def run(self, mbs, x, y):
# setup system
sim.setup(model_binary_module=(
speed_tracker_with_protocol_search_c_code_version))
# build verts
reader = SDRAMReaderAndTransmitterWithProtocol(mbs)
reader.add_constraint(ChipAndCoreConstraint(x=x, y=y))
receiver = PacketGathererWithProtocol()
# add verts to graph
sim.add_machine_vertex_instance(reader)
sim.add_machine_vertex_instance(receiver)
# build and add edge to graph
sim.add_machine_edge_instance(MachineEdge(reader, receiver),
"TRANSMIT")
machine = sim.machine()
if machine.is_chip_at(x, y):
return self._do_run(reader, receiver, mbs)
else:
sim.stop()
return None, False, False, "", 0
def _get_gatherer_for_monitor(monitor):
placement = sim.placements().get_placement_of_vertex(monitor)
chip = sim.machine().get_chip_at(placement.x, placement.y)
the_sim = sim.globals_variables.get_simulator()
# pylint: disable=protected-access
gatherers = the_sim._vertex_to_ethernet_connected_chip_mapping
return (gatherers, gatherers[chip.nearest_ethernet_x,
chip.nearest_ethernet_y])
def _get_gatherer_for_monitor(monitor):
placement = sim.placements().get_placement_of_vertex(monitor)
chip = sim.machine().get_chip_at(placement.x, placement.y)
the_sim = sim.globals_variables.get_simulator()
# pylint: disable=protected-access
gatherers = the_sim._last_run_outputs[_GATHERER_MAP]
return (gatherers, gatherers[chip.nearest_ethernet_x,
chip.nearest_ethernet_y])
def run(self, mbs):
# setup system
sim.setup(model_binary_module=test_extra_monitor_core_data_extraction,
n_chips_required=2)
# build verts
writer = SDRAMWriter(mbs)
# add verts to graph
sim.add_machine_vertex_instance(writer)
sim.run(12)
# get placements for extraction
placements = sim.placements()
machine = sim.machine()
writer_placement = placements.get_placement_of_vertex(writer)
writer_chip = \
machine.get_chip_at(writer_placement.x, writer_placement.y)
writer_nearest_ethernet = machine.get_chip_at(
writer_chip.nearest_ethernet_x, writer_chip.nearest_ethernet_y)
extra_monitor_vertices = sim.globals_variables.\
get_simulator()._last_run_outputs['MemoryExtraMonitorVertices']
extra_monitor_gatherers = sim.globals_variables.\
get_simulator()._last_run_outputs[
'MemoryMCGatherVertexToEthernetConnectedChipMapping']
receiver = None
gatherer = extra_monitor_gatherers[(writer_nearest_ethernet.x,
writer_nearest_ethernet.y)]
for vertex in extra_monitor_vertices:
placement = placements.get_placement_of_vertex(vertex)
if (placement.x == writer_placement.x
and placement.y == writer_placement.y):
receiver = vertex
start = float(time.time())
gatherer.set_cores_for_data_extraction(sim.transceiver(),
extra_monitor_vertices,
placements)
data = gatherer.get_data(
sim.transceiver(), placements.get_placement_of_vertex(receiver),
self._get_data_region_address(sim.transceiver(), writer_placement),
writer.mbs_in_bytes)
gatherer.unset_cores_for_data_extraction(sim.transceiver(),
extra_monitor_vertices,
placements)
end = float(time.time())
print("time taken to extract {} MB is {}. MBS of {}".format(
mbs, end - start, (mbs * 8) / (end - start)))
self._check_data(data)
def run(self, mbs, number_of_repeats):
# setup system
sim.setup(model_binary_module=(
test_extra_monitor_core_data_extraction_multiple_locations),
n_chips_required=49 * 2)
# build vertices
locs = [(0, 0), (2, 2), (7, 7), (3, 0), (1, 0), (0, 1), (3, 3), (4, 4),
(5, 5), (3, 5), (4, 0), (7, 4), (8, 4), (4, 8), (11, 11),
(11, 0), (0, 11), (6, 3), (0, 6)]
writers = list()
for chip_x, chip_y in locs:
writer = SDRAMWriter(mbs,
constraint=ChipAndCoreConstraint(
chip_x, chip_y))
# add vertices to graph
sim.add_machine_vertex_instance(writer)
writers.append(writer)
sim.run(12)
# get placements for extraction
placements = sim.placements()
machine = sim.machine()
extra_monitor_vertices = sim.globals_variables. \
get_simulator()._last_run_outputs[
'MemoryExtraMonitorVertices']
extra_monitor_gatherers = sim.globals_variables. \
get_simulator()._last_run_outputs[
'MemoryMCGatherVertexToEthernetConnectedChipMapping']
time_out_setter = extra_monitor_gatherers[(0, 0)]
time_out_setter.set_cores_for_data_extraction(sim.transceiver(),
extra_monitor_vertices,
placements)
for _ in range(0, number_of_repeats):
for writer in writers:
writer_placement = placements.get_placement_of_vertex(writer)
writer_chip = \
machine.get_chip_at(writer_placement.x, writer_placement.y)
writer_nearest_ethernet = machine.get_chip_at(
writer_chip.nearest_ethernet_x,
writer_chip.nearest_ethernet_y)
receiver = None
gatherer = extra_monitor_gatherers[(writer_nearest_ethernet.x,
writer_nearest_ethernet.y)]
for vertex in extra_monitor_vertices:
placement = placements.get_placement_of_vertex(vertex)
if (placement.x == writer_placement.x
and placement.y == writer_placement.y):
receiver = vertex
start = float(time.time())
data = gatherer.get_data(
sim.transceiver(),
placements.get_placement_of_vertex(receiver),
self._get_data_region_address(sim.transceiver(),
writer_placement),
writer.mbs_in_bytes)
end = float(time.time())
print("time taken to extract {} MB is {}. MBS of {}".format(
mbs, end - start, (mbs * 8) / (end - start)))
self._check_data(data)
time_out_setter.unset_cores_for_data_extraction(
sim.transceiver(), extra_monitor_vertices, placements)
def run_mcmc(model,
data,
n_samples,
burn_in=2000,
thinning=5,
degrees_of_freedom=3.0,
seed=None,
n_chips=None,
n_boards=None):
""" Executes an MCMC model, returning the received samples
:param model: The MCMCModel to be used
:param data: The data to sample
:param n_samples: The number of samples to generate
:param burn_in:\
no of MCMC transitions to reach apparent equilibrium before\
generating inference samples
:param thinning:\
sampling rate i.e. 5 = 1 sample for 5 generated steps
:param degrees_of_freedom:\
The number of degrees of freedom to jump around with
:param seed: The random seed to use
:param n_chips: The number of chips to run the model on
:param root_finder: Use the root finder by adding root finder vertices
:param cholesky: Use the Cholesky algorithm by adding Cholesky vertices
:return: The samples read
:rtype: A numpy array with fields for each model state variable
"""
# Set up the simulation
g.setup(n_boards_required=n_boards,
n_chips_required=n_chips,
model_binary_module=model_binaries)
# Get the number of cores available for use
n_cores = 0
machine = g.machine()
# Create a coordinator for each board
coordinators = dict()
boards = dict()
for chip in machine.ethernet_connected_chips:
# Create a coordinator
coordinator = MCMCCoordinatorVertex(model, data, n_samples, burn_in,
thinning, degrees_of_freedom, seed)
g.add_machine_vertex_instance(coordinator)
# Put the coordinator on the Ethernet chip
coordinator.add_constraint(ChipAndCoreConstraint(chip.x, chip.y))
coordinators[chip.x, chip.y] = coordinator
boards[chip.x, chip.y] = chip.ip_address
# Go through all the chips and add the workhorses
n_chips_on_machine = machine.n_chips
n_workers = 0
if (model.root_finder):
n_root_finders = 0
if (model.cholesky):
n_cholesky = 0
for chip in machine.chips:
# Count the cores in the processor
# (-1 if this chip also has a coordinator)
n_cores = len([p for p in chip.processors if not p.is_monitor])
if (chip.x, chip.y) in coordinators:
n_cores -= 3 # coordinator and extra_monitor_support (2)
if (model.root_finder):
if (model.cholesky):
n_cores = n_cores // 3
else:
n_cores = n_cores // 2
else:
n_cores -= 1 # just extra_monitor_support
if (model.root_finder):
if (model.cholesky):
n_cores = n_cores // 3
else:
n_cores = n_cores // 2
# Find the coordinator for the board (or 0, 0 if it is missing)
eth_x = chip.nearest_ethernet_x
eth_y = chip.nearest_ethernet_y
coordinator = coordinators.get((eth_x, eth_y))
if coordinator is None:
print("Warning - couldn't find {}, {} for chip {}, {}".format(
eth_x, eth_y, chip.x, chip.y))
coordinator = coordinators[0, 0]
print("Using coordinator ", coordinator)
# hard-code remove some cores (chip power monitor etc.) just
# to see what happens
# n_cores -= non_worker_cores_per_chip
# print 'n_cores: ', n_cores
# Add a vertex for each core
for _ in range(n_cores):
# Create the vertex and add it to the graph
vertex = MCMCVertex(coordinator, model)
n_workers += 1
g.add_machine_vertex_instance(vertex)
# Put the vertex on the same board as the coordinator
vertex.add_constraint(ChipAndCoreConstraint(chip.x, chip.y))
# Add an edge from the coordinator to the vertex, to send the data
g.add_machine_edge_instance(MachineEdge(coordinator, vertex),
coordinator.data_partition_name)
# Add an edge from the vertex to the coordinator,
# to send acknowledgement
g.add_machine_edge_instance(MachineEdge(vertex, coordinator),
coordinator.acknowledge_partition_name)
if (model.root_finder):
# Create a root finder vertex
rf_vertex = MCMCRootFinderVertex(vertex, model)
n_root_finders += 1
g.add_machine_vertex_instance(rf_vertex)
# put it on the same chip as the standard mcmc vertex?
# no - put it on a "nearby" chip, however that works
rf_vertex.add_constraint(ChipAndCoreConstraint(chip.x, chip.y))
# Add an edge from mcmc vertex to root finder vertex,
# to "send" the data - need to work this out
g.add_machine_edge_instance(MachineEdge(vertex, rf_vertex),
vertex.parameter_partition_name)
# Add edge from root finder vertex back to mcmc vertex
# to send acknowledgement / result - need to work this out
g.add_machine_edge_instance(MachineEdge(rