def update_context(self, context, x, pool_dim_name):
"""Update the length dimension, sequence_id and position information."""
pooled_seq_length = x.shape.get_dim_by_name(pool_dim_name).size
# For position, we slice the first `pooled_seq_length` indices instead of
# striding. This ensures that the 3rd position before the pooling becomes
# 2nd position after pooling instead of remembering its position before
# pooling.
new_context_position = mtf.slice(
context.position,
begin=0,
size=pooled_seq_length,
slice_dim_name=pool_dim_name)
context.position = new_context_position
pooled_seq_length = x.shape.get_dim_by_name(pool_dim_name).size
new_length_dim = mtf.Dimension(
name=pool_dim_name, size=pooled_seq_length)
new_sequence_id = mtf.stride_tensor_1d(
context.sequence_id,
pool_dim=context.length_dim,
pool_size=self.pooling_size)
context.length_dim = new_length_dim
context.sequence_id = new_sequence_id
def halo_reduce(x, blocks_dim, block_size_dim, halo_size, wrap=True):
"""Reduce each block with the margins of adjacent blocks.
Get left and right blocks_dim and sum overlap along block_size_dim.
Only supports halo size smaller than block_size/2
Args:
x: a Tensor.
blocks_dim: a Dimension in x.shape
block_size_dim: a Dimension in x.shape
halo_size: an integer
wrap: a boolean
Returns:
a Tensor with the same shape as x, other than in block_size_dim, whose
size is increased by 2*halo_size.
"""
if halo_size == 0:
return x
block_size = block_size_dim.size
assert halo_size <= block_size // 2
left_margin = mtf.slice(x, 0, 2 * halo_size, block_size_dim.name)
right_margin = mtf.slice(x, block_size_dim.size - 2 * halo_size,
2 * halo_size, block_size_dim.name)
center = mtf.slice(x, 2 * halo_size, block_size_dim.size - 4 * halo_size,
block_size_dim.name)
# Perform halo exchange sum margins
left = mtf.shift(right_margin, 1, blocks_dim, wrap) + left_margin
right = mtf.shift(left_margin, -1, blocks_dim, wrap) + right_margin
# Recompose block
left = mtf.pad(left, [0, block_size_dim.size - 2 * halo_size],
block_size_dim.name)
right = mtf.pad(right, [block_size_dim.size - 2 * halo_size, 0],
block_size_dim.name)
center = mtf.pad(center, [2 * halo_size, 2 * halo_size],
block_size_dim.name)
x = left + center + right
return x
def call(self, context, x, losses=None):
"""Call the layer."""
if self.canine_mode:
# This is the canine-like ByT5 + LASC baseline in paper.
return self.call_canine_encoder(context, x, losses=losses)
if self.conv_type:
if self.conv_type == "conv1d":
tf.logging.info("Using 1d conv")
tmp_output = mtf.Dimension("tmp_dim", x.shape[-1].size)
orig_dim = x.shape[-1]
x = mtf.layers.conv1d(x,
tmp_output,
filter_size=self.filter_size,
stride=1)
x = mtf.rename_dimension(x, "tmp_dim", orig_dim.name)
tf.logging.info(x)
if self.norm:
x = sublayer_rms_norm(x, None, context)
o = x
olength = o.shape.get_dim_by_name("length")
o = custom_attention.gradient_based_subword_tokenization(
o,
olength,
downsample=self.downsample_query,
use_offsets=self.use_offsets,
consider_chars_as_blocks=self.consider_chars_as_blocks,
use_block_pos_embedding=self.use_block_pos_embedding,
memory_embeddings=self.num_memory_slots,
context=context,
block_mixing_mode=self.block_mixing_mode,
activation=self.rank_activation,
downsample_function=self.gbst_pool)
new_length_dim = o.shape.get_dim_by_name("length")
context.length_dim = new_length_dim
new_context_position = context.get_position()
context.position = new_context_position
context.sequence_id = mtf.slice(context.sequence_id,
begin=0,
size=new_length_dim.size,
slice_dim_name=new_length_dim.name)
if self.use_ffn:
# not actually used in Charformer.
tf.logging.info("Using FFN")
o2 = self.ffn.call(context, o)
o = o + o2
if self.norm:
o = sublayer_rms_norm(o, None, context)
olength = o.shape.get_dim_by_name("length")
return o, context
def call_canine_encoder(self, context, x, losses=None):
"""Call Canine baseline encoder (Byte level T5 + LASC in paper)."""
# local attention
params = self.make_params(context)
q = params.compute_q(x)
if self.shared_kv:
kv = params.compute_kv(x)
k = kv
v = kv
else:
k = params.compute_k(x)
v = params.compute_v(x)
# local attention
output_shape = x.shape
x = custom_attention.local_attention_1d(
q,
k,
v,
length_dim=context.length_dim,
length_dim_num_splits=1,
key_dim=self.kv_dim,
value_dim=self.kv_dim,
fully_autoregressive=False,
radius=self.radius,
sequence_id=context.sequence_id,
write_priority=context.write_priority,
read_priority=context.read_priority,
context=context,
attention_kwargs=self.attention_kwargs_from_context(context))
o = params.compute_output(x, output_shape=output_shape)
# strided convolutions
tmp_output = mtf.Dimension("tmp_dim", o.shape[-1].size)
# downsample query args is reused here for "r"
o = mtf.layers.conv1d(o,
tmp_output,
filter_size=self.filter_size,
stride=int(self.downsample_query))
o = mtf.rename_dimension(o, "tmp_dim", "d_model")
tf.logging.info(o)
new_length_dim = o.shape.get_dim_by_name("length")
context.length_dim = new_length_dim
new_context_position = context.get_position()
context.position = new_context_position
context.sequence_id = mtf.slice(context.sequence_id,
begin=0,
size=new_length_dim.size,
slice_dim_name=new_length_dim.name)
return o, context
def downsample_hr_to_lr(field, lr_shape, hr_shape, downsampling_factor, halo_size, splittables, mesh):
# Reshaping array into high resolution mesh
field = mtf.reshape(field, field.shape+[mtf.Dimension('h_dim', 1)])
low = mesh_utils.downsample(field, downsampling_factor, antialias=True)
low = mtf.reshape(low, low.shape[:-1])
for block_size_dim in hr_shape[-3:]:
low = mtf.slice(low, halo_size//2**downsampling_factor, block_size_dim.size//2**downsampling_factor, block_size_dim.name)
# Hack usisng custom reshape because mesh is pretty dumb
low = mtf.slicewise(lambda x: x[:,0,0,0],
[low],
output_dtype=field.dtype,
output_shape=lr_shape,
name='my_dumb_reshape',
splittable_dims=splittables)
return low
def cic_paint_fr(field, state, output_shape, hr_shape, halo_size, splittables, mesh, weights=None):
'''paint the position from state to a field of batch+3D tensor
Ops performed :
- reshape to hr_shape
- pad
- paint
- halo_reduce
- slice to remove pad
- reshape to output_shape
'''
lnc = field.shape[-1].size
field = mtf.slicewise(lambda x:tf.expand_dims(tf.expand_dims(tf.expand_dims(x, axis=1),axis=1),axis=1),
[field],
output_dtype=tf.float32,
output_shape=mtf.Shape(hr_shape[0:4]+[
mtf.Dimension('sx_block', lnc//hr_shape[1].size),
mtf.Dimension('sy_block', lnc//hr_shape[2].size),
mtf.Dimension('sz_block', lnc//hr_shape[3].size)]),
name='my_reshape',
splittable_dims=splittables)
for block_size_dim in hr_shape[-3:]:
field = mtf.pad(field, [halo_size, halo_size], block_size_dim.name)
field = mesh_utils.cic_paint(field, state[0], halo_size, weights)
# Halo exchange
for blocks_dim, block_size_dim in zip(hr_shape[1:4], field.shape[-3:]):
field = mesh_ops.halo_reduce(field, blocks_dim, block_size_dim, halo_size)
# Remove borders
for block_size_dim in hr_shape[-3:]:
field = mtf.slice(field, halo_size, block_size_dim.size, block_size_dim.name)
field = mtf.slicewise(lambda x: x[:,0,0,0],
[field],
output_dtype=field.dtype,
output_shape=output_shape,
name='my_dumb_reshape',
splittable_dims=splittables)
return field
def synthetic_attention(q,
k,
v,
memory_length_dim,
key_dim,
value_dim,
bias=None,
dropout_rate=0.0,
dropout_broadcast_dims=None,
extra_logit=None,
synthesize=True,
synthesize_mode="random_plus_alpha",
factorized_dim=16,
max_length=512,
context=None):
"""Synthetic Attention from Synthesizers (https://arxiv.org/abs/2005.00743).
key_dim is a Dimension representing the channels in the queries and keys
value_dim is a Dimension representing the channels in values
memory_length_dim is a Dimension representing the different key/value pairs.
Dimensions of q: other_query_dims + {key_dim}
Dimensions of k: other_memory_dims + {memory_length_dim, key_dim}
Dimensions of v: other_memory_dims + {memory_length_dim, value_dim}
other_memory_dims is a subset of other_query_dims
Typically, other_query_dims={batch, heads, length}
Typically, other_memory_dims={batch, heads}
Args:
q: a Tensor
k: a Tensor
v: a Tensor
memory_length_dim: a Dimension
key_dim: a Dimension
value_dim: a Dimension
bias: a Tensor to be added into the attention logits.
dropout_rate: a float.
dropout_broadcast_dims: an optional list of mtf.Dimension
extra_logit: an optional scalar or tensor
synthesize: flag to use synthetic attention or not
synthesize_mode: which variant of synthesizer to use
factorized_dim: factorized dim for synthesizers
max_length: max length of input sequence
context: context since we need context mode
Returns:
Tensor with shape q.shape - key_dim + value_dim
"""
if synthesize:
num_heads = v.shape.get_dim_by_name("heads")
tf.logging.info("Using synthesizer")
if synthesize_mode == "random":
tf.logging.info("Using Random Synthesizers")
r_shape = mtf.Shape([mtf.Dimension("length", max_length),
mtf.Dimension("heads", num_heads.size),
mtf.Dimension("memory_length", max_length)])
r = mtf.get_variable(context.mesh, "R", r_shape,
initializer=None,
dtype=context.variable_dtype)
r = mtf.slice(r, 0, memory_length_dim.size, memory_length_dim.name)
if context.mode == "incremental":
r = mtf.gather(r, context.position, r.shape.get_dim_by_name("length"))
else:
length_dim = q.shape.get_dim_by_name("length")
r = mtf.slice(r, 0, length_dim.size, "length")
logits = r
r_shape = logits.shape
elif synthesize_mode == "factorized":
tf.logging.info("Using Factorized Random Synthesizers")
k = factorized_dim
r1_shape = mtf.Shape([mtf.Dimension("tmp", k),
mtf.Dimension("heads", num_heads.size),
mtf.Dimension("memory_length", 512)])
r2_shape = mtf.Shape([mtf.Dimension("tmp", k),
mtf.Dimension("heads", num_heads.size),
mtf.Dimension("memory_length", 512)])
r_shape = mtf.Shape([mtf.Dimension("length", 512),
mtf.Dimension("heads", num_heads.size),
mtf.Dimension("memory_length", 512)])
r1 = mtf.get_variable(context.mesh, "R1", r1_shape,
initializer=None,
dtype=context.variable_dtype)
r2 = mtf.get_variable(context.mesh, "R2", r2_shape,
initializer=None,
dtype=context.variable_dtype)
r = mtf.einsum([r1, r2], r_shape)
r = mtf.slice(r, 0, memory_length_dim.size, memory_length_dim.name)
if context.mode == "incremental":
r = mtf.gather(r, context.position, r.shape.get_dim_by_name("length"))
else:
length_dim = q.shape.get_dim_by_name("length")
r = mtf.slice(r, 0, length_dim.size, "length")
logits = r
elif synthesize_mode == "dense_minus":
# Dense Synthesizer Model
tmp_dim = mtf.Dimension("memory_length", max_length)
logits = mtf.layers.dense(mtf.relu(q), [tmp_dim],
use_bias=False,
name="pi",
reduced_dims=[key_dim],
variable_dtype=None)
logits = mtf.slice(logits, 0, memory_length_dim.size,
memory_length_dim.name)
if context.mode == "incremental":
pass
else:
length_dim = q.shape.get_dim_by_name("length")
logits = mtf.slice(logits, 0, length_dim.size, "length")
elif synthesize_mode == "random_plus_alpha" or \
synthesize_mode == "random_plus":
# Mixture Random Synthesizer with learnable Alpha
tf.logging.info("Using Random Plus Alpha")
logits = mtf.einsum([q, k], reduced_dims=[key_dim])
num_heads = logits.shape.get_dim_by_name("heads")
r_shape = mtf.Shape([mtf.Dimension("length", 512),
mtf.Dimension("heads", num_heads.size),
mtf.Dimension("memory_length", 512)])
r = mtf.get_variable(context.mesh, "R", r_shape,
initializer=None,
dtype=context.variable_dtype)
r = mtf.slice(r, 0, memory_length_dim.size, memory_length_dim.name)
if context.mode == "incremental":
r = mtf.gather(r, context.position, r.shape.get_dim_by_name("length"))
else:
length_dim = q.shape.get_dim_by_name("length")
r = mtf.slice(r, 0, length_dim.size, length_dim.name)
if "alpha" in synthesize_mode:
alpha = mtf.get_variable(context.mesh,
"alpha",
mtf.Shape([mtf.Dimension("alpha", 1)]),
initializer=tf.zeros_initializer(),
dtype=context.variable_dtype)
alpha = mtf.sigmoid(alpha)
logits = ((1-alpha) * logits) + (alpha * r)
else:
logits = logits + r
elif synthesize_mode == "dense_plus_alpha" or \
synthesize_mode == "dense_plus":
# Mixture Dense Synthesizer with learnable alpha
tf.logging.info("Using Dense Plus Alpha Scaling")
logits = mtf.einsum([q, k], reduced_dims=[key_dim])
tmp_dim = mtf.Dimension("memory_length", 512)
r = mtf.layers.dense(mtf.relu(q), [tmp_dim],
use_bias=False,
name="pi",
reduced_dims=[key_dim],
variable_dtype=None)
r = mtf.slice(r, 0, memory_length_dim.size, memory_length_dim.name)
if context.mode == "incremental":
pass
else:
length_dim = q.shape.get_dim_by_name("length")
r = mtf.slice(r, 0, length_dim.size, "length")
if "alpha" in synthesize_mode:
alpha = mtf.get_variable(context.mesh,
"alpha",
mtf.Shape([mtf.Dimension("alpha", 1)]),
initializer=tf.zeros_initializer(),
dtype=context.variable_dtype)
alpha = mtf.sigmoid(alpha)
logits = ((1-alpha) * logits) + (alpha * r)
else:
logits = logits + r
if bias is not None:
logits += bias
weights = mtf.softmax(logits, memory_length_dim, extra_logit=extra_logit)
weights = mtf.dropout(
weights, context.train, 1.0 - dropout_rate,
noise_shape=weights.shape - dropout_broadcast_dims)
if synthesize and "plus" not in synthesize_mode:
if synthesize_mode == "dense_minus":
outputs_shape = mtf.Shape(q.shape.dims[:-1] + [value_dim])
else:
outputs_shape = mtf.Shape(q.shape.dims[:-1] + [num_heads, value_dim])
else:
outputs_shape = q.shape - [key_dim] + value_dim
outputs = mtf.einsum([weights, v], outputs_shape)
return outputs
def nbody_prototype(mesh,
infield=False,
nc=FLAGS.nc,
bs=FLAGS.box_size,
batch_size=FLAGS.batch_size,
a0=FLAGS.a0,
a=FLAGS.af,
nsteps=FLAGS.nsteps,
dtype=tf.float32):
"""
Prototype of function computing LPT deplacement.
Returns output tensorflow and mesh tensorflow tensors
"""
# Compute a few things first, using simple tensorflow
stages = np.linspace(a0, a, nsteps, endpoint=True)
# Define the named dimensions
# Parameters of the small scales decomposition
n_block_x = FLAGS.nx
n_block_y = FLAGS.ny
n_block_z = 1
halo_size = FLAGS.hsize
# Parameters of the large scales decomposition
fx_dim = mtf.Dimension("nx", nc)
fy_dim = mtf.Dimension("ny", nc)
fz_dim = mtf.Dimension("nz", nc)
tfx_dim = mtf.Dimension("tx", nc)
tfy_dim = mtf.Dimension("ty", nc)
tfz_dim = mtf.Dimension("tz", nc)
tx_dim = mtf.Dimension("tx_lr", nc)
ty_dim = mtf.Dimension("ty_lr", nc)
tz_dim = mtf.Dimension("tz_lr", nc)
nx_dim = mtf.Dimension('nx_block', n_block_x)
ny_dim = mtf.Dimension('ny_block', n_block_y)
nz_dim = mtf.Dimension('nz_block', n_block_z)
sx_dim = mtf.Dimension('sx_block', nc // n_block_x)
sy_dim = mtf.Dimension('sy_block', nc // n_block_y)
sz_dim = mtf.Dimension('sz_block', nc // n_block_z)
k_dims = [tx_dim, ty_dim, tz_dim]
batch_dim = mtf.Dimension("batch", batch_size)
klin = np.loadtxt('../flowpm/data/Planck15_a1p00.txt').T[0]
plin = np.loadtxt('../flowpm/data/Planck15_a1p00.txt').T[1]
ipklin = iuspline(klin, plin)
pk_dim = mtf.Dimension("npk", len(plin))
pk = mtf.import_tf_tensor(mesh, plin, shape=[pk_dim])
# Compute necessary Fourier kernels
kvec = flowpm.kernels.fftk((nc, nc, nc), symmetric=False)
kx = mtf.import_tf_tensor(mesh,
kvec[0].squeeze().astype('float32'),
shape=[tfx_dim])
ky = mtf.import_tf_tensor(mesh,
kvec[1].squeeze().astype('float32'),
shape=[tfy_dim])
kz = mtf.import_tf_tensor(mesh,
kvec[2].squeeze().astype('float32'),
shape=[tfz_dim])
kv = [ky, kz, kx]
# kvec for low resolution grid
kvec_lr = flowpm.kernels.fftk([nc, nc, nc], symmetric=False)
kx_lr = mtf.import_tf_tensor(mesh,
kvec_lr[0].squeeze().astype('float32'),
shape=[tx_dim])
ky_lr = mtf.import_tf_tensor(mesh,
kvec_lr[1].squeeze().astype('float32'),
shape=[ty_dim])
kz_lr = mtf.import_tf_tensor(mesh,
kvec_lr[2].squeeze().astype('float32'),
shape=[tz_dim])
kv_lr = [ky_lr, kz_lr, kx_lr]
shape = [batch_dim, fx_dim, fy_dim, fz_dim]
lr_shape = [batch_dim, fx_dim, fy_dim, fz_dim]
hr_shape = [batch_dim, nx_dim, ny_dim, nz_dim, sx_dim, sy_dim, sz_dim]
part_shape = [batch_dim, fx_dim, fy_dim, fz_dim]
# Begin simulation
## Compute initial initial conditions distributed
input_field = tf.placeholder(dtype, [batch_size, nc, nc, nc])
if infield:
initc = mtf.import_tf_tensor(mesh, input_field, shape=part_shape)
else:
initc = mtfpm.linear_field(mesh, shape, bs, nc, pk, kv)
# Here we can run our nbody
if FLAGS.nbody:
state = mtfpm.lpt_init_single(
initc,
a0,
kv_lr,
halo_size,
lr_shape,
hr_shape,
part_shape[1:],
antialias=True,
)
# Here we can run our nbody
final_state = mtfpm.nbody_single(state, stages, lr_shape, hr_shape,
kv_lr, halo_size)
else:
final_state = mtfpm.lpt_init_single(
initc,
stages[-1],
kv_lr,
halo_size,
lr_shape,
hr_shape,
part_shape[1:],
antialias=True,
)
# paint the field
final_field = mtf.zeros(mesh, shape=hr_shape)
for block_size_dim in hr_shape[-3:]:
final_field = mtf.pad(final_field, [halo_size, halo_size],
block_size_dim.name)
final_field = mesh_utils.cic_paint(final_field, final_state[0], halo_size)
# Halo exchange
for blocks_dim, block_size_dim in zip(hr_shape[1:4],
final_field.shape[-3:]):
final_field = mpm.halo_reduce(final_field, blocks_dim, block_size_dim,
halo_size)
# Remove borders
for block_size_dim in hr_shape[-3:]:
final_field = mtf.slice(final_field, halo_size, block_size_dim.size,
block_size_dim.name)
final_field = mtf.slicewise(
lambda x: x[:, 0, 0, 0], [final_field],
output_dtype=dtype,
output_shape=[batch_dim, fx_dim, fy_dim, fz_dim],
name='my_dumb_reshape',
splittable_dims=part_shape[:-1] + hr_shape[:4])
return initc, final_field, input_field
def unet_with_spatial_partition(mesh, mesh_impl, dataset_str, images, labels):
"""Builds the UNet model graph, train op and eval metrics.
Args:
mesh: a MeshTensorflow.mesh object.
mesh_impl: a mesh implementation, such as SimdMeshImpl and
PlacementMeshImpl.
dataset_str: a string of either train or eval. This is used for batch_norm.
images: a laid out Tensor with shape [batch, x, y, num_channels]
or [batch, x, y, z, num_channels].
labels: a laid out Tensor with shape [batch, x, y, num_classes]
or [batch, x, y, z, num_classes].
Returns:
Prediction and loss.
"""
is_training = (dataset_str == 'train')
if dataset_str == 'train':
batch_dim = mtf.Dimension('batch', FLAGS.batch_size_train)
else:
assert dataset_str == 'eval'
batch_dim = mtf.Dimension('batch', FLAGS.batch_size_eval)
image_nx_dim = mtf.Dimension('image_nx_block', FLAGS.image_nx_block)
image_ny_dim = mtf.Dimension('image_ny_block', FLAGS.image_ny_block)
image_sx_dim = mtf.Dimension('image_sx_block',
FLAGS.ct_resolution // FLAGS.image_nx_block)
image_sy_dim = mtf.Dimension('image_sy_block',
FLAGS.ct_resolution // FLAGS.image_ny_block)
image_sz_dim = mtf.Dimension('image_sz_block', FLAGS.ct_resolution)
image_c_dim = mtf.Dimension('image_c', FLAGS.image_c)
label_c_dim = mtf.Dimension('label_c', FLAGS.label_c)
mtf_images_shape, mtf_labels_shape = get_input_mtf_shapes(dataset_str)
mtf_dtype = tf.as_dtype(FLAGS.mtf_dtype)
variable_dtype = mtf.VariableDType(mtf_dtype, mtf_dtype, mtf_dtype)
# Import input features.
x = mtf.import_laid_out_tensor(mesh, mesh_impl.LaidOutTensor(images),
mtf_images_shape)
x = mtf.cast(x, mtf_dtype)
# Import ground truth labels.
t = mtf.import_laid_out_tensor(mesh, mesh_impl.LaidOutTensor(labels),
mtf_labels_shape)
t = mtf.cast(t, mtf_dtype)
# Transpose the blocks.
if FLAGS.sampled_2d_slices:
x = mtf.transpose(x, [
batch_dim, image_nx_dim, image_ny_dim, image_sx_dim, image_sy_dim,
image_c_dim
])
t = mtf.transpose(t, [
batch_dim, image_nx_dim, image_ny_dim, image_sx_dim, image_sy_dim,
label_c_dim
])
else:
x = mtf.transpose(x, [
batch_dim, image_nx_dim, image_ny_dim, image_sx_dim, image_sy_dim,
image_sz_dim, image_c_dim
])
t = mtf.transpose(t, [
batch_dim, image_nx_dim, image_ny_dim, image_sx_dim, image_sy_dim,
image_sz_dim, label_c_dim
])
# Network.
levels = []
all_bn_update_ops = []
# add levels with convolution or down-sampling
for depth in range(FLAGS.network_depth):
for n_conv in range(FLAGS.n_conv_per_block):
if depth == 0 and n_conv == 0:
# no dropout in 1st layer.
dropout_keep_p = 1.0
else:
dropout_keep_p = FLAGS.dropout_keep_p
x, bn_update_ops = conv_with_spatial_partition(
x, FLAGS.sampled_2d_slices, image_nx_dim, image_ny_dim,
FLAGS.n_base_filters * (2**depth), dropout_keep_p,
FLAGS.with_batch_norm, is_training,
'conv_{}_{}'.format(depth, n_conv), variable_dtype,
'conv_down_{}_{}'.format(depth, n_conv))
all_bn_update_ops.extend(bn_update_ops)
levels.append(x)
if depth < FLAGS.network_depth - 1:
if FLAGS.sampled_2d_slices:
x = mtf.layers.max_pool2d(x, ksize=(2, 2))
else:
x = mtf.layers.max_pool3d(x, ksize=(2, 2, 2))
# add levels with up-convolution or up-sampling
for depth in range(FLAGS.network_depth - 1)[::-1]:
x = deconv_with_spatial_partition(
x, FLAGS.sampled_2d_slices, image_nx_dim, image_ny_dim,
FLAGS.n_base_filters * (2**depth), FLAGS.dropout_keep_p,
'conv_{}_{}'.format(depth, FLAGS.n_conv_per_block - 1),
variable_dtype, 'deconv_{}_0'.format(depth))
x = mtf.concat([x, levels[depth]],
concat_dim_name='conv_{}_{}'.format(
depth, FLAGS.n_conv_per_block - 1))
for n_conv in range(FLAGS.n_conv_per_block):
x, bn_update_ops = conv_with_spatial_partition(
x, FLAGS.sampled_2d_slices, image_nx_dim, image_ny_dim,
FLAGS.n_base_filters * (2**depth), FLAGS.dropout_keep_p,
FLAGS.with_batch_norm, is_training,
'conv_{}_{}'.format(depth, n_conv), variable_dtype,
'conv_up_{}_{}'.format(depth, n_conv))
all_bn_update_ops.extend(bn_update_ops)
# no dropout in the final layer.
if FLAGS.sampled_2d_slices:
y = mtf.layers.conv2d_with_blocks(
x,
mtf.Dimension('label_c', FLAGS.label_c),
filter_size=(1, 1),
strides=(1, 1),
padding='SAME',
h_blocks_dim=image_nx_dim,
w_blocks_dim=image_ny_dim,
variable_dtype=variable_dtype,
name='final_conv_{}'.format(FLAGS.label_c),
)
else:
y = mtf.layers.conv3d_with_blocks(
x,
mtf.Dimension('label_c', FLAGS.label_c),
filter_size=(1, 1, 1),
strides=(1, 1, 1),
padding='SAME',
d_blocks_dim=image_nx_dim,
h_blocks_dim=image_ny_dim,
variable_dtype=variable_dtype,
name='final_conv_{}'.format(FLAGS.label_c),
)
# use mtf.constant to make sure there is no CPU-side constants.
def scalar(v, dtype):
return mtf.constant(mesh, v, shape=[], dtype=dtype)
argmax_t = mtf.argmax(t, label_c_dim)
liver_t = mtf.cast(mtf.equal(argmax_t, scalar(1, tf.int32)), mtf_dtype)
lesion_t = mtf.cast(mtf.equal(argmax_t, scalar(2, tf.int32)), mtf_dtype)
argmax_y = mtf.argmax(y, label_c_dim)
lesion_y = mtf.cast(mtf.equal(argmax_y, scalar(2, tf.int32)), mtf_dtype)
# summary of class ratios.
lesion_pred_ratio = mtf.reduce_mean(lesion_y)
lesion_label_ratio = mtf.reduce_mean(lesion_t)
# summary of accuracy.
accuracy = mtf.reduce_mean(
mtf.cast(mtf.equal(argmax_y, argmax_t), mtf_dtype))
# Cross-entropy loss. Up-weight the liver region.
pixel_loss = mtf.layers.softmax_cross_entropy_with_logits(
y, t, label_c_dim)
pixel_weight = scalar(1, mtf_dtype) + \
liver_t * scalar(FLAGS.xen_liver_weight - 1, mtf_dtype) + \
lesion_t * scalar(FLAGS.xen_lesion_weight - FLAGS.xen_liver_weight,
mtf_dtype)
loss_xen = mtf.reduce_mean(pixel_loss * pixel_weight)
# Dice loss
y_prob = mtf.softmax(y, reduced_dim=label_c_dim)
lesion_prob = mtf.reduce_sum(mtf.slice(y_prob, 2, 1, 'label_c'),
reduced_dim=mtf.Dimension('label_c', 1))
prob_intersect = mtf.reduce_sum(lesion_prob * lesion_t,
output_shape=mtf.Shape([batch_dim]))
prob_area_sum = mtf.reduce_sum(lesion_prob + lesion_t,
output_shape=mtf.Shape([batch_dim]))
loss_dice_per_case = mtf.reduce_mean(
scalar(-2, mtf_dtype) * prob_intersect /
(prob_area_sum + scalar(FLAGS.dice_epsilon, mtf_dtype)))
loss_dice_global = scalar(-2, mtf_dtype) * mtf.reduce_sum(
prob_intersect) / (mtf.reduce_sum(prob_area_sum) +
scalar(FLAGS.dice_epsilon, mtf_dtype))
loss_dice = (loss_dice_per_case + loss_dice_global) * scalar(
0.5, mtf_dtype)
loss = scalar(FLAGS.dice_loss_weight, mtf_dtype) * loss_dice + scalar(
1 - FLAGS.dice_loss_weight, mtf_dtype) * loss_xen
intersect = mtf.reduce_sum(lesion_y * lesion_t,
output_shape=mtf.Shape([batch_dim]))
area_sum = mtf.reduce_sum(lesion_y + lesion_t,
output_shape=mtf.Shape([batch_dim]))
# summary of dice.
dice_per_case = mtf.reduce_mean(
scalar(2, mtf_dtype) * intersect /
(area_sum + scalar(0.000001, mtf_dtype)))
dice_global = scalar(2, mtf_dtype) * mtf.reduce_sum(intersect) / (
mtf.reduce_sum(area_sum) + scalar(0.000001, mtf_dtype))
eval_metrics = {
'lesion_pred_ratio': lesion_pred_ratio,
'lesion_label_ratio': lesion_label_ratio,
'accuracy_of_all_classes': accuracy,
'lesion_dice_per_case': dice_per_case,
'lesion_dice_global': dice_global,
'loss_xen': loss_xen,
'loss_dice': loss_dice,
'loss_dice_per_case': loss_dice_per_case,
'loss_dice_global': loss_dice_global,
}
if FLAGS.sampled_2d_slices:
y_prob_downsampled = mtf.layers.avg_pool2d(
y_prob, ksize=(FLAGS.pred_downsample, ) * 2)
if FLAGS.output_ground_truth:
lesion_gt_downsampled = mtf.layers.avg_pool2d(
mtf.slice(t, 2, 1, 'label_c'),
ksize=(FLAGS.pred_downsample, ) * 2)
else:
y_prob_downsampled = mtf.layers.avg_pool3d(
y_prob, ksize=(FLAGS.pred_downsample, ) * 3)
if FLAGS.output_ground_truth:
lesion_gt_downsampled = mtf.layers.avg_pool3d(
mtf.slice(t, 2, 1, 'label_c'),
ksize=(FLAGS.pred_downsample, ) * 3)
liver_prob_downsampled = mtf.slice(y_prob_downsampled, 1, 1, 'label_c')
lesion_prob_downsampled = mtf.slice(y_prob_downsampled, 2, 1, 'label_c')
preds = [
mtf.reduce_sum(liver_prob_downsampled,
reduced_dim=mtf.Dimension('label_c', 1)),
mtf.reduce_sum(lesion_prob_downsampled,
reduced_dim=mtf.Dimension('label_c', 1))
]
if FLAGS.output_ground_truth:
preds.append(
mtf.reduce_sum(lesion_gt_downsampled,
reduced_dim=mtf.Dimension('label_c', 1)))
preds.extend([intersect, area_sum])
return preds, loss, eval_metrics, all_bn_update_ops
def nbody_fn(mesh,
klin,
plin,
nc=FLAGS.nc,
bs=FLAGS.box_size,
batch_size=FLAGS.batch_size,
a0=FLAGS.a0,
a=FLAGS.af,
nsteps=FLAGS.nsteps,
dtype=tf.float32):
""" Pyramid N-body function
"""
stages = np.linspace(a0, a, nsteps, endpoint=True)
# Define the named dimensions
# Parameters of the small scales decomposition
n_block_x = FLAGS.nx
n_block_y = FLAGS.ny
n_block_z = 1
halo_size = FLAGS.hsize
# Parameters of the large scales decomposition
downsampling_factor = FLAGS.dsample
lnc = nc // 2**downsampling_factor
fx_dim = mtf.Dimension("nx", nc)
fy_dim = mtf.Dimension("ny", nc)
fz_dim = mtf.Dimension("nz", nc)
tfx_dim = mtf.Dimension("tx", nc)
tfy_dim = mtf.Dimension("ty", nc)
tfz_dim = mtf.Dimension("tz", nc)
# Dimensions of the low resolution grid
x_dim = mtf.Dimension("nx_lr", lnc)
y_dim = mtf.Dimension("ny_lr", lnc)
z_dim = mtf.Dimension("nz_lr", lnc)
tx_dim = mtf.Dimension("tx_lr", lnc)
ty_dim = mtf.Dimension("ty_lr", lnc)
tz_dim = mtf.Dimension("tz_lr", lnc)
nx_dim = mtf.Dimension('nx_block', n_block_x)
ny_dim = mtf.Dimension('ny_block', n_block_y)
nz_dim = mtf.Dimension('nz_block', n_block_z)
sx_dim = mtf.Dimension('sx_block', nc // n_block_x)
sy_dim = mtf.Dimension('sy_block', nc // n_block_y)
sz_dim = mtf.Dimension('sz_block', nc // n_block_z)
batch_dim = mtf.Dimension("batch", batch_size)
pk_dim = mtf.Dimension("npk", len(plin))
pk = mtf.import_tf_tensor(mesh, plin.astype('float32'), shape=[pk_dim])
# Compute necessary Fourier kernels
kvec = flowpm.kernels.fftk((nc, nc, nc), symmetric=False)
kx = mtf.import_tf_tensor(
mesh, kvec[0].squeeze().astype('float32'), shape=[tfx_dim])
ky = mtf.import_tf_tensor(
mesh, kvec[1].squeeze().astype('float32'), shape=[tfy_dim])
kz = mtf.import_tf_tensor(
mesh, kvec[2].squeeze().astype('float32'), shape=[tfz_dim])
kv = [ky, kz, kx]
# kvec for low resolution grid
kvec_lr = flowpm.kernels.fftk([lnc, lnc, lnc], symmetric=False)
kx_lr = mtf.import_tf_tensor(
mesh,
kvec_lr[0].squeeze().astype('float32') / 2**downsampling_factor,
shape=[tx_dim])
ky_lr = mtf.import_tf_tensor(
mesh,
kvec_lr[1].squeeze().astype('float32') / 2**downsampling_factor,
shape=[ty_dim])
kz_lr = mtf.import_tf_tensor(
mesh,
kvec_lr[2].squeeze().astype('float32') / 2**downsampling_factor,
shape=[tz_dim])
kv_lr = [ky_lr, kz_lr, kx_lr]
# kvec for high resolution blocks
padded_sx_dim = mtf.Dimension('padded_sx_block',
