def test_touched_overlap_area():
sig_shape = (505, 407)
overlap = (11, 9)
n_seg = (8, 4)
segments = Segmentation(n_seg=n_seg,
signal_shape=sig_shape,
overlap=overlap)
for i_seg in range(segments.effective_n_seg):
seg_shape = segments.get_seg_shape(i_seg)
seg_slice = segments.get_seg_slice(i_seg)
seg_inner_slice = segments.get_seg_slice(i_seg, inner=True)
if i_seg != 0:
with pytest.raises(AssertionError):
segments.check_area_contained(i_seg, (0, 0), overlap)
for pt0 in [
overlap, (overlap[0], 25), (25, overlap[1]), (25, 25),
(seg_shape[0] - overlap[0] - 1, 25),
(25, seg_shape[1] - overlap[1] - 1),
(seg_shape[0] - overlap[0] - 1, seg_shape[1] - overlap[1] - 1)
]:
assert segments.is_contained_coordinate(i_seg, pt0, inner=True)
segments.check_area_contained(i_seg, pt0, overlap)
z = np.zeros(sig_shape)
pt_global = segments.get_global_coordinate(i_seg, pt0)
update_slice = tuple([
slice(max(v - r, 0), v + r + 1)
for v, r in zip(pt_global, overlap)
])
z[update_slice] += 1
z[seg_inner_slice] = 0
# The returned slice are given in local coordinates. Take the
# segment in z to use local coordinate.
z_seg = z[seg_slice]
updated_slices = segments.get_touched_overlap_slices(
i_seg, pt0, overlap)
# Assert that all selected coordinate are indeed in the update area
for u_slice in updated_slices:
assert np.all(z_seg[u_slice] == 1)
# Assert that all coordinate updated in the overlap area have been
# selected with at least one slice.
for u_slice in updated_slices:
z_seg[u_slice] *= 0
assert np.all(z == 0)
class DICODWorker:
"""Worker for DICOD, running LGCD locally and using MPI for communications
Parameters
----------
backend: str
Backend used to communicate between workers. Available backends are
{ 'mpi' }.
"""
def __init__(self, backend):
self._backend = backend
def recv_task(self):
# Retrieve different constants from the base communicator and store
# then in the class.
params = self.get_params()
if self.timeout:
self.timeout *= 3
self.random_state = params['random_state']
if isinstance(self.random_state, int):
self.random_state += self.rank
self.size_msg = len(params['valid_shape']) + 2
# Compute the shape of the worker segment.
self.D = self.get_D()
n_atoms, n_channels, *atom_support = self.D.shape
self.overlap = np.array(atom_support) - 1
self.workers_segments = Segmentation(
n_seg=params['workers_topology'],
signal_shape=params['valid_shape'],
overlap=self.overlap)
# Receive X and z from the master node.
worker_shape = self.workers_segments.get_seg_shape(self.rank)
X_shape = (n_channels, ) + get_full_shape(worker_shape, atom_support)
if params['has_z0']:
z0_shape = (n_atoms, ) + worker_shape
self.z0 = self.get_signal(z0_shape, params['debug'])
else:
self.z0 = None
self.X_worker = self.get_signal(X_shape, params['debug'])
# Compute the local segmentation for LGCD algorithm
# If n_seg is not specified, compute the shape of the local segments
# as the size of an interfering zone.
n_seg = self.n_seg
local_seg_shape = None
if self.n_seg == 'auto':
n_seg = None
local_seg_shape = 2 * np.array(atom_support) - 1
# Get local inner bounds. First, compute the seg_bound without overlap
# in local coordinates and then convert the bounds in the local
# coordinate system.
inner_bounds = self.workers_segments.get_seg_bounds(self.rank,
inner=True)
inner_bounds = np.transpose([
self.workers_segments.get_local_coordinate(self.rank, bound)
for bound in np.transpose(inner_bounds)
])
self.local_segments = Segmentation(n_seg=n_seg,
seg_shape=local_seg_shape,
inner_bounds=inner_bounds,
full_shape=worker_shape)
# Initialize the solution
n_atoms = self.D.shape[0]
seg_shape = self.workers_segments.get_seg_shape(self.rank)
if self.z0 is None:
self.z_hat = np.zeros((n_atoms, ) + seg_shape)
else:
self.z_hat = self.z0
self.info(
"Start DICOD with {} workers, strategy '{}', soft_lock"
"={} and n_seg={}({})",
self.n_jobs,
self.strategy,
self.soft_lock,
self.n_seg,
self.local_segments.effective_n_seg,
global_msg=True)
self.synchronize_workers()
def compute_z_hat(self):
# Initialization of the algorithm variables
random_state = check_random_state(self.random_state)
i_seg = -1
n_coordinate_updates = 0
accumulator = 0
k0, pt0 = 0, None
self.n_paused_worker = 0
# compute the number of coordinates
n_atoms, *_ = self.D.shape
seg_in_shape = self.workers_segments.get_seg_shape(self.rank,
inner=True)
n_coordinates = n_atoms * np.prod(seg_in_shape)
self.init_cd_variables()
diverging = False
if flags.INTERACTIVE_PROCESSES and self.n_jobs == 1:
import ipdb
ipdb.set_trace() # noqa: E702
self.t_start = t_start = time.time()
if self.timeout is not None:
deadline = t_start + self.timeout
else:
deadline = None
for ii in range(self.max_iter):
# Display the progress of the algorithm
self.progress(ii, max_ii=self.max_iter, unit="iterations")
# Process incoming messages
self.process_messages()
# Increment the segment and select the coordinate to update
try:
i_seg = self.local_segments.increment_seg(i_seg)
except ZeroDivisionError:
print(self.local_segments.signal_shape,
self.local_segments.n_seg_per_axis)
raise
if self.local_segments.is_active_segment(i_seg):
k0, pt0, dz = _select_coordinate(self.dz_opt,
self.dE,
self.local_segments,
i_seg,
strategy=self.strategy,
random_state=random_state)
assert self.workers_segments.is_contained_coordinate(
self.rank, pt0, inner=True), pt0
else:
k0, pt0, dz = None, None, 0
# update the accumulator for 'random' strategy
accumulator = max(abs(dz), accumulator)
# If requested, check that the update chosen only have an impact on
# the segment and its overlap area.
if flags.CHECK_UPDATE_CONTAINED and pt0 is not None:
self.workers_segments.check_area_contained(
self.rank, pt0, self.overlap)
# Check if the coordinate is soft-locked or not.
soft_locked = False
if (pt0 is not None and abs(dz) > self.tol
and self.soft_lock != 'none'):
n_lock = 1 if self.soft_lock == "corner" else 0
lock_slices = self.workers_segments.get_touched_overlap_slices(
self.rank, pt0,
np.array(self.overlap) + 1)
# Only soft lock in the corners
if len(lock_slices) > n_lock:
max_on_lock = 0
for u_slice in lock_slices:
max_on_lock = max(
abs(self.dz_opt[u_slice]).max(), max_on_lock)
soft_locked = max_on_lock > abs(dz)
# Update the selected coordinate and beta, only if the update is
# greater than the convergence tolerance and is contained in the
# worker. If the update is not in the worker, this will
# effectively work has a soft lock to prevent interferences.
if abs(dz) > self.tol and not soft_locked:
n_coordinate_updates += 1
# update the selected coordinate and beta
self.coordinate_update(k0, pt0, dz)
# Notify neighboring workers of the update if needed.
pt_global = self.workers_segments.get_global_coordinate(
self.rank, pt0)
workers = self.workers_segments.get_touched_segments(
pt=pt_global, radius=np.array(self.overlap) + 1)
msg = np.array([k0, *pt_global, dz], 'd')
self.notify_neighbors(msg, workers)
if self.timing:
t_update = time.time() - t_start
self._log_updates.append(
(t_update, ii, self.rank, k0, pt_global, dz))
