def init_from_orbit(self,
period,
lighttime,
tref=0.0,
eccen=1e-5,
varpi=0.0):
"""Initialize the parameters based on an orbit estimate
Args:
period: The orbital period in units of ``time``.
lighttime: The projected light travel time in units of ``time``
(:math:`a_1\,\sin(i)/c`).
tref: The reference time in units of ``time``.
eccen: The orbital eccentricity.
varpi: The angle of the ascending node in radians.
"""
ops = []
ops.append(tf.assign(self.period, period))
ops.append(
tf.assign(self.lighttime,
lighttime + tf.zeros_like(self.lighttime)))
ops.append(tf.assign(self.tref, tref))
if self.with_eccen:
ops.append(
tf.assign(self.eccen_param,
np.log(eccen) - np.log(1.0 - eccen)))
ops.append(tf.assign(self.varpi, varpi))
self.run(ops)
def _init_references(self):
# print ('DeepLIFT: computing references...')
sys.stdout.flush()
self._deeplift_ref.clear()
ops = []
# Original: Full set of operations
if self.init_ref is 'default':
g = tf.get_default_graph()
ops_check = g.get_operations()
elif self.init_ref is 'custom':
## Custom: limit operations to those downstream of the input
print('Custom: limit operations to those downstream of the input')
ops_check = [descendants(op) for op in self.X.consumers()]
ops_check = list(set(chain.from_iterable(ops_check)))
for op in ops_check:
if len(op.inputs) > 0 and not op.name.startswith('gradients'):
if op.type in SUPPORTED_ACTIVATIONS:
ops.append(op)
YR = self._session_run([o.inputs[0] for o in ops], self.baseline)
for (r, op) in zip(YR, ops):
self._deeplift_ref[op.name] = r
# print('DeepLIFT: references ready')
sys.stdout.flush()
def states2states(self, states, to_states):
ops = []
for i in xrange(len(states)):
copy_c = to_states[i].c.assign(states[i].c)
copy_h = to_states[i].h.assign(states[i].h)
ops.append(copy_c)
ops.append(copy_h)
return ops
def tranform2transform(self, top_status, top_status_transform,
to_statuses):
ops = []
copy_s = to_statuses[0].assign(top_status)
copy_st = to_statuses[1].assign(top_status_transform)
ops.append(copy_s)
ops.append(copy_st)
return ops
def _setup_graph(self):
vars = tf.trainable_variables()
ops = []
for v in vars:
n = v.op.name
if not n.startswith('discrim/'):
continue
logger.info("Clip {}".format(n))
ops.append(tf.assign(v, tf.clip_by_value(v, -0.01, 0.01)))
self._op = tf.group(*ops, name='clip')
def output_after2before(self, beam_parent):
# beam_parent : [beam_size]
ops = []
for i in xrange(len(self.after_output)):
o = self.after_output
new_o = tf.nn.embedding_lookup(o, beam_parent)
copy_o = self.before_state[i].c.assign(new_o)
ops.append(copy_o)
return ops
def setup_as_moving_average_of(self, src_net, beta=0.99, beta_nontrainable=0.0):
assert isinstance(src_net, Network)
with absolute_name_scope(self.scope):
with tf.name_scope('MovingAvg'):
ops = []
for name, var in self.vars.items():
if name in src_net.vars:
cur_beta = beta if name in self.trainables else beta_nontrainable
new_value = lerp(src_net.vars[name], var, cur_beta)
ops.append(var.assign(new_value))
return tf.group(*ops)
def states2states_shuffle(self, states, to_states, beam_parent):
ops = []
for i in xrange(len(states)):
copy_c = self.state2state_shuffle(to_states[i].c, states[i].c,
beam_parent)
copy_h = self.state2state_shuffle(to_states[i].h, states[i].h,
beam_parent)
ops.append(copy_c)
ops.append(copy_h)
return ops
def relaxed_distance(rx_step):
"""Distance between relaxed variables and their average."""
