def setup(data_reader_file,
name='classifier',
num_labels=200,
mini_batch_size=128,
num_epochs=1000,
learning_rate=0.1,
bn_statistics_group_size=2,
fc_data_layout='model_parallel',
warmup_epochs=50,
learning_rate_drop_interval=50,
learning_rate_drop_factor=0.25,
checkpoint_interval=None):
# Setup input data
input = lbann.Input(target_mode = 'classification')
images = lbann.Identity(input)
labels = lbann.Identity(input)
# Classification network
head_cnn = modules.ResNet(bn_statistics_group_size=bn_statistics_group_size)
class_fc = lbann.modules.FullyConnectedModule(num_labels,
activation=lbann.Softmax,
name=f'{name}_fc',
data_layout=fc_data_layout)
x = head_cnn(images)
probs = class_fc(x)
# Setup objective function
cross_entropy = lbann.CrossEntropy([probs, labels])
l2_reg_weights = set()
for l in lbann.traverse_layer_graph(input):
if type(l) == lbann.Convolution or type(l) == lbann.FullyConnected:
l2_reg_weights.update(l.weights)
l2_reg = lbann.L2WeightRegularization(weights=l2_reg_weights, scale=0.0002)
obj = lbann.ObjectiveFunction([cross_entropy, l2_reg])
# Setup model
metrics = [lbann.Metric(lbann.CategoricalAccuracy([probs, labels]),
name='accuracy', unit='%')]
callbacks = [lbann.CallbackPrint(), lbann.CallbackTimer()]
if checkpoint_interval:
callbacks.append(
lbann.CallbackCheckpoint(
checkpoint_dir='ckpt',
checkpoint_epochs=5
)
)
# Learning rate schedules
if warmup_epochs:
callbacks.append(
lbann.CallbackLinearGrowthLearningRate(
target=learning_rate * mini_batch_size / 128,
num_epochs=warmup_epochs
)
)
if learning_rate_drop_factor:
callbacks.append(
lbann.CallbackDropFixedLearningRate(
drop_epoch=list(range(0, num_epochs, learning_rate_drop_interval)),
amt=learning_rate_drop_factor)
)
# Construct model
model = lbann.Model(num_epochs,
layers=lbann.traverse_layer_graph(input),
objective_function=obj,
metrics=metrics,
callbacks=callbacks)
# Setup optimizer
# opt = lbann.Adam(learn_rate=learning_rate, beta1=0.9, beta2=0.999, eps=1e-8)
opt = lbann.SGD(learn_rate=learning_rate, momentum=0.9)
# Load data reader from prototext
data_reader_proto = lbann.lbann_pb2.LbannPB()
with open(data_reader_file, 'r') as f:
google.protobuf.text_format.Merge(f.read(), data_reader_proto)
data_reader_proto = data_reader_proto.data_reader
for reader_proto in data_reader_proto.reader:
reader_proto.python.module_dir = os.path.dirname(os.path.realpath(__file__))
# Return experiment objects
return model, data_reader_proto, opt
def construct_model(run_args):
"""Construct LBANN model.
Initial model for ATOM molecular VAE
"""
import lbann
pad_index = run_args.pad_index
assert pad_index is not None
sequence_length = run_args.sequence_length
assert sequence_length is not None
print("sequence length is {}".format(sequence_length))
data_layout = "data_parallel"
# Layer graph
input_ = lbann.Identity(lbann.Input(name='inp', target_mode="N/A"),
name='inp1')
vae_loss = []
input_feature_dims = sequence_length
embedding_size = run_args.embedding_dim
dictionary_size = run_args.num_embeddings
assert embedding_size is not None
assert dictionary_size is not None
kl, recon = molvae.MolVAE(input_feature_dims, dictionary_size,
embedding_size, pad_index)(input_)
vae_loss.append(kl)
vae_loss.append(recon)
print("LEN vae loss ", len(vae_loss))
layers = list(lbann.traverse_layer_graph(input_))
# Setup objective function
weights = set()
for l in layers:
weights.update(l.weights)
l2_reg = lbann.L2WeightRegularization(weights=weights, scale=5e-4)
obj = lbann.ObjectiveFunction(vae_loss)
# Initialize check metric callback
metrics = [
lbann.Metric(kl, name='kl_loss'),
lbann.Metric(recon, name='recon')
]
callbacks = [lbann.CallbackPrint(), lbann.CallbackTimer()]
if (run_args.dump_weights_interval > 0):
callbacks.append(
lbann.CallbackDumpWeights(
directory=run_args.dump_weights_dir,
epoch_interval=run_args.dump_weights_interval))
if (run_args.ltfb):
send_name = ('' if run_args.weights_to_send == 'All' else
run_args.weights_to_send) #hack for Merlin empty string
weights_to_ex = [w.name for w in weights if send_name in w.name]
print("LTFB Weights to exchange ", weights_to_ex)
callbacks.append(
lbann.CallbackLTFB(batch_interval=run_args.ltfb_batch_interval,
metric='recon',
weights=list2str(weights_to_ex),
low_score_wins=True,
exchange_hyperparameters=True))
if (run_args.warmup):
callbacks.append(
lbann.CallbackLinearGrowthLearningRate(target=run_args.lr / 512 *
run_args.batch_size,
num_epochs=5))
# Construct model
return lbann.Model(run_args.num_epochs,
weights=weights,
layers=layers,
objective_function=obj,
metrics=metrics,
callbacks=callbacks)
def setup(num_patches=3,
mini_batch_size=512,
num_epochs=75,
learning_rate=0.005,
bn_statistics_group_size=2,
fc_data_layout='model_parallel',
warmup=True,
checkpoint_interval=None):
# Data dimensions
patch_dims = patch_generator.patch_dims
num_labels = patch_generator.num_labels(num_patches)
# Extract tensors from data sample
input = lbann.Input()
slice_points = [0]
for _ in range(num_patches):
patch_size = functools.reduce(operator.mul, patch_dims)
slice_points.append(slice_points[-1] + patch_size)
slice_points.append(slice_points[-1] + num_labels)
sample = lbann.Slice(input, slice_points=str_list(slice_points))
patches = [
lbann.Reshape(sample, dims=str_list(patch_dims))
for _ in range(num_patches)
]
labels = lbann.Identity(sample)
# Siamese network
head_cnn = modules.ResNet(
bn_statistics_group_size=bn_statistics_group_size)
heads = [head_cnn(patch) for patch in patches]
heads_concat = lbann.Concatenation(heads)
# Classification network
class_fc1 = modules.FcBnRelu(
4096,
statistics_group_size=bn_statistics_group_size,
name='siamese_class_fc1',
data_layout=fc_data_layout)
class_fc2 = modules.FcBnRelu(
4096,
statistics_group_size=bn_statistics_group_size,
name='siamese_class_fc2',
data_layout=fc_data_layout)
class_fc3 = lbann.modules.FullyConnectedModule(num_labels,
activation=lbann.Softmax,
name='siamese_class_fc3',
data_layout=fc_data_layout)
x = class_fc1(heads_concat)
x = class_fc2(x)
probs = class_fc3(x)
# Setup objective function
cross_entropy = lbann.CrossEntropy([probs, labels])
l2_reg_weights = set()
for l in lbann.traverse_layer_graph(input):
if type(l) == lbann.Convolution or type(l) == lbann.FullyConnected:
l2_reg_weights.update(l.weights)
l2_reg = lbann.L2WeightRegularization(weights=l2_reg_weights, scale=0.0002)
obj = lbann.ObjectiveFunction([cross_entropy, l2_reg])
# Setup model
metrics = [
lbann.Metric(lbann.CategoricalAccuracy([probs, labels]),
name='accuracy',
unit='%')
]
callbacks = [lbann.CallbackPrint(), lbann.CallbackTimer()]
if checkpoint_interval:
callbacks.append(
lbann.CallbackCheckpoint(checkpoint_dir='ckpt',
checkpoint_epochs=5))
# Learning rate schedules
if warmup:
callbacks.append(
lbann.CallbackLinearGrowthLearningRate(target=learning_rate *
mini_batch_size / 128,
num_epochs=5))
callbacks.append(
lbann.CallbackDropFixedLearningRate(drop_epoch=list(range(0, 100, 15)),
amt=0.25))
# Construct model
model = lbann.Model(num_epochs,
layers=lbann.traverse_layer_graph(input),
objective_function=obj,
metrics=metrics,
callbacks=callbacks)
# Setup optimizer
opt = lbann.SGD(learn_rate=learning_rate, momentum=0.9)
# opt = lbann.Adam(learn_rate=learning_rate, beta1=0.9, beta2=0.999, eps=1e-8)
# Setup data reader
data_reader = make_data_reader(num_patches)
# Return experiment objects
return model, data_reader, opt
obj = lbann.ObjectiveFunction([cross_entropy, l2_reg])
# Setup model
metrics = [
lbann.Metric(top1, name='top-1 accuracy', unit='%'),
lbann.Metric(top5, name='top-5 accuracy', unit='%')
]
callbacks = [
lbann.CallbackPrint(),
lbann.CallbackTimer(),
lbann.CallbackDropFixedLearningRate(drop_epoch=[30, 60, 80], amt=0.1)
]
if args.warmup:
callbacks.append(
lbann.CallbackLinearGrowthLearningRate(target=0.1 *
args.mini_batch_size / 256,
num_epochs=5))
model = lbann.Model(args.num_epochs,
layers=layers,
objective_function=obj,
metrics=metrics,
callbacks=callbacks)
# Setup optimizer
opt = lbann.contrib.args.create_optimizer(args)
# Setup data reader
data_reader = data.imagenet.make_data_reader(num_classes=args.num_classes)
# Setup trainer
trainer = lbann.Trainer(mini_batch_size=args.mini_batch_size,
def construct_model(run_args):
"""Construct LBANN model.
Initial model for ATOM molecular VAE
"""
import lbann
pad_index = run_args.pad_index
assert pad_index is not None
sequence_length = run_args.sequence_length
assert sequence_length is not None
print("sequence length is {}".format(sequence_length))
data_layout = "data_parallel"
# Layer graph
input_ = lbann.Identity(lbann.Input(name='inp', target_mode="N/A"),
name='inp1')
vae_loss = []
input_feature_dims = sequence_length
embedding_size = run_args.embedding_dim
dictionary_size = run_args.num_embeddings
assert embedding_size is not None
assert dictionary_size is not None
save_output = True if run_args.dump_outputs_dir else False
print("save output? ", save_output, "out dir ", run_args.dump_outputs_dir)
z = lbann.Gaussian(mean=0.0, stdev=1.0, neuron_dims="128")
recon, d1_real, d1_fake, d_adv, arg_max = molwae.MolWAE(
input_feature_dims, dictionary_size, embedding_size, pad_index,
save_output)(input_, z)
zero = lbann.Constant(value=0.0, num_neurons='1', name='zero')
one = lbann.Constant(value=1.0, num_neurons='1', name='one')
d1_real_bce = lbann.SigmoidBinaryCrossEntropy([d1_real, one],
name='d1_real_bce')
d1_fake_bce = lbann.SigmoidBinaryCrossEntropy([d1_fake, zero],
name='d1_fake_bce')
d_adv_bce = lbann.SigmoidBinaryCrossEntropy([d_adv, one], name='d_adv_bce')
vae_loss.append(recon)
layers = list(lbann.traverse_layer_graph(input_))
# Setup objective function
weights = set()
src_layers = []
dst_layers = []
for l in layers:
if (l.weights and "disc0" in l.name and "instance1" in l.name):
src_layers.append(l.name)
#freeze weights in disc2
if (l.weights and "disc1" in l.name):
dst_layers.append(l.name)
for idx in range(len(l.weights)):
l.weights[idx].optimizer = lbann.NoOptimizer()
weights.update(l.weights)
l2_reg = lbann.L2WeightRegularization(weights=weights, scale=1e-4)
vae_loss.append(d1_real_bce)
vae_loss.append(d_adv_bce)
vae_loss.append(d1_fake_bce)
vae_loss.append(l2_reg)
print("LEN vae loss ", len(vae_loss))
obj = lbann.ObjectiveFunction(vae_loss)
# Initialize check metric callback
metrics = [
lbann.Metric(d_adv_bce, name='adv_loss'),
lbann.Metric(recon, name='recon')
]
callbacks = [
lbann.CallbackPrint(),
#lbann.CallbackStepLearningRate(step=10, amt=0.5),
lbann.CallbackTimer()
]
if (run_args.dump_weights_interval > 0):
callbacks.append(
lbann.CallbackDumpWeights(
directory=run_args.dump_weights_dir,
epoch_interval=run_args.dump_weights_interval))
if (run_args.ltfb):
send_name = ('' if run_args.weights_to_send == 'All' else
run_args.weights_to_send) #hack for Merlin empty string
weights_to_ex = [w.name for w in weights if send_name in w.name]
print("LTFB Weights to exchange ", weights_to_ex)
callbacks.append(
lbann.CallbackLTFB(batch_interval=run_args.ltfb_batch_interval,
metric='recon',
weights=list2str(weights_to_ex),
low_score_wins=True,
exchange_hyperparameters=True))
callbacks.append(
lbann.CallbackReplaceWeights(source_layers=list2str(src_layers),
destination_layers=list2str(dst_layers),
batch_interval=2))
#Dump final weight for inference
if (run_args.dump_model_dir):
callbacks.append(lbann.CallbackSaveModel(dir=run_args.dump_model_dir))
#Dump output (activation) for post processing
if (run_args.dump_outputs_dir):
pred_tensor = lbann.Concatenation(arg_max, name='pred_tensor')
callbacks.append(
lbann.CallbackDumpOutputs(
batch_interval=run_args.dump_outputs_interval,
execution_modes='test',
directory=run_args.dump_outputs_dir,
layers='inp pred_tensor'))
if (run_args.warmup):
callbacks.append(
lbann.CallbackLinearGrowthLearningRate(target=run_args.lr / 512 *
run_args.batch_size,
num_epochs=5))
# Construct model
return lbann.Model(run_args.num_epochs,
weights=weights,
layers=layers,
objective_function=obj,
metrics=metrics,
callbacks=callbacks)