nc // n_block_x + 2 * halo_size)
padded_sy_dim = mtf.Dimension('padded_sy_block',
nc // n_block_y + 2 * halo_size)
padded_sz_dim = mtf.Dimension('padded_sz_block',
nc // n_block_z + 2 * halo_size)
kvec_hr = flowpm.kernels.fftk([
nc // n_block_x + 2 * halo_size, nc // n_block_y + 2 * halo_size,
nc // n_block_z + 2 * halo_size
],
symmetric=False)
kx_hr = mtf.import_tf_tensor(
mesh, kvec_hr[0].squeeze().astype('float32'), shape=[padded_sx_dim])
ky_hr = mtf.import_tf_tensor(
mesh, kvec_hr[1].squeeze().astype('float32'), shape=[padded_sy_dim])
kz_hr = mtf.import_tf_tensor(
mesh, kvec_hr[2].squeeze().astype('float32'), shape=[padded_sz_dim])
kv_hr = [ky_hr, kz_hr, kx_hr]
shape = [batch_dim, fx_dim, fy_dim, fz_dim]
lr_shape = [batch_dim, x_dim, y_dim, z_dim]
hr_shape = [batch_dim, nx_dim, ny_dim, nz_dim, sx_dim, sy_dim, sz_dim]
part_shape = [batch_dim, fx_dim, fy_dim, fz_dim]
# Compute initial initial conditions distributed
initc = mtfpm.linear_field(mesh, shape, bs, nc, pk, kv)
# Reshaping array into high resolution mesh
field = mtf.slicewise(
lambda x: tf.expand_dims(
tf.expand_dims(tf.expand_dims(x, axis=1), axis=1), axis=1), [initc],
output_dtype=tf.float32,
output_shape=hr_shape,
name='my_reshape',
splittable_dims=lr_shape[:-1] + hr_shape[1:4] + part_shape[1:3])
for block_size_dim in hr_shape[-3:]:
field = mtf.pad(field, [halo_size, halo_size], block_size_dim.name)
for blocks_dim, block_size_dim in zip(hr_shape[1:4], field.shape[-3:]):
field = mpm.halo_reduce(field, blocks_dim, block_size_dim, halo_size)
field = mtf.reshape(field, field.shape + [mtf.Dimension('h_dim', 1)])
high = field
low = mesh_utils.downsample(field, downsampling_factor, antialias=True)
low = mtf.reshape(low, low.shape[:-1])
high = mtf.reshape(high, high.shape[:-1])
for block_size_dim in hr_shape[-3:]:
low = mtf.slice(low, halo_size // 2**downsampling_factor,
block_size_dim.size // 2**downsampling_factor,
block_size_dim.name)
# Hack usisng custom reshape because mesh is pretty dumb
low = mtf.slicewise(
lambda x: x[:, 0, 0, 0], [low],
output_dtype=tf.float32,
output_shape=lr_shape,
name='my_dumb_reshape',
splittable_dims=lr_shape[:-1] + hr_shape[:4])
state = mtfpm.lpt_init(
low,
high,
0.1,
kv_lr,
kv_hr,
halo_size,
hr_shape,
lr_shape,
part_shape[1:],
downsampling_factor=downsampling_factor,
antialias=True,
)
final_state = mtfpm.nbody(
state,
stages,
lr_shape,
hr_shape,
kv_lr,
kv_hr,
halo_size,
downsampling_factor=downsampling_factor)
# paint the field
final_field = mtf.zeros(mesh, shape=hr_shape)
for block_size_dim in hr_shape[-3:]:
final_field = mtf.pad(final_field, [halo_size, halo_size],
block_size_dim.name)
final_field = mesh_utils.cic_paint(final_field, final_state[0], halo_size)
# Halo exchange
for blocks_dim, block_size_dim in zip(hr_shape[1:4], final_field.shape[-3:]):
final_field = mpm.halo_reduce(final_field, blocks_dim, block_size_dim,
halo_size)
# Remove borders
for block_size_dim in hr_shape[-3:]:
final_field = mtf.slice(final_field, halo_size, block_size_dim.size,
block_size_dim.name)
final_field = mtf.slicewise(
lambda x: x[:, 0, 0, 0], [final_field],
output_dtype=tf.float32,
output_shape=[batch_dim, fx_dim, fy_dim, fz_dim],
name='my_dumb_reshape',
splittable_dims=part_shape[:-1] + hr_shape[:4])
return initc, final_field
def benchmark_model(mesh):
"""
Initializes a 3D volume with random noise, and execute a forward FFT
"""
# Setup parameters
bs = FLAGS.box_size
nc = FLAGS.cube_size
batch_size = FLAGS.batch_size
a0 = FLAGS.a0
a = 1.0
nsteps = FLAGS.pm_steps
# Compute a few things first, using simple tensorflow
klin = np.loadtxt('../flowpm/data/Planck15_a1p00.txt').T[0]
plin = np.loadtxt('../flowpm/data/Planck15_a1p00.txt').T[1]
ipklin = iuspline(klin, plin)
stages = np.linspace(a0, a, nsteps, endpoint=True)
# Initialize the integration steps
stages = np.linspace(FLAGS.a0, 1.0, FLAGS.pm_steps, endpoint=True)
# Generate a batch of 3D initial conditions
initial_conditions = flowpm.linear_field(
nc, # size of the cube
bs, # Physical size of the cube
ipklin, # Initial power spectrum
batch_size=batch_size)
# Compute necessary Fourier kernels
kvec = flowpm.kernels.fftk((nc, nc, nc), symmetric=False)
from flowpm.kernels import laplace_kernel, gradient_kernel
lap = tf.cast(laplace_kernel(kvec), tf.complex64)
grad_x = gradient_kernel(kvec, 0)
grad_y = gradient_kernel(kvec, 1)
grad_z = gradient_kernel(kvec, 2)
# Define the named dimensions
# Parameters of the small scales decomposition
n_block_x = 8
n_block_y = 4
n_block_z = 1
halo_size = 4
# Parameters of the large scales decomposition
downsampling_factor = 2
lnc = nc // 2**downsampling_factor
fx_dim = mtf.Dimension("nx", nc)
fy_dim = mtf.Dimension("ny", nc)
fz_dim = mtf.Dimension("nz", nc)
tfx_dim = mtf.Dimension("tx", nc)
tfy_dim = mtf.Dimension("ty", nc)
tfz_dim = mtf.Dimension("tz", nc)
# Dimensions of the low resolution grid
tx_dim = mtf.Dimension("tx_lr", nc)
ty_dim = mtf.Dimension("ty_lr", nc)
tz_dim = mtf.Dimension("tz_lr", nc)
nx_dim = mtf.Dimension('nx_block', n_block_x)
ny_dim = mtf.Dimension('ny_block', n_block_y)
nz_dim = mtf.Dimension('nz_block', n_block_z)
sx_dim = mtf.Dimension('sx_block', nc // n_block_x)
sy_dim = mtf.Dimension('sy_block', nc // n_block_y)
sz_dim = mtf.Dimension('sz_block', nc // n_block_z)
batch_dim = mtf.Dimension("batch", batch_size)
pk_dim = mtf.Dimension("npk", len(plin))
pk = mtf.import_tf_tensor(mesh, plin.astype('float32'), shape=[pk_dim])
# Compute necessary Fourier kernels
kvec = flowpm.kernels.fftk((nc, nc, nc), symmetric=False)
kx = mtf.import_tf_tensor(mesh,
kvec[0].squeeze().astype('float32'),
shape=[tfx_dim])
ky = mtf.import_tf_tensor(mesh,
kvec[1].squeeze().astype('float32'),
shape=[tfy_dim])
kz = mtf.import_tf_tensor(mesh,
kvec[2].squeeze().astype('float32'),
shape=[tfz_dim])
kv = [ky, kz, kx]
kvec_lr = flowpm.kernels.fftk([nc, nc, nc], symmetric=False)
kx_lr = mtf.import_tf_tensor(mesh,
kvec_lr[0].squeeze().astype('float32'),
shape=[tx_dim])
ky_lr = mtf.import_tf_tensor(mesh,
kvec_lr[1].squeeze().astype('float32'),
shape=[ty_dim])
kz_lr = mtf.import_tf_tensor(mesh,
kvec_lr[2].squeeze().astype('float32'),
shape=[tz_dim])
kv_lr = [ky_lr, kz_lr, kx_lr]
# kvec for high resolution blocks
shape = [batch_dim, fx_dim, fy_dim, fz_dim]
lr_shape = [batch_dim, fx_dim, fy_dim, fz_dim]
hr_shape = [batch_dim, nx_dim, ny_dim, nz_dim, sx_dim, sy_dim, sz_dim]
part_shape = [batch_dim, fx_dim, fy_dim, fz_dim]
initc = mtfpm.linear_field(mesh, shape, bs, nc, pk, kv)
state = mtfpm.lpt_init_single(
initc,
a0,
kv_lr,
halo_size,
lr_shape,
hr_shape,
part_shape[1:],
antialias=True,
)
#state = mtfpm.lpt_init(low, high, 0.1, kv_lr, kv_hr, halo_size, hr_shape, lr_shape,
# part_shape[1:], downsampling_factor=downsampling_factor, antialias=True,)
# Here we can run our nbody
final_state = state #mtfpm.nbody(state, stages, lr_shape, hr_shape, kv_lr, kv_hr, halo_size, downsampling_factor=downsampling_factor)
# paint the field
final_field = mtf.zeros(mesh, shape=hr_shape)
for block_size_dim in hr_shape[-3:]:
final_field = mtf.pad(final_field, [halo_size, halo_size],
block_size_dim.name)
final_field = mesh_utils.cic_paint(final_field, final_state[0], halo_size)
# Halo exchange
for blocks_dim, block_size_dim in zip(hr_shape[1:4], final_field.shape[-3:]):
final_field = mpm.halo_reduce(final_field, blocks_dim, block_size_dim,
halo_size)
# Remove borders
for block_size_dim in hr_shape[-3:]:
final_field = mtf.slice(final_field, halo_size, block_size_dim.size,
block_size_dim.name)
#final_field = mtf.reshape(final_field, [batch_dim, fx_dim, fy_dim, fz_dim])
# Hack usisng custom reshape because mesh is pretty dumb
final_field = mtf.slicewise(lambda x: x[:, 0, 0, 0], [final_field],
output_dtype=tf.float32,
output_shape=[batch_dim, fx_dim, fy_dim, fz_dim],
name='my_dumb_reshape',
splittable_dims=part_shape[:-1] + hr_shape[:4])
return mtf.reduce_sum(final_field)
def lpt_prototype(mesh,
initial_conditions,
derivs,
nc=FLAGS.nc,
bs=FLAGS.box_size,
batch_size=FLAGS.batch_size,
a0=FLAGS.a0,
a=FLAGS.af,
nsteps=FLAGS.nsteps):
"""
Prototype of function computing LPT deplacement.
Returns output tensorflow and mesh tensorflow tensors
"""
stages = np.linspace(a0, a, nsteps, endpoint=True)
lap, grad_x, grad_y, grad_z = derivs
klin = np.loadtxt('../flowpm/data/Planck15_a1p00.txt').T[0]
plin = np.loadtxt('../flowpm/data/Planck15_a1p00.txt').T[1]
ipklin = iuspline(klin, plin)
stages = np.linspace(a0, a, nsteps, endpoint=True)
# Define the named dimensions
# Parameters of the small scales decomposition
n_block_x = FLAGS.nx
n_block_y = FLAGS.ny
n_block_z = 1
halo_size = FLAGS.hsize
# Parameters of the large scales decomposition
downsampling_factor = FLAGS.dsample
lnc = nc // 2**downsampling_factor
#
fx_dim = mtf.Dimension("nx", nc)
fy_dim = mtf.Dimension("ny", nc)
fz_dim = mtf.Dimension("nz", nc)
# Dimensions of the low resolution grid
x_dim = mtf.Dimension("nx_lr", lnc)
y_dim = mtf.Dimension("ny_lr", lnc)
z_dim = mtf.Dimension("nz_lr", lnc)
tx_dim = mtf.Dimension("tx_lr", lnc)
ty_dim = mtf.Dimension("ty_lr", lnc)
tz_dim = mtf.Dimension("tz_lr", lnc)
nx_dim = mtf.Dimension('nx_block', n_block_x)
ny_dim = mtf.Dimension('ny_block', n_block_y)
nz_dim = mtf.Dimension('nz_block', n_block_z)
sx_dim = mtf.Dimension('sx_block', nc // n_block_x)
sy_dim = mtf.Dimension('sy_block', nc // n_block_y)
sz_dim = mtf.Dimension('sz_block', nc // n_block_z)
k_dims = [tx_dim, ty_dim, tz_dim]
batch_dim = mtf.Dimension("batch", batch_size)
pk_dim = mtf.Dimension("npk", len(plin))
pk = mtf.import_tf_tensor(mesh, plin.astype('float32'), shape=[pk_dim])
# kvec for low resolution grid
kvec_lr = flowpm.kernels.fftk([lnc, lnc, lnc], symmetric=False)
kx_lr = mtf.import_tf_tensor(mesh,
kvec_lr[0].squeeze().astype('float32') /
2**downsampling_factor,
shape=[tx_dim])
ky_lr = mtf.import_tf_tensor(mesh,
kvec_lr[1].squeeze().astype('float32') /
2**downsampling_factor,
shape=[ty_dim])
kz_lr = mtf.import_tf_tensor(mesh,
kvec_lr[2].squeeze().astype('float32') /
2**downsampling_factor,
shape=[tz_dim])
kv_lr = [ky_lr, kz_lr, kx_lr]
# kvec for high resolution blocks
padded_sx_dim = mtf.Dimension('padded_sx_block',
nc // n_block_x + 2 * halo_size)
padded_sy_dim = mtf.Dimension('padded_sy_block',
nc // n_block_y + 2 * halo_size)
padded_sz_dim = mtf.Dimension('padded_sz_block',
nc // n_block_z + 2 * halo_size)
kvec_hr = flowpm.kernels.fftk([
nc // n_block_x + 2 * halo_size, nc // n_block_y + 2 * halo_size,
nc // n_block_z + 2 * halo_size
],
symmetric=False)
kx_hr = mtf.import_tf_tensor(mesh,
kvec_hr[0].squeeze().astype('float32'),
shape=[padded_sx_dim])
ky_hr = mtf.import_tf_tensor(mesh,
kvec_hr[1].squeeze().astype('float32'),
shape=[padded_sy_dim])
kz_hr = mtf.import_tf_tensor(mesh,
kvec_hr[2].squeeze().astype('float32'),
shape=[padded_sz_dim])
kv_hr = [kx_hr, ky_hr, kz_hr]
lr_shape = [batch_dim, x_dim, y_dim, z_dim]
hr_shape = [batch_dim, nx_dim, ny_dim, nz_dim, sx_dim, sy_dim, sz_dim]
part_shape = [batch_dim, fx_dim, fy_dim, fz_dim]
initc = tf.reshape(
initial_conditions,
[1, n_block_x, nc // n_block_x, n_block_y, nc // n_block_y, 1, nc])
initc = tf.transpose(initc, [0, 1, 3, 5, 2, 4, 6])
field = mtf.import_tf_tensor(mesh, initc, shape=hr_shape)
for block_size_dim in hr_shape[-3:]:
field = mtf.pad(field, [halo_size, halo_size], block_size_dim.name)
for blocks_dim, block_size_dim in zip(hr_shape[1:4], field.shape[-3:]):
field = mpm.halo_reduce(field, blocks_dim, block_size_dim, halo_size)
field = mtf.reshape(field, field.shape + [mtf.Dimension('h_dim', 1)])
high = field
low = mesh_utils.downsample(field, downsampling_factor, antialias=True)
low = mtf.reshape(low, low.shape[:-1])
high = mtf.reshape(high, high.shape[:-1])
for block_size_dim in hr_shape[-3:]:
low = mtf.slice(low, halo_size // 2**downsampling_factor,
block_size_dim.size // 2**downsampling_factor,
block_size_dim.name)
# Hack usisng custom reshape because mesh is pretty dumb
low = mtf.slicewise(lambda x: x[:, 0, 0, 0], [low],
output_dtype=tf.float32,
output_shape=lr_shape,
name='my_dumb_reshape',
splittable_dims=lr_shape[:-1] + hr_shape[:4])
# Hack to handle reshape acrosss multiple dimensions
#low = mtf.reshape(low, [batch_dim, x_dim, low.shape[2], low.shape[5], z_dim])
#low = mtf.reshape(low, lr_shape)
state = mtfpm.lpt_init(
low,
high,
a0,
kv_lr,
kv_hr,
halo_size,
hr_shape,
lr_shape,
k_dims,
part_shape[1:],
downsampling_factor=downsampling_factor,
antialias=True,
)
# Here we can run our nbody
final_state = state #mtfpm.nbody(state, stages, lr_shape, hr_shape, k_dims, kv_lr, kv_hr, halo_size, downsampling_factor=downsampling_factor)
# paint the field
final_field = mtf.zeros(mesh, shape=hr_shape)
for block_size_dim in hr_shape[-3:]:
final_field = mtf.pad(final_field, [halo_size, halo_size],
block_size_dim.name)
final_field = mesh_utils.cic_paint(final_field, final_state[0], halo_size)
# Halo exchange
for blocks_dim, block_size_dim in zip(hr_shape[1:4],
final_field.shape[-3:]):
final_field = mpm.halo_reduce(final_field, blocks_dim, block_size_dim,
halo_size)
# Remove borders
for block_size_dim in hr_shape[-3:]:
final_field = mtf.slice(final_field, halo_size, block_size_dim.size,
block_size_dim.name)
#final_field = mtf.reshape(final_field, [batch_dim, fx_dim, fy_dim, fz_dim])
# Hack usisng custom reshape because mesh is pretty dumb
final_field = mtf.slicewise(
lambda x: x[:, 0, 0, 0], [final_field],
output_dtype=tf.float32,
output_shape=[batch_dim, fx_dim, fy_dim, fz_dim],
name='my_dumb_reshape',
splittable_dims=part_shape[:-1] + hr_shape[:4])
return final_field
def __init__(self,
config,
is_training,
input_ids,
input_mask=None,
token_type_ids=None,
scope=None,
mesh_shape="",
layout=""):
self.config = copy.deepcopy(config)
del config
if not is_training:
self.config.layer_output_dropout_prob = 0.0
self.config.attention_probs_dropout_prob = 0.0
self.config.feedforward_intermediate_dropout_prob = 0.0
input_shape = input_ids.shape
assert input_shape.ndims == 2
self._seq_dim = input_shape.dims[1]
self._memory_seq_dim = mtf.Dimension("memory_seq", self.seq_dim.size)
self._extra_losses = []
mesh = input_ids.mesh
if token_type_ids is None:
token_type_ids = mtf.zeros(mesh, input_shape, dtype=tf.int32)
with tf.variable_scope(scope, default_name="bert"):
with tf.variable_scope("embeddings"):
# Perform embedding lookup on the word ids.
self.embedding_table = mtf.get_variable(
mesh, "word_embeddings",
mtf.Shape([self.vocab_dim, self.model_dim]),
initializer=self.embedding_initializer)
self.word_embedding_output = mtf.gather(
self.embedding_table, input_ids, self.vocab_dim)
# Add positional embeddings and token type embeddings, then layer
# normalize and perform dropout.
self.embedding_output = self.word_embedding_output
token_type_table = mtf.get_variable(
mesh, "token_type_embeddings",
mtf.Shape([self.token_type_vocab_dim, self.model_dim]),
initializer=self.embedding_initializer)
if token_type_ids is not None:
self.embedding_output += mtf.gather(
token_type_table, token_type_ids, self.token_type_vocab_dim)
if self.config.position_signal == "embedding":
full_position_table = mtf.get_variable(
mesh, "position_embeddings",
mtf.Shape([self.max_position_embeddings_dim, self.model_dim]),
initializer=self.embedding_initializer)
short_position_table = mtf.rename_dimension(
mtf.slice(full_position_table, 0, self.seq_dim.size,
self.max_position_embeddings_dim.name),
self.max_position_embeddings_dim.name, self.seq_dim.name)
self.embedding_output += short_position_table
self.embedding_output = self.normalize(self.embedding_output)
self.embedding_output = mtf.dropout(
self.embedding_output, is_training,
keep_prob=1.0 - self.config.layer_output_dropout_prob)
with tf.variable_scope("encoder"):
attention_biases = []
if input_mask:
# [batch_dim, memory_seq_dim]
attention_biases.append(
(1.0 - mtf.to_float(mtf.replace_dimensions(
input_mask, self.seq_dim, self.memory_seq_dim))) * -10000.0)
if self.config.position_signal == "relative_attention_bias":
buckets_dim = mtf.Dimension("buckets", 32)
rp_bucket = _relative_position_bucket(
mtf.range(mesh, self.memory_seq_dim, tf.int32)
- mtf.range(mesh, self.seq_dim, tf.int32),
num_buckets=buckets_dim.size)
bias_var = mtf.get_variable(
mesh, "relative_attention_bias",
[self.num_heads_dim, buckets_dim],
initializer=tf.zeros_initializer())
attention_biases.append(mtf.gather(bias_var, rp_bucket, buckets_dim))
attention_bias = mtf.add_n(attention_biases)
prev_layer_output = self.embedding_output
self.all_encoder_layers = []
for block_num in range(self.config.num_blocks):
with tf.variable_scope("block_%d" % block_num):
for layer_idx, layer_type in enumerate(self.config.block_layers):
layer_name = layer_type
count = self.config.block_layers[:layer_idx].count(layer_type)
if count:
layer_name += "_%d" % count
with tf.variable_scope(layer_name):
x = prev_layer_output
if self.config.residual_structure == "direct":
x = self.normalize(x)
if layer_type == "attention":
x = self.self_attention(x, attention_bias)
elif layer_type == "feedforward":
x = self.feedforward(x)
elif layer_type == "moe":
x = self.moe(x, layout, mesh_shape, input_mask, is_training)
else:
raise ValueError("unknown layer type " + layer_type)
x = mtf.dropout(
x, is_training,
keep_prob=1.0 - self.config.layer_output_dropout_prob)
layer_output = prev_layer_output + x
if self.config.residual_structure == "original":
layer_output = self.normalize(layer_output)
prev_layer_output = layer_output
self.all_encoder_layers.append(layer_output)
self.sequence_output = prev_layer_output
if self.config.residual_structure == "direct":
self.sequence_output = self.normalize(self.sequence_output)
# The "pooler" converts the encoded sequence tensor of shape
# [batch_dim, seq_dim, hidden_size] to a tensor of shape
# [batch_dim, hidden_size]. This is necessary for segment-level
# (or segment-pair-level) classification tasks where we need a fixed
# dimensional representation of the segment.
with tf.variable_scope("pooler"):
# We "pool" the model by simply taking the hidden state corresponding
# to the first token. We assume that this has been pre-trained
first_token_tensor = mtf.gather(self.sequence_output, 0, self.seq_dim)
self.pooled_output = mtf.layers.dense(
first_token_tensor,
reduced_dims=[self.model_dim],
new_dims=[self.model_dim],
activation=mtf.tanh,
kernel_initializer=self.dense_initializer,
use_bias=self.config.use_bias)
def lpt_prototype(mesh,
initial_conditions,
derivs,
nc=FLAGS.nc,
bs=FLAGS.box_size,
batch_size=FLAGS.batch_size,
a0=FLAGS.a0,
a=FLAGS.af,
nsteps=FLAGS.nsteps):
"""
Prototype of function computing LPT deplacement.
Returns output tensorflow and mesh tensorflow tensors
"""
stages = np.linspace(a0, a, nsteps, endpoint=True)
lap, grad_x, grad_y, grad_z = derivs
klin = np.loadtxt('../flowpm/data/Planck15_a1p00.txt').T[0]
plin = np.loadtxt('../flowpm/data/Planck15_a1p00.txt').T[1]
ipklin = iuspline(klin, plin)
stages = np.linspace(a0, a, nsteps, endpoint=True)
# Define the named dimensions
# Parameters of the small scales decomposition
n_block_x = FLAGS.nx
n_block_y = FLAGS.ny
n_block_z = 1
halo_size = FLAGS.hsize
# Parameters of the large scales decomposition
downsampling_factor = 0
lnc = nc // 2**downsampling_factor
#
ffx_dim = mtf.Dimension("fnx", nc)
ffy_dim = mtf.Dimension("fny", nc)
ffz_dim = mtf.Dimension("fnz", nc)
fx_dim = mtf.Dimension("nx", nc)
fy_dim = mtf.Dimension("ny", nc)
fz_dim = mtf.Dimension("nz", nc)
tx_dim = mtf.Dimension("tx_lr", nc)
ty_dim = mtf.Dimension("ty_lr", nc)
tz_dim = mtf.Dimension("tz_lr", nc)
nx_dim = mtf.Dimension('nx_block', n_block_x)
ny_dim = mtf.Dimension('ny_block', n_block_y)
nz_dim = mtf.Dimension('nz_block', n_block_z)
sx_dim = mtf.Dimension('sx_block', nc // n_block_x)
sy_dim = mtf.Dimension('sy_block', nc // n_block_y)
sz_dim = mtf.Dimension('sz_block', nc // n_block_z)
k_dims = [tx_dim, ty_dim, tz_dim]
batch_dim = mtf.Dimension("batch", batch_size)
pk_dim = mtf.Dimension("npk", len(plin))
pk = mtf.import_tf_tensor(mesh, plin.astype('float32'), shape=[pk_dim])
# kvec for low resolution grid
kvec_lr = flowpm.kernels.fftk([nc, nc, nc], symmetric=False)
kx_lr = mtf.import_tf_tensor(mesh,
kvec_lr[0].squeeze().astype('float32'),
shape=[tx_dim])
ky_lr = mtf.import_tf_tensor(mesh,
kvec_lr[1].squeeze().astype('float32'),
shape=[ty_dim])
kz_lr = mtf.import_tf_tensor(mesh,
kvec_lr[2].squeeze().astype('float32'),
shape=[tz_dim])
kv_lr = [ky_lr, kz_lr, kx_lr]
lr_shape = [batch_dim, fx_dim, fy_dim, fz_dim]
hr_shape = [batch_dim, nx_dim, ny_dim, nz_dim, sx_dim, sy_dim, sz_dim]
part_shape = [batch_dim, fx_dim, fy_dim, fz_dim]
field = mtf.import_tf_tensor(mesh, initial_conditions, shape=part_shape)
state = mtfpm.lpt_init_single(
field,
a,
kv_lr,
halo_size,
lr_shape,
hr_shape,
part_shape[1:],
antialias=True,
)
print('TOTO', state)
# Here we can run our nbody
final_state = state
# final_state = mtfpm.nbody_single(state, stages, lr_shape, hr_shape,
# kv_lr, halo_size)
# paint the field
final_field = mtf.zeros(mesh, shape=hr_shape)
for block_size_dim in hr_shape[-3:]:
final_field = mtf.pad(final_field, [halo_size, halo_size],
block_size_dim.name)
final_field = mesh_utils.cic_paint(final_field, final_state[0], halo_size)
# Halo exchange
for blocks_dim, block_size_dim in zip(hr_shape[1:4],
final_field.shape[-3:]):
final_field = mpm.halo_reduce(final_field, blocks_dim, block_size_dim,
halo_size)
# Remove borders
for block_size_dim in hr_shape[-3:]:
final_field = mtf.slice(final_field, halo_size, block_size_dim.size,
block_size_dim.name)
#final_field = mtf.reshape(final_field, [batch_dim, fx_dim, fy_dim, fz_dim])
# Hack usisng custom reshape because mesh is pretty dumb
final_field = mtf.slicewise(
lambda x: x[:, 0, 0, 0], [final_field],
output_dtype=tf.float32,
output_shape=[batch_dim, fx_dim, fy_dim, fz_dim],
name='my_dumb_reshape',
splittable_dims=part_shape[:-1] + hr_shape[:4])
final_field = mtf.reshape(final_field,
[batch_dim, ffx_dim, ffy_dim, ffz_dim])
return final_field
def transformer_moe_layer_v1(inputs,
output_dim,
hparams,
train,
variable_dtype,
layout=None,
mesh_shape=None,
nonpadding=None,
activation=mtf.relu,
num_microbatches=None,
token_embeddings=None,
context=None):
"""Local heterogenous mixture of experts.
See transformer_moe_layer_v1 in moe.py for a more detailed explanation for
a generic moe layer.
The heterogeneous mask outputted by generate_heterogeneous_expert_masks has
dimension [maximum hidden size, maximum # layers, # experts] and its shape
will overwrite the parameters moe_num_layers and moe_hidden_size in hparams.
The layer-specific mask slice is applied at each expert layer to the
activation which is [expert width, # experts]. If the heterogeneous_mask_info
is None, there is no mask applied and the code is equivalent to the
homogeneous case.
The input is n-dimensional: [<batch_and_length_dims>, input_dim], consisting
of the representations of all positions in a batch of sequences.
Each position of each sequence is sent to 0-2 experts. The expert
choices and the combination weights are determined by a learned gating
function.
This function returns a small auxiliary loss that should be added to the
training loss of the model. This loss helps to balance expert usage.
Without the loss, it is very likely that a few experts will be trained and
the rest will starve.
Dimensions cheat sheet:
B: batch dim(s)
L: original sequence length
M: input depth
N: output depth
G: number of groups
S: group size
E: number of experts
C: expert capacity
Args:
inputs: a mtf.Tensor with shape [batch_dim(s), length_dim, input_dim]
output_dim: a mtf.Dimension (for Transformer, this is input_dim)
hparams: model hyperparameters
train: a boolean
variable_dtype: a mtf.VariableDType
layout: optional - an input to mtf.convert_to_layout_rules
mesh_shape: optional - an input to mtf.convert_to_shape
nonpadding: an optional Tensor with shape [batch_dim(s), length_dim]
and the same dtype as inputs, consisting of ones(nonpadding)
and zeros(padding).
activation: a function.
num_microbatches: number of microbatches.
token_embeddings: a mtf.Tensor with shape
[batch_dim(s), length_dim, input_dim]. These are the word embeddings for
that correspond to the inputs. These can optionally be used to make
routing decisions.
context: a Context.
Returns:
outputs: a Tensor with shape [batch_dim(s), length_dim, output_dim]
loss: a mtf scalar
Raises:
ValueError: on unrecognized hparams.moe_gating
"""
orig_inputs = inputs
experts_dim = mtf.Dimension("experts", hparams.moe_num_experts)
if hparams.moe_heterogeneous_mask_info is not None:
tf.logging.info("moe_heterogeneous_mask_info: {}".format(
hparams.moe_heterogeneous_mask_info))
heterogeneous_mask = generate_heterogeneous_expert_masks(
hparams.moe_heterogeneous_mask_info,
hparams.moe_num_experts,
experts_dim,
mesh=inputs.mesh,
expert_width=hparams.moe_hidden_size)
# overwrite depth and width with the mask maximum dimension
hparams.moe_num_layers = heterogeneous_mask.shape[1].size
hparams.moe_hidden_size = heterogeneous_mask.shape[0].size
hidden_dim = mtf.Dimension("expert_hidden", hparams.moe_hidden_size)
# We "cheat" here and look at the mesh shape and layout. This is to ensure
# that the number of groups is a multiple of the mesh dimension
# over which those groups are split.
batch_and_length_dims, input_dim = (orig_inputs.shape.dims[:-1],
orig_inputs.shape.dims[-1])
# Hack: we assume that
# "outer_batch" == replication of experts
# mesh_dim_size can be derived from mesh_shape and orig_batch_dim
#
# We then reqire num_groups to be a multiple of mesh_dim_size.
if orig_inputs.shape.dims[0].name == "outer_batch":
outer_batch_dim, orig_batch_dim = orig_inputs.shape.dims[:2]
else:
outer_batch_dim, orig_batch_dim = (mtf.Dimension("outer_batch", 1),
orig_inputs.shape.dims[0])
# Number of MoE inputs (total number of position across batch_and_length_dims
# per replica.
n = 1
for d in batch_and_length_dims:
n *= d.size
n = n // outer_batch_dim.size
mesh_dim_size = mtf.tensor_dim_to_mesh_dim_size(layout, mesh_shape,
orig_batch_dim)
num_groups, group_size = moe._split_into_groups( # pylint: disable=protected-access
n, hparams.moe_group_size, mesh_dim_size)
# TODO(barretzoph): implementation without pylint calls?
group_size_dim = mtf.Dimension("group", group_size)
num_groups_dim = mtf.Dimension(orig_batch_dim.name, num_groups)
moe_input_dims = [
outer_batch_dim, num_groups_dim, group_size_dim, input_dim
]
# OGSM Tensor
inputs = mtf.reshape(inputs, moe_input_dims)
# Token embeddings that can be optionally used in the router for determining
# where to send tokens.
if hparams.moe_word_embed_mode is not None:
token_embeddings = mtf.cast(
mtf.reshape(token_embeddings, moe_input_dims), inputs.dtype)
# Each sequence sends expert_capacity positions to each expert.
if train:
capacity_factor = hparams.moe_capacity_factor_train
else:
capacity_factor = hparams.moe_capacity_factor_eval
expert_capacity = min(
group_size_dim.size,
int((group_size_dim.size * capacity_factor) / experts_dim.size))
expert_capacity = max(expert_capacity, hparams.moe_min_expert_capacity)
tf.logging.info("expert_capacity: %d" % expert_capacity)
expert_capacity_dim = mtf.Dimension("expert_capacity", expert_capacity)
experts_dim_unsplit = mtf.Dimension("expert_unsplit", experts_dim.size)
batch_dim_unsplit = mtf.Dimension("batch_unsplit", num_groups_dim.size)
if nonpadding is not None:
nonpadding = mtf.zeros(inputs.mesh,
batch_and_length_dims,
dtype=inputs.dtype) + nonpadding
nonpadding = mtf.reshape(nonpadding, moe_input_dims[:-1])
if hparams.moe_gating == "top_2":
# combine_tensor,
# dispatch_tensor OG`SEC Tensors
# (G is generally split along mesh dim)
dispatch_tensor, combine_tensor, loss = moe._top_2_gating( # pylint: disable=protected-access
inputs=inputs,
outer_expert_dims=None,
experts_dim=experts_dim_unsplit,
expert_capacity_dim=expert_capacity_dim,
hparams=hparams,
train=train,
variable_dtype=variable_dtype,
importance=nonpadding,
num_microbatches=num_microbatches,
token_embeddings=token_embeddings)
elif hparams.moe_gating == "top_n":
dispatch_tensor, combine_tensor, loss = moe._top_n_gating( # pylint: disable=protected-access
inputs=inputs,
outer_expert_dims=None,
experts_dim=experts_dim_unsplit,
expert_capacity_dim=expert_capacity_dim,
hparams=hparams,
train=train,
variable_dtype=variable_dtype,
importance=nonpadding,
num_microbatches=num_microbatches,
token_embeddings=token_embeddings)
elif hparams.moe_gating == "switch":
dispatch_tensor, combine_tensor, loss = moe._switch_gating( # pylint: disable=protected-access
inputs=inputs,
outer_expert_dims=None,
experts_dim=experts_dim_unsplit,
expert_capacity_dim=expert_capacity_dim,
hparams=hparams,
train=train,
variable_dtype=variable_dtype,
importance=nonpadding,
num_microbatches=num_microbatches,
token_embeddings=token_embeddings)
elif hparams.moe_gating == "ntlb":
dispatch_tensor, combine_tensor, loss = moe._ntlb_gating( # pylint: disable=protected-access
inputs=inputs,
outer_expert_dims=None,
experts_dim=experts_dim_unsplit,
expert_capacity_dim=expert_capacity_dim,
hparams=hparams,
train=train,
variable_dtype=variable_dtype,
importance=nonpadding,
num_microbatches=num_microbatches,
token_embeddings=token_embeddings)
elif hparams.moe_gating == "switch_max":
dispatch_tensor, combine_tensor, loss = moe._switch_max_gating( # pylint: disable=protected-access
inputs=inputs,
outer_expert_dims=None,
experts_dim=experts_dim_unsplit,
expert_capacity_dim=expert_capacity_dim,
hparams=hparams,
train=train,
variable_dtype=variable_dtype,
importance=nonpadding,
num_microbatches=num_microbatches,
token_embeddings=token_embeddings)
elif hparams.moe_gating == "expert_selection":
dispatch_tensor, combine_tensor, loss = moe._expert_selection_gating( # pylint: disable=protected-access
inputs=inputs,
outer_expert_dims=None,
experts_dim=experts_dim_unsplit,
group_size_dim=group_size_dim,
expert_capacity_dim=expert_capacity_dim,
hparams=hparams,
train=train,
variable_dtype=variable_dtype,
importance=nonpadding,
name="expert_selection_gating",
num_microbatches=num_microbatches,
token_embeddings=token_embeddings)
else:
raise ValueError("unknown hparams.moe_gating=%s" % hparams.moe_gating)
expert_inputs = mtf.einsum([inputs, dispatch_tensor],
mtf.Shape([
outer_batch_dim, experts_dim_unsplit,
num_groups_dim, expert_capacity_dim,
input_dim
]))
# Extra reshape reduces communication cost for model-parallel versions.
# For model-parallel versions, this reshape causes an mtf.slice and for non-
# model-parallel versions, this has no effect.
d_model_split_dim = mtf.Dimension("d_model_split", input_dim.size)
expert_inputs = mtf.reshape(
expert_inputs,
mtf.Shape([
outer_batch_dim, experts_dim, batch_dim_unsplit,
expert_capacity_dim, d_model_split_dim
]))
# Split over batch -> split over experts
expert_inputs = mtf.reshape(
expert_inputs,
mtf.Shape([
outer_batch_dim, experts_dim, batch_dim_unsplit,
expert_capacity_dim, input_dim
]))
# Pretend we have heterogeneous_mask with shape [moe_num_layers, num_experts]
for layer_idx in range(hparams.moe_num_layers):
with tf.variable_scope("expert_layer_{}".format(layer_idx)):
res_h = 0.0
if layer_idx > 0:
res_h = expert_inputs
expert_inputs = transformer.sublayer_rms_norm(
expert_inputs, None, context)
# Now feed the expert inputs through the experts.
h = mtf.layers.dense_product(
expert_inputs,
reduced_dims=expert_inputs.shape.dims[-1:],
new_dims=[hidden_dim],
expert_dims=[experts_dim],
activation_functions=activation,
use_bias=False,
variable_dtype=variable_dtype,
name="wi")
# apply dropout
if hparams.moe_dropout_rate != 0.0:
h = mtf.dropout(h,
is_training=train,
keep_prob=1.0 - hparams.moe_dropout_rate)
# only if heterogeneous
if hparams.moe_heterogeneous_mask_info is not None:
# Get mask for current layer by slicing heterogeneous mask
heterogeneous_mask_slice = mtf.slice(heterogeneous_mask,
layer_idx, 1,
"num_expert_layers")
# Get rid of the expert layers dimension.
heterogeneous_mask_slice = mtf.reshape(
heterogeneous_mask_slice, [
heterogeneous_mask_slice.shape[0],
heterogeneous_mask_slice.shape[-1]
])
h *= mtf.cast(heterogeneous_mask_slice, h.dtype)
expert_output = mtf.layers.dense(h,
output_dim,
expert_dims=[experts_dim],
use_bias=False,
reduced_dims=h.shape.dims[-1:],
variable_dtype=variable_dtype,
name="wo")
if layer_idx < (hparams.moe_num_layers - 1):
expert_output = transformer.sublayer_dropout(
expert_output, None, context)
expert_output += res_h
expert_inputs = expert_output
# Extra reshape reduces communication cost for model-parallel versions.
# For model-parallel versions, this reshape causes an mtf.slice and for non-
# model-parallel versions, this has no effect.
expert_output = mtf.reshape(
expert_output,
mtf.Shape([
outer_batch_dim, experts_dim_unsplit, num_groups_dim,
expert_capacity_dim, d_model_split_dim
]))
# Split over experts -> split over batch
expert_output = mtf.reshape(
expert_output,
mtf.Shape([
outer_batch_dim,
experts_dim_unsplit,
num_groups_dim,
expert_capacity_dim,
output_dim,
]))
moe_output_dims = moe_input_dims[:-1] + [output_dim]
output = mtf.einsum([expert_output, combine_tensor],
mtf.Shape(moe_output_dims))
output = mtf.reshape(output, batch_and_length_dims + [output_dim])
return output, loss * hparams.moe_loss_coef
def recon_prototype(mesh,
data,
nc=FLAGS.nc,
bs=FLAGS.box_size,
batch_size=FLAGS.batch_size,
a0=FLAGS.a0,
a=FLAGS.af,
nsteps=FLAGS.nsteps,
dtype=tf.float32):
"""
Prototype of function computing LPT deplacement.
Returns output tensorflow and mesh tensorflow tensors
"""
if dtype == tf.float32:
npdtype = "float32"
cdtype = tf.complex64
elif dtype == tf.float64:
npdtype = "float64"
cdtype = tf.complex128
print("Dtype : ", dtype, npdtype)
# Compute a few things first, using simple tensorflow
kny = 1 * np.pi * nc / bs
R1, R2 = 3., 3 * 1.2
stages = np.linspace(a0, a, nsteps, endpoint=True)
#graph = mtf.Graph()
#mesh = mtf.Mesh(graph, "my_mesh")
# Define the named dimensions
# Parameters of the small scales decomposition
n_block_x = FLAGS.nx
n_block_y = FLAGS.ny
n_block_z = 1
halo_size = FLAGS.hsize
if halo_size >= 0.5 * min(nc // n_block_x, nc // n_block_y,
nc // n_block_z):
new_size = int(0.5 *
min(nc // n_block_x, nc // n_block_y, nc // n_block_z))
print('WARNING: REDUCING HALO SIZE from %d to %d' %
(halo_size, new_size))
halo_size = new_size
# Parameters of the large scales decomposition
scalar = mtf.Dimension("scalar", 1)
fx_dim = mtf.Dimension("nx", nc)
fy_dim = mtf.Dimension("ny", nc)
fz_dim = mtf.Dimension("nz", nc)
tfx_dim = mtf.Dimension("tx", nc)
tfy_dim = mtf.Dimension("ty", nc)
tfz_dim = mtf.Dimension("tz", nc)
tx_dim = mtf.Dimension("tx_lr", nc)
ty_dim = mtf.Dimension("ty_lr", nc)
tz_dim = mtf.Dimension("tz_lr", nc)
nx_dim = mtf.Dimension('nx_block', n_block_x)
ny_dim = mtf.Dimension('ny_block', n_block_y)
nz_dim = mtf.Dimension('nz_block', n_block_z)
sx_dim = mtf.Dimension('sx_block', nc // n_block_x)
sy_dim = mtf.Dimension('sy_block', nc // n_block_y)
sz_dim = mtf.Dimension('sz_block', nc // n_block_z)
#k_dims = [tx_dim, ty_dim, tz_dim]
batch_dim = mtf.Dimension("batch", batch_size)
klin = np.loadtxt('../flowpm/data/Planck15_a1p00.txt').T[0]
plin = np.loadtxt('../flowpm/data/Planck15_a1p00.txt').T[1]
ipklin = iuspline(klin, plin)
pk_dim = mtf.Dimension("npk", len(plin))
pk = mtf.import_tf_tensor(mesh, plin.astype(npdtype), shape=[pk_dim])
# Compute necessary Fourier kernels
kvec = flowpm.kernels.fftk((nc, nc, nc), symmetric=False)
kx = mtf.import_tf_tensor(mesh,
kvec[0].squeeze().astype('float32'),
shape=[tfx_dim])
ky = mtf.import_tf_tensor(mesh,
kvec[1].squeeze().astype('float32'),
shape=[tfy_dim])
kz = mtf.import_tf_tensor(mesh,
kvec[2].squeeze().astype('float32'),
shape=[tfz_dim])
kv = [ky, kz, kx]
# kvec for low resolution grid
kvec_lr = flowpm.kernels.fftk([nc, nc, nc], symmetric=False)
kx_lr = mtf.import_tf_tensor(mesh,
kvec_lr[0].squeeze().astype('float32'),
shape=[tx_dim])
ky_lr = mtf.import_tf_tensor(mesh,
kvec_lr[1].squeeze().astype('float32'),
shape=[ty_dim])
kz_lr = mtf.import_tf_tensor(mesh,
kvec_lr[2].squeeze().astype('float32'),
shape=[tz_dim])
kv_lr = [ky_lr, kz_lr, kx_lr]
shape = [batch_dim, fx_dim, fy_dim, fz_dim]
lr_shape = [batch_dim, fx_dim, fy_dim, fz_dim]
hr_shape = [batch_dim, nx_dim, ny_dim, nz_dim, sx_dim, sy_dim, sz_dim]
part_shape = [batch_dim, fx_dim, fy_dim, fz_dim]
#
# Begin simulation
## Compute initial initial conditions distributed
#initc = mtfpm.linear_field(mesh, shape, bs, nc, pk, kv)
fieldvar = mtf.get_variable(mesh, 'linear', part_shape)
input_field = tf.placeholder(data.dtype, [batch_size, nc, nc, nc])
mtfinp = mtf.import_tf_tensor(mesh, input_field, shape=part_shape)
linearop = mtf.assign(fieldvar, mtfinp)
#field = fieldvar
initc = fieldvar
print("initc : ", initc)
# Here we can run our nbody
if FLAGS.nbody:
state = mtfpm.lpt_init_single(
fieldvar,
a0,
kv_lr,
halo_size,
lr_shape,
hr_shape,
part_shape[1:],
antialias=True,
)
# Here we can run our nbody
final_state = mtfpm.nbody_single(state, stages, lr_shape, hr_shape,
kv_lr, halo_size)
else:
final_state = mtfpm.lpt_init_single(
initc,
stages[-1],
kv_lr,
halo_size,
lr_shape,
hr_shape,
part_shape[1:],
antialias=True,
)
# paint the field
final_field = mtf.zeros(mesh, shape=hr_shape)
for block_size_dim in hr_shape[-3:]:
final_field = mtf.pad(final_field, [halo_size, halo_size],
block_size_dim.name)
final_field = mesh_utils.cic_paint(final_field, final_state[0], halo_size)
# Halo exchange
for blocks_dim, block_size_dim in zip(hr_shape[1:4],
final_field.shape[-3:]):
final_field = mpm.halo_reduce(final_field, blocks_dim, block_size_dim,
halo_size)
# Remove borders
for block_size_dim in hr_shape[-3:]:
final_field = mtf.slice(final_field, halo_size, block_size_dim.size,
block_size_dim.name)
final_field = mtf.slicewise(
lambda x: x[:, 0, 0, 0], [final_field],
output_dtype=dtype,
output_shape=[batch_dim, fx_dim, fy_dim, fz_dim],
name='my_dumb_reshape',
splittable_dims=part_shape[:-1] + hr_shape[:4])
##
x = final_field
ppars, mpars, kernel = setupfnn()
pwts, pbias, pmx, psx = ppars
mwts, mbias, mmx, msx, mmy, msy = mpars
msy, mmy = msy[0], mmy[0]
print("mmy : ", mmy)
size = 3
k_dims = [d.shape[0] for d in kv]
k_dims = [k_dims[2], k_dims[0], k_dims[1]]
tfnc, tfbs = float_to_mtf(nc * 1., mesh,
scalar), float_to_mtf(bs, mesh, scalar)
x1f = mesh_utils.r2c3d(x, k_dims, dtype=cdtype)
x1f = mtf.cwise(cwise_decic, [x1f] + kv + [tfnc, tfbs],
output_dtype=cdtype)
x1d = mesh_utils.c2r3d(x1f, x.shape[-3:], dtype=dtype)
x1d = mtf.add(x1d, -1.)
x1f0 = mesh_utils.r2c3d(x1d, k_dims, dtype=cdtype)
x1f = mtf.cwise(cwise_fingauss,
[x1f0, float_to_mtf(R1, mesh, scalar)] + kv + [tfnc, tfbs],
output_dtype=cdtype)
x1 = mesh_utils.c2r3d(x1f, x1d.shape[-3:], dtype=dtype)
x2f = mtf.cwise(cwise_fingauss,
[x1f0, float_to_mtf(R2, mesh, scalar)] + kv + [tfnc, tfbs],
output_dtype=cdtype)
x2 = mesh_utils.c2r3d(x2f, x1d.shape[-3:], dtype=dtype)
x12 = x1 - x2
width = tf.placeholder(tf.float32, shape=())
def apply_pwts(x, x1, x2):
#y = tf.expand_dims(x, axis=-1)
y = tf.nn.conv3d(tf.expand_dims(x, axis=-1), kernel, [1, 1, 1, 1, 1],
'SAME')
y1 = tf.nn.conv3d(tf.expand_dims(x1, axis=-1), kernel, [1, 1, 1, 1, 1],
'SAME')
y2 = tf.nn.conv3d(tf.expand_dims(x2, axis=-1), kernel, [1, 1, 1, 1, 1],
'SAME')
#y = tf.nn.conv3d(tf.expand_dims(tfwrap3D(x), -1), kernel, [1, 1, 1, 1, 1], 'VALID')
#y1 = tf.nn.conv3d(tf.expand_dims(tfwrap3D(x1), -1), kernel, [1, 1, 1, 1, 1], 'VALID')
#y2 = tf.nn.conv3d(tf.expand_dims(tfwrap3D(x12), -1), kernel, [1, 1, 1, 1, 1], 'VALID')
yy = tf.concat([y, y1, y2], axis=-1)
yy = yy - pmx
yy = yy / psx
yy1 = tf.nn.relu(tf.matmul(yy, pwts[0]) + pbias[0])
yy2 = tf.nn.relu(tf.matmul(yy1, pwts[1]) + pbias[1])
yy3 = tf.matmul(yy2, pwts[2]) + pbias[2]
pmodel = tf.nn.sigmoid(width * yy3)
return pmodel[..., 0]
pmodel = mtf.slicewise(
apply_pwts,
[x, x1, x12],
output_dtype=tf.float32,
output_shape=part_shape, # + [mtf.Dimension('c_dim', 81)],
name='apply_pwts',
splittable_dims=lr_shape[:-1] + hr_shape[1:4] + part_shape[1:3])
def apply_mwts(x, x1, x2):
#y = tf.expand_dims(x, axis=-1)
zz = tf.concat([
tf.expand_dims(x, -1),
tf.expand_dims(x1, -1),
tf.expand_dims(x2, -1)
],
axis=-1)
zz = zz - mmx
zz = zz / msx
zz1 = tf.nn.elu(tf.matmul(zz, mwts[0]) + mbias[0])
zz2 = tf.nn.elu(tf.matmul(zz1, mwts[1]) + mbias[1])
zz3 = tf.matmul(zz2, mwts[2]) + mbias[2]
mmodel = zz3 * msy + mmy
return mmodel[..., 0]
mmodel = mtf.slicewise(
apply_mwts,
[x, x1, x12],
output_dtype=tf.float32,
output_shape=part_shape, # + [mtf.Dimension('c_dim', 81)],
name='apply_mwts',
splittable_dims=lr_shape[:-1] + hr_shape[1:4] + part_shape[1:3])
model = pmodel * mmodel
mtfdata = mtf.import_tf_tensor(mesh,
tf.convert_to_tensor(data),
shape=shape)
# Get prior
#k_dims = [d.shape[0] for d in kv]
#k_dims = [k_dims[2], k_dims[0], k_dims[1]]
k_dims_pr = [d.shape[0] for d in kv]
k_dims_pr = [k_dims_pr[2], k_dims_pr[0], k_dims_pr[1]]
cfield = mesh_utils.r2c3d(fieldvar, k_dims_pr, dtype=cdtype)
def _cwise_prior(kfield, pk, kx, ky, kz):
kx = tf.reshape(kx, [-1, 1, 1])
ky = tf.reshape(ky, [1, -1, 1])
kz = tf.reshape(kz, [1, 1, -1])
kk = tf.sqrt((kx / bs * nc)**2 + (ky / bs * nc)**2 + (kz / bs * nc)**2)
kshape = kk.shape
kk = tf.reshape(kk, [-1])
pkmesh = tfp.math.interp_regular_1d_grid(
x=kk,
x_ref_min=1e-05,
x_ref_max=1000.0,
y_ref=pk,
grid_regularizing_transform=tf.log)
priormesh = tf.reshape(pkmesh, kshape)
return tf.abs(kfield) / priormesh**0.5
cpfield = mtf.cwise(_cwise_prior, [cfield, pk] + kv,
output_dtype=tf.float32)
prior = mtf.reduce_sum(mtf.square(cpfield)) * bs**3 * nc**3
# Total loss
#diff = (model - mtfdata)
modelf = mesh_utils.r2c3d(model, k_dims, dtype=cdtype)
modelsmf = mtf.cwise(cwise_fingauss,
[modelf, float_to_mtf(R1, mesh, scalar)] + kv +
[tfnc, tfbs],
output_dtype=cdtype)
modelsm = mesh_utils.c2r3d(modelsmf, x1d.shape[-3:], dtype=dtype)
#dataf = mesh_utils.r2c3d(mtfdata, k_dims, dtype=cdtype)
#datasmf = mtf.cwise(cwise_fingauss, [dataf, float_to_mtf(R1, mesh, scalar)] + kv + [tfnc, tfbs], output_dtype=cdtype)
#datasm = mesh_utils.c2r3d(datasmf, x1d.shape[-3:], dtype=dtype)
##Anneal
R0 = tf.placeholder(tf.float32, shape=())
M0 = tf.placeholder(tf.float32, shape=())
off, istd = tf.placeholder(tf.float32, shape=data.shape), tf.placeholder(
tf.float32, shape=data.shape)
mtfoff = mtf.import_tf_tensor(mesh, off, shape=shape)
mtfistd = mtf.import_tf_tensor(mesh, istd, shape=shape)
diff = mtf.log(modelsm + M0) - mtf.log(mtfdata + M0)
#diff = diff / 0.25
#diff = (diff + mtfoff)*mtfistd #For some reason, doing things wrong this one
diff = (diff + mtfoff) / 0.25
def _cwise_smooth(kfield, kx, ky, kz):
kx = tf.reshape(kx, [-1, 1, 1])
ky = tf.reshape(ky, [1, -1, 1])
kz = tf.reshape(kz, [1, 1, -1])
kk = (kx / bs * nc)**2 + (ky / bs * nc)**2 + (kz / bs * nc)**2
wts = tf.cast(tf.exp(-kk * (R0 * bs / nc)**2), kfield.dtype)
return kfield * wts
cdiff = mesh_utils.r2c3d(diff, k_dims_pr, dtype=cdtype)
cdiff = mtf.cwise(_cwise_smooth, [cdiff] + kv, output_dtype=cdtype)
diff = mesh_utils.c2r3d(cdiff, diff.shape[-3:], dtype=dtype)
chisq = mtf.reduce_sum(mtf.square(diff))
loss = chisq + prior
#return initc, final_field, loss, linearop, input_field
nyq = np.pi * nc / bs
def _cwise_highpass(kfield, kx, ky, kz):
kx = tf.reshape(kx, [-1, 1, 1])
ky = tf.reshape(ky, [1, -1, 1])
kz = tf.reshape(kz, [1, 1, -1])
kk = (kx / bs * nc)**2 + (ky / bs * nc)**2 + (kz / bs * nc)**2
wts = tf.cast(tf.exp(-kk * (R0 * bs / nc + 1 / nyq)**2), kfield.dtype)
return kfield * (1 - wts)
var_grads = mtf.gradients([loss], [fieldvar])
cgrads = mesh_utils.r2c3d(var_grads[0], k_dims_pr, dtype=cdtype)
cgrads = mtf.cwise(_cwise_highpass, [cgrads] + kv, output_dtype=cdtype)
var_grads = [mesh_utils.c2r3d(cgrads, diff.shape[-3:], dtype=dtype)]
lr = tf.placeholder(tf.float32, shape=())
update_op = mtf.assign(fieldvar, fieldvar - var_grads[0] * lr)
return initc, model, loss, var_grads, update_op, linearop, input_field, lr, R0, M0, width, chisq, prior, off, istd
def _call_internal(self,
context,
inputs,
targets=None,
attributes=None,
z=None):
"""Compute logits based on inputs (all positions in parallel).
Also updates context if applicable.
Args:
context: a Context
inputs: a Tensor
targets: an optional Tensor
attributes: an optional Tensor
Returns:g
logits: a Tensor with shape [<batch_dims>, length_dim, output_vocab_dim]
"""
mesh = inputs.mesh
if self.ensemble_dim and self.ensemble_dim not in inputs.shape.dims:
# Training an ensemble where all models are trained on the same examples.
inputs = mtf.broadcast(inputs,
[self.ensemble_dim] + inputs.shape.dims)
if self.ensemble_dim not in attributes.shape.dims:
attributes = mtf.broadcast(attributes, [self.ensemble_dim] +
attributes.shape.dims)
if targets:
targets = mtf.broadcast(targets, [self.ensemble_dim] +
targets.shape.dims)
if "embedding" in context.shared_params:
vocab_embedding = context.shared_params["embedding"]
else:
vocab_embedding = VocabEmbedding(mesh,
self.input_vocab_dim,
self.model_dim,
context.variable_dtype,
name="embedding",
ensemble_dim=self.ensemble_dim)
x = vocab_embedding.ids_to_embedding(inputs)
if self.positional_embedding:
if "positional_embedding" in context.shared_params:
pos_emb_var = context.shared_params["positional_embedding"]
else:
pos_emb_var = mtf.layers.embedding_weights(
mesh,
self.max_length_dim,
self.model_dim,
context.variable_dtype,
"positional_embedding",
ensemble_dim=self.ensemble_dim)
if (context.length_dim is not None
and context.length_dim.size > self.max_length_dim.size):
message = (
"Length dimenison exceeds size of positional embedding table. "
"length_dim.size > max_length_dim.size %s vs %s." %
(context.length_dim, self.max_length_dim))
if context.position_is_default:
# Definitely getting overflow in this case.
raise ValueError(message)
else:
tf.logging.warning(
message +
" This may be OK if there are several shorter sequences packed "
"together. Otherwise, the later positions will get zeros."
)
if context.position_is_default:
pos_emb = mtf.rename_dimension(
mtf.slice(pos_emb_var, 0, context.length_dim.size,
self.max_length_dim.name),
self.max_length_dim.name, context.length_dim.name)
else:
pos_emb = mtf.gather(pos_emb_var,
context.position,
self.max_length_dim,
output_shape=x.shape)
x += pos_emb
if self.attribute_embedding:
if "attribute_embedding" in context.shared_params:
att_emb_var = context.shared_params["attribute_embedding"]
else:
att_emb_var = mtf.layers.embedding_weights(
mesh,
self.attribute_dim,
self.model_dim,
context.variable_dtype,
"attribute_embedding",
ensemble_dim=self.ensemble_dim)
att_emb = mtf.gather(att_emb_var,
attributes,
self.attribute_dim,
output_shape=x.shape)
# Addition of x and attribute
# x *= LAMBDA_ATTRIBUTE * sty_emb #
# Concatenation of x and attribute
x_attribute = mtf.concat([x, att_emb], self.model_dim.name)
x = mtf.layers.dense(x_attribute,
self.model_dim,
activation=None,
variable_dtype=context.variable_dtype,
name="comb_x_attribute")
if z:
z = mtf.layers.dense(z,
self.model_dim,
activation=None,
variable_dtype=context.variable_dtype,
name="z")
# raise ValueError("x shape=%s , z shape=%s" % (x.shape, z.shape))
x += z
x = self.layer_stack.call(context, x)
if self.output_vocab_dim is None:
return x
if self.shared_embedding_and_softmax_weights:
logits = vocab_embedding.hidden_to_logits(x)
else:
logits = mtf.layers.dense(x,
self.output_vocab_dim,
use_bias=False,
variable_dtype=context.variable_dtype,
reduced_dims=x.shape.dims[-1:],
name="logits")
if targets is not None and context.losses is not None:
context.losses.append(
self._compute_loss(context, logits, targets,
self.output_vocab_dim))
if self.ensemble_dim:
logits = reduce_ensemble_logits(logits, self.ensemble_dim,
self.output_vocab_dim)
return logits
def recon_model(mesh,
data,
R0,
x0,
nc=FLAGS.nc,
bs=FLAGS.box_size,
batch_size=FLAGS.batch_size,
a0=FLAGS.a0,
a=FLAGS.af,
nsteps=FLAGS.nsteps,
dtype=tf.float32):
"""
Prototype of function computing LPT deplacement.
Returns output tensorflow and mesh tensorflow tensors
"""
if dtype == tf.float32:
npdtype = "float32"
cdtype = tf.complex64
elif dtype == tf.float64:
npdtype = "float64"
cdtype = tf.complex128
print(dtype, npdtype)
# Compute a few things first, using simple tensorflow
stages = np.linspace(a0, a, nsteps, endpoint=True)
# Define the named dimensions
# Parameters of the small scales decomposition
n_block_x = FLAGS.nx
n_block_y = FLAGS.ny
n_block_z = 1
halo_size = FLAGS.hsize
if halo_size >= 0.5 * min(nc // n_block_x, nc // n_block_y,
nc // n_block_z):
new_size = int(0.5 *
min(nc // n_block_x, nc // n_block_y, nc // n_block_z))
print('WARNING: REDUCING HALO SIZE from %d to %d' %
(halo_size, new_size))
halo_size = new_size
# Parameters of the large scales decomposition
fx_dim = mtf.Dimension("nx", nc)
fy_dim = mtf.Dimension("ny", nc)
fz_dim = mtf.Dimension("nz", nc)
tfx_dim = mtf.Dimension("tx", nc)
tfy_dim = mtf.Dimension("ty", nc)
tfz_dim = mtf.Dimension("tz", nc)
tx_dim = mtf.Dimension("tx_lr", nc)
ty_dim = mtf.Dimension("ty_lr", nc)
tz_dim = mtf.Dimension("tz_lr", nc)
nx_dim = mtf.Dimension('nx_block', n_block_x)
ny_dim = mtf.Dimension('ny_block', n_block_y)
nz_dim = mtf.Dimension('nz_block', n_block_z)
sx_dim = mtf.Dimension('sx_block', nc // n_block_x)
sy_dim = mtf.Dimension('sy_block', nc // n_block_y)
sz_dim = mtf.Dimension('sz_block', nc // n_block_z)
k_dims = [tx_dim, ty_dim, tz_dim]
batch_dim = mtf.Dimension("batch", batch_size)
klin = np.loadtxt('../data/Planck15_a1p00.txt').T[0]
plin = np.loadtxt('../data/Planck15_a1p00.txt').T[1]
ipklin = iuspline(klin, plin)
pk_dim = mtf.Dimension("npk", len(plin))
pk = mtf.import_tf_tensor(mesh, plin.astype(npdtype), shape=[pk_dim])
# Compute necessary Fourier kernels
kvec = flowpm.kernels.fftk((nc, nc, nc), symmetric=False)
kx = mtf.import_tf_tensor(mesh,
kvec[0].squeeze().astype('float32'),
shape=[tfx_dim])
ky = mtf.import_tf_tensor(mesh,
kvec[1].squeeze().astype('float32'),
shape=[tfy_dim])
kz = mtf.import_tf_tensor(mesh,
kvec[2].squeeze().astype('float32'),
shape=[tfz_dim])
kv = [ky, kz, kx]
# kvec for low resolution grid
kvec_lr = flowpm.kernels.fftk([nc, nc, nc], symmetric=False)
kx_lr = mtf.import_tf_tensor(mesh,
kvec_lr[0].squeeze().astype('float32'),
shape=[tx_dim])
ky_lr = mtf.import_tf_tensor(mesh,
kvec_lr[1].squeeze().astype('float32'),
shape=[ty_dim])
kz_lr = mtf.import_tf_tensor(mesh,
kvec_lr[2].squeeze().astype('float32'),
shape=[tz_dim])
kv_lr = [ky_lr, kz_lr, kx_lr]
shape = [batch_dim, fx_dim, fy_dim, fz_dim]
lr_shape = [batch_dim, fx_dim, fy_dim, fz_dim]
hr_shape = [batch_dim, nx_dim, ny_dim, nz_dim, sx_dim, sy_dim, sz_dim]
part_shape = [batch_dim, fx_dim, fy_dim, fz_dim]
# Begin simulation
if x0 is None:
fieldvar = mtf.get_variable(mesh,
'linear',
part_shape,
initializer=tf.random_normal_initializer(
mean=0.0, stddev=1, seed=None))
else:
fieldvar = mtf.get_variable(mesh,
'linear',
part_shape,
initializer=tf.constant_initializer(x0))
print("\nfieldvar : \n", fieldvar)
# Here we can run our nbody
if FLAGS.nbody:
state = mtfpm.lpt_init_single(
fieldvar,
a0,
kv_lr,
halo_size,
lr_shape,
hr_shape,
part_shape[1:],
antialias=True,
)
# Here we can run our nbody
final_state = mtfpm.nbody_single(state, stages, lr_shape, hr_shape,
kv_lr, halo_size)
else:
final_state = mtfpm.lpt_init_single(
fieldvar,
stages[-1],
kv_lr,
halo_size,
lr_shape,
hr_shape,
part_shape[1:],
antialias=True,
)
# paint the field
final_field = mtf.zeros(mesh, shape=hr_shape)
for block_size_dim in hr_shape[-3:]:
final_field = mtf.pad(final_field, [halo_size, halo_size],
block_size_dim.name)
final_field = mesh_utils.cic_paint(final_field, final_state[0], halo_size)
# Halo exchange
for blocks_dim, block_size_dim in zip(hr_shape[1:4],
final_field.shape[-3:]):
final_field = mpm.halo_reduce(final_field, blocks_dim, block_size_dim,
halo_size)
# Remove borders
for block_size_dim in hr_shape[-3:]:
final_field = mtf.slice(final_field, halo_size, block_size_dim.size,
block_size_dim.name)
final_field = mtf.slicewise(
lambda x: x[:, 0, 0, 0], [final_field],
output_dtype=dtype,
output_shape=[batch_dim, fx_dim, fy_dim, fz_dim],
name='my_dumb_reshape',
splittable_dims=part_shape[:-1] + hr_shape[:4])
mtfdata = mtf.import_tf_tensor(mesh,
tf.convert_to_tensor(data),
shape=shape)
# Get prior
k_dims_pr = [d.shape[0] for d in kv]
k_dims_pr = [k_dims_pr[2], k_dims_pr[0], k_dims_pr[1]]
cfield = mesh_utils.r2c3d(fieldvar, k_dims_pr, dtype=cdtype)
def _cwise_prior(kfield, pk, kx, ky, kz):
kx = tf.reshape(kx, [-1, 1, 1])
ky = tf.reshape(ky, [1, -1, 1])
kz = tf.reshape(kz, [1, 1, -1])
kk = tf.sqrt((kx / bs * nc)**2 + (ky / bs * nc)**2 + (kz / bs * nc)**2)
kshape = kk.shape
kk = tf.reshape(kk, [-1])
pkmesh = tfp.math.interp_regular_1d_grid(
x=kk,
x_ref_min=1e-05,
x_ref_max=1000.0,
y_ref=pk,
grid_regularizing_transform=tf.log)
priormesh = tf.reshape(pkmesh, kshape)
return tf.abs(kfield) / priormesh**0.5
cpfield = mtf.cwise(_cwise_prior, [cfield, pk] + kv,
output_dtype=tf.float32)
prior = mtf.reduce_sum(mtf.square(cpfield)) * bs**3 #*nc**3
# Total loss
diff = (final_field - mtfdata)
R0 = tf.constant(R0)
print("R0 in the recon_model : ", R0)
def _cwise_smooth(kfield, kx, ky, kz):
kx = tf.reshape(kx, [-1, 1, 1])
ky = tf.reshape(ky, [1, -1, 1])
kz = tf.reshape(kz, [1, 1, -1])
kk = (kx / bs * nc)**2 + (ky / bs * nc)**2 + (kz / bs * nc)**2
wts = tf.cast(tf.exp(-kk * (R0 * bs / nc)**2), kfield.dtype)
return kfield * wts
# Element-wise function that applies a Fourier kernel
plambda = FLAGS.plambda
def _cwise_logprob(finalfield, data):
galmean = tfp.distributions.Poisson(rate=plambda * (1 + finalfield))
logprob = galmean.log_prob(data)
return -1 * logprob
cfield = mesh_utils.r2c3d(final_field, k_dims_pr, dtype=cdtype)
cfield = mtf.cwise(_cwise_smooth, [cfield] + kv, output_dtype=cdtype)
final_fieldsm = mesh_utils.c2r3d(cfield, diff.shape[-3:], dtype=dtype)
chisq = mtf.cwise(_cwise_logprob, [final_fieldsm, mtfdata],
output_dtype=tf.float32) #
chisq = mtf.reduce_sum(chisq)
## #
loss = chisq + prior
def _cwise_sample(finalfield, data):
galmean = tfp.distributions.Poisson(rate=plambda * (1 + finalfield))
sample = galmean.sample()
return sample
sample = mtf.cwise(_cwise_sample, [final_fieldsm, mtfdata],
output_dtype=tf.float32) #
fields = [fieldvar, sample]
metrics = [chisq, prior, loss]
return fields, metrics, kv
def force(state,
lr_shape,
hr_shape,
kvec_lr,
kvec_hr,
halo_size,
cosmology=Planck15,
downsampling_factor=2,
pm_nc_factor=1,
antialias=True,
**kwargs):
"""
Estimate force on the particles given a state.
Parameters:
-----------
state: tensor
Input state tensor of shape (3, batch_size, npart, 3)
boxsize: float
Size of the simulation volume (Mpc/h) TODO: check units
cosmology: astropy.cosmology
Cosmology object
pm_nc_factor: int
TODO: @modichirag please add doc
"""
X, P, F = state
#TODO: support different factor
assert pm_nc_factor == 1
lnc = lr_shape[-1].size
part_shape = X.shape
k_dims_lr = [d.shape[0] for d in kvec_lr]
k_dims_hr = [d.shape[0] for d in kvec_hr]
# Reorder the FFTs which where transposed# y,z,x
k_dims_lr = [k_dims_lr[2], k_dims_lr[0], k_dims_lr[1]]
k_dims_hr = [k_dims_hr[2], k_dims_hr[0], k_dims_hr[1]]
# Paint the particles on the high resolution mesh
field = mtf.zeros(X.mesh, shape=hr_shape)
for block_size_dim in hr_shape[-3:]:
field = mtf.pad(field, [halo_size, halo_size], block_size_dim.name)
field = mesh_utils.cic_paint(field, X, halo_size)
for blocks_dim, block_size_dim in zip(hr_shape[1:4], field.shape[-3:]):
field = mesh_ops.halo_reduce(field, blocks_dim, block_size_dim,
halo_size)
# Split the field into low and high resolution
field = mtf.reshape(field, field.shape + [mtf.Dimension('h_dim', 1)])
high = field
low = mesh_utils.downsample(field, downsampling_factor, antialias=True)
low = mtf.reshape(low, low.shape[:-1])
hr_field = mtf.reshape(high, high.shape[:-1])
for block_size_dim in hr_shape[-3:]:
low = mtf.slice(low, halo_size // 2**downsampling_factor,
block_size_dim.size // 2**downsampling_factor,
block_size_dim.name)
# Hack usisng custom reshape because mesh is pretty dumb
lr_field = mtf.slicewise(lambda x: x[:, 0, 0, 0], [low],
output_dtype=tf.float32,
output_shape=lr_shape,
name='my_dumb_reshape',
splittable_dims=lr_shape[:-1] + hr_shape[:4])
lr_kfield = mesh_utils.r2c3d(lr_field, k_dims_lr)
hr_kfield = mesh_utils.r2c3d(hr_field, k_dims_hr)
kfield_lr = mesh_kernels.apply_longrange_kernel(lr_kfield,
kvec_lr,
r_split=0)
kfield_lr = mesh_kernels.apply_gradient_laplace_kernel(lr_kfield, kvec_lr)
kfield_hr = mesh_kernels.apply_longrange_kernel(hr_kfield,
kvec_hr,
r_split=0)
kfield_hr = mesh_kernels.apply_gradient_laplace_kernel(kfield_hr, kvec_hr)
# Reorder the low res FFTs which where transposed# y,z,x
kfield_lr = [kfield_lr[2], kfield_lr[0], kfield_lr[1]]
kfield_hr = [kfield_hr[2], kfield_hr[0], kfield_hr[1]]
displacement = []
for f, g in zip(kfield_lr, kfield_hr):
f = mesh_utils.c2r3d(f, lr_shape[-3:])
f = mtf.slicewise(
lambda x: tf.expand_dims(
tf.expand_dims(tf.expand_dims(x, axis=1), axis=1), axis=1),
[f],
output_dtype=tf.float32,
output_shape=mtf.Shape(hr_shape[0:4] + [
mtf.Dimension('sx_block', lnc // hr_shape[1].size),
mtf.Dimension('sy_block', lnc // hr_shape[2].size),
mtf.Dimension('sz_block', lnc // hr_shape[3].size)
]),
name='my_reshape',
splittable_dims=lr_shape[:-1] + hr_shape[1:4] + part_shape[1:3])
for block_size_dim in hr_shape[-3:]:
f = mtf.pad(f, [
halo_size // 2**downsampling_factor,
halo_size // 2**downsampling_factor
], block_size_dim.name)
for blocks_dim, block_size_dim in zip(hr_shape[1:4], f.shape[-3:]):
f = mesh_ops.halo_reduce(f, blocks_dim, block_size_dim,
halo_size // 2**downsampling_factor)
f = mtf.reshape(f, f.shape + [mtf.Dimension('h_dim', 1)])
f = mesh_utils.upsample(f, downsampling_factor)
f = mtf.reshape(f, f.shape[:-1])
g = mesh_utils.c2r3d(g, f.shape[-3:])
high_shape = g.shape
# And now we remove the large scales
g = mtf.reshape(g, g.shape + [mtf.Dimension('h_dim', 1)])
_low = mesh_utils.downsample(g,
downsampling_factor,
antialias=antialias)
g = g - mtf.reshape(mesh_utils.upsample(_low, downsampling_factor),
g.shape)
g = mtf.reshape(g, high_shape)
d = mesh_utils.cic_readout(f + g, X, halo_size)
displacement.append(d)
# Readout the force to particle positions
F = mtf.stack([d for d in displacement], "ndim", axis=4)
F = F * 1.5 * cosmology.Om0
return X, P, F
def gradient_based_subword_tokenization(x,
length_dim,
max_subword_length=4,
downsample=None,
use_offsets=False,
consider_chars_as_blocks=False,
use_block_pos_embedding=False,
share_block_kernel=False,
memory_embeddings=0,
context=None,
block_mixing_mode=None,
activation="softmax",
downsample_function="mean"):
"""Implements GBSWT from Charformer.
Args:
x: a Tensor containing length_dim
length_dim: a Dimension
max_subword_length: integer
downsample: integer.
use_offsets: boolean.
consider_chars_as_blocks: boolean.
use_block_pos_embedding: boolean.
share_block_kernel: boolean.
memory_embeddings: integer.
context: Context.
block_mixing_mode: Str for block mixing.
activation: Str for block ranking.
downsample_function: Str, supports mean/linformer for now.
Returns:
a Tensor with the same shape as x.
Raises:
ValueError: if channels or depth don't match.
"""
# don't use this for now.
del max_subword_length
del memory_embeddings
all_blocks = []
all_scores = []
tf.logging.info("GSW block layer")
def _tile(x, n, tile_dim):
# Simple tile function in MTF.
return mtf.concat([x] * n, tile_dim.name)
def _repeat(x, n, repeat_dim):
# repeat function in MTF
tmp_dim = mtf.Dimension("tmp", 1)
expand_shape = mtf.Shape(x.shape.dims + [tmp_dim])
x = mtf.reshape(x, expand_shape)
x = _tile(x, n, tmp_dim)
output_shape = []
for dim in x.shape.dims:
if dim.name == "tmp":
continue
if dim.name == repeat_dim.name:
dim = mtf.Dimension(dim.name, dim.size * n)
output_shape.append(dim)
output_shape = mtf.Shape(output_shape)
x = mtf.reshape(x, output_shape)
return x
def _combined_dim(dims):
return mtf.Dimension(dims[0].name, mtf.Shape(dims).size)
# compute all subword blocks
# TODO(yitay): handle offsets to get all blocks
if activation == "sigtanh":
# one score for sigmoid
tmp_dim = mtf.Dimension("block_score", 2)
else:
tmp_dim = mtf.Dimension("block_score", 1)
model_dim = x.shape[-1]
subword_blocks_width = [2, 3, 4]
if consider_chars_as_blocks:
subword_blocks_width += [1]
if share_block_kernel:
block_kernel_shape = mtf.Shape([model_dim, tmp_dim])
block_kernel = mtf.get_variable(x.mesh,
"block_kernel",
block_kernel_shape,
initializer=None,
dtype=context.variable_dtype)
else:
block_kernel = None
for subword_len in subword_blocks_width:
if use_block_pos_embedding:
# this is turn off by default. It is meant to support cases like
# parameterized pooling or other features.
block_len_dim = mtf.Dimension(length_dim.name, subword_len)
# TODO(vqtran): Consider other positional embeddings.
block_pos_emb = sinusoid_positional_embedding_weights(
context.mesh, block_len_dim, x.shape[-1],
context.variable_dtype.activation_dtype)
block_pos_emb = _repeat(
block_pos_emb, math.ceil(length_dim.size / float(subword_len)),
block_len_dim)
if use_offsets:
offset_space = subword_len
else:
offset_space = 1
for offsets in range(offset_space):
if offsets > 0:
xoff = mtf.shift(x, offsets, length_dim, wrap=False)
if use_block_pos_embedding:
block_pos_emb = mtf.shift(block_pos_emb,
offsets,
block_pos_emb.shape[-2],
wrap=False)
else:
xoff = x
tf.logging.info("SW len=%d offset=%d", subword_len, offsets)
if length_dim.size % subword_len != 0:
tf.logging.info("Not divisible by length")
# add extra padding tokens
pad_amt = int(subword_len) - int(length_dim.size % subword_len)
kp = mtf.pad(xoff, [0, pad_amt], length_dim.name)
else:
kp = xoff
if use_block_pos_embedding:
kp += block_pos_emb
bx = mtf.pool_tensor_1d(
kp,
pool_dim=kp.shape.get_dim_by_name("length"),
reduce_fn=mtf.reduce_mean,
pool_size=int(subword_len))
block_score = mtf.layers.dense(bx, [tmp_dim],
use_bias=False,
name="bx",
reduced_dims=[model_dim],
variable_dtype=None,
kernel_weights=block_kernel)
expand_bx = _repeat(bx, subword_len, length_dim)
expand_scores = _repeat(block_score, subword_len, length_dim)
if offsets > 0:
# add offset.
expand_bx = mtf.pad(expand_bx, [offsets, 0], length_dim.name)
expand_scores = mtf.pad(expand_scores, [offsets, 0],
length_dim.name)
new_len = expand_bx.shape.get_dim_by_name(length_dim.name)
if new_len.size < length_dim.size:
pad_amt = new_len.size - length_dim.size
expand_bx = mtf.pad(expand_bx, [0, pad_amt], length_dim.name)
expand_scores = mtf.pad(expand_scores, [0, pad_amt],
length_dim.name)
elif new_len.size > length_dim.size:
expand_bx = mtf.slice(expand_bx, 0, length_dim.size,
length_dim.name)
expand_scores = mtf.slice(expand_scores, 0, length_dim.size,
length_dim.name)
new_tmp_dim = mtf.Dimension("extra_dim", 1)
expand_shape = mtf.Shape(expand_bx.shape.dims + [new_tmp_dim])
expand_scores_shape = mtf.Shape(expand_scores.shape.dims +
[new_tmp_dim])
expand_bx = mtf.reshape(expand_bx, expand_shape)
expand_scores = mtf.reshape(expand_scores, expand_scores_shape)
all_blocks.append(expand_bx)
all_scores.append(expand_scores)
all_blocks = mtf.concat(all_blocks, new_tmp_dim.name)
all_scores = mtf.concat(all_scores, new_tmp_dim.name)
tf.logging.info(all_blocks)
new_tmp_dim = all_blocks.shape.get_dim_by_name("extra_dim")
combined_dim = _combined_dim([new_tmp_dim, tmp_dim])
block_net_shape = all_scores.shape - tmp_dim - new_tmp_dim + combined_dim
block_net = mtf.reshape(all_scores, block_net_shape)
if block_mixing_mode == "score_attention":
tf.logging.info("Using score attention")
att = mtf.einsum([block_net, block_net], reduced_dims=[new_tmp_dim])
tf.logging.info(block_net)
att = mtf.softmax(att, reduced_dim=att.shape[-1])
block_net = mtf.einsum([att, block_net], output_shape=block_net.shape)
tf.logging.info(block_net)
if activation == "softmax":
block_net = mtf.softmax(block_net, reduced_dim=new_tmp_dim)
elif activation == "tanh":
tf.logging.info("Using tanh")
block_net = mtf.tanh(block_net)
all_blocks = block_net * all_blocks
all_blocks = mtf.reduce_sum(all_blocks, reduced_dim=new_tmp_dim)
output = all_blocks
if downsample:
output_length = output.shape.get_dim_by_name("length")
if output_length.size % int(downsample) != 0:
pad_amt = int(downsample) - int(
output_length.size % int(downsample))
output = mtf.pad(output, [0, pad_amt], output_length.name)
if downsample_function == "mean":
output = mtf.pool_tensor_1d(
output,
pool_dim=output.shape.get_dim_by_name("length"),
reduce_fn=mtf.reduce_mean,
pool_size=int(downsample))
else:
raise ValueError("Downsampling function not implemeneted.")
return output
def force_single(state,
lr_shape,
hr_shape,
kvec_lr,
halo_size,
cosmology=Planck15,
pm_nc_factor=1,
**kwargs):
"""
Estimate force on the particles given a state.
Parameters:
-----------
state: tensor
Input state tensor of shape (3, batch_size, npart, 3)
boxsize: float
Size of the simulation volume (Mpc/h) TODO: check units
cosmology: astropy.cosmology
Cosmology object
pm_nc_factor: int
TODO: @modichirag please add doc
"""
X, P, F = state
#TODO: support different factor
assert pm_nc_factor == 1
lnc = lr_shape[-1].size
part_shape = X.shape
# Paint the particles on the high resolution mesh
field = mtf.zeros(X.mesh, shape=hr_shape)
for block_size_dim in hr_shape[-3:]:
field = mtf.pad(field, [halo_size, halo_size], block_size_dim.name)
field = mesh_utils.cic_paint(field, X, halo_size)
for blocks_dim, block_size_dim in zip(hr_shape[1:4], field.shape[-3:]):
field = mesh_ops.halo_reduce(field, blocks_dim, block_size_dim,
halo_size)
# Remove borders
for block_size_dim in hr_shape[-3:]:
field = mtf.slice(field, halo_size, block_size_dim.size,
block_size_dim.name)
# Hack usisng custom reshape because mesh is pretty dumb
lr_field = mtf.slicewise(lambda x: x[:, 0, 0, 0], [field],
output_dtype=tf.float32,
output_shape=lr_shape,
name='my_dumb_reshape',
splittable_dims=lr_shape[:-1] + hr_shape[:4])
k_dims_lr = [d.shape[0] for d in kvec_lr]
k_dims_lr = [k_dims_lr[2], k_dims_lr[0], k_dims_lr[1]]
lr_kfield = mesh_utils.r2c3d(lr_field, k_dims_lr)
kfield_lr = mesh_kernels.apply_gradient_laplace_kernel(lr_kfield, kvec_lr)
# Reorder the low res FFTs which where transposed# y,z,x
kfield_lr = [kfield_lr[2], kfield_lr[0], kfield_lr[1]]
displacement = []
for f in kfield_lr:
f = mesh_utils.c2r3d(f, lr_shape[-3:])
f = mtf.slicewise(
lambda x: tf.expand_dims(
tf.expand_dims(tf.expand_dims(x, axis=1), axis=1), axis=1),
[f],
output_dtype=tf.float32,
output_shape=mtf.Shape(hr_shape[0:4] + [
mtf.Dimension('sx_block', lnc // hr_shape[1].size),
mtf.Dimension('sy_block', lnc // hr_shape[2].size),
mtf.Dimension('sz_block', lnc // hr_shape[3].size)
]),
name='my_reshape',
splittable_dims=lr_shape[:-1] + hr_shape[1:4] + part_shape[1:3])
for block_size_dim in hr_shape[-3:]:
f = mtf.pad(f, [halo_size, halo_size], block_size_dim.name)
for blocks_dim, block_size_dim in zip(hr_shape[1:4], f.shape[-3:]):
f = mesh_ops.halo_reduce(f, blocks_dim, block_size_dim, halo_size)
d = mesh_utils.cic_readout(f, X, halo_size)
displacement.append(d)
# Readout the force to particle positions
F = mtf.stack([d for d in displacement], "ndim", axis=4)
F = F * 1.5 * cosmology.Om0
return X, P, F
def lpt_prototype(mesh,
nc=FLAGS.nc,
bs=FLAGS.box_size,
batch_size=FLAGS.batch_size,
a0=FLAGS.a0,
a=FLAGS.af,
nsteps=FLAGS.nsteps):
"""
Prototype of function computing LPT deplacement.
Returns output tensorflow and mesh tensorflow tensors
"""
klin = np.loadtxt('../flowpm/data/Planck15_a1p00.txt').T[0]
plin = np.loadtxt('../flowpm/data/Planck15_a1p00.txt').T[1]
ipklin = iuspline(klin, plin)
stages = np.linspace(a0, a, nsteps, endpoint=True)
# Define the named dimensions
# Parameters of the small scales decomposition
n_block_x = FLAGS.nx
n_block_y = FLAGS.ny
n_block_z = 1
halo_size = FLAGS.hsize
if halo_size >= 0.5 * min(nc // n_block_x, nc // n_block_y,
nc // n_block_z):
new_size = int(0.5 *
min(nc // n_block_x, nc // n_block_y, nc // n_block_z))
print('WARNING: REDUCING HALO SIZE from %d to %d' %
(halo_size, new_size))
halo_size = new_size
# Parameters of the large scales decomposition
downsampling_factor = 0
lnc = nc // 2**downsampling_factor
#
fx_dim = mtf.Dimension("nx", nc)
fy_dim = mtf.Dimension("ny", nc)
fz_dim = mtf.Dimension("nz", nc)
tfx_dim = mtf.Dimension("tx", nc)
tfy_dim = mtf.Dimension("ty", nc)
tfz_dim = mtf.Dimension("tz", nc)
tx_dim = mtf.Dimension("tx_lr", nc)
ty_dim = mtf.Dimension("ty_lr", nc)
tz_dim = mtf.Dimension("tz_lr", nc)
nx_dim = mtf.Dimension('nx_block', n_block_x)
ny_dim = mtf.Dimension('ny_block', n_block_y)
nz_dim = mtf.Dimension('nz_block', n_block_z)
sx_dim = mtf.Dimension('sx_block', nc // n_block_x)
sy_dim = mtf.Dimension('sy_block', nc // n_block_y)
sz_dim = mtf.Dimension('sz_block', nc // n_block_z)
k_dims = [tx_dim, ty_dim, tz_dim]
batch_dim = mtf.Dimension("batch", batch_size)
pk_dim = mtf.Dimension("npk", len(plin))
pk = mtf.import_tf_tensor(mesh, plin.astype('float32'), shape=[pk_dim])
# Compute necessary Fourier kernels
kvec = flowpm.kernels.fftk((nc, nc, nc), symmetric=False)
kx = mtf.import_tf_tensor(mesh,
kvec[0].squeeze().astype('float32'),
shape=[tfx_dim])
ky = mtf.import_tf_tensor(mesh,
kvec[1].squeeze().astype('float32'),
shape=[tfy_dim])
kz = mtf.import_tf_tensor(mesh,
kvec[2].squeeze().astype('float32'),
shape=[tfz_dim])
kv = [ky, kz, kx]
# kvec for low resolution grid
kvec_lr = flowpm.kernels.fftk([nc, nc, nc], symmetric=False)
kx_lr = mtf.import_tf_tensor(mesh,
kvec_lr[0].squeeze().astype('float32'),
shape=[tx_dim])
ky_lr = mtf.import_tf_tensor(mesh,
kvec_lr[1].squeeze().astype('float32'),
shape=[ty_dim])
kz_lr = mtf.import_tf_tensor(mesh,
kvec_lr[2].squeeze().astype('float32'),
shape=[tz_dim])
kv_lr = [ky_lr, kz_lr, kx_lr]
shape = [batch_dim, fx_dim, fy_dim, fz_dim]
lr_shape = [batch_dim, fx_dim, fy_dim, fz_dim]
hr_shape = [batch_dim, nx_dim, ny_dim, nz_dim, sx_dim, sy_dim, sz_dim]
part_shape = [batch_dim, fx_dim, fy_dim, fz_dim]
# Begin simulation
initc = mtfpm.linear_field(mesh, shape, bs, nc, pk, kv)
# # Reshaping array into high resolution mesh
# field = mtf.slicewise(lambda x:tf.expand_dims(tf.expand_dims(tf.expand_dims(x, axis=1),axis=1),axis=1),
# [initc],
# output_dtype=tf.float32,
# output_shape=hr_shape,
# name='my_reshape',
# splittable_dims=lr_shape[:-1]+hr_shape[1:4]+part_shape[1:3])
#
state = mtfpm.lpt_init_single(
initc,
a0,
kv_lr,
halo_size,
lr_shape,
hr_shape,
part_shape[1:],
antialias=True,
)
# Here we can run our nbody
final_state = state #mtfpm.nbody(state, stages, lr_shape, hr_shape, k_dims, kv_lr, kv_hr, halo_size, downsampling_factor=downsampling_factor)
# paint the field
final_field = mtf.zeros(mesh, shape=hr_shape)
for block_size_dim in hr_shape[-3:]:
final_field = mtf.pad(final_field, [halo_size, halo_size],
block_size_dim.name)
final_field = mesh_utils.cic_paint(final_field, final_state[0], halo_size)
# Halo exchange
for blocks_dim, block_size_dim in zip(hr_shape[1:4],
final_field.shape[-3:]):
final_field = mpm.halo_reduce(final_field, blocks_dim, block_size_dim,
halo_size)
# Remove borders
for block_size_dim in hr_shape[-3:]:
final_field = mtf.slice(final_field, halo_size, block_size_dim.size,
block_size_dim.name)
#final_field = mtf.reshape(final_field, [batch_dim, fx_dim, fy_dim, fz_dim])
# Hack usisng custom reshape because mesh is pretty dumb
final_field = mtf.slicewise(
lambda x: x[:, 0, 0, 0], [final_field],
output_dtype=tf.float32,
output_shape=[batch_dim, fx_dim, fy_dim, fz_dim],
name='my_dumb_reshape',
splittable_dims=part_shape[:-1] + hr_shape[:4])
return initc, final_field
def _call_internal(self, context, inputs, targets=None):
"""Compute logits based on inputs (all positions in parallel).
Also updates context if applicable.
Args:
context: a Context
inputs: a Tensor
targets: an optional Tensor
Returns:
logits: a Tensor with shape [<batch_dims>, length_dim, output_vocab_dim]
"""
mesh = inputs.mesh
if "embedding" in context.shared_params:
embedding_weights = context.shared_params["embedding"]
else:
embedding_weights = mtf.layers.embedding_weights(
mesh, self.input_vocab_dim, self.model_dim, context.variable_dtype,
name="embedding")
x = mtf.gather(embedding_weights, inputs, self.input_vocab_dim)
if "positional_embedding" in context.shared_params:
pos_emb_var = context.shared_params["positional_embedding"]
else:
pos_emb_var = mtf.layers.embedding_weights(
mesh, self.max_length_dim, self.model_dim, context.variable_dtype,
"positional_embedding")
if context.position_is_default:
pos_emb = mtf.rename_dimension(
mtf.slice(pos_emb_var, 0, context.length_dim.size,
self.max_length_dim.name),
self.max_length_dim.name, context.length_dim.name)
else:
pos_emb = mtf.gather(
pos_emb_var, context.position, self.max_length_dim,
output_shape=x.shape)
x += pos_emb
x = self.layer_stack.call(context, x)
if self.output_vocab_dim is None:
return x
if self.shared_embedding_and_softmax_weights:
logits = mtf.einsum(
[x * (self.model_dim.size ** -0.5), embedding_weights],
reduced_dims=[self.model_dim])
else:
logits = mtf.layers.dense(
x, self.output_vocab_dim, use_bias=False,
variable_dtype=context.variable_dtype,
name="logits")
if targets is not None and context.losses is not None:
off_value = self.label_smoothing / self.output_vocab_dim.size
on_value = 1.0 - self.label_smoothing + off_value
soft_targets = mtf.one_hot(
targets, self.output_vocab_dim,
dtype=context.activation_dtype,
on_value=on_value,
off_value=off_value)
loss = mtf.layers.softmax_cross_entropy_with_logits(
logits, soft_targets, self.output_vocab_dim,
z_loss=self.z_loss if context.train else 0.0)
weights = mtf.layers.weights_nonzero(
targets, dtype=context.activation_dtype)
loss = mtf.reduce_mean(loss * weights)
context.losses.append(loss)
return logits
def recon_prototype(mesh,
data,
nc=FLAGS.nc,
bs=FLAGS.box_size,
batch_size=FLAGS.batch_size,
a0=FLAGS.a0,
a=FLAGS.af,
nsteps=FLAGS.nsteps,
dtype=tf.float32):
"""
Prototype of function computing LPT deplacement.
Returns output tensorflow and mesh tensorflow tensors
"""
if dtype == tf.float32:
npdtype = "float32"
cdtype = tf.complex64
elif dtype == tf.float64:
npdtype = "float64"
cdtype = tf.complex128
print(dtype, npdtype)
# Compute a few things first, using simple tensorflow
stages = np.linspace(a0, a, nsteps, endpoint=True)
#graph = mtf.Graph()
#mesh = mtf.Mesh(graph, "my_mesh")
# Define the named dimensions
# Parameters of the small scales decomposition
n_block_x = FLAGS.nx
n_block_y = FLAGS.ny
n_block_z = 1
halo_size = FLAGS.hsize
if halo_size >= 0.5 * min(nc // n_block_x, nc // n_block_y,
nc // n_block_z):
new_size = int(0.5 *
min(nc // n_block_x, nc // n_block_y, nc // n_block_z))
print('WARNING: REDUCING HALO SIZE from %d to %d' %
(halo_size, new_size))
halo_size = new_size
# Parameters of the large scales decomposition
downsampling_factor = 2
lnc = nc // 2**downsampling_factor
fx_dim = mtf.Dimension("nx", nc)
fy_dim = mtf.Dimension("ny", nc)
fz_dim = mtf.Dimension("nz", nc)
tfx_dim = mtf.Dimension("tx", nc)
tfy_dim = mtf.Dimension("ty", nc)
tfz_dim = mtf.Dimension("tz", nc)
# Dimensions of the low resolution grid
x_dim = mtf.Dimension("nx_lr", lnc)
y_dim = mtf.Dimension("ny_lr", lnc)
z_dim = mtf.Dimension("nz_lr", lnc)
tx_dim = mtf.Dimension("tx_lr", lnc)
ty_dim = mtf.Dimension("ty_lr", lnc)
tz_dim = mtf.Dimension("tz_lr", lnc)
nx_dim = mtf.Dimension('nx_block', n_block_x)
ny_dim = mtf.Dimension('ny_block', n_block_y)
nz_dim = mtf.Dimension('nz_block', n_block_z)
sx_dim = mtf.Dimension('sx_block', nc // n_block_x)
sy_dim = mtf.Dimension('sy_block', nc // n_block_y)
sz_dim = mtf.Dimension('sz_block', nc // n_block_z)
k_dims = [tx_dim, ty_dim, tz_dim]
batch_dim = mtf.Dimension("batch", batch_size)
klin = np.loadtxt('../flowpm/data/Planck15_a1p00.txt').T[0]
plin = np.loadtxt('../flowpm/data/Planck15_a1p00.txt').T[1]
ipklin = iuspline(klin, plin)
pk_dim = mtf.Dimension("npk", len(plin))
pk = mtf.import_tf_tensor(mesh, plin.astype(npdtype), shape=[pk_dim])
# Compute necessary Fourier kernels
kvec = flowpm.kernels.fftk((nc, nc, nc), symmetric=False, dtype=npdtype)
kx = mtf.import_tf_tensor(mesh,
kvec[0].squeeze().astype(npdtype),
shape=[tfx_dim])
ky = mtf.import_tf_tensor(mesh,
kvec[1].squeeze().astype(npdtype),
shape=[tfy_dim])
kz = mtf.import_tf_tensor(mesh,
kvec[2].squeeze().astype(npdtype),
shape=[tfz_dim])
kv = [ky, kz, kx]
# kvec for low resolution grid
kvec_lr = flowpm.kernels.fftk([lnc, lnc, lnc],
symmetric=False,
dtype=npdtype)
kx_lr = mtf.import_tf_tensor(mesh,
kvec_lr[0].squeeze().astype(npdtype) /
2**downsampling_factor,
shape=[tx_dim])
ky_lr = mtf.import_tf_tensor(mesh,
kvec_lr[1].squeeze().astype(npdtype) /
2**downsampling_factor,
shape=[ty_dim])
kz_lr = mtf.import_tf_tensor(mesh,
kvec_lr[2].squeeze().astype(npdtype) /
2**downsampling_factor,
shape=[tz_dim])
kv_lr = [ky_lr, kz_lr, kx_lr]
# kvec for high resolution blocks
padded_sx_dim = mtf.Dimension('padded_sx_block',
nc // n_block_x + 2 * halo_size)
padded_sy_dim = mtf.Dimension('padded_sy_block',
nc // n_block_y + 2 * halo_size)
padded_sz_dim = mtf.Dimension('padded_sz_block',
nc // n_block_z + 2 * halo_size)
kvec_hr = flowpm.kernels.fftk([
nc // n_block_x + 2 * halo_size, nc // n_block_y + 2 * halo_size,
nc // n_block_z + 2 * halo_size
],
symmetric=False,
dtype=npdtype)
kx_hr = mtf.import_tf_tensor(mesh,
kvec_hr[0].squeeze().astype(npdtype),
shape=[padded_sx_dim])
ky_hr = mtf.import_tf_tensor(mesh,
kvec_hr[1].squeeze().astype(npdtype),
shape=[padded_sy_dim])
kz_hr = mtf.import_tf_tensor(mesh,
kvec_hr[2].squeeze().astype(npdtype),
shape=[padded_sz_dim])
kv_hr = [ky_hr, kz_hr, kx_hr]
# kvec for prior blocks
prior_sx_dim = mtf.Dimension('prior_sx_block', nc // n_block_x)
prior_sy_dim = mtf.Dimension('prior_sy_block', nc // n_block_y)
prior_sz_dim = mtf.Dimension('prior_sz_block', nc // n_block_z)
kvec_pr = flowpm.kernels.fftk(
[nc // n_block_x, nc // n_block_y, nc // n_block_z],
symmetric=False,
dtype=npdtype)
kx_pr = mtf.import_tf_tensor(mesh,
kvec_pr[0].squeeze().astype(npdtype),
shape=[prior_sx_dim])
ky_pr = mtf.import_tf_tensor(mesh,
kvec_pr[1].squeeze().astype(npdtype),
shape=[prior_sy_dim])
kz_pr = mtf.import_tf_tensor(mesh,
kvec_pr[2].squeeze().astype(npdtype),
shape=[prior_sz_dim])
kv_pr = [ky_pr, kz_pr, kx_pr]
shape = [batch_dim, fx_dim, fy_dim, fz_dim]
lr_shape = [batch_dim, x_dim, y_dim, z_dim]
hr_shape = [batch_dim, nx_dim, ny_dim, nz_dim, sx_dim, sy_dim, sz_dim]
part_shape = [batch_dim, fx_dim, fy_dim, fz_dim]
## Compute initial initial conditions distributed
fieldvar = mtf.get_variable(mesh, 'linear', hr_shape)
input_field = tf.placeholder(data.dtype, [
batch_size, n_block_x, n_block_y, n_block_z, nc // n_block_x,
nc // n_block_y, nc // n_block_z
])
mtfinp = mtf.import_tf_tensor(mesh, input_field, shape=hr_shape)
linearop = mtf.assign(fieldvar, mtfinp)
#
field = fieldvar
initc = mtf.slicewise(lambda x: x[:, 0, 0, 0], [field],
output_dtype=tf.float32,
output_shape=[batch_dim, fx_dim, fy_dim, fz_dim],
name='my_dumb_reshape',
splittable_dims=part_shape[:-1] + hr_shape[:4])
#
for block_size_dim in hr_shape[-3:]:
field = mtf.pad(field, [halo_size, halo_size], block_size_dim.name)
for blocks_dim, block_size_dim in zip(hr_shape[1:4], field.shape[-3:]):
field = mpm.halo_reduce(field, blocks_dim, block_size_dim, halo_size)
field = mtf.reshape(field, field.shape + [mtf.Dimension('h_dim', 1)])
high = field
low = mesh_utils.downsample(field, downsampling_factor, antialias=True)
low = mtf.reshape(low, low.shape[:-1])
high = mtf.reshape(high, high.shape[:-1])
for block_size_dim in hr_shape[-3:]:
low = mtf.slice(low, halo_size // 2**downsampling_factor,
block_size_dim.size // 2**downsampling_factor,
block_size_dim.name)
# Hack usisng custom reshape because mesh is pretty dumb
low = mtf.slicewise(lambda x: x[:, 0, 0, 0], [low],
output_dtype=initc.dtype,
output_shape=lr_shape,
name='my_dumb_reshape',
splittable_dims=lr_shape[:-1] + hr_shape[:4])
# Here we can run our nbody
if FLAGS.nbody:
state = mtfpm.lpt_init(low,
high,
0.1,
kv_lr,
kv_hr,
halo_size,
hr_shape,
lr_shape,
part_shape[1:],
downsampling_factor=downsampling_factor,
antialias=True)
final_state = mtfpm.nbody(state,
stages,
lr_shape,
hr_shape,
kv_lr,
kv_hr,
halo_size,
downsampling_factor=downsampling_factor)
else:
final_state = mtfpm.lpt_init(low,
high,
stages[-1],
kv_lr,
kv_hr,
halo_size,
hr_shape,
lr_shape,
part_shape[1:],
downsampling_factor=downsampling_factor,
antialias=True)
# paint the field
final_field = mtf.zeros(mesh, shape=hr_shape)
for block_size_dim in hr_shape[-3:]:
final_field = mtf.pad(final_field, [halo_size, halo_size],
block_size_dim.name)
final_field = mesh_utils.cic_paint(final_field, final_state[0], halo_size)
# Halo exchange
for blocks_dim, block_size_dim in zip(hr_shape[1:4],
final_field.shape[-3:]):
final_field = mpm.halo_reduce(final_field, blocks_dim, block_size_dim,
halo_size)
# Remove borders
for block_size_dim in hr_shape[-3:]:
final_field = mtf.slice(final_field, halo_size, block_size_dim.size,
block_size_dim.name)
final_field = mtf.slicewise(
lambda x: x[:, 0, 0, 0], [final_field],
output_dtype=dtype,
output_shape=[batch_dim, fx_dim, fy_dim, fz_dim],
name='my_dumb_reshape',
splittable_dims=part_shape[:-1] + hr_shape[:4])
mtfdata = mtf.import_tf_tensor(mesh,
tf.convert_to_tensor(data),
shape=shape)
# Get prior
k_dims_pr = [d.shape[0] for d in kv_pr]
k_dims_pr = [k_dims_pr[2], k_dims_pr[0], k_dims_pr[1]]
cfield = mesh_utils.r2c3d(fieldvar, k_dims_pr, dtype=cdtype)
def _cwise_prior(kfield, pk, kx, ky, kz):
kx = tf.reshape(kx, [-1, 1, 1])
ky = tf.reshape(ky, [1, -1, 1])
kz = tf.reshape(kz, [1, 1, -1])
kk = tf.sqrt((kx / bs * nc)**2 + (ky / bs * nc)**2 + (kz / bs * nc)**2)
kshape = kk.shape
kk = tf.reshape(kk, [-1])
pkmesh = tfp.math.interp_regular_1d_grid(
x=kk,
x_ref_min=1e-05,
x_ref_max=1000.0,
y_ref=pk,
grid_regularizing_transform=tf.log)
priormesh = tf.reshape(pkmesh, kshape)
return tf.abs(kfield) / priormesh**0.5
cpfield = mtf.cwise(_cwise_prior, [cfield, pk] + kv_pr,
output_dtype=tf.float32)
prior = mtf.reduce_sum(mtf.square(cpfield)) * bs**3
# Total loss
diff = (final_field - mtfdata)
R0 = tf.placeholder(tf.float32, shape=())
def _cwise_smooth(kfield, kx, ky, kz):
kx = tf.reshape(kx, [-1, 1, 1])
ky = tf.reshape(ky, [1, -1, 1])
kz = tf.reshape(kz, [1, 1, -1])
kk = (kx / bs * nc)**2 + (ky / bs * nc)**2 + (kz / bs * nc)**2
wts = tf.cast(tf.exp(-kk * (R0 * bs / nc)**2), kfield.dtype)
return kfield * wts
cdiff = mesh_utils.r2c3d(diff, k_dims_pr, dtype=cdtype)
cdiff = mtf.cwise(_cwise_smooth, [cdiff] + kv_pr, output_dtype=cdtype)
diff = mesh_utils.c2r3d(cdiff, diff.shape[-3:], dtype=dtype)
chisq = mtf.reduce_sum(mtf.square(diff))
loss = chisq + prior
#return initc, final_field, loss, linearop, input_field
nyq = np.pi * nc / bs
def _cwise_highpass(kfield, kx, ky, kz):
kx = tf.reshape(kx, [-1, 1, 1])
ky = tf.reshape(ky, [1, -1, 1])
kz = tf.reshape(kz, [1, 1, -1])
kk = (kx / bs * nc)**2 + (ky / bs * nc)**2 + (kz / bs * nc)**2
wts = tf.cast(tf.exp(-kk * (R0 * bs / nc + 1 / nyq)**2), kfield.dtype)
return kfield * (1 - wts)
var_grads = mtf.gradients([loss], [fieldvar])
cgrads = mesh_utils.r2c3d(var_grads[0], k_dims_pr, dtype=cdtype)
cgrads = mtf.cwise(_cwise_highpass, [cgrads] + kv_pr, output_dtype=cdtype)
var_grads = [
mesh_utils.c2r3d(cgrads, var_grads[0].shape[-3:], dtype=dtype)
]
lr = tf.placeholder(tf.float32, shape=())
update_op = mtf.assign(fieldvar, fieldvar - var_grads[0] * lr)
return initc, final_field, loss, var_grads, update_op, linearop, input_field, lr, R0