res, ops, rx_done = [], [], {}
for v in tf.trainable_variables():
if v.name[0:2] == "RX":
rx_name = v.op.name[v.name.find("/") + 1:]
if rx_name not in rx_done:
avg, dist_loss = relaxed_average(rx_name, rx_step)
res.append(dist_loss)
rx_done[rx_name] = avg
ops.append(v.assign(rx_done[rx_name]))
return tf.add_n(res), tf.group(*ops)
def get_parents(grad, op_type):
ops = list()
wave = set([grad.op])
while wave:
new_wave = set()
for op in wave:
for op in (t.op for t in op.inputs):
if op.type == op_type:
ops.append(op)
else:
new_wave.add(op)
wave = new_wave
return ops
def set_vars(var_to_value_dict):
ops = []
feed_dict = {}
for var, value in var_to_value_dict.items():
assert is_tf_expression(var)
try:
setter = tf.get_default_graph().get_tensor_by_name(var.name.replace(':0', '/setter:0')) # look for existing op
except KeyError:
with absolute_name_scope(var.name.split(':')[0]):
with tf.control_dependencies(None): # ignore surrounding control_dependencies
setter = tf.assign(var, tf.placeholder(var.dtype, var.shape, 'new_value'), name='setter') # create new setter
ops.append(setter)
feed_dict[setter.op.inputs[1]] = value
run(ops, feed_dict)
def after2before(self, beam_parent):
# beam_parent : [beam_size]
ops = []
for i in xrange(len(self.after_state)):
c = self.after_state[i].c
h = self.after_state[i].h
new_c = tf.nn.embedding_lookup(c, beam_parent)
new_h = tf.nn.embedding_lookup(h, beam_parent)
copy_c = self.before_state[i].c.assign(new_c)
copy_h = self.before_state[i].h.assign(new_h)
ops.append(copy_c)
ops.append(copy_h)
return ops
def check(self, *args, **keys):
if not self.frozen:
heartbeat()
ops = []
seen = set()
for name, action in self.commands:
full = self.full_path(name)
if not os.path.isdir(full):
if name not in seen:
seen.add(name)
ops.append(name)
for op in ops:
self.run(op, *args, **keys)
return ops
def restore(self, sess, path, index):
ops = []
feed = {}
for k, net in self._nets.items():
filename = os.path.join(path, "{}.l2l-{}".format(k, index))
data = pickle.load(open(filename, "rb"))
vars = snt.get_variables_in_module(net)
for v in vars:
split = v.name.split(":")[0].split("/")
module_name = split[-2]
variable_name = split[-1]
feed[self.restore_pl[k][module_name][variable_name]] = data[module_name][variable_name]
ops.append(self.assigns[k][module_name][variable_name])
sess.run(ops, feed_dict=feed)
def sync_variables_op(mpi_rank, num_comms=2, prereduce=0):
ops = list()
prev = []
with tf.device("/gpu:0"):
for var in tf.trainable_variables():
with tf.control_dependencies(prev):
op = tf.assign(
var,
allreduce(var if mpi_rank == 0 else var * 0.0,
num_comms=num_comms,
prereduce=prereduce))
prev = [op]
ops.append(op)
return tf.group(*ops)
def _init_references(self):
# print ('DeepLIFT: computing references...')
sys.stdout.flush()
self._deeplift_ref.clear()
ops = []
g = tf.get_default_graph()
for op in g.get_operations():
if len(op.inputs) > 0 and not op.name.startswith('gradients'):
if op.type in SUPPORTED_ACTIVATIONS:
ops.append(op)
YR = self.session_run([o.inputs[0] for o in ops], self.baseline)
for (r, op) in zip(YR, ops):
self._deeplift_ref[op.name] = r
# print('DeepLIFT: references ready')
sys.stdout.flush()
def ft_optimizer_list(cost, opt_vars, optimizer, lrs, grad_clip=False):
"""Efficient optimization for fine tuning a net."""
ops = []
gvs = []
for v, l in zip(opt_vars, lrs):
if grad_clip:
optim = optimizer(l)
gvs = optim.compute_gradients(cost, var_list=v)
capped_gvs = [(tf.clip_by_norm(grad, 10.),
var) if grad is not None else (grad, var)
for grad, var in gvs]
ops.append(optim.apply_gradients(capped_gvs))
else:
ops.append(optimizer(l).minimize(cost, var_list=v))
return tf.group(*ops), gvs
def _init_references(self):
