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#!/usr/bin/env python
"""A rectangular domain partitioner and associated communication
functionality for solving PDEs in (1D,2D) using FDM
written in the python language
The global solution domain is assumed to be of rectangular shape,
where the number of cells in each direction is stored in nx, ny, nz
The numerical scheme is fully explicit
Authors
-------
* Xing Cai
* Min Ragan-Kelley
"""
from numpy import ascontiguousarray, frombuffer, zeros
try:
from mpi4py import MPI
except ImportError:
pass
else:
mpi = MPI.COMM_WORLD
class RectPartitioner:
"""
Responsible for a rectangular partitioning of a global domain,
which is expressed as the numbers of cells in the different
spatial directions. The partitioning info is expressed as an
array of integers, each indicating the number of subdomains in
one spatial direction.
"""
def __init__(self, my_id=-1, num_procs=-1, global_num_cells=[], num_parts=[]):
self.nsd = 0
self.my_id = my_id
self.num_procs = num_procs
self.redim(global_num_cells, num_parts)
def redim(self, global_num_cells, num_parts):
nsd_ = len(global_num_cells)
# print("Inside the redim function, nsd=%d" %nsd_)
if nsd_ < 1 | nsd_ > 3 | nsd_ != len(num_parts):
print('The input global_num_cells is not ok!')
return
self.nsd = nsd_
self.global_num_cells = global_num_cells
self.num_parts = num_parts
def prepare_communication(self):
"""
Find the subdomain rank (tuple) for each processor and
determine the neighbor info.
"""
nsd_ = self.nsd
if nsd_ < 1:
print('Number of space dimensions is %d, nothing to do' % nsd_)
return
self.subd_rank = [-1, -1, -1]
self.subd_lo_ix = [-1, -1, -1]
self.subd_hi_ix = [-1, -1, -1]
self.lower_neighbors = [-1, -1, -1]
self.upper_neighbors = [-1, -1, -1]
num_procs = self.num_procs
my_id = self.my_id
num_subds = 1
for i in range(nsd_):
num_subds = num_subds * self.num_parts[i]
if my_id == 0:
print("# subds=", num_subds)
# should check num_subds againt num_procs
offsets = [1, 0, 0]
# find the subdomain rank
self.subd_rank[0] = my_id % self.num_parts[0]
if nsd_ >= 2:
offsets[1] = self.num_parts[0]
self.subd_rank[1] = my_id / offsets[1]
if nsd_ == 3:
offsets[1] = self.num_parts[0]
offsets[2] = self.num_parts[0] * self.num_parts[1]
self.subd_rank[1] = (my_id % offsets[2]) / self.num_parts[0]
self.subd_rank[2] = my_id / offsets[2]
print("my_id=%d, subd_rank: " % my_id, self.subd_rank)
if my_id == 0:
print("offsets=", offsets)
# find the neighbor ids
for i in range(nsd_):
rank = self.subd_rank[i]
if rank > 0:
self.lower_neighbors[i] = my_id - offsets[i]
if rank < self.num_parts[i] - 1:
self.upper_neighbors[i] = my_id + offsets[i]
k = self.global_num_cells[i] / self.num_parts[i]
m = self.global_num_cells[i] % self.num_parts[i]
ix = rank * k + max(0, rank + m - self.num_parts[i])
self.subd_lo_ix[i] = ix
ix = ix + k
if rank >= (self.num_parts[i] - m):
ix = ix + 1 # load balancing
if rank < self.num_parts[i] - 1:
ix = ix + 1 # one cell of overlap
self.subd_hi_ix[i] = ix
print(
"subd_rank:",
self.subd_rank,
"lower_neig:",
self.lower_neighbors,
"upper_neig:",
self.upper_neighbors,
)
print(
"subd_rank:",
self.subd_rank,
"subd_lo_ix:",
self.subd_lo_ix,
"subd_hi_ix:",
self.subd_hi_ix,
)
class RectPartitioner1D(RectPartitioner):
"""
Subclass of RectPartitioner, for 1D problems
"""
def prepare_communication(self):
"""
Prepare the buffers to be used for later communications
"""
RectPartitioner.prepare_communication(self)
if self.lower_neighbors[0] >= 0:
self.in_lower_buffers = [zeros(1, float)]
self.out_lower_buffers = [zeros(1, float)]
if self.upper_neighbors[0] >= 0:
self.in_upper_buffers = [zeros(1, float)]
self.out_upper_buffers = [zeros(1, float)]
def get_num_loc_cells(self):
return [self.subd_hi_ix[0] - self.subd_lo_ix[0]]
class RectPartitioner2D(RectPartitioner):
"""
Subclass of RectPartitioner, for 2D problems
"""
def prepare_communication(self):
"""
Prepare the buffers to be used for later communications
"""
RectPartitioner.prepare_communication(self)
self.in_lower_buffers = [[], []]
self.out_lower_buffers = [[], []]
self.in_upper_buffers = [[], []]
self.out_upper_buffers = [[], []]
size1 = self.subd_hi_ix[1] - self.subd_lo_ix[1] + 1
if self.lower_neighbors[0] >= 0:
self.in_lower_buffers[0] = zeros(size1, float)
self.out_lower_buffers[0] = zeros(size1, float)
if self.upper_neighbors[0] >= 0:
self.in_upper_buffers[0] = zeros(size1, float)
self.out_upper_buffers[0] = zeros(size1, float)
size0 = self.subd_hi_ix[0] - self.subd_lo_ix[0] + 1
if self.lower_neighbors[1] >= 0:
self.in_lower_buffers[1] = zeros(size0, float)
self.out_lower_buffers[1] = zeros(size0, float)
if self.upper_neighbors[1] >= 0:
self.in_upper_buffers[1] = zeros(size0, float)
self.out_upper_buffers[1] = zeros(size0, float)
def get_num_loc_cells(self):
return [
self.subd_hi_ix[0] - self.subd_lo_ix[0],
self.subd_hi_ix[1] - self.subd_lo_ix[1],
]
class MPIRectPartitioner2D(RectPartitioner2D):
"""
Subclass of RectPartitioner2D, which uses MPI via mpi4py for communication
"""
def __init__(
self, my_id=-1, num_procs=-1, global_num_cells=[], num_parts=[], slice_copy=True
):
RectPartitioner.__init__(self, my_id, num_procs, global_num_cells, num_parts)
self.slice_copy = slice_copy
def update_internal_boundary(self, solution_array):
nsd_ = self.nsd
if nsd_ != len(self.in_lower_buffers) | nsd_ != len(self.out_lower_buffers):
print("Buffers for communicating with lower neighbors not ready")
return
if nsd_ != len(self.in_upper_buffers) | nsd_ != len(self.out_upper_buffers):
print("Buffers for communicating with upper neighbors not ready")
return
loc_nx = self.subd_hi_ix[0] - self.subd_lo_ix[0]
loc_ny = self.subd_hi_ix[1] - self.subd_lo_ix[1]
lower_x_neigh = self.lower_neighbors[0]
upper_x_neigh = self.upper_neighbors[0]
lower_y_neigh = self.lower_neighbors[1]
upper_y_neigh = self.upper_neighbors[1]
# communicate in the x-direction first
if lower_x_neigh > -1:
if self.slice_copy:
self.out_lower_buffers[0] = ascontiguousarray(solution_array[1, :])
else:
for i in range(0, loc_ny + 1):
self.out_lower_buffers[0][i] = solution_array[1, i]
mpi.Isend(self.out_lower_buffers[0], lower_x_neigh)
if upper_x_neigh > -1:
mpi.Recv(self.in_upper_buffers[0], upper_x_neigh)
if self.slice_copy:
solution_array[loc_nx, :] = self.in_upper_buffers[0]
self.out_upper_buffers[0] = ascontiguousarray(
solution_array[loc_nx - 1, :]
)
else:
for i in range(0, loc_ny + 1):
solution_array[loc_nx, i] = self.in_upper_buffers[0][i]
self.out_upper_buffers[0][i] = solution_array[loc_nx - 1, i]
mpi.Isend(self.out_upper_buffers[0], upper_x_neigh)
if lower_x_neigh > -1:
mpi.Recv(self.in_lower_buffers[0], lower_x_neigh)
if self.slice_copy:
solution_array[0, :] = self.in_lower_buffers[0]
else:
for i in range(0, loc_ny + 1):
solution_array[0, i] = self.in_lower_buffers[0][i]
# communicate in the y-direction afterwards
if lower_y_neigh > -1:
if self.slice_copy:
self.out_lower_buffers[1] = ascontiguousarray(solution_array[:, 1])
else:
for i in range(0, loc_nx + 1):
self.out_lower_buffers[1][i] = solution_array[i, 1]
mpi.Isend(self.out_lower_buffers[1], lower_y_neigh)
if upper_y_neigh > -1:
mpi.Recv(self.in_upper_buffers[1], upper_y_neigh)
if self.slice_copy:
solution_array[:, loc_ny] = self.in_upper_buffers[1]
self.out_upper_buffers[1] = ascontiguousarray(
solution_array[:, loc_ny - 1]
)
else:
for i in range(0, loc_nx + 1):
solution_array[i, loc_ny] = self.in_upper_buffers[1][i]
self.out_upper_buffers[1][i] = solution_array[i, loc_ny - 1]
mpi.Isend(self.out_upper_buffers[1], upper_y_neigh)
if lower_y_neigh > -1:
mpi.Recv(self.in_lower_buffers[1], lower_y_neigh)
if self.slice_copy:
solution_array[:, 0] = self.in_lower_buffers[1]
else:
for i in range(0, loc_nx + 1):
solution_array[i, 0] = self.in_lower_buffers[1][i]
class ZMQRectPartitioner2D(RectPartitioner2D):
"""
Subclass of RectPartitioner2D, which uses 0MQ via pyzmq for communication
The first two arguments must be `comm`, an EngineCommunicator object,
and `addrs`, a dict of connection information for other EngineCommunicator
objects.
"""
def __init__(
self,
comm,
addrs,
my_id=-1,
num_procs=-1,
global_num_cells=[],
num_parts=[],
slice_copy=True,
):
RectPartitioner.__init__(self, my_id, num_procs, global_num_cells, num_parts)
self.slice_copy = slice_copy
self.comm = comm # an Engine
self.addrs = addrs
def prepare_communication(self):
RectPartitioner2D.prepare_communication(self)
# connect west/south to east/north
west_id, south_id = self.lower_neighbors[:2]
west = self.addrs.get(west_id, None)
south = self.addrs.get(south_id, None)
self.comm.connect(south, west)
def update_internal_boundary_x_y(self, solution_array):
"""update the inner boundary with the same send/recv pattern as the MPIPartitioner"""
nsd_ = self.nsd
dtype = solution_array.dtype
if nsd_ != len(self.in_lower_buffers) | nsd_ != len(self.out_lower_buffers):
print("Buffers for communicating with lower neighbors not ready")
return
if nsd_ != len(self.in_upper_buffers) | nsd_ != len(self.out_upper_buffers):
print("Buffers for communicating with upper neighbors not ready")
return
loc_nx = self.subd_hi_ix[0] - self.subd_lo_ix[0]
loc_ny = self.subd_hi_ix[1] - self.subd_lo_ix[1]
lower_x_neigh = self.lower_neighbors[0]
upper_x_neigh = self.upper_neighbors[0]
lower_y_neigh = self.lower_neighbors[1]
upper_y_neigh = self.upper_neighbors[1]
trackers = []
flags = dict(copy=False, track=False)
# communicate in the x-direction first
if lower_x_neigh > -1:
if self.slice_copy:
self.out_lower_buffers[0] = ascontiguousarray(solution_array[1, :])
else:
for i in range(0, loc_ny + 1):
self.out_lower_buffers[0][i] = solution_array[1, i]
t = self.comm.west.send(self.out_lower_buffers[0], **flags)
trackers.append(t)
if upper_x_neigh > -1:
msg = self.comm.east.recv(copy=False)
self.in_upper_buffers[0] = frombuffer(msg, dtype=dtype)
if self.slice_copy:
solution_array[loc_nx, :] = self.in_upper_buffers[0]
self.out_upper_buffers[0] = ascontiguousarray(
solution_array[loc_nx - 1, :]
)
else:
for i in range(0, loc_ny + 1):
solution_array[loc_nx, i] = self.in_upper_buffers[0][i]
self.out_upper_buffers[0][i] = solution_array[loc_nx - 1, i]
t = self.comm.east.send(self.out_upper_buffers[0], **flags)
trackers.append(t)
if lower_x_neigh > -1:
msg = self.comm.west.recv(copy=False)
self.in_lower_buffers[0] = frombuffer(msg, dtype=dtype)
if self.slice_copy:
solution_array[0, :] = self.in_lower_buffers[0]
else:
for i in range(0, loc_ny + 1):
solution_array[0, i] = self.in_lower_buffers[0][i]
# communicate in the y-direction afterwards
if lower_y_neigh > -1:
if self.slice_copy:
self.out_lower_buffers[1] = ascontiguousarray(solution_array[:, 1])
else:
for i in range(0, loc_nx + 1):
self.out_lower_buffers[1][i] = solution_array[i, 1]
t = self.comm.south.send(self.out_lower_buffers[1], **flags)
trackers.append(t)
if upper_y_neigh > -1:
msg = self.comm.north.recv(copy=False)
self.in_upper_buffers[1] = frombuffer(msg, dtype=dtype)
if self.slice_copy:
solution_array[:, loc_ny] = self.in_upper_buffers[1]
self.out_upper_buffers[1] = ascontiguousarray(
solution_array[:, loc_ny - 1]
)
else:
for i in range(0, loc_nx + 1):
solution_array[i, loc_ny] = self.in_upper_buffers[1][i]
self.out_upper_buffers[1][i] = solution_array[i, loc_ny - 1]
t = self.comm.north.send(self.out_upper_buffers[1], **flags)
trackers.append(t)
if lower_y_neigh > -1:
msg = self.comm.south.recv(copy=False)
self.in_lower_buffers[1] = frombuffer(msg, dtype=dtype)
if self.slice_copy:
solution_array[:, 0] = self.in_lower_buffers[1]
else:
