def init_horovod_if_needed(self):
for _ in range(DEFAULT_MAX_ALLREDUCE_RETRY_NUM):
rank_response = self._master_client.get_comm_rank()
if rank_response.rank_id < 0:
logger.warning(
"The master has not added the worker host into "
"rendezvous yet. Retrying to get rank"
)
time.sleep(5)
else:
break
# If the rendezvous from master is unequal to self._rendezvous_id,
# the worker should rebuild the communication because the master
# has updated the communication group.
if rank_response.rendezvous_id != self._rendezvous_id:
os.environ[HorovodEnv.RENDEZVOUS_PORT] = str(
rank_response.rendezvous_port
)
os.environ[HorovodEnv.RANK] = str(rank_response.rank_id)
os.environ[HorovodEnv.SIZE] = str(rank_response.world_size)
hvd.shutdown()
hvd.init()
self._world_size = hvd.size()
self._rendezvous_id = rank_response.rendezvous_id
self._need_broadcast = True
def test_train_minibatch(self):
self._trainer.init_horovod_if_needed()
features = tf.constant([[0.5], [0.6], [0.7]])
labels = tf.constant([[1.0], [0.0], [1.0]])
_, version, loss = self._trainer.train_minibatch(features, labels)
self.assertEqual(version, 1)
self.assertIsNotNone(loss)
hvd.shutdown()
def test_training_process_with_fault_tolerance(self):
self._trainer.init_horovod_if_needed()
features = tf.constant([[0.5], [0.6], [0.7]])
labels = tf.constant([[1.0], [0.0], [1.0]])
version, _ = self._trainer.training_process_with_fault_tolerance(
features, labels)
# Firstly, we will call model locally to create variables
# for the model and optimizer. Then, we will train the
# model using Horovod. So, the iteration step = 2.
self.assertEqual(version, 2)
hvd.shutdown()
def stop_train(rank):
# hvd shutdown
logging.info('hvd shutdown at rank %d', rank)
hvd.shutdown()
def test_static(self):
mpi_rank, mpi_size = mpi_env_rank_and_size()
gloo_rank = int(os.getenv('HOROVOD_RANK', -1))
gloo_size = int(os.getenv('HOROVOD_SIZE', -1))
is_mpi = gloo_rank == -1
rank = max(mpi_rank, gloo_rank)
size = max(mpi_size, gloo_size)
# This test does not apply if there is only one worker.
if size == 1:
self.skipTest("Only one worker available")
if is_mpi:
try:
import mpi4py
mpi4py.rc.initialize = False
except ImportError:
pass
if rank == 0:
my_process_sets = [
hvd.ProcessSet([0]),
hvd.ProcessSet(range(1, size)),
hvd.ProcessSet(range(size - 1, -1, -1)), # duplicate
hvd.ProcessSet([0]) # duplicate
]
else:
my_process_sets = [
hvd.ProcessSet([0]),
hvd.ProcessSet(reversed(range(
1, size))), # permuting a process set does not matter
hvd.ProcessSet(range(size - 1, -1, -1)), # duplicate
hvd.ProcessSet([0]) # duplicate
]
with self.assertRaises(ValueError):
hvd.init(process_sets=my_process_sets)
if rank == 0:
my_process_sets = [
hvd.ProcessSet([0]),
hvd.ProcessSet(range(1, size)),
]
else:
my_process_sets = [
hvd.ProcessSet([0]),
hvd.ProcessSet(reversed(range(
1, size))), # permuting a process set does not matter
]
hvd.init(process_sets=my_process_sets)
self.assertEqual(hvd.global_process_set.process_set_id, 0)
self.assertListEqual(hvd.global_process_set.ranks, list(range(size)))
# Here we test some implementation details (numeric process set id values) using an internal function.
ps = hvd.mpi_ops._basics._get_process_set_ids_and_ranks()
self.assertDictEqual(ps, {
0: list(range(size)),
1: [0],
2: list(range(1, size))
})
# If another process initiates shutdown while this process is still processing _get_process_set_ids_and_ranks(),
# a race condition may be triggered. Avoid with a barrier.
try:
if is_mpi:
# barrier before shutdown
from mpi4py import MPI
MPI.COMM_WORLD.barrier()
else:
time.sleep(0.1)
except ImportError:
time.sleep(0.1)
hvd.shutdown()
def main(unused_argv):
# Horovod: initialize Horovod.
hvd.init()
# Keras automatically creates a cache directory in ~/.keras/datasets for
# storing the downloaded MNIST data. This creates a race
# condition among the workers that share the same filesystem. If the
# directory already exists by the time this worker gets around to creating
# it, ignore the resulting exception and continue.
cache_dir = os.path.join(os.path.expanduser('~'), '.keras', 'datasets')
if not os.path.exists(cache_dir):
try:
os.mkdir(cache_dir)
except OSError as e:
if e.errno == errno.EEXIST and os.path.isdir(cache_dir):
pass
else:
raise
# Download and load MNIST dataset.
#(train_data, train_labels), (eval_data, eval_labels) = \
# keras.datasets.mnist.load_data('MNIST-data-%d' % hvd.rank())
f = np.load("/opt/ml/input/data/training/mnist.npz")
train_data, train_labels = f['x_train'], f['y_train']
eval_data, eval_labels = f['x_test'], f['y_test']
print('train_labels: ', train_labels[0], 'rank: ', hvd.rank())
# The shape of downloaded data is (-1, 28, 28), hence we need to reshape it
# into (-1, 784) to feed into our network. Also, need to normalize the
# features between 0 and 1.
train_data = np.reshape(train_data, (-1, 784)) / 255.0
eval_data = np.reshape(eval_data, (-1, 784)) / 255.0
# Horovod: pin GPU to be used to process local rank (one GPU per process)
config = tf.ConfigProto()
config.gpu_options.allow_growth = True
config.gpu_options.visible_device_list = str(hvd.local_rank())
starttime = time.time()
# Horovod: save checkpoints only on worker 0 to prevent other workers from
# corrupting them.
model_dir = '/opt/ml/model/' if hvd.rank() == 0 else None
# Create the Estimator
mnist_classifier = tf.estimator.Estimator(
model_fn=cnn_model_fn,
model_dir=model_dir,
config=tf.estimator.RunConfig(session_config=config))
# Set up logging for predictions
# Log the values in the "Softmax" tensor with label "probabilities"
tensors_to_log = {"probabilities": "softmax_tensor"}
logging_hook = tf.train.LoggingTensorHook(tensors=tensors_to_log,
every_n_iter=1000)
# Horovod: BroadcastGlobalVariablesHook broadcasts initial variable states from
# rank 0 to all other processes. This is necessary to ensure consistent
# initialization of all workers when training is started with random weights or
# restored from a checkpoint.
bcast_hook = hvd.BroadcastGlobalVariablesHook(0)
# Train the model
train_input_fn = tf.estimator.inputs.numpy_input_fn(x={"x": train_data},
y=train_labels,
batch_size=100,
num_epochs=None,
shuffle=True)
# Horovod: adjust number of steps based on number of GPUs.
mnist_classifier.train(input_fn=train_input_fn,
steps=1000 // hvd.size(),
hooks=[logging_hook, bcast_hook])
# Evaluate the model and print results
eval_input_fn = tf.estimator.inputs.numpy_input_fn(x={"x": eval_data},
y=eval_labels,
num_epochs=1,
shuffle=False)
eval_results = mnist_classifier.evaluate(input_fn=eval_input_fn)
print(eval_results)
print('total time: ', time.time() - starttime, 'rank: ', hvd.rank())
print(hvd.rank(), " shutdown")
hvd.shutdown()
def test_multi_comm(self):
gloo_size = int(os.getenv('HOROVOD_SIZE', -1))
if gloo_size != -1:
self.skipTest("This test is specific to MPI and does not apply with Gloo controller.")
try:
from mpi4py import MPI
except ImportError:
self.skipTest("This test requires mpi4py.")
# This will be our baseline world communicator
comm = MPI.COMM_WORLD
size = comm.size
if size < 2:
self.skipTest("This test requires multiple workers.")
# Split COMM_WORLD into subcommunicators
subcomm = MPI.COMM_WORLD.Split(color=MPI.COMM_WORLD.rank % 2,
key=MPI.COMM_WORLD.rank)
comm_clone = comm.Dup()
subcomm_clone = subcomm.Dup()
subcomm_effective_clone = hvd.ProcessSet(range(0, comm.size, 2)) # identified as a clone on even ranks
# 3+ duplicates
my_process_sets = [hvd.ProcessSet(subcomm),
hvd.ProcessSet(comm_clone),
hvd.ProcessSet(subcomm_clone),
subcomm_effective_clone,
hvd.ProcessSet([0]),
]
with self.assertRaises(ValueError):
hvd.init(comm=comm, process_sets=my_process_sets)
## Internally Horovod has been initialized successfully, but we need to call hvd.init() with a valid list of
## process sets to proceed.
# 2+ duplicates
my_process_sets = [hvd.ProcessSet(subcomm),
hvd.ProcessSet(comm_clone),
subcomm_effective_clone,
hvd.ProcessSet([0]),
]
with self.assertRaises(ValueError):
hvd.init(comm=comm, process_sets=my_process_sets)
# 1+ duplicates
my_process_sets = [hvd.ProcessSet(subcomm),
hvd.ProcessSet(comm_clone),
hvd.ProcessSet([0]),
]
with self.assertRaises(ValueError):
hvd.init(comm=comm, process_sets=my_process_sets)
# 1+ duplicates
my_process_sets = [hvd.ProcessSet(subcomm),
subcomm_effective_clone,
hvd.ProcessSet([0]),
]
if hvd.size() == 2 or hvd.rank() % 2 == 0:
with self.assertRaises(ValueError):
hvd.init(comm=comm, process_sets=my_process_sets)
else:
hvd.init(comm=comm, process_sets=my_process_sets)
# no duplicates
if size > 2:
my_process_sets = [hvd.ProcessSet(subcomm),
hvd.ProcessSet([0]),
]
hvd.init(comm=comm, process_sets=my_process_sets)
else:
my_process_sets = [hvd.ProcessSet(subcomm), ]
hvd.init(comm=comm, process_sets=my_process_sets)
self.assertEqual(hvd.global_process_set.process_set_id, 0)
self.assertListEqual(hvd.global_process_set.ranks, list(range(size)))
self.assertEqual(hvd.global_process_set.mpi_comm, comm)
# Here we test some implementation details (numeric process set id values) using an internal function.
ps = hvd.mpi_ops._basics._get_process_set_ids_and_ranks()
if size > 2:
self.assertDictEqual(ps, {0: list(range(size)),
1: list(range(0, size, 2)),
2: list(range(1, size, 2)),
3: [0],
})
else:
self.assertDictEqual(ps, {0: list(range(size)),
1: list(range(0, size, 2)),
2: list(range(1, size, 2)),
})
if hvd.rank() % 2 == 0:
self.assertEqual(my_process_sets[0].process_set_id, 1)
else:
self.assertEqual(my_process_sets[0].process_set_id, 2)
# If another process initiates shutdown while this process is still processing _get_process_set_ids_and_ranks(),
# a race condition may be triggered. Avoid with a barrier.
MPI.COMM_WORLD.barrier()
hvd.shutdown()
def test_horovod_linear_regression(self):
import horovod.tensorflow as hvd
# Horovod: initialize Horovod.
hvd.init()
logdir = args.logdir + '/horovod_test/'
if hvd.rank() == 0:
if not os.path.exists(logdir):
os.makedirs(logdir)
assert args.training_size % hvd.size() == 0
assert (args.training_size // hvd.size()) % args.batch_size == 0
training_data_filename = logdir + 'training_data.npy'
if hvd.rank() == 0:
with open(training_data_filename, 'w') as f:
full_training_data = np.random.random(
size=(args.training_size, ))
full_training_data.tofile(f)
print("Full training data:")
print(full_training_data)
hvd.allgather(tf.constant([0]))
with open(training_data_filename, 'r') as f:
training_data = np.fromfile(f)
training_data_size = training_data.shape[0]
local_training_data_size = (training_data.shape[0] + hvd.size() -
1) // hvd.size()
local_training_data_begin = hvd.rank() * local_training_data_size
if hvd.rank() == hvd.size(
) - 1 and training_data.shape[0] % local_training_data_size != 0:
local_training_data_size = training_data.shape[
0] % local_training_data_size
local_training_data = training_data[
local_training_data_begin:local_training_data_begin +
local_training_data_size]
print("Local training data:")
print(local_training_data)
# Define Tensorflow graph
graph = tf.Graph()
with graph.as_default():
x_ph = tf.placeholder(tf.float32,
shape=[None, training_data_size],
name='x')
y_ph = tf.placeholder(tf.float32, shape=[None], name='y')
w = tf.Variable(np.zeros((training_data_size, )),
dtype=tf.float32,
name='w')
loss_func = tf.constant(0.5) * tf.reduce_sum(
tf.square(y_ph - tf.tensordot(x_ph, w, axes=1)))
opt = tf.train.GradientDescentOptimizer(learning_rate=hvd.size() *
1.0)
# Horovod: wrap local optimizer in distributed Horovod optimizer.
opt = hvd.DistributedOptimizer(opt)
#train_step = opt.minimize(loss_func)
#grads_and_vars = opt.compute_gradients(loss_func)
train_step = opt.minimize(
loss_func) # apply_gradients(grads_and_vars)
config = tf.ConfigProto()
config.intra_op_parallelism_threads = 22
config.inter_op_parallelism_threads = 8
config.gpu_options.allow_growth = True
config.allow_soft_placement = True
# Horovod
# Add variable initializer.
init = tf.global_variables_initializer()
# Horovod: broadcast initial variable states from rank 0 to all other processes.
# This is necessary to ensure consistent initialization of all workers when
# training is started with random weights or restored from a checkpoint.
bcast = hvd.broadcast_global_variables(0)
print("Local training data:")
print(local_training_data)
print('Opening tf.Session...')
with tf.Session(graph=graph, config=config) as sess:
# We must initialize all variables before we use them.
init.run()
bcast.run()
print('Initialized all Horovod ranks.')
print('Begin training - batch size = {}.'.format(args.batch_size),
flush=True)
if hvd.rank() == 0:
training_writer = tf.summary.FileWriter(logdir,
graph=sess.graph)
for i in range((local_training_data_size + args.batch_size - 1) //
args.batch_size):
batch_begin = i * args.batch_size
batch_size = args.batch_size \
if i != (local_training_data_size+args.batch_size-1)//args.batch_size else \
local_training_data_size % args.batch_size
x = np.zeros(shape=(batch_size, training_data_size))
x[np.arange(x.shape[0]), local_training_data_begin +
batch_begin + np.arange(x.shape[0])] = 1.0
y = local_training_data[batch_begin:batch_begin + batch_size]
feed_train = {x_ph: x, y_ph: y}
# Only compute shuffle indices, do not compute shuffled data set to avoid memory error
time_before = time.time()
#grad_op = grads_and_vars[0][0]
loss, _ = sess.run([loss_func, train_step],
feed_dict=feed_train)
time_after = time.time()
print(
'Step {0:5d} - loss: {1:6.2f} - latency: {2:6.2f} ms.'.
format(i, loss, 1000 * (time_after - time_before)),
flush=True)
print('Finished training - local residual w - y_training is:')
local_residual = sess.run([
w[local_training_data_begin:local_training_data_begin +
local_training_data_size] - y_ph
],
feed_dict={y_ph: local_training_data})
print(local_residual)
print('Locally trained variable components')
print(
sess.run([
w[local_training_data_begin:local_training_data_begin +
local_training_data_size]
]))
print('Local training data')
print(local_training_data)
self.assertTrue(
np.allclose(local_residual,
np.zeros(len(local_residual), ),
rtol=1e-7))
if hvd.rank() == 0:
os.remove(training_data_filename)
hvd.allgather(tf.constant([0]))
hvd.shutdown()
def run_gnn(args,model_ops,test_items,train_items=None,optimizer=None):
# Split ops.
inputs_p_ph, inputs_l_ph, targets_ph, inputs_p_op, inputs_l_op, targets_op, output_ops, loss_op, step_op = model_ops
# Create new TF session.
banner_print("Create TF config / session.")
config = tf.ConfigProto(allow_soft_placement=True, log_device_placement=False)
config.gpu_options.allow_growth = True
if args.hvd:
import horovod.tensorflow as hvd
config.gpu_options.visible_device_list = str(hvd.local_rank())
#Some versions of tensorflow(version<1.15) have issues with allocating all device memory
#In this case, uncomment the following line
#config.gpu_options.per_process_gpu_memory_fraction = 0.5
checkpoint_dir = './checkpoints' if RANK == 0 else './checkpoints_test'
else:
config.gpu_options.visible_device_list = str(0)
checkpoint_dir = './checkpoints'
try:
os.mkdir(checkpoint_dir)
except OSError:
print ("Creation of directory %s failed!"%checkpoint_dir)
else:
print ("Successfully created directory %s."%checkpoint_dir)
sess = tf.Session(config=config)
# Initialize Model.
if(RANK==0):
print("All workers are initializing global variables...")
#All ranks should initialize their variables before
#loading checkpoints or getting broadcast variables
#from rank 0
sess.run(tf.global_variables_initializer())
if(RANK==0):
print("Done global variables init.")
saver = tf.train.Saver()
model_path = checkpoint_dir + '/model%s.ckpt'%RANK
restore_path = model_path
if RANK==0:
# Test Save / Restore model with Rank 0.
save_path = saver.save(sess, model_path)
print("Coordinator Test checkpoint saved to: %s"%save_path)
else:
save_path = saver.save(sess, model_path)
print("Worker test checkpoint saved to: %s"%save_path)
if args.restore != None:
restore_path = args.restore
print("Restoring model from: %s"%restore_path)
saver.restore(sess,restore_path)
print("Model restored sucessfully.")
print("To resume training use --restore %s"%str(os.getcwd()+"/"+restore_path))
else:
restore_path=model_path
saver.restore(sess, restore_path)
print("Worker fresh checkpoint restore test success.")
print("To resume training use --restore %s"%str(os.getcwd()+"/"+restore_path))
print("Training new model.")
# Print total model parameters.
if 0:
total_parameters = 0
for variable in tf.trainable_variables():
variable_parameters = 1
for dim in variable.get_shape():
variable_parameters *= dim.value
total_parameters += variable_parameters
print("Total trainable params: ", total_parameters)
if args.hvd:
print("Broadcasting...")
import horovod.tensorflow as hvd
bcast_op = hvd.broadcast_global_variables(0)
sess.run(bcast_op)
time.sleep(10)
print("Done broadcast")
# Training / inference loop.
banner_print("Start training / testing loop.")
acc_best = 0.0
epoch_best = 0
log_epochs, solveds_tr, solveds_ge, losses_tr, losses_ge, lr_hist = ([],[],[],[],[],[])
for epoch in range(args.epochs):
if RANK == 0:
print("Epoch %d:"%(epoch))
log_epochs.append(epoch)
# Run training step.
if not INFERENCE_ONLY:
if RANK == 0:
print(" Training.")
elapsed, solved, loss, count = run_batches(sess, lambda: item_batch_iter(train_items,args.batch_size),
inputs_p_ph, inputs_l_ph, targets_ph,
inputs_p_op, inputs_l_op, targets_op,
output_ops, step_op, loss_op)
acc = solved / count
loss = loss / count
lr = sess.run(optimizer._learning_rate)
if args.hvd:
acc, solved, loss = average_distributed_metrics(sess, acc, solved, loss)
count = hvd.size()*count
solved = hvd.size()*solved
if RANK == 0:
print(" Time: %.1fs"%(elapsed))
print(" LrnR: %.6f"%lr)
print(" Loss: %f"%(loss))
print(" Acc.: %f (%.1f/%.1f)"%(acc,solved,count))
solveds_tr.append(acc)
losses_tr.append(loss)
lr_hist.append(lr)
# Run a test step.
if RANK == 0:
print(" Testing.")
elapsed, solved, loss, count = run_batches(sess, lambda: item_batch_iter(test_items,args.batch_size_test, shuffle=False),
inputs_p_ph, inputs_l_ph, targets_ph,
inputs_p_op, inputs_l_op, targets_op,
output_ops, None, loss_op)
acc = solved / count
loss = loss / count
if args.hvd:
acc, solved, loss = average_distributed_metrics(sess, acc, solved, loss)
count = hvd.size()*count
solved = hvd.size()*solved
if RANK == 0:
print(" Time: %.1fs"%(elapsed))
print(" Loss: %f"%(loss))
print(" Acc.: %f (%.1f/%.1f)"%(acc,solved,count))
solveds_ge.append(acc)
losses_ge.append(loss)
if(args.plot_history):
plot_history(log_epochs, solveds_tr, solveds_ge, 'PharML-Accuracy', 'accuracy')
plot_history(log_epochs, losses_tr, losses_ge, 'PharML-Loss','loss')
plot_history(log_epochs, lr_hist, lr_hist, 'PharML-LR','learning rate')
# Checkpoint if needed.
if acc > acc_best and not INFERENCE_ONLY:
acc_best = acc
epoch_best = epoch
if RANK == 0:
print(" New Best Test Acc: ", acc_best)
print(" -> Occurred at epoch ", epoch_best)
sys.stdout.flush()
save_path = saver.save(sess, model_path)
print(" -> Saved checkpoint to %s"%(save_path))
if INFERENCE_ONLY:
# Exit loop after first inference if in inference only-mode.
print("Inference only mode, done with single pass so exiting...")
hvd.shutdown()
break;
# If test accuracy has not improved for more than
# 15 epochs, call it converged and exit - this is what
# was used in paper, but since we've found lowering
# this to 5 epochs is sufficient in some cases
if( (epoch-epoch_best) >= 15 and not INFERENCE_ONLY):
print("Model Converged! Exiting Nicely...")
#sys.exit(0)
hvd.shutdown()
break;
# Success!
banner_print("Success!")
