def watch(configs, gen, num_workers, output_dir, num_survive, fitness_direction):
dump_dir = output_dir + "/to_master/" + str(gen)
t_start = time.time()
popn, num_finished, dir_checks = [], 0,0
ids = [str(i) for i in range(1, num_workers + 1)]
while (num_finished < num_workers):
time.sleep(1)
dir_checks+=1
for root, dirs, files in os.walk(dump_dir):
for f in files:
if f in ids:
if (os.path.getmtime(root + "/" + f) + 1 < time.time()):
dump_file = output_dir + "/to_master/" + str(gen) + "/" + str(f)
with open(dump_file, 'rb') as file:
try:
worker_pop = pickle.load(file)
popn += worker_pop[:num_survive]
num_finished += 1
ids.remove(f)
except: pass
#sort and delete some
sorted_popn = fitness.eval_fitness(popn, fitness_direction)
popn = sorted_popn[:num_survive]
del sorted_popn
assert (not ids)
t_end = time.time()
time_elapsed = t_end - t_start
if (gen % 100 == 0): util.cluster_print(output_dir,"master finished extracting workers after " + str(time_elapsed) + " seconds, and making " + str(dir_checks) + " dir checks.")
return popn
def parse_worker_popn (num_workers, gen, output_dir, num_survive, fitness_direction):
popn = []
print('master.parse_worker_popn(): num workers = ' + str(num_workers) + " and gen " + str(gen))
print("parse worker pop params: dir = " + str(output_dir) + ".")
for w in range(1,num_workers+1):
dump_file = output_dir + "/to_master/" + str(gen) + "/" + str(w)
with open(dump_file, 'rb') as file:
worker_pop = pickle.load(file)
i=0
for indiv in worker_pop:
popn.append(indiv)
i+=1
sorted_popn = fitness.eval_fitness(popn, fitness_direction)
return sorted_popn[:num_survive]
def evolve_minion(worker_file, gen, rank, output_dir):
t_start = time.time()
with open(str(worker_file), 'rb') as file:
worker_ID, seed, worker_gens, pop_size, num_return, randSeed, curr_gen, configs = pickle.load(
file)
file.close()
survive_fraction = float(configs['worker_percent_survive']) / 100
num_survive = math.ceil(survive_fraction * pop_size)
output_dir = configs['output_directory'].replace(
"v4nu_minknap_1X_both_reverse/", '')
#output_dir += str(worker_ID)
max_gen = int(configs['max_generations'])
control = configs['control']
if (control == "None"): control = None
fitness_direction = str(configs['fitness_direction'])
node_edge_ratio = float(configs['edge_to_node_ratio'])
random.seed(randSeed)
population = gen_population_from_seed(seed, pop_size)
start_size = len(seed.net.nodes())
pressurize_time = 0
mutate_time = 0
for g in range(worker_gens):
gen_percent = float(curr_gen / max_gen)
if (g != 0):
for p in range(num_survive, pop_size):
population[p] = population[p % num_survive].copy()
#assert (population[p] != population[p%num_survive])
#assert (population[p].net != population[p % num_survive].net)
for p in range(pop_size):
t0 = ptime()
mutate.mutate(configs, population[p].net, gen_percent,
node_edge_ratio)
t1 = ptime()
mutate_time += t1 - t0
if (control == None):
pressure_results = pressurize.pressurize(
configs, population[p].net, None
) # false: don't track node fitness, None: don't write instances to file
population[p].fitness_parts[0], population[p].fitness_parts[
1], population[p].fitness_parts[2] = pressure_results[
0], pressure_results[1], pressure_results[2]
else:
util.cluster_print(
output_dir, "ERROR in minion(): unknown control config: " +
str(control))
old_popn = population
population = fitness.eval_fitness(old_popn, fitness_direction)
del old_popn
#debug(population,worker_ID, output_dir)
curr_gen += 1
write_out_worker(output_dir + "/to_master/" + str(gen) + "/" + str(rank),
population, num_return)
# some output, probably outdated
if (worker_ID == 0):
orig_dir = configs['output_directory']
end_size = len(population[0].net.nodes())
growth = end_size - start_size
output.minion_csv(orig_dir, pressurize_time, growth, end_size)
#debug(population, worker_ID, output_dir)
#if (worker_ID==0): util.cluster_print(output_dir,"Pressurizing took " + str(pressurize_time) + " secs, while mutate took " + str(mutate_time) + " secs.")
t_end = time.time()
time_elapsed = t_end - t_start
if (rank == 1 or rank == 32 or rank == 63):
util.cluster_print(
output_dir, "Worker #" + str(rank) + " finishing after " +
str(time_elapsed) + " seconds")
def sort_popn(population, fitness_direction):
old_popn = population
population = fitness.eval_fitness(old_popn, fitness_direction)
del old_popn
return population