# print ('DeepLIFT: computing references...')
sys.stdout.flush()
self._deeplift_ref.clear()
ops = []
g = tf.get_default_graph()
for op in g.get_operations():
if len(op.inputs) > 0 and not op.name.startswith('gradients'):
if op.type in SUPPORTED_ACTIVATIONS:
ops.append(op)
for op in ops:
r = self.session_run(op.inputs[0], self.train_x[0:0 + 1, :])
for i in range(1, self.train_x.shape[0]):
r += self.session_run(op.inputs[0], self.train_x[i:i + 1, :])
self._deeplift_ref[op.name] = r / self.train_x.shape[0]
# print('DeepLIFT: references ready')
sys.stdout.flush()
def apply_gradients(self, grads_and_vars, global_step=None, name=None):
ops = []
if not self.stage_weights:
return tf.train.MomentumOptimizer(
self.lr,
momentum=self.momentum).apply_gradients(grads_and_vars, name)
for stage, weights in self.stage_weights.items():
lr_decay = self.stage_lr_decay[stage]
mom_decay = self.stage_mom_decay[stage]
lr = self.lr * lr_decay
mom = self.momentum * mom_decay
grads_and_vars_opt = [(g, v) for g, v in grads_and_vars
if v.name in weights]
ops.append(
tf.train.MomentumOptimizer(lr, momentum=mom).apply_gradients(
grads_and_vars_opt, name))
return tf.group(ops)
def cast_variables(variables, graph=None, cache_ops=None):
if graph is None:
graph = get_default_graph()
if cache_ops is None:
cache_ops = state.cache_ops
if graph not in cache_ops:
cache_ops[graph] = {}
cache = cache_ops[graph]
ops = []
for variable in variables:
if variable in cache:
op = cache[variable]
elif variable.dtype == dtypes.bfloat16_ref or variable.dtype == tf.bfloat16:
op = tf.cast(variable, tf.float32)
else:
op = variable
cache[variable] = op
ops.append(op)
return ops
def get_parents(grad, op_type):
if grad.op.type == op_type:
return [grad.op]
ops = list()
wave = set([grad.op])
while wave:
new_wave = set()
for op in wave:
# print(op.name)
# for i in op.inputs:
# print(" ", i.name)
# print()
for op in (t.op for t in op.inputs):
if op.type == op_type:
ops.append(op)
else:
new_wave.add(op)
wave = new_wave
return ops
def _init_references(self):
sys.stdout.flush()
self._deeplift_ref.clear()
ops = []
g = self.session.graph
# get subgraph starting from the target node down
subgraph = tf.graph_util.extract_sub_graph(g.as_graph_def(), [self.T.name.split(':')[0]])
for n in subgraph.node:
op = g.get_operation_by_name(n.name)
if len(op.inputs) > 0 and not op.name.startswith('gradients'):
if op.type in SUPPORTED_ACTIVATIONS:
ops.append(op)
print(op.name)
ins = [o.inputs[0] for o in ops]
print('ins', ins)
YR = self.session_run(ins, self.baseline)
for (r, op) in zip(YR, ops):
self._deeplift_ref[op.name] = r
sys.stdout.flush()
def sync_globals_zero_init_op(num_comms=2, prereduce=0):
ops = list()
prev = []
with tf.device("/gpu:0"):
for var in tf.global_variables():
if var.dtype.base_dtype not in [tf.float32, tf.float16]:
cast_back = True
to_reduce = tf.cast(var, tf.float32)
else:
to_reduce = var
cast_back = False
with tf.control_dependencies(prev):
reduced = allreduce(to_reduce,
num_comms=num_comms,
prereduce=prereduce)
if cast_back:
reduced = tf.cast(reduced, var.dtype.base_dtype)
op = tf.assign(var, reduced)
prev = [op]
ops.append(op)
return tf.group(*ops)
def _apply_dense(self, grad, var):
var_dtype = var.dtype.base_dtype
lr = math_ops.cast(self._lr_t, var_dtype)
beta = self._beta
epsilon = self._epsilon
t = math_ops.cast(self.iterations + 1, var_dtype)
ops = []
# Update running sum
s = self.get_slot(var, 'sum')
grad_sq = math_ops.square(grad)
s_new = s + grad_sq
ops.append(state_ops.assign(s, s_new, use_locking=self._use_locking))
# Update running counter
if self._sparse_counter:
n = self.get_slot(var, 'counter')
n_new = n + math_ops.sign(grad_sq)
ops.append(
state_ops.assign(n, n_new, use_locking=self._use_locking))
else:
# Counter is not sparse; just use the current timestep instead
n_new = t
# Compute step size
average = math_ops.div_no_nan(s_new, n_new)
step = grad / (epsilon + math_ops.sqrt(average))
# Update momentum
if self._use_momentum:
m = self.get_slot(var, 'momentum')
m_new = beta * m + (1.0 - beta) * step
ops.append(
state_ops.assign(m, m_new, use_locking=self._use_locking))
# Bias correction
lr = lr / (1.0 - pow(beta, t))
else:
# No momentum; just use the current step instead
m_new = step
# Update parameters
ops.append(
state_ops.assign_sub(var,
lr * m_new,
use_locking=self._use_locking))
return control_flow_ops.group(*ops)
def hatt_after2before(self,beam_parent):
ops = []
new_h_att = tf.nn.embedding_lookup(self.after_h_att,beam_parent)
copy_op = self.before_h_att.assign(new_h_att)
ops.append(copy_op)
return ops
def group_lstm_grads(grads, params, scope="grouped_lstm", group_size=None):
grad = None
grad_idx = None
for i, (g, p) in enumerate(zip(grads, params)):
if scope in p.name and "kernel" in p.name:
grad = g
grad_idx = i
break
assert grad is not None
# backward walk param grad to find dw MatMul ops
# walk should terminate with each MatMul op
ops = list()
wave = set([grad.op])
while wave:
new_wave = set()
for op in wave:
for op in (t.op for t in op.inputs):
# TN MatMul ops
if op.type == "MatMul" and op.get_attr(
"transpose_a") and not op.get_attr("transpose_b"):
ops.append(op)
else:
new_wave.add(op)
wave = new_wave
# sort op names descending and split out the lstms (if weights are shared)
last_lstm = None
lstms = list()
ops.sort(key=lambda op: op.name, reverse=True)
for op in ops:
# gradients/grouped_lstm/lstm_2/step_00_grad/MatMul_1 => lstm_2
lstm = op.name.split("/")[-3]
if last_lstm != lstm:
lstms.insert(0, list())
last_lstm = lstm
lstms[0].append(op)
# we're going to be using absolute names, so clear name_scope
with tf.name_scope(None):
lstm_grads = list()
for lstm_ops in lstms:
# default dw op to one big matmul per lstm
if group_size is None:
group_size = len(lstm_ops)
# use the lstm scope for the new ops
# gradients/grouped_lstm/lstm_2/step_00_grad/MatMul_1 => gradients/grouped_lstm/lstm_2
scope = lstm_ops[-1].name.split('/')
scope = '/'.join(scope[0:-2])
offset = 0
while offset < len(lstm_ops):
xs = tf.concat([
op.inputs[0] for op in lstm_ops[offset:offset + group_size]
],
axis=0)
gs = tf.concat([
op.inputs[1] for op in lstm_ops[offset:offset + group_size]
],
axis=0)
mmop = tf.matmul(xs,
gs,
transpose_a=True,
transpose_b=False,
name="%s/dw_%04d" % (scope, offset))
grad = mmop if offset == 0 else ew.add(
grad, mmop, name="%s/add_%04d" % (scope, offset))
offset += group_size
lstm_grads.append(grad)
if len(lstms) > 1:
from blocksparse.ewops import add_n
# gradients/grouped_lstm/lstm_2/step_00_grad/MatMul_1 => gradients/grouped_lstm
scope = lstms[0][-1].name.split('/')
scope = '/'.join(scope[0:-3])
grads[grad_idx] = tf.add_n(lstm_grads, name="%s/add_n" % scope)
else:
grads[grad_idx] = lstm_grads[0]
#grads modified in place
# lstm_scopes = dict()
# # rediculous amount of code just to be able to re-enter a variable scope without its name being re-numbered.
# # https://github.com/tensorflow/tensorflow/pull/14390
# global lstm_scopes
# if scope not in lstm_scopes:
# with tf.variable_scope(scope) as lstm_scope:
# lstm_scopes[scope] = lstm_scope
# lstm_scope = lstm_scopes[scope]
# with tf.variable_scope(lstm_scope, auxiliary_name_scope=False), tf.name_scope(lstm_scope.original_name_scope):
# with tf.variable_scope(weights_scope, reuse=weights_reuse):
# w = tf.get_variable('kernel', shape=[in_width + width, 4 * width])
# if bias_scope is None:
# b = tf.get_variable('bias', shape=[4 * width])
# if layernorm:
# g = tf.get_variable('gain', shape=[4 * width])
# if bias_scope is not None:
# with tf.variable_scope(bias_scope, reuse=bias_reuse):
# b = tf.get_variable('bias', shape=[4 * width])
# if layernorm:
# g = tf.get_variable('gain', shape=[4 * width])
def output2output(self, output, to_output):
ops = []
copy_o = to_output.assign(output)
ops.append(copy_o)
return ops
def apply_updates(self):
assert not self._updates_applied
self._updates_applied = True
devices = list(self._dev_grads.keys())
total_grads = sum(len(grads) for grads in self._dev_grads.values())
assert len(devices) >= 1 and total_grads >= 1
ops = []
with absolute_name_scope(self.scope):
# Cast gradients to FP32 and calculate partial sum within each device.
dev_grads = OrderedDict() # device => [(grad, var), ...]
