def _test_ad(self, sess, model, hp_dict, neval):
"""Test automatic differentiation.
Args:
model: Mode object.
hp_dict: A dictionary of hyperparameter name and initial values.
"""
hyperparams = dict(
[(hp_name, model.optimizer.hyperparams[hp_name]) for hp_name in hp_dict.keys()])
grads = model.optimizer.grads
accumulators = model.optimizer.accumulators
new_accumulators = model.optimizer.new_accumulators
loss = model.cost
# Build look ahead graph.
look_ahead_ops, grad_ops, zero_out_ops = look_ahead_grads(
hyperparams, grads, accumulators, new_accumulators, loss, dtype=self._dtype)
# Gets variables to be checkpointed.
ckpt_var_list = []
for var_list in model.optimizer.accumulators.values():
ckpt_var_list.extend(var_list)
ckpt_var_list.append(model.global_step)
# Build checkpoint ops.
ckpt = build_checkpoint(ckpt_var_list)
read_checkpoint_op = read_checkpoint(ckpt, ckpt_var_list)
write_checkpoint_op = write_checkpoint(ckpt, ckpt_var_list)
# Initialize weights parameters.
sess.run(tf.global_variables_initializer())
# Checkpoint weights and momentum parameters.
sess.run(write_checkpoint_op)
# Initialize hyperparameters.
for hp_name, init_hp in hp_dict.items():
model.optimizer.assign_hyperparam(sess, hp_name, init_hp)
_, grad_hp = self.run_loss(sess, model, self._batch_size, look_ahead_ops, grad_ops)
# Check the gradient of loss wrt. each hp.
for ii, (hp_name, init_hp) in enumerate(hp_dict.items()):
sess.run(read_checkpoint_op)
sess.run(zero_out_ops)
model.optimizer.assign_hyperparam(sess, hp_name, init_hp - self._eps)
l1, _ = self.run_loss(sess, model, self._batch_size, look_ahead_ops, grad_ops)
sess.run(read_checkpoint_op)
sess.run(zero_out_ops)
model.optimizer.assign_hyperparam(sess, hp_name, init_hp + self._eps)
l2, _ = self.run_loss(sess, model, self._batch_size, look_ahead_ops, grad_ops)
grad_hp_fd = (l2 - l1) / (2 * self._eps)
model.optimizer.assign_hyperparam(sess, hp_name, init_hp)
np.testing.assert_allclose(grad_hp[ii], grad_hp_fd, rtol=self._rtol, atol=self._atol)
def main_raxml_runner(args, op):
""" Run pargenes from the parsed arguments op """
start = time.time()
output_dir = op.output_dir
checkpoint_index = checkpoint.read_checkpoint(output_dir)
if (os.path.exists(output_dir) and not op.do_continue):
logger.info(
"[Error] The output directory " + output_dir +
" already exists. Please use another output directory or run with --continue."
)
sys.exit(1)
commons.makedirs(output_dir)
logger.init_logger(op.output_dir)
print_header(args)
msas = None
logger.timed_log("end of MSAs initializations")
scriptdir = os.path.dirname(os.path.realpath(__file__))
modeltest_run_path = os.path.join(output_dir, "modeltest_run")
raxml_run_path = os.path.join(output_dir, "mlsearch_run")
binaries_dir = os.path.join(scriptdir, "..", "pargenes_binaries")
print("Binaries directory: " + binaries_dir)
if (op.scheduler != "split"):
raxml_library = os.path.join(binaries_dir, "raxml-ng")
modeltest_library = os.path.join(binaries_dir, "modeltest-ng")
else:
raxml_library = os.path.join(binaries_dir, "raxml-ng-mpi.so")
modeltest_library = os.path.join(binaries_dir, "modeltest-ng-mpi.so")
astral_jar = os.path.join(binaries_dir, "astral.jar")
if (len(op.raxml_binary) > 1):
raxml_library = op.raxml_binary
if (len(op.modeltest_binary) > 1):
modeltest_library = op.modeltest_binary
if (len(op.astral_jar) > 1):
astral_jar = op.astral_jar
astral_jar = os.path.abspath(astral_jar)
if (checkpoint_index < 1):
msas = commons.init_msas(op)
raxml.run_parsing_step(msas, raxml_library, op.scheduler,
os.path.join(output_dir, "parse_run"), op.cores,
op)
raxml.analyse_parsed_msas(msas, op)
checkpoint.write_checkpoint(output_dir, 1)
logger.timed_log("end of parsing mpi-scheduler run")
else:
msas = raxml.load_msas(op)
if (op.dry_run):
logger.info("End of the dry run. Exiting")
return 0
logger.timed_log("end of anlysing parsing results")
if (op.use_modeltest):
if (checkpoint_index < 2):
modeltest.run(msas, output_dir, modeltest_library,
modeltest_run_path, op)
logger.timed_log("end of modeltest mpi-scheduler run")
modeltest.parse_modeltest_results(op.modeltest_criteria, msas,
output_dir)
logger.timed_log("end of parsing modeltest results")
# then recompute the binary MSA files to put the correct model, and reevaluate the MSA sizes with the new models
shutil.move(os.path.join(output_dir, "parse_run"),
os.path.join(output_dir, "old_parse_run"))
raxml.run_parsing_step(msas, raxml_library, op.scheduler,
os.path.join(output_dir, "parse_run"),
op.cores, op)
raxml.analyse_parsed_msas(msas, op)
logger.timed_log("end of the second parsing step")
checkpoint.write_checkpoint(output_dir, 2)
if (checkpoint_index < 3):
raxml.run(msas, op.random_starting_trees, op.parsimony_starting_trees,
op.bootstraps, raxml_library, op.scheduler, raxml_run_path,
op.cores, op)
logger.timed_log("end of mlsearch mpi-scheduler run")
checkpoint.write_checkpoint(output_dir, 3)
if (op.random_starting_trees + op.parsimony_starting_trees > 1):
if (checkpoint_index < 4):
raxml.select_best_ml_tree(msas, op)
logger.timed_log("end of selecting the best ML tree")
checkpoint.write_checkpoint(output_dir, 4)
if (op.bootstraps != 0):
if (checkpoint_index < 5):
bootstraps.concatenate_bootstraps(output_dir, min(16, op.cores))
logger.timed_log("end of bootstraps concatenation")
checkpoint.write_checkpoint(output_dir, 5)
starting_trees = op.random_starting_trees + op.parsimony_starting_trees
if (checkpoint_index < 6 and starting_trees > 0):
bootstraps.run(msas, output_dir, raxml_library, op.scheduler,
os.path.join(output_dir, "supports_run"), op.cores,
op)
logger.timed_log("end of supports mpi-scheduler run")
checkpoint.write_checkpoint(output_dir, 6)
if (op.use_astral):
if (checkpoint_index < 7):
astral.run_astral_pargenes(astral_jar, op)
checkpoint.write_checkpoint(output_dir, 7)
all_invalid = True
for name, msa in msas.items():
if (msa.valid):
all_invalid = False
if (all_invalid):
print("[Error] ParGenes failed to analyze all MSAs.")
report.report_and_exit(op.output_dir, 1)
print_stats(op)
return 0
def online_smd(dataset_name='mnist',
init_lr=1e-1,
momentum=0.001,
num_steps=20000,
middle_decay=False,
steps_per_update=10,
smd=True,
steps_look_ahead=5,
num_meta_steps=10,
steps_per_eval=100,
batch_size=100,
meta_lr=1e-2,
print_step=False,
effective_lr=True,
negative_momentum=True,
optimizer='momentum',
stochastic=True,
exp_folder='.'):
"""Train an MLP for MNIST.
Args:
dataset_name: String. Name of the dataset.
init_lr: Float. Initial learning rate, default 0.1.
momentum: Float. Initial momentum, default 0.9.
num_steps: Int. Total number of steps, default 20000.
middle_decay: Whether applying manual learning rate decay to 1e-4 from the middle, default False.
steps_per_update: Int. Number of steps per update, default 10.
smd: Bool. Whether run SMD.
steps_look_ahead: Int. Number of steps to look ahead, default 5.
num_meta_steps: Int. Number of meta steps, default 10.
steps_per_eval: Int. Number of training steps per evaluation, default 100.
batch_size: Int. Mini-batch size, default 100.
meta_lr: Float. Meta learning rate, default 1e-2.
print_step: Bool. Whether to print loss during training, default True.
effective_lr: Bool. Whether to re-parameterize learning rate as lr / (1 - momentum), default True.
negative_momentum: Bool. Whether to re-parameterize momentum as (1 - momentum), default True.
optimizer: String. Name of the optimizer. Options: `momentum`, `adam, default `momentum`.
stochastic: Bool. Whether to do stochastic or deterministic look ahead, default True.
Returns:
results: Results tuple object.
"""
dataset = get_dataset(dataset_name)
dataset_train = get_dataset(
dataset_name) # For evaluate training progress (full epoch).
dataset_test = get_dataset(
dataset_name, test=True) # For evaluate test progress (full epoch).
if dataset_name == 'mnist':
input_shape = [None, 28, 28, 1]
elif dataset_name.startswith('cifar'):
input_shape = [None, 32, 32, 3]
x = tf.placeholder(tf.float32, input_shape, name="x")
y = tf.placeholder(tf.int64, [None], name="y")
if effective_lr:
init_lr_ = init_lr / (1.0 - momentum)
else:
init_lr_ = init_lr
if negative_momentum:
init_mom_ = 1.0 - momentum
else:
init_mom_ = momentum
if dataset_name == 'mnist':
config = get_mnist_mlp_config(
init_lr_,
init_mom_,
effective_lr=effective_lr,
negative_momentum=negative_momentum)
elif dataset_name == 'cifar-10':
config = get_cifar_cnn_config(
init_lr_,
init_mom_,
effective_lr=effective_lr,
negative_momentum=negative_momentum)
else:
raise NotImplemented
with tf.name_scope('Train'):
with tf.variable_scope('Model'):
if dataset_name == 'mnist':
m = get_mnist_mlp_model(
config, x, y, optimizer=optimizer, training=True)
model = m
elif dataset_name == 'cifar-10':
m = get_cifar_cnn_model(
config, x, y, optimizer=optimizer, training=True)
model = m
with tf.name_scope('Test'):
with tf.variable_scope('Model', reuse=True):
if dataset_name == 'mnist':
mtest = get_mnist_mlp_model(config, x, y, training=False)
elif dataset_name == 'cifar-10':
mtest = get_cifar_cnn_model(config, x, y, training=False)
final_lr = 1e-4
midpoint = num_steps // 2
if dataset_name == 'mnist':
num_train = 60000
num_test = 10000
elif dataset_name.startswith('cifar'):
num_train = 50000
num_test = 10000
lr_ = init_lr_
mom_ = init_mom_
bsize = batch_size
steps_per_epoch = num_train // bsize
steps_test_per_epoch = num_test // bsize
train_xent_list = []
train_acc_list = []
test_xent_list = []
test_acc_list = []
lr_list = []
mom_list = []
step_list = []
log.info(
'Applying decay at midpoint with final learning rate = {:.3e}'.format(
final_lr))
if 'momentum' in optimizer:
mom_name = 'mom'
elif 'adam' in optimizer:
mom_name = 'beta1'
else:
raise ValueError('Unknown optimizer')
hp_dict = {'lr': init_lr} #, mom_name: momentum}
hp_names = hp_dict.keys()
hyperparams = dict([(hp_name, model.optimizer.hyperparams[hp_name])
for hp_name in hp_names])
grads = model.optimizer.grads
accumulators = model.optimizer.accumulators
new_accumulators = model.optimizer.new_accumulators
loss = model.cost
# Build look ahead graph.
look_ahead_ops, hp_grad_ops, zero_out_ops = look_ahead_grads(
hyperparams, grads, accumulators, new_accumulators, loss)
# Meta optimizer, use Adam on the log space.
meta_opt = LogOptimizer(tf.train.AdamOptimizer(meta_lr))
hp = [model.optimizer.hyperparams[hp_name] for hp_name in hp_names]
hp_grads_dict = {
'lr': tf.placeholder(tf.float32, [], name='lr_grad'),
# mom_name: tf.placeholder(
# tf.float32, [], name='{}_grad'.format(mom_name))
}
hp_grads_plh = [hp_grads_dict[hp_name] for hp_name in hp_names]
hp_grads_and_vars = list(zip(hp_grads_plh, hp))
cgrad = {'lr': (-1e1, 1e1)} #, mom_name: (-1e1, 1e1)}
cval = {'lr': (1e-4, 1e1)} #, mom_name: (1e-4, 1e0)}
cgrad_ = [cgrad[hp_name] for hp_name in hp_names]
cval_ = [cval[hp_name] for hp_name in hp_names]
meta_train_op = meta_opt.apply_gradients(
hp_grads_and_vars, clip_gradients=cgrad_, clip_values=cval_)
var_list = tf.global_variables()
ckpt = build_checkpoint(tf.global_variables())
write_op = write_checkpoint(ckpt, var_list)
read_op = read_checkpoint(ckpt, var_list)
with tf.Session() as sess:
sess.run(tf.global_variables_initializer())
exp_logger = _get_exp_logger(sess, exp_folder)
def log_hp(hp_dict):
lr_ = hp_dict['lr']
mom_ = hp_dict['mom']
# Log current learning rate and momentum.
if negative_momentum:
exp_logger.log(ii, 'mom', 1.0 - mom_)
exp_logger.log(ii, 'log neg mom', np.log10(mom_))
mom__ = 1.0 - mom_
else:
exp_logger.log(ii, 'mom', mom_)
exp_logger.log(ii, 'log neg mom', np.log10(1.0 - mom_))
mom__ = mom_
if effective_lr:
lr__ = lr_ * (1.0 - mom__)
eflr_ = lr_
else:
lr__ = lr_
eflr_ = lr_ / (1.0 - mom__)
exp_logger.log(ii, 'eff lr', eflr_)
exp_logger.log(ii, 'log eff lr', np.log10(eflr_))
exp_logger.log(ii, 'lr', lr__)
exp_logger.log(ii, 'log lr', np.log10(lr__))
exp_logger.flush()
return lr__, mom__
# Assign initial learning rate and momentum.
m.optimizer.assign_hyperparam(sess, 'lr', lr_)
m.optimizer.assign_hyperparam(sess, 'mom', mom_)
train_iter = six.moves.xrange(num_steps)
if not print_step:
train_iter = tqdm(train_iter, ncols=0)
for ii in train_iter:
# Meta-optimization loop.
if ii == 0 or ii % steps_per_update == 0:
if ii < midpoint and smd:
if stochastic:
data_list = [
dataset.next_batch(bsize)
for step in six.moves.xrange(steps_look_ahead)
]
# Take next few batches for last step evaluation.
eval_data_list = [
dataset.next_batch(bsize)
for step in six.moves.xrange(steps_look_ahead)
]
else:
data_entry = dataset.next_batch(bsize)
data_list = [data_entry] * steps_look_ahead
# Use the deterministic batch for last step evaluation.
eval_data_list = [data_list[0]]
sess.run(write_op)
for ms in six.moves.xrange(num_meta_steps):
cost, hp_dict = meta_step(sess, model, data_list,
look_ahead_ops, hp_grad_ops,
hp_grads_plh, meta_train_op,
eval_data_list)
sess.run(read_op)
for hpname, hpval in hp_dict.items():
model.optimizer.assign_hyperparam(
sess, hpname, hpval)
lr_ = hp_dict['lr']
# mom_ = hp_dict['mom']
else:
hp_dict = sess.run(model.optimizer.hyperparams)
lr_log, mom_log = log_hp(hp_dict)
lr_list.append(lr_log)
mom_list.append(mom_log)
if ii == midpoint // 2:
m.optimizer.assign_hyperparam(sess, 'mom', 1 - 0.9)
if ii == midpoint:
lr_before_mid = hp_dict['lr']
tau = (num_steps - midpoint) / np.log(lr_before_mid / final_lr)
if ii > midpoint:
lr_ = np.exp(-(ii - midpoint) / tau) * lr_before_mid
m.optimizer.assign_hyperparam(sess, 'lr', lr_)
# Run regular training.
if lr_ > 1e-6:
# Use CBL for first half of training
xd, yd = data_entry if (smd and not stochastic and ii < midpoint) else dataset.next_batch(bsize)
cost_, _ = sess.run(
[m.cost, m.train_op], feed_dict={
m.x: xd,
m.y: yd
})
if ii < midpoint:
sess.run(m._retrieve_ema_op)
# Evaluate every certain number of steps.
if ii == 0 or (ii + 1) % steps_per_eval == 0:
test_acc = 0.0
test_xent = 0.0
train_acc = 0.0
train_xent = 0.0
# Report full epoch training loss.
for jj in six.moves.xrange(steps_per_epoch):
xd, yd = dataset_train.next_batch(bsize)
xent_, acc_ = sess.run(
[m.cost, m.acc], feed_dict={
x: xd,
y: yd
})
train_xent += xent_ / float(steps_per_epoch)
train_acc += acc_ / float(steps_per_epoch)
step_list.append(ii + 1)
train_xent_list.append(train_xent)
train_acc_list.append(train_acc)
dataset_train.reset()
# Report full epoch validation loss.
for jj in six.moves.xrange(steps_test_per_epoch):
xd, yd = dataset_test.next_batch(bsize)
xent_, acc_ = sess.run(
[mtest.cost, mtest.acc], feed_dict={
x: xd,
y: yd
})
test_xent += xent_ / float(steps_test_per_epoch)
test_acc += acc_ / float(steps_test_per_epoch)
test_xent_list.append(test_xent)
test_acc_list.append(test_acc)
dataset_test.reset()
# Log training progress.
exp_logger.log(ii, 'train loss', train_xent)
exp_logger.log(ii, 'log train loss', np.log10(train_xent))
exp_logger.log(ii, 'test loss', test_xent)
exp_logger.log(ii, 'log test loss', np.log10(test_xent))
exp_logger.log(ii, 'train acc', train_acc)
exp_logger.log(ii, 'test acc', test_acc)
exp_logger.flush()
if print_step:
log.info((
'Steps {:d} T Xent {:.3e} T Acc {:.3f} V Xent {:.3e} V Acc {:.3f} '
'LR {:.3e}').format(ii + 1, train_xent,
train_acc * 100.0, test_xent,
test_acc * 100.0, lr_))
return Results(
step=np.array(step_list),
train_xent=np.array(train_xent_list),
train_acc=np.array(train_acc_list),
test_xent=np.array(test_xent_list),
test_acc=np.array(test_acc_list),
lr=np.array(lr_list),
momentum=np.array(mom_list))
def run_offline_smd(num_steps,
init_lr,
init_decay,
meta_lr,
num_meta_steps,
momentum=MOMENTUM,
effective_lr=False,
negative_momentum=False,
pretrain_ckpt=None,
output_fname=None,
seed=0):
"""Run offline SMD experiments.
Args:
init_lr: Initial learning rate.
init_decay: Initial decay constant.
data_list: List of tuples of inputs and labels.
meta_lr: Float. Meta descent learning rate.
num_meta_steps: Int. Number of meta descent steps.
momentum: Float. Momentum.
effective_lr: Bool. Whether to optimize in the effective LR space.
negative_momentum: Bool. Whether to optimize in the negative momentum space.
"""
bsize = BATCH_SIZE
if output_fname is not None:
log_folder = os.path.dirname(output_fname)
else:
log_folder = os.path.join('results', 'mnist', 'offline', 'smd')
log_folder = os.path.join(log_folder, _get_run_number(log_folder))
if not os.path.exists(log_folder):
os.makedirs(log_folder)
with tf.Graph().as_default(), tf.Session() as sess:
dataset = get_dataset('mnist')
exp_logger = _get_exp_logger(sess, log_folder)
if effective_lr:
init_lr_ = init_lr / float(1.0 - momentum)
else:
init_lr_ = init_lr
if negative_momentum:
init_mom_ = 1.0 - momentum
else:
init_mom_ = momentum
config = get_mnist_mlp_config(
init_lr_,
init_mom_,
decay=init_decay,
effective_lr=effective_lr,
negative_momentum=negative_momentum)
x = tf.placeholder(tf.float32, [None, 28, 28, 1], name="x")
y = tf.placeholder(tf.int64, [None], name="y")
with tf.name_scope('Train'):
with tf.variable_scope('Model'):
model = get_mnist_mlp_model(
config,
x,
y,
optimizer='momentum_inv_decay',
training=True)
all_vars = tf.global_variables()
var_to_restore = list(
filter(lambda x: 'momentum' not in x.name.lower(), all_vars))
var_to_restore = list(
filter(lambda x: 'global_step' not in x.name.lower(),
var_to_restore))
var_to_restore = list(
filter(lambda x: 'lr' not in x.name.lower(), var_to_restore))
var_to_restore = list(
filter(lambda x: 'mom' not in x.name.lower(), var_to_restore))
var_to_restore = list(
filter(lambda x: 'decay' not in x.name.lower(), var_to_restore))
saver = tf.train.Saver(var_to_restore)
rnd = np.random.RandomState(seed)
hp_dict = {'lr': init_lr, 'decay': init_decay}
hp_names = hp_dict.keys()
hyperparams = dict([(hp_name, model.optimizer.hyperparams[hp_name])
for hp_name in hp_names])
grads = model.optimizer.grads
accumulators = model.optimizer.accumulators
new_accumulators = model.optimizer.new_accumulators
loss = model.cost
# Build look ahead graph.
look_ahead_ops, hp_grad_ops, zero_out_ops = look_ahead_grads(
hyperparams, grads, accumulators, new_accumulators, loss)
# Meta optimizer, use Adam on the log space.
# meta_opt = LogOptimizer(tf.train.AdamOptimizer(meta_lr))
meta_opt = LogOptimizer(tf.train.MomentumOptimizer(meta_lr, 0.9))
hp = [model.optimizer.hyperparams[hp_name] for hp_name in hp_names]
hp_grads_dict = {
'lr': tf.placeholder(tf.float32, [], name='lr_grad'),
'decay': tf.placeholder(tf.float32, [], name='decay_grad')
}
hp_grads_plh = [hp_grads_dict[hp_name] for hp_name in hp_names]
hp_grads_and_vars = list(zip(hp_grads_plh, hp))
cgrad = {'lr': (-1e1, 1e1), 'decay': (-1e1, 1e1)}
cval = {'lr': (1e-4, 1e1), 'decay': (1e-4, 1e3)}
cgrad_ = [cgrad[hp_name] for hp_name in hp_names]
cval_ = [cval[hp_name] for hp_name in hp_names]
meta_train_op = meta_opt.apply_gradients(
hp_grads_and_vars, clip_gradients=cgrad_, clip_values=cval_)
if output_fname is not None:
msg = '{} exists, please remove previous experiment data.'.format(
output_fname)
assert not os.path.exists(output_fname), msg
log.info('Writing to {}'.format(output_fname))
with open(output_fname, 'w') as f:
f.write('Step,LR,Mom,Decay,Loss\n')
# Initialize all variables.
sess.run(tf.global_variables_initializer())
var_list = tf.global_variables()
if pretrain_ckpt is not None:
saver.restore(sess, pretrain_ckpt)
ckpt = build_checkpoint(var_list)
write_op = write_checkpoint(ckpt, var_list)
read_op = read_checkpoint(ckpt, var_list)
sess.run(write_op)
# Progress bar.
it = tqdm(
six.moves.xrange(num_meta_steps),
ncols=0,
desc='look_{}_ilr_{:.0e}_decay_{:.0e}'.format(
num_steps, init_lr, init_decay))
for run in it:
# Stochastic data list makes the SMD converge faster.
data_list = [
dataset.next_batch(bsize)
for step in six.moves.xrange(num_steps)
]
eval_data_list = [
dataset.next_batch(bsize)
for step in six.moves.xrange(NUM_TRAIN // bsize)
]
# Run meta descent step.
cost, hp_dict = meta_step(sess, model, data_list, look_ahead_ops,
hp_grad_ops, hp_grads_plh, meta_train_op,
eval_data_list)
# Early stop if hits NaN.
if np.isnan(cost):
break
# Restore parameters.
sess.run(read_op)
for hpname, hpval in hp_dict.items():
model.optimizer.assign_hyperparam(sess, hpname, hpval)
# Read out hyperparameters in normal parameterization.
if negative_momentum:
mom = 1 - hp_dict['mom']
else:
mom = hp_dict['mom']
if effective_lr:
lr = hp_dict['lr'] * (1 - mom)
else:
lr = hp_dict['lr']
# Write to logs.
if output_fname is not None:
with open(output_fname, 'a') as f:
f.write('{:d},{:f},{:f},{:f},{:f}\n'.format(
run, lr, hp_dict['mom'], hp_dict['decay'], cost))
# Log to TensorBoard.
exp_logger.log(run, 'lr', lr)
exp_logger.log(run, 'decay', hp_dict['decay'])
exp_logger.log(run, 'log loss', np.log10(cost))
exp_logger.flush()
# Update progress bar.
it.set_postfix(
lr='{:.3e}'.format(lr),
decay='{:.3e}'.format(hp_dict['decay']),
loss='{:.3e}'.format(cost))
exp_logger.close()
def main_raxml_runner(op):
""" Run pargenes from the parsed arguments op """
start = time.time()
output_dir = op.output_dir
checkpoint_index = checkpoint.read_checkpoint(output_dir)
print("Checkpoint: " + str(checkpoint_index))
if (os.path.exists(output_dir) and not op.do_continue):
print(
"[Error] The output directory " + output_dir +
" already exists. Please use another output directory or run with --continue."
)
sys.exit(1)
commons.makedirs(output_dir)
logs = commons.get_log_file(output_dir, "pargenes_logs")
print("Redirecting logs to " + logs)
sys.stdout = open(logs, "w")
print_header()
msas = commons.init_msas(op)
timed_print(start, "end of MSAs initializations")
scriptdir = os.path.dirname(os.path.realpath(__file__))
modeltest_run_path = os.path.join(output_dir, "modeltest_run")
raxml_run_path = os.path.join(output_dir, "mlsearch_run")
if (op.scheduler == "onecore"):
raxml_library = os.path.join(scriptdir, "..", "raxml-ng", "bin",
"raxml-ng")
modeltest_library = os.path.join(scriptdir, "..", "modeltest", "bin",
"modeltest-ng")
else:
raxml_library = os.path.join(scriptdir, "..", "raxml-ng", "bin",
"raxml-ng-mpi.so")
modeltest_library = os.path.join(scriptdir, "..", "modeltest", "build",
"src", "modeltest-ng-mpi.so")
if (checkpoint_index < 1):
raxml.run_parsing_step(msas, raxml_library, op.scheduler,
os.path.join(output_dir, "parse_run"), op.cores,
op)
checkpoint.write_checkpoint(output_dir, 1)
timed_print(start, "end of parsing mpi-scheduler run")
raxml.analyse_parsed_msas(msas, op, output_dir)
if (op.dry_run):
print("End of the dry run. Exiting")
return 0
timed_print(start, "end of anlysing parsing results")
if (op.use_modeltest):
if (checkpoint_index < 2):
modeltest.run(msas, output_dir, modeltest_library,
modeltest_run_path, op)
timed_print(start, "end of modeltest mpi-scheduler run")
modeltest.parse_modeltest_results(op.modeltest_criteria, msas,
output_dir)
timed_print(start, "end of parsing modeltest results")
# then recompute the binary MSA files to put the correct model, and reevaluate the MSA sizes with the new models
shutil.move(os.path.join(output_dir, "parse_run"),
os.path.join(output_dir, "old_parse_run"))
raxml.run_parsing_step(msas, raxml_library, op.scheduler,
os.path.join(output_dir, "parse_run"),
op.cores, op)
raxml.analyse_parsed_msas(msas, op, output_dir)
timed_print(start, "end of the second parsing step")
checkpoint.write_checkpoint(output_dir, 2)
if (checkpoint_index < 3):
raxml.run(msas, op.random_starting_trees, op.parsimony_starting_trees,
op.bootstraps, raxml_library, op.scheduler, raxml_run_path,
op.cores, op)
timed_print(start, "end of mlsearch mpi-scheduler run")
checkpoint.write_checkpoint(output_dir, 3)
if (op.random_starting_trees + op.parsimony_starting_trees > 1):
if (checkpoint_index < 4):
raxml.select_best_ml_tree(msas, op)
timed_print(start, "end of selecting the best ML tree")
checkpoint.write_checkpoint(output_dir, 4)
if (op.bootstraps != 0):
if (checkpoint_index < 5):
bootstraps.concatenate_bootstraps(output_dir, min(16, op.cores))
timed_print(start, "end of bootstraps concatenation")
checkpoint.write_checkpoint(output_dir, 5)
if (checkpoint_index < 6):
bootstraps.run(output_dir, raxml_library, op.scheduler,
os.path.join(output_dir, "supports_run"), op.cores,
op)
timed_print(start, "end of supports mpi-scheduler run")
checkpoint.write_checkpoint(output_dir, 6)
return 0