Unregister unpicklable methods before sending the toolbox.
toolbox.unregister("attr_bool")
toolbox.unregister("individual")
toolbox.unregister("population")
NGEN, FREQ = 40, 5
toolbox.register("algorithm", algorithms.eaSimple, toolbox=toolbox,
cxpb=0.5, mutpb=0.2, ngen=FREQ, verbose=False)
for i in range(0, NGEN, FREQ):
results = toolbox.map(toolbox.algorithm, islands)
islands = [pop for pop, logbook in results]
tools.migRing(islands, 15, tools.selBest)
return islands
def main():
random.seed(64)
NISLES = 5
islands = [toolbox.population(n=300) for i in range(NISLES)]
# Unregister unpicklable methods before sending the toolbox.
toolbox.unregister("attr_bool")
toolbox.unregister("individual")
toolbox.unregister("population")
NGEN, FREQ = 40, 5
toolbox.register("algorithm",
algorithms.eaSimple,
toolbox=toolbox,
cxpb=0.5,
mutpb=0.2,
ngen=FREQ,
verbose=False)
for i in range(0, NGEN, FREQ):
results = toolbox.map(toolbox.algorithm, islands)
islands = [pop for pop, logbook in results]
tools.migRing(islands, 15, tools.selBest)
return islands
size = comm.Get_size()
rank = comm.Get_rank()
random.seed(4)
N_ISLES = size
FREQ = 5
if rank == 0:
pob = int(500/N_ISLES)
islands = [toolbox.population(n=pob) for i in range(N_ISLES)]
else:
islands = None
toolbox.unregister("indices")
toolbox.unregister("individual")
toolbox.unregister("population")
if rank == 0 :
start_time = time.time()
for i in range (0, 400, FREQ):
islands = comm.scatter(islands,root = 0)
resultsT = algorithms.eaSimple(islands,toolbox=toolbox, cxpb=0.8, mutpb=0.2, ngen=5, verbose=False)
results = comm.gather(resultsT,root=0)
if rank== 0:
islands = [pop for pop, logbook in results]
tools.migRing(islands, 15, tools.selBest)
if rank == 0:
print("--- %s seconds ---" % (time.time() - start_time))
start_time = time.perf_counter()
for it in range(max_iter):
for island in controlIslands:
island.evolution_step()
for island in islands:
island.evolution_step()
# migrate
if np.random.rand() < migration_probability:
populations = [
island.get_population() for island in controlIslands
]
tools.migRing(populations,
k=3,
selection=toolbox.selectMig,
replacement=toolbox.selectRepl)
populations = [island.get_population() for island in islands]
tools.migRing(populations,
k=3,
selection=toolbox.selectMig,
replacement=toolbox.selectRepl)
positions = [island.estimate_position()[0] for island in islands]
mean_position_std = np.std(positions)
diversity_logger.info("{}, {}".format(it, mean_position_std))
results = [island.get_results() for island in islands]
best_result = min([island.get_avg_fitness() for island in islands])
def __call__(self, fixed_schedule_part, initial_schedule, current_time=0, initial_population=None, only_new_pops=False):
##==========================
## create populations
##==========================
##TODO: remake it
creator.create("FitnessMax", base.Fitness, weights=(1.0,))
creator.create("Individual", dict, fitness=creator.FitnessMax)
toolbox = base.Toolbox()
toolbox.register("evaluate", ga_functions.build_fitness(fixed_schedule_part, current_time))
toolbox.register("attr_bool", ga_functions.build_initial(fixed_schedule_part, current_time))
# Structure initializers
toolbox.register("individual", tools.initIterate, creator.Individual, toolbox.attr_bool)
toolbox.register("population", tools.initRepeat, list, toolbox.individual)
## TODO: replace it with strategy and specilized builder
if only_new_pops is True:
## TODO: replace this magic number with parameter
populations = [toolbox.population(n=POPSIZE) for i in range(3)]
else:
## create populations
old_pop = initial_population
newpop = toolbox.population(n=POPSIZE)
#heft_initial = GAFunctions2.schedule_to_chromosome(initial_schedule)
# TODO: this is a stub. Rearchitect information flows and entities responsibilities as soon as you will get the first positive results.
heft_initial = initial_schedule
heft_initial = tools.initIterate(creator.Individual, lambda: heft_initial)
heft_pop = [ga_functions.mutation(deepcopy(heft_initial)) for i in range(POPSIZE)]
populations = [old_pop, newpop, heft_pop]
## TODO: replace this more effective implementation
def quick_save():
whole_pop = reduce(lambda x, y: x+y, populations)
## choose new old pop for the next run
sorted_whole_pop = sorted(whole_pop, key=lambda x: x.fitness.values, reverse=True)
best = sorted_whole_pop[0]
new_oldpop = sorted_whole_pop[0:POPSIZE]
## construct final result
## TODO: implement constructor of final result here
result = ((best, new_oldpop, None, None), common_logbook)
self._save_result(result)
return result
##==========================
## run for several migration periods
##==========================
common_logbook = tools.Logbook()
result = None
for k in range(MIGRATIONS):
new_pops = []
iter_map = {}
for pop in populations:
((best, npop, schedule, stopped_iteration), logbook) = ga_alg(fixed_schedule_part,
None,
current_time=current_time,
initial_population=pop)
new_pops.append(npop)
for rec in logbook:
iter = k*GENERATIONS + rec["iter"]
mp = iter_map.get(iter, [])
mp.append({"worst": rec["worst"], "best": rec["best"], "avr": rec["avr"]})
iter_map[iter] = mp
pass
for iter, items in iter_map.items():
best = max(it["best"] for it in items)
avr = sum(it["avr"] for it in items)/len(items)
worst = min(it["worst"] for it in items)
common_logbook.record(iter=iter, worst=worst, best=best, avr=avr)
pass
populations = new_pops
migRing(populations, migrCount, emigrant_selection)
result = quick_save()
pass
# merge all populations in one and evaluate for some time
# TODO: test this changes
common_pop = functools.reduce(operator.add, populations, [])
for k in range(MERGED_POP):
((best, npop, schedule, stopped_iteration), logbook) = ga_alg(fixed_schedule_part,
None,
current_time=current_time,
initial_population=common_pop)
common_pop = npop
for rec in logbook:
iter = (all_iters_count - MERGED_POP) + rec["iter"]
common_logbook.record(iter=iter, worst=rec["worst"], best=rec["best"], avr=rec["avr"])
pass
result = quick_save()
pass
((best, new_oldpop, x1, x2), x3) = result
result = ((best, new_oldpop, ga_functions.build_schedule(best, fixed_schedule_part, current_time), None), common_logbook)
self._save_result(result[0])
return result
def __call__(self,
fixed_schedule_part,
initial_schedule,
current_time=0,
initial_population=None,
only_new_pops=False):
##==========================
## create populations
##==========================
##TODO: remake it
creator.create("FitnessMax", base.Fitness, weights=(1.0, ))
creator.create("Individual", dict, fitness=creator.FitnessMax)
toolbox = base.Toolbox()
toolbox.register(
"evaluate",
ga_functions.build_fitness(fixed_schedule_part, current_time))
toolbox.register(
"attr_bool",
ga_functions.build_initial(fixed_schedule_part, current_time))
# Structure initializers
toolbox.register("individual", tools.initIterate,
creator.Individual, toolbox.attr_bool)
toolbox.register("population", tools.initRepeat, list,
toolbox.individual)
## TODO: replace it with strategy and specilized builder
if only_new_pops is True:
## TODO: replace this magic number with parameter
populations = [toolbox.population(n=POPSIZE) for i in range(3)]
else:
## create populations
old_pop = initial_population
newpop = toolbox.population(n=POPSIZE)
#heft_initial = GAFunctions2.schedule_to_chromosome(initial_schedule)
# TODO: this is a stub. Rearchitect information flows and entities responsibilities as soon as you will get the first positive results.
heft_initial = initial_schedule if not isinstance(
initial_schedule,
Schedule) else GAFunctions2.schedule_to_chromosome(
initial_schedule, fixed_schedule_part)
heft_initial = tools.initIterate(creator.Individual,
lambda: heft_initial)
heft_pop = [
ga_functions.mutation(deepcopy(heft_initial))
for i in range(POPSIZE)
]
populations = [old_pop, newpop, heft_pop]
## TODO: replace this more effective implementation
def quick_save():
whole_pop = reduce(lambda x, y: x + y, populations)
## choose new old pop for the next run
sorted_whole_pop = sorted(whole_pop,
key=lambda x: x.fitness.values,
reverse=True)
best = sorted_whole_pop[0]
new_oldpop = sorted_whole_pop[0:POPSIZE]
## construct final result
## TODO: implement constructor of final result here
result = ((best, new_oldpop, None, None), common_logbook)
self._save_result(result)
return result
##==========================
## run for several migration periods
##==========================
common_logbook = tools.Logbook()
result = None
for k in range(MIGRATIONS):
new_pops = []
iter_map = {}
for pop in populations:
((best, npop, schedule, stopped_iteration),
logbook) = ga_alg(fixed_schedule_part,
None,
current_time=current_time,
initial_population=pop)
new_pops.append(npop)
# for rec in logbook:
# iter = k*GENERATIONS + rec["iter"]
# mp = iter_map.get(iter, [])
# mp.append({"worst": rec["worst"], "best": rec["best"], "avr": rec["avr"]})
# iter_map[iter] = mp
# pass
for iter, items in iter_map.items():
best = max(it["best"] for it in items)
avr = sum(it["avr"] for it in items) / len(items)
worst = min(it["worst"] for it in items)
common_logbook.record(iter=iter,
worst=worst,
best=best,
avr=avr)
pass
populations = new_pops
migRing(populations, migrCount, emigrant_selection)
result = quick_save()
pass
# merge all populations in one and evaluate for some time
# TODO: test this changes
common_pop = functools.reduce(operator.add, populations, [])
for k in range(MERGED_POP):
((best, npop, schedule, stopped_iteration),
logbook) = ga_alg(fixed_schedule_part,
None,
current_time=current_time,
initial_population=common_pop)
common_pop = npop
# for rec in logbook:
# iter = (all_iters_count - MERGED_POP) + rec["iter"]
# common_logbook.record(iter=iter, worst=rec["worst"], best=rec["best"], avr=rec["avr"])
# pass
result = quick_save()
pass
((best, new_oldpop, x1, x2), x3) = result
result = ((best, new_oldpop,
ga_functions.build_schedule(best, fixed_schedule_part,
current_time), None),
common_logbook)
self._save_result(result[0])
return result