# Inactivate the current segment if the magnitude of the update is
# too small. This only work when using LGCD.
if abs(dz) <= self.tol and self.strategy == "greedy":
self.local_segments.set_inactive_segments(i_seg)
# When workers are diverging, finish the worker to avoid having to
# wait until max_iter for stopping the algorithm.
if abs(dz) >= 1e3:
self.info("diverging worker")
self.wait_status_changed(status=constants.STATUS_FINISHED)
diverging = True
break
# Check the stopping criterion and if we have locally converged,
# wait either for an incoming message or for full convergence.
if _check_convergence(self.local_segments,
self.tol,
ii,
self.dz_opt,
n_coordinates,
self.strategy,
accumulator=accumulator):
if flags.CHECK_ACTIVE_SEGMENTS:
inner_slice = (Ellipsis, ) + tuple([
slice(start, end)
for start, end in self.local_segments.inner_bounds
])
assert np.all(abs(self.dz_opt[inner_slice]) <= self.tol)
if self.check_no_transitting_message():
status = self.wait_status_changed()
if status == constants.STATUS_STOP:
self.debug(
"LGCD converged with {} coordinate "
"updates", n_coordinate_updates)
break
# Check is we reach the timeout
if deadline is not None and time.time() >= deadline:
self.stop_before_convergence("Reached timeout",
n_coordinate_updates)
break
else:
self.stop_before_convergence("Reached max_iter",
n_coordinate_updates)
self.synchronize_workers()
assert diverging or self.check_no_transitting_message()
runtime = time.time() - t_start
comm = MPI.Comm.Get_parent()
comm.gather([n_coordinate_updates, runtime], root=0)
return n_coordinate_updates, runtime
def run(self):
self.recv_task()
n_coordinate_updates, runtime = self.compute_z_hat()
self.send_result(n_coordinate_updates, runtime)
def stop_before_convergence(self, msg, n_coordinate_updates):
self.info("{}. Done {} coordinate updates. Max of |dz|={}.", msg,
n_coordinate_updates,
abs(self.dz_opt).max())
self.wait_status_changed(status=constants.STATUS_FINISHED)
def init_cd_variables(self):
t_start = time.time()
# Pre-compute some quantities
constants = {}
constants['norm_atoms'] = compute_norm_atoms(self.D)
constants['DtD'] = compute_DtD(self.D)
self.constants = constants
# List of all pending messages sent
self.messages = []
# Log all updates for logging purpose
self._log_updates = []
# Avoid printing progress too often
self._last_progress = 0
# Initialization of the auxillary variable for LGCD
return_dE = self.strategy == "gs-q"
self.beta, self.dz_opt, self.dE = _init_beta(
self.X_worker,
self.D,
self.reg,
z_i=self.z0,
constants=constants,
z_positive=self.z_positive,
return_dE=return_dE)
# Make sure all segments are activated
self.local_segments.reset()
if self.z0 is not None:
self.freezed_support = None
self.correct_beta_z0()
if flags.CHECK_WARM_BETA:
pt_global = self.workers_segments.get_seg_shape(0, inner=True)
pt = self.workers_segments.get_local_coordinate(
self.rank, pt_global)
if self.workers_segments.is_contained_coordinate(self.rank, pt):
_, _, *atom_support = self.D.shape
beta_slice = (Ellipsis, ) + tuple([
slice(v - size_ax + 1, v + size_ax - 1)
for v, size_ax in zip(pt, atom_support)
])
sum_beta = np.array(self.beta[beta_slice].sum(), dtype='d')
self.return_array(sum_beta)
if self.freeze_support:
assert self.z0 is not None
self.freezed_support = self.z0 == 0
self.dz_opt[self.freezed_support] = 0
else:
self.freezed_support = None
self.synchronize_workers()
t_local_init = time.time() - t_start
self.info("End local initialization in {:.2f}s",
t_local_init,
global_msg=True)
def coordinate_update(self, k0, pt0, dz, coordinate_exist=True):
self.beta, self.dz_opt, self.dE = coordinate_update(
k0,
pt0,
dz,
beta=self.beta,
dz_opt=self.dz_opt,
dE=self.dE,
z_hat=self.z_hat,
D=self.D,
reg=self.reg,
constants=self.constants,
z_positive=self.z_positive,
freezed_support=self.freezed_support,
coordinate_exist=coordinate_exist)
# Re-activate the segments where beta have been updated to ensure
# convergence.
touched_segments = self.local_segments.get_touched_segments(
pt=pt0, radius=self.overlap)
n_changed_status = self.local_segments.set_active_segments(
touched_segments)
# If requested, check that all inactive segments have no coefficients
# to update over the tolerance.
if flags.CHECK_ACTIVE_SEGMENTS and n_changed_status:
self.local_segments.test_active_segments(self.dz_opt, self.tol)
def process_messages(self, worker_status=constants.STATUS_RUNNING):
mpi_status = MPI.Status()
while MPI.COMM_WORLD.Iprobe(status=mpi_status):
src = mpi_status.source
tag = mpi_status.tag
if tag == constants.TAG_DICOD_UPDATE_BETA:
if worker_status == constants.STATUS_PAUSED:
self.notify_worker_status(
constants.TAG_DICOD_RUNNING_WORKER, wait=True)
worker_status = constants.STATUS_RUNNING
elif tag == constants.TAG_DICOD_STOP:
worker_status = constants.STATUS_STOP
elif tag == constants.TAG_DICOD_PAUSED_WORKER:
self.n_paused_worker += 1
assert self.n_paused_worker <= self.n_jobs
elif tag == constants.TAG_DICOD_RUNNING_WORKER:
self.n_paused_worker -= 1
assert self.n_paused_worker >= 0
msg = np.empty(self.size_msg, 'd')
MPI.COMM_WORLD.Recv([msg, MPI.DOUBLE], source=src, tag=tag)
if tag == constants.TAG_DICOD_UPDATE_BETA:
self.message_update_beta(msg)
if self.n_paused_worker == self.n_jobs:
worker_status = constants.STATUS_STOP
return worker_status
def message_update_beta(self, msg):
k0, *pt_global, dz = msg
k0 = int(k0)
pt_global = tuple([int(v) for v in pt_global])
pt0 = self.workers_segments.get_local_coordinate(self.rank, pt_global)
assert not self.workers_segments.is_contained_coordinate(
self.rank, pt0, inner=True), (pt_global, pt0)
coordinate_exist = self.workers_segments.is_contained_coordinate(
self.rank, pt0, inner=False)
self.coordinate_update(k0, pt0, dz, coordinate_exist=coordinate_exist)
if flags.CHECK_BETA and np.random.rand() > 0.99:
# Only check beta 1% of the time to avoid the check being too long
inner_slice = (Ellipsis, ) + tuple([
slice(start, end)
for start, end in self.local_segments.inner_bounds
])
beta, *_ = _init_beta(self.X_worker,
self.D,
self.reg,
z_i=self.z_hat,
constants=self.constants,
z_positive=self.z_positive)
assert np.allclose(beta[inner_slice], self.beta[inner_slice])
def notify_neighbors(self, msg, neighbors):
assert self.rank in neighbors
for i_neighbor in neighbors:
if i_neighbor != self.rank:
req = self.send_message(msg,
constants.TAG_DICOD_UPDATE_BETA,
i_neighbor,
wait=False)
self.messages.append(req)
def notify_worker_status(self, tag, i_worker=0, wait=False):
# handle the messages from Worker0 to himself.
if self.rank == 0 and i_worker == 0:
if tag == constants.TAG_DICOD_PAUSED_WORKER:
self.n_paused_worker += 1
assert self.n_paused_worker <= self.n_jobs
elif tag == constants.TAG_DICOD_RUNNING_WORKER:
self.n_paused_worker -= 1
assert self.n_paused_worker >= 0
elif tag == constants.TAG_DICOD_INIT_DONE:
pass
else:
raise ValueError("Got tag {}".format(tag))
return
# Else send the message to the required destination
msg = np.empty(self.size_msg, 'd')
self.send_message(msg, tag, i_worker, wait=wait)
def wait_status_changed(self, status=constants.STATUS_PAUSED):
if status == constants.STATUS_FINISHED:
# Make sure to flush the messages
while not self.check_no_transitting_message():
self.process_messages(worker_status=status)
time.sleep(0.001)
self.notify_worker_status(constants.TAG_DICOD_PAUSED_WORKER)
self.debug("paused worker")
# Wait for all sent message to be processed
count = 0
while status not in [constants.STATUS_RUNNING, constants.STATUS_STOP]:
time.sleep(.005)
status = self.process_messages(worker_status=status)
if (count % 500) == 0:
self.progress(self.n_paused_worker,
max_ii=self.n_jobs,
unit="done workers")
if self.rank == 0 and status == constants.STATUS_STOP:
for i_worker in range(1, self.n_jobs):
self.notify_worker_status(constants.TAG_DICOD_STOP,
i_worker,
wait=True)
elif status == constants.STATUS_RUNNING:
self.debug("wake up")
else:
assert status == constants.STATUS_STOP
return status
def compute_sufficient_statistics(self):
_, _, *atom_support = self.D.shape
z_slice = (Ellipsis, ) + tuple([
slice(start, end)
for start, end in self.local_segments.inner_bounds
])
X_slice = (Ellipsis, ) + tuple([
slice(start, end + size_atom_ax - 1)
for (start, end), size_atom_ax in zip(
self.local_segments.inner_bounds, atom_support)
])
ztX = compute_ztX(self.z_hat[z_slice], self.X_worker[X_slice])
padding_shape = self.workers_segments.get_padding_to_overlap(self.rank)
ztz = compute_ztz(self.z_hat,
atom_support,
padding_shape=padding_shape)
return np.array(ztz, dtype='d'), np.array(ztX, dtype='d')
def correct_beta_z0(self):
# Send coordinate updates to neighbors for all nonzero coordinates in
# z0
msg_send, msg_recv = [0] * self.n_jobs, [0] * self.n_jobs
for k0, *pt0 in zip(*self.z0.nonzero()):
# Notify neighboring workers of the update if needed.
pt_global = self.workers_segments.get_global_coordinate(
self.rank, pt0)
workers = self.workers_segments.get_touched_segments(
pt=pt_global, radius=np.array(self.overlap) + 1)
msg = np.array([k0, *pt_global, self.z0[(k0, *pt0)]], 'd')
self.notify_neighbors(msg, workers)
for i in workers:
msg_send[i] += 1
n_init_done = 0
done_pt = set()
no_msg, init_done = False, False
mpi_status = MPI.Status()
while not init_done:
if n_init_done == self.n_jobs:
for i_worker in range(1, self.n_jobs):
self.notify_worker_status(constants.TAG_DICOD_INIT_DONE,
i_worker=i_worker)
init_done = True
if not no_msg:
if self.check_no_transitting_message(check_incoming=False):
self.notify_worker_status(constants.TAG_DICOD_INIT_DONE)
if self.rank == 0:
n_init_done += 1
assert len(self.messages) == 0
no_msg = True
if MPI.COMM_WORLD.Iprobe(status=mpi_status):
tag = mpi_status.tag
src = mpi_status.source
if tag == constants.TAG_DICOD_INIT_DONE:
if self.rank == 0:
n_init_done += 1
else:
init_done = True
msg = np.empty(self.size_msg, 'd')
MPI.COMM_WORLD.Recv([msg, MPI.DOUBLE], source=src, tag=tag)
if tag == constants.TAG_DICOD_UPDATE_BETA:
msg_recv[src] += 1
k0, *pt_global, dz = msg
k0 = int(k0)
pt_global = tuple([int(v) for v in pt_global])
pt0 = self.workers_segments.get_local_coordinate(
self.rank, pt_global)
pt_exist = self.workers_segments.is_contained_coordinate(
self.rank, pt0, inner=False)
if not pt_exist and (k0, *pt0) not in done_pt:
done_pt.add((k0, *pt0))
self.coordinate_update(k0,
pt0,
dz,
coordinate_exist=False)
else:
time.sleep(.001)
def compute_cost(self):
X_hat_worker = reconstruct(self.z_hat, self.D)
inner_bounds = self.local_segments.inner_bounds
inner_slice = tuple(
[Ellipsis] +
[slice(start_ax, end_ax) for start_ax, end_ax in inner_bounds])
X_hat_slice = list(inner_slice)
i_seg = self.rank
ax_rank_offset = self.workers_segments.effective_n_seg
for ax, n_seg_ax in enumerate(self.workers_segments.n_seg_per_axis):
ax_rank_offset //= n_seg_ax
ax_i_seg = i_seg // ax_rank_offset
i_seg % ax_rank_offset
if (ax_i_seg + 1) % n_seg_ax == 0:
s = inner_slice[ax + 1]
X_hat_slice[ax + 1] = slice(s.start, None)
X_hat_slice = tuple(X_hat_slice)
diff = (X_hat_worker[X_hat_slice] - self.X_worker[X_hat_slice]).ravel()
cost = .5 * np.dot(diff, diff)
return cost + self.reg * abs(self.z_hat[inner_slice]).sum()
def return_z_hat(self):
if flags.GET_OVERLAP_Z_HAT:
res_slice = (Ellipsis, )
else:
res_slice = (Ellipsis, ) + tuple([
slice(start, end)
for start, end in self.local_segments.inner_bounds
])
z_worker = self.z_hat[res_slice].ravel()
self.return_array(z_worker)
def return_z_nnz(self):
res_slice = (Ellipsis, ) + tuple([
slice(start, end)
for start, end in self.local_segments.inner_bounds
])
z_nnz = self.z_hat[res_slice] != 0
z_nnz = np.sum(z_nnz, axis=tuple(range(1, z_nnz.ndim)))
self.reduce_sum_array(z_nnz)
def return_sufficient_statistics(self):
ztz, ztX = self.compute_sufficient_statistics()
self.reduce_sum_array(ztz)
self.reduce_sum_array(ztX)
def return_cost(self):
cost = self.compute_cost()
cost = np.array(cost, dtype='d')
self.reduce_sum_array(cost)
###########################################################################
# Display utilities
###########################################################################
def progress(self, ii, max_ii, unit):
t_progress = time.time()
if t_progress - self._last_progress < 1:
return
self._last_progress = t_progress
self._log("{:.0f}s - progress : {:7.2%} {}",
time.time() - self.t_start,
ii / max_ii,
unit,
level=1,
level_name="PROGRESS",
global_msg=True,
endline=False)
def info(self, msg, *fmt_args, global_msg=False, **fmt_kwargs):
self._log(msg,
*fmt_args,
level=1,
level_name="INFO",
global_msg=global_msg,
**fmt_kwargs)
def debug(self, msg, *fmt_args, global_msg=False, **fmt_kwargs):
self._log(msg,
*fmt_args,
level=5,
level_name="DEBUG",
global_msg=global_msg,
**fmt_kwargs)
def _log(self,
msg,
*fmt_args,
level=0,
level_name="None",
global_msg=False,
endline=True,
**fmt_kwargs):
if self.verbose >= level:
if global_msg:
if self.rank != 0:
return
msg_fmt = constants.GLOBAL_OUTPUT_TAG + msg
identity = self.n_jobs
else:
msg_fmt = constants.WORKER_OUTPUT_TAG + msg
identity = self.rank
if endline:
kwargs = {}
else:
kwargs = {'end': '', 'flush': True}
msg_fmt = msg_fmt.ljust(80)
print(
msg_fmt.format(
*fmt_args,
identity=identity,
level_name=level_name,
**fmt_kwargs,
), **kwargs)
###########################################################################
# Communication primitives
###########################################################################
def synchronize_workers(self):
if self._backend == "mpi":
self._synchronize_workers_mpi()
else:
raise NotImplementedError("Backend {} is not implemented".format(
self._backend))
def get_params(self):
"""Receive the parameter of the algorithm from the master node."""
if self._backend == "mpi":
self.rank, self.n_jobs, params = self._get_params_mpi()
else:
raise NotImplementedError("Backend {} is not implemented".format(
self._backend))
self.tol = params['tol']
self.reg = params['reg']
self.n_seg = params['n_seg']
self.timing = params['timing']
self.timeout = params['timeout']
self.verbose = params['verbose']
self.strategy = params['strategy']
self.max_iter = params['max_iter']
self.soft_lock = params['soft_lock']
self.z_positive = params['z_positive']
self.return_ztz = params['return_ztz']
self.freeze_support = params['freeze_support']
self.debug("tol updated to {:.2e}", self.tol, global_msg=True)
return params
def get_signal(self, X_shape, debug=False):
"""Receive the part of the signal to encode from the master node."""
if self._backend == "mpi":
return self._get_signal_mpi(X_shape, debug=debug)
else:
raise NotImplementedError("Backend {} is not implemented".format(
self._backend))
def send_message(self, msg, tag, i_worker, wait=False):
"""Send a message to a specified worker."""
assert self.rank != i_worker
if self._backend == "mpi":
return self._send_message_mpi(msg, tag, i_worker, wait=wait)
else:
raise NotImplementedError("Backend {} is not implemented".format(
self._backend))
def send_result(self, iterations, runtime):
if self._backend == "mpi":
self._send_result_mpi(iterations, runtime)
else:
raise NotImplementedError("Backend {} is not implemented".format(
self._backend))
def get_D(self):
"""Receive a dictionary D"""
if self._backend == "mpi":
comm = MPI.Comm.Get_parent()
self.D = recv_broadcasted_array(comm)
return self.D
else:
raise NotImplementedError("Backend {} is not implemented".format(
self._backend))
def return_array(self, sig):
if self._backend == "mpi":
self._return_array_mpi(sig)
else:
raise NotImplementedError("Backend {} is not implemented".format(
self._backend))
def reduce_sum_array(self, arr):
if self._backend == "mpi":
self._reduce_sum_array_mpi(arr)
else:
raise NotImplementedError("Backend {} is not implemented".format(
self._backend))
def shutdown(self):
if self._backend == "mpi":
self._shutdown_mpi()
else:
raise NotImplementedError("Backend {} is not implemented".format(
self._backend))
###########################################################################
# mpi4py implementation
###########################################################################
def _synchronize_workers_mpi(self):
comm = MPI.Comm.Get_parent()
comm.Barrier()
def check_no_transitting_message(self, check_incoming=True):
"""Check no message is in waiting to complete to or from this worker"""
if check_incoming and MPI.COMM_WORLD.Iprobe():
return False
while self.messages:
if not self.messages[0].Test() or (check_incoming
and MPI.COMM_WORLD.Iprobe()):
return False
self.messages.pop(0)
assert len(self.messages) == 0, len(self.messages)
return True
def _get_params_mpi(self):
comm = MPI.Comm.Get_parent()
rank = comm.Get_rank()
n_jobs = comm.Get_size()
params = comm.bcast(None, root=0)
return rank, n_jobs, params
def _get_signal_mpi(self, sig_shape, debug):
comm = MPI.Comm.Get_parent()
rank = comm.Get_rank()
sig_worker = np.empty(sig_shape, dtype='d')
comm.Recv([sig_worker.ravel(), MPI.DOUBLE],
source=0,
tag=constants.TAG_ROOT + rank)
if debug:
X_alpha = 0.25 * np.ones(sig_shape)
self.return_array(X_alpha)
return sig_worker
def _send_message_mpi(self, msg, tag, i_worker, wait=False):
if wait:
return MPI.COMM_WORLD.Ssend([msg, MPI.DOUBLE], i_worker, tag=tag)
else:
return MPI.COMM_WORLD.Issend([msg, MPI.DOUBLE], i_worker, tag=tag)
def _send_result_mpi(self, iterations, runtime):
comm = MPI.Comm.Get_parent()
self.info("Reducing the distributed results", global_msg=True)
self.return_z_hat()
if self.return_ztz:
self.return_sufficient_statistics()
self.return_cost()
if self.timing:
comm.send(self._log_updates, dest=0)
comm.Barrier()
def _return_array_mpi(self, arr):
comm = MPI.Comm.Get_parent()
arr.astype('d')
comm.Send([arr, MPI.DOUBLE],
dest=0,
tag=constants.TAG_ROOT + self.rank)
def _reduce_sum_array_mpi(self, arr):
comm = MPI.Comm.Get_parent()
arr = np.array(arr, dtype='d')
comm.Reduce([arr, MPI.DOUBLE], None, op=MPI.SUM, root=0)
def _shutdown_mpi(self):
comm = MPI.Comm.Get_parent()
self.debug("clean shutdown")
comm.Barrier()
comm.Disconnect()
def test_inner_coordinate():
sig_support = (505, 407)
overlap = (11, 11)
n_seg = (4, 4)
segments = Segmentation(n_seg=n_seg, signal_support=sig_support,
overlap=overlap)
for h_rank in range(n_seg[0]):
for w_rank in range(n_seg[1]):
i_seg = h_rank * n_seg[1] + w_rank
seg_support = segments.get_seg_support(i_seg)
assert segments.is_contained_coordinate(i_seg, overlap,
inner=True)
if h_rank == 0:
assert segments.is_contained_coordinate(i_seg, (0, overlap[1]),
inner=True)
else:
assert not segments.is_contained_coordinate(
i_seg, (overlap[0] - 1, overlap[1]), inner=True)
if w_rank == 0:
assert segments.is_contained_coordinate(i_seg, (overlap[0], 0),
inner=True)
else:
assert not segments.is_contained_coordinate(
i_seg, (overlap[0], overlap[1] - 1), inner=True)
if h_rank == 0 and w_rank == 0:
assert segments.is_contained_coordinate(i_seg, (0, 0),
inner=True)
else:
assert not segments.is_contained_coordinate(
i_seg, (overlap[0] - 1, overlap[1] - 1), inner=True)
if h_rank == n_seg[0] - 1:
assert segments.is_contained_coordinate(
i_seg,
(seg_support[0] - 1, seg_support[1] - overlap[1] - 1),
inner=True)
else:
assert not segments.is_contained_coordinate(
i_seg, (seg_support[0] - overlap[0],
seg_support[1] - overlap[1] - 1), inner=True)
if w_rank == n_seg[1] - 1:
assert segments.is_contained_coordinate(
i_seg,
(seg_support[0] - overlap[0] - 1, seg_support[1] - 1),
inner=True)
else:
assert not segments.is_contained_coordinate(
i_seg, (seg_support[0] - overlap[0] - 1,
seg_support[1] - overlap[1]), inner=True)
if h_rank == n_seg[0] - 1 and w_rank == n_seg[1] - 1:
assert segments.is_contained_coordinate(
i_seg, (seg_support[0] - 1, seg_support[1] - 1),
inner=True)
else:
assert not segments.is_contained_coordinate(
i_seg, (seg_support[0] - overlap[0],
seg_support[1] - overlap[1]), inner=True)