# remove exported and ghost particles
pa.remove_particles(exportLocalids)
# place incoming particles at the end of the array
# after resizing
displacement = pa.get_number_of_particles()
# how many particles are being sent from each process
recv_particles = np.empty(size, dtype=np.int32)
comm.Alltoall(sendbuf=send_particles, recvbuf=recv_particles)
# resize arrays to give room for incoming particles and update
# the new number of real particles in the container
num_incoming_particles = np.sum(recv_particles)
pa.extend(num_incoming_particles)
exchange_particles(pa, send_data, send_particles, recv_particles, displacement,
comm)
# after the exchange each proc should have 6 particles except for proc 0
numParticles = 6
if rank == 0:
numParticles = 7
assert (pa.get_number_of_particles() == numParticles)
for i in xrange(pa.get_number_of_particles()):
assert (abs(X[pa['gid'][i]] - pa['position-x'][i]) < 1e-15)
assert (abs(Y[pa['gid'][i]] - pa['position-y'][i]) < 1e-15)
assert (GID[pa['gid'][i]] == pa['gid'][i])
def create_ghost_particles(self, particles, mesh, domain, load_balance, comm, iteration=6):
"""Create initial ghost particles that hug the boundary after
load balance
"""
rank = comm.Get_rank()
size = comm.Get_size()
# remove current (if any) ghost particles
particles.remove_tagged_particles(ParticleTAGS.Ghost)
current_size = particles.get_number_of_particles()
# create initial ghost particles, particles is now larger
# these particles are centered in neighboring boundary leaf
# cells of the octree
load_balance.create_boundary_particles(particles, rank)
# reorder ghost in processors order: exterior have a process id of -1 so
# their put before interior ghost particles
ghost_proc = np.array(particles["process"][current_size:])
ind = np.argsort(ghost_proc)
ghost_proc = ghost_proc[ind]
for field in particles.properties.keys():
array = particles[field][current_size:]
array[:] = array[ind]
# allocate arrays for boundary indices
indices = LongArray()
corner_ghost = ParticleContainer()
# sides
boundary_indices = {
"left" : LongArray(),
"right" : LongArray(),
"bottom" : LongArray(),
"top" : LongArray(),
"left-top" : LongArray(),
"left-bottom" : LongArray(),
"right-top" : LongArray(),
"right-bottom" : LongArray()
}
send_particles = np.zeros(size, dtype=np.int32)
recv_particles = np.zeros(size, dtype=np.int32)
# create ghost interior and exterior particles by iteration, using
# the mesh to extract the needed neighbors
for i in range(iteration):
# build the mesh
mesh.tessellate()
cumsum_neighbors = mesh["number of neighbors"].cumsum()
#---------- create exterior ghost particles ----------#
# create indices for ghost particles
ghost_indices = np.arange(current_size, particles.get_number_of_particles())
# label current ghost as old ghost
particles['tag'][ghost_indices] = ParticleTAGS.OldGhost
# select exterior ghost particles
exterior_ghost = ghost_proc == -1
exterior_ghost_indices = ghost_indices[exterior_ghost]
if np.sum(exterior_ghost_indices) > 0:
num_exterior_ghost = create_reflect_ghost(particles, boundary_indices,
domain, exterior_ghost_indices, ghost_indices,
mesh['neighbors'], mesh['number of neighbors'], cumsum_neighbors, -1)
#---------- create interior ghost particles ----------#
interior_ghost_indices = ghost_indices[~exterior_ghost]
interior_ghost_proc = ghost_proc[~exterior_ghost]
# bin processors - they are in order
interior_ghost_proc_bin = np.bincount(interior_ghost_proc, minlength=size)
send_particles[:] = 0
recv_particles[:] = 0
indices.reset()
# collect the indices of particles to be export to each process
cumsum_proc = interior_ghost_proc_bin.cumsum()
for proc in range(size):
if interior_ghost_proc_bin[proc] != 0:
start = cumsum_proc[proc] - interior_ghost_proc_bin[proc]
end = cumsum_proc[proc]
send_particles[proc] = find_boundary_particles(indices, interior_ghost_indices[start:end], ghost_indices,
mesh['neighbors'], mesh['number of neighbors'], cumsum_neighbors, False)
# extract data to send and remove the particles
send_data = {}
for prop in particles.properties.keys():
send_data[prop] = np.ascontiguousarray(particles[prop][indices.get_npy_array()])
send_data["tag"][:] = ParticleTAGS.Ghost
# how many particles are being sent from each process
comm.Alltoall(sendbuf=send_particles, recvbuf=recv_particles)
num_interior_ghost = np.sum(recv_particles)
# resize arrays to give room for incoming particles
sp = particles.get_number_of_particles()
#particles.resize(current_size + num_exterior_ghost + num_interior_ghost)
particles.extend(num_interior_ghost)
exchange_particles(particles, send_data, send_particles, recv_particles,
sp, comm)
#---------- create exterior corner ghost particles ----------#
indices.reset()
send_particles[:] = 0
recv_particles[:] = 0
# clear out corner ghost
corner_ghost.resize(0)
if boundary_indices['left'].length > 0:
export_reflect(particles, corner_ghost, boundary_indices["left"], indices, send_particles, 'x', domain.xmin, ghost_indices,
mesh['neighbors'], mesh['number of neighbors'], cumsum_neighbors, load_balance, current_size, rank, size)
if boundary_indices['right'].length > 0:
export_reflect(particles, corner_ghost, boundary_indices["right"], indices, send_particles, 'x', domain.xmax, ghost_indices,
mesh['neighbors'], mesh['number of neighbors'], cumsum_neighbors, load_balance, current_size, rank, size)
if boundary_indices['bottom'].length > 0:
export_reflect(particles, corner_ghost, boundary_indices["bottom"], indices, send_particles, 'y', domain.ymin, ghost_indices,
mesh['neighbors'], mesh['number of neighbors'], cumsum_neighbors, load_balance, current_size, rank, size)
if boundary_indices['top'].length > 0:
export_reflect(particles, corner_ghost, boundary_indices["top"], indices, send_particles, 'y', domain.ymax, ghost_indices,
mesh['neighbors'], mesh['number of neighbors'], cumsum_neighbors, load_balance, current_size, rank, size)
#print rank, current_size, particles.get_number_of_particles(), current_size + num_exterior_ghost + num_interior_ghost
sp = particles.get_number_of_particles()
comm.Alltoall(sendbuf=send_particles, recvbuf=recv_particles)
particles.extend(np.sum(recv_particles))
# to export corners have to be reorderd by process
if corner_ghost.get_number_of_particles() > 0:
ind = np.argsort(corner_ghost['process'])
for field in corner_ghost.properties.keys():
array = corner_ghost[field]
array[:] = array[ind]
corner_ghost["process"][:] = -1
# exchange patch corners
exchange_particles(particles, corner_ghost, send_particles, recv_particles,
sp, comm)
for bd in boundary_indices:
boundary_indices[bd].reset()
particles.remove_tagged_particles(ParticleTAGS.OldGhost)
# put particles in process order for next loop
ind = np.argsort(particles["process"][current_size:])
for field in particles.properties.keys():
array = particles[field][current_size:]
array[:] = array[ind]
ghost_proc = np.array(particles["process"][current_size:])
print 'rank:', rank, 'fraction of real to ghost:', (particles.get_number_of_particles()-current_size)*1.0/particles.get_number_of_particles()
def update_ghost_particles(self, particles, mesh, domain, load_balance, comm):
rank = comm.Get_rank()
size = comm.Get_size()
# allocate arrays for boundary indices
indices = LongArray()
corner_ghost = ParticleContainer()
send_particles = np.zeros(size, dtype=np.int32)
recv_particles = np.zeros(size, dtype=np.int32)
# we are puting new ghost at the end of the array
current_size = particles.get_number_of_particles()
boundary_indices = {
"left" : LongArray(),
"right" : LongArray(),
"bottom" : LongArray(),
"top" : LongArray(),
"left-top" : LongArray(),
"left-bottom" : LongArray(),
"right-top" : LongArray(),
"right-bottom" : LongArray()
}
# relabel all particles
particles["tag"][:] = ParticleTAGS.Undefined
particles["type"][:] = ParticleTAGS.Undefined
# flag particles that have left the domain and particles
# that remained
load_balance.flag_migrate_particles(particles, rank)
# find particles that have left the domain
export_indices = np.where(particles["type"] == ParticleTAGS.ExportInterior)[0]
if export_indices.size > 0:
# extract export particles
export_particles = particles.extract_items(export_indices)
# put particles in process order
ind = np.argsort(export_particles["process"])
for field in export_particles.properties.keys():
array = export_particles[field]
array[:] = array[ind]
export_particles["tag"][:] = ParticleTAGS.Real
export_particles["type"][:] = ParticleTAGS.Undefined
else:
export_particles = ParticleContainer()
# bin particle process
send_particles[:] = np.bincount(export_particles["process"], minlength=size)
# how many particles are being sent from each process
comm.Alltoall(sendbuf=send_particles, recvbuf=recv_particles)
# create container for incoming particles
import_particles = ParticleContainer(np.sum(recv_particles))
exchange_particles(import_particles, export_particles, send_particles, recv_particles,
0, comm)
# copy import particle data to ghost place holders and turn to real particles
migrate.transfer_migrate_particles(particles, import_particles)
# flag export particles back to interior ghost particles
particles["type"][export_indices] = ParticleTAGS.Interior
ghost_indices = np.where(particles["tag"] == ParticleTAGS.OldGhost)[0]
# find indices of interior/exterior ghost particles
cumsum_neighbors = mesh["number of neighbors"].cumsum()
exterior_ghost_indices = np.where(particles["type"] == ParticleTAGS.Exterior)[0]
interior_ghost_indices = np.where(particles["type"] == ParticleTAGS.Interior)[0]
#---------- create exterior ghost particles ----------#
num_exterior_ghost = 0
if exterior_ghost_indices.size > 0:
num_exterior_ghost = create_reflect_ghost(particles, boundary_indices,
domain, exterior_ghost_indices, ghost_indices,
mesh['neighbors'], mesh['number of neighbors'], cumsum_neighbors, -1)
#---------- create interior ghost particles ----------#
send_particles[:] = 0
recv_particles[:] = 0
interior_ghost_proc = particles["process"][interior_ghost_indices]
# arrange particles in process order
ind = interior_ghost_proc.argsort()
interior_ghost_proc = interior_ghost_proc[ind]
interior_ghost_indices = interior_ghost_indices[ind]
# bin processors
interior_ghost_proc_bin = np.bincount(interior_ghost_proc, minlength=size)
cumsum_neighbors = mesh["number of neighbors"].cumsum()
# collect the indices of particles to be export to each process
cumsum_proc = interior_ghost_proc_bin.cumsum()
for proc in range(size):
if interior_ghost_proc_bin[proc] != 0:
start = cumsum_proc[proc] - interior_ghost_proc_bin[proc]
end = cumsum_proc[proc]
send_particles[proc] = find_boundary_particles(indices, interior_ghost_indices[start:end], ghost_indices,
mesh['neighbors'], mesh['number of neighbors'], cumsum_neighbors, False)
# extract data to send and remove the particles
send_data = {}
for prop in particles.properties.keys():
send_data[prop] = np.ascontiguousarray(particles[prop][indices.get_npy_array()])
send_data["tag"][:] = ParticleTAGS.Ghost
# how many particles are being sent from each process
comm.Alltoall(sendbuf=send_particles, recvbuf=recv_particles)
num_interior_ghost = np.sum(recv_particles)
# resize arrays to give room for incoming particles
sp = particles.get_number_of_particles()
particles.extend(num_interior_ghost)
exchange_particles(particles, send_data, send_particles, recv_particles,
sp, comm)
#---------- create exterior corner ghost particles ----------#
indices.reset()
send_particles[:] = 0
recv_particles[:] = 0
if boundary_indices['left'].length > 0:
export_reflect(particles, corner_ghost, boundary_indices["left"], indices, send_particles, 'x', domain.xmin, ghost_indices,
mesh['neighbors'], mesh['number of neighbors'], cumsum_neighbors, load_balance, current_size, rank, size)
if boundary_indices['right'].length > 0:
export_reflect(particles, corner_ghost, boundary_indices["right"], indices, send_particles, 'x', domain.xmax, ghost_indices,
mesh['neighbors'], mesh['number of neighbors'], cumsum_neighbors, load_balance, current_size, rank, size)
if boundary_indices['bottom'].length > 0:
export_reflect(particles, corner_ghost, boundary_indices["bottom"], indices, send_particles, 'y', domain.ymin, ghost_indices,
mesh['neighbors'], mesh['number of neighbors'], cumsum_neighbors, load_balance, current_size, rank, size)
if boundary_indices['top'].length > 0:
export_reflect(particles, corner_ghost, boundary_indices["top"], indices, send_particles, 'y', domain.ymax, ghost_indices,
mesh['neighbors'], mesh['number of neighbors'], cumsum_neighbors, load_balance, current_size, rank, size)
comm.Alltoall(sendbuf=send_particles, recvbuf=recv_particles)
sp = particles.get_number_of_particles()
particles.extend(np.sum(recv_particles))
# to export corners have to be reorderd by process
if corner_ghost.get_number_of_particles() > 0:
ind = np.argsort(corner_ghost['process'])
for field in corner_ghost.properties.keys():
array = corner_ghost[field]
array[:] = array[ind]
corner_ghost["process"][:] = -1
# exchange patch corners
exchange_particles(particles, corner_ghost, send_particles, recv_particles,
sp, comm)
# finally remove old ghost particles from previous time step
# and also put real particles in front and ghost in the back
particles.remove_tagged_particles(ParticleTAGS.OldGhost)
particles.align_particles()
particles['type'][:] = ParticleTAGS.Undefined
def decomposition(self):
"""Perform domain decomposition
"""
# remove current (if any) ghost particles
self.particles.remove_tagged_particles(ParticleTAGS.Ghost)
# generate hilbert keys for real particles and create
# global tree over all process
calculate_hilbert_keys()
self.calculate_hilbert_keys()
global_tree = self.build_global_tree()
# partion tree leaves by the amount work done
# in each leaf
self.calculate_global_work(global_tree)
self.find_split_in_work()
# count the number of particles that need to be exported
num_export = global_tree.count_particles_export(
self.keys, self.leaf_proc, self.rank)
self.export_ids = np.empty(num_export, dtype=np.int32)
self.export_proc = np.empty(num_export, dtype=np.int32)
# collect particles to be exported with their process location
global_tree.collect_particles_export(self.keys, self.export_ids,
self.export_proc, self.leaf_proc,
self.rank)
# arrange particles in process order
ind = self.export_proc.argsort()
self.export_proc = self.export_proc[ind]
self.export_ids = self.export_ids[ind]
# count the number of particles to send to each process
send_particles = np.bincount(self.export_proc,
minlength=self.size).astype(np.int32)
# extract particles to send
send_data = self.particles.get_sendbufs(self.export_ids)
# remove exported particles
self.particles.remove_items(self.export_ids)
# how many particles are being sent from each process
recv_particles = np.empty(self.size, dtype=np.int32)
self.comm.Alltoall(sendbuf=send_particles, recvbuf=recv_particles)
# resize particle array and place incoming particles at the
# end of the array
displacement = self.particles.get_number_of_particles()
num_incoming_particles = np.sum(recv_particles)
self.particles.extend(num_incoming_particles)
# exchange load balance particles
exchange_particles(self.particles, send_data, send_particles,
recv_particles, displacement, self.comm)
# align particles and count the number of real particles
self.particles.align_particles()
# label all new particles to current process
self.particles['process'][:] = self.rank
self.global_tree = global_tree