for i in range(0, loc_nx + 1):
solution_array[i, 0] = self.in_lower_buffers[1][i]
# wait for sends to complete:
if flags['track']:
for t in trackers:
t.wait()
def update_internal_boundary_send_recv(self, solution_array):
"""update the inner boundary, sending first, then receiving"""
nsd_ = self.nsd
dtype = solution_array.dtype
if nsd_ != len(self.in_lower_buffers) | nsd_ != len(self.out_lower_buffers):
print("Buffers for communicating with lower neighbors not ready")
return
if nsd_ != len(self.in_upper_buffers) | nsd_ != len(self.out_upper_buffers):
print("Buffers for communicating with upper neighbors not ready")
return
loc_nx = self.subd_hi_ix[0] - self.subd_lo_ix[0]
loc_ny = self.subd_hi_ix[1] - self.subd_lo_ix[1]
lower_x_neigh = self.lower_neighbors[0]
upper_x_neigh = self.upper_neighbors[0]
lower_y_neigh = self.lower_neighbors[1]
upper_y_neigh = self.upper_neighbors[1]
trackers = []
flags = dict(copy=False, track=False)
# send in all directions first
if lower_x_neigh > -1:
if self.slice_copy:
self.out_lower_buffers[0] = ascontiguousarray(solution_array[1, :])
else:
for i in range(0, loc_ny + 1):
self.out_lower_buffers[0][i] = solution_array[1, i]
t = self.comm.west.send(self.out_lower_buffers[0], **flags)
trackers.append(t)
if lower_y_neigh > -1:
if self.slice_copy:
self.out_lower_buffers[1] = ascontiguousarray(solution_array[:, 1])
else:
for i in range(0, loc_nx + 1):
self.out_lower_buffers[1][i] = solution_array[i, 1]
t = self.comm.south.send(self.out_lower_buffers[1], **flags)
trackers.append(t)
if upper_x_neigh > -1:
if self.slice_copy:
self.out_upper_buffers[0] = ascontiguousarray(
solution_array[loc_nx - 1, :]
)
else:
for i in range(0, loc_ny + 1):
self.out_upper_buffers[0][i] = solution_array[loc_nx - 1, i]
t = self.comm.east.send(self.out_upper_buffers[0], **flags)
trackers.append(t)
if upper_y_neigh > -1:
if self.slice_copy:
self.out_upper_buffers[1] = ascontiguousarray(
solution_array[:, loc_ny - 1]
)
else:
for i in range(0, loc_nx + 1):
self.out_upper_buffers[1][i] = solution_array[i, loc_ny - 1]
t = self.comm.north.send(self.out_upper_buffers[1], **flags)
trackers.append(t)
# now start receiving
if upper_x_neigh > -1:
msg = self.comm.east.recv(copy=False)
self.in_upper_buffers[0] = frombuffer(msg, dtype=dtype)
if self.slice_copy:
solution_array[loc_nx, :] = self.in_upper_buffers[0]
else:
for i in range(0, loc_ny + 1):
solution_array[loc_nx, i] = self.in_upper_buffers[0][i]
if lower_x_neigh > -1:
msg = self.comm.west.recv(copy=False)
self.in_lower_buffers[0] = frombuffer(msg, dtype=dtype)
if self.slice_copy:
solution_array[0, :] = self.in_lower_buffers[0]
else:
for i in range(0, loc_ny + 1):
solution_array[0, i] = self.in_lower_buffers[0][i]
if upper_y_neigh > -1:
msg = self.comm.north.recv(copy=False)
self.in_upper_buffers[1] = frombuffer(msg, dtype=dtype)
if self.slice_copy:
solution_array[:, loc_ny] = self.in_upper_buffers[1]
else:
for i in range(0, loc_nx + 1):
solution_array[i, loc_ny] = self.in_upper_buffers[1][i]
if lower_y_neigh > -1:
msg = self.comm.south.recv(copy=False)
self.in_lower_buffers[1] = frombuffer(msg, dtype=dtype)
if self.slice_copy:
solution_array[:, 0] = self.in_lower_buffers[1]
else:
for i in range(0, loc_nx + 1):
solution_array[i, 0] = self.in_lower_buffers[1][i]
# wait for sends to complete:
if flags['track']:
for t in trackers:
t.wait()
# use send/recv pattern instead of x/y sweeps
update_internal_boundary = update_internal_boundary_send_recv
|