for dev_idx, dev in enumerate(devices):
with tf.name_scope('ProcessGrads%d' % dev_idx), tf.device(dev):
sums = []
for gv in zip(*self._dev_grads[dev]):
assert all(v is gv[0][1] for g, v in gv)
g = [tf.cast(g, tf.float32) for g, v in gv]
g = g[0] if len(g) == 1 else tf.add_n(g)
sums.append((g, gv[0][1]))
dev_grads[dev] = sums
# Sum gradients across devices.
if len(devices) > 1:
with tf.name_scope('SumAcrossGPUs'), tf.device(None):
for var_idx, grad_shape in enumerate(self._grad_shapes):
g = [dev_grads[dev][var_idx][0] for dev in devices]
if np.prod(
grad_shape
): # nccl does not support zero-sized tensors
g = tf.contrib.nccl.all_sum(g)
for dev, gg in zip(devices, g):
dev_grads[dev][var_idx] = (
gg, dev_grads[dev][var_idx][1])
# Apply updates separately on each device.
for dev_idx, (dev, grads) in enumerate(dev_grads.items()):
with tf.name_scope('ApplyGrads%d' % dev_idx), tf.device(dev):
# Scale gradients as needed.
if self.use_loss_scaling or total_grads > 1:
with tf.name_scope('Scale'):
coef = tf.constant(np.float32(1.0 / total_grads),
name='coef')
coef = self.undo_loss_scaling(coef)
grads = [(g * coef, v) for g, v in grads]
# Check for overflows.
with tf.name_scope('CheckOverflow'):
grad_ok = tf.reduce_all(
tf.stack([
tf.reduce_all(tf.is_finite(g))
for g, v in grads
]))
# Update weights and adjust loss scaling.
with tf.name_scope('UpdateWeights'):
opt = self._dev_opt[dev]
ls_var = self.get_loss_scaling_var(dev)
if not self.use_loss_scaling:
ops.append(
tf.cond(grad_ok,
lambda: opt.apply_gradients(grads),
tf.no_op))
else:
ops.append(
tf.cond(
grad_ok, lambda: tf.group(
tf.assign_add(ls_var, self.
loss_scaling_inc),
opt.apply_gradients(grads)),
lambda: tf.group(
tf.assign_sub(ls_var, self.
loss_scaling_dec))))
# Report statistics on the last device.
if dev == devices[-1]:
with tf.name_scope('Statistics'):
ops.append(
autosummary(self.id + '/learning_rate',
self.learning_rate))
ops.append(
autosummary(self.id + '/overflow_frequency',
tf.where(grad_ok, 0, 1)))
if self.use_loss_scaling:
ops.append(
autosummary(self.id + '/loss_scaling_log2',
ls_var))
# Initialize variables and group everything into a single op.
self.reset_optimizer_state()
init_uninited_vars(list(self._dev_ls_var.values()))
return tf.group(*ops, name='TrainingOp')
def assign_vars(distribution, variables, values):
ops = []
for variable, value in zip(variables, values):
ops.append(variable.assign(value))
return ops
context = create_test_xla_compile_context()
context.Enter()
o = a.assign(2)
context.Exit()
return o
op = lambda x: tpu_ops.tpu_ops.collective_permute(x, [[0, 1], [1, 0], [2, 3], [3, 2], [4, 5], [5, 4], [6, 7], [7, 6]])
zz = tpu_ops.shard(op, outputs_from_all_shards=True, num_shards=8, inputs=[[tf.constant([x+1], dtype=tf.float32) for x in range(8)]]); sess.run(zz)
ops = []
for core in range(8):
for step in range(8):
with tf.control_dependencies(ops):
ops.append(tpu_ops.tpu_ops.infeed_enqueue([tf.constant(step, tf.float32)], shape=[1], device_ordinal=core))
topology = tpu_topology
topology_rank = len(topology.mesh_shape)
mesh_shape = topology.mesh_shape
computation_shape = None
computation_stride = None
num_replicas = 3
if computation_shape is None:
computation_shape = np.array([1] * topology_rank, dtype=np.int32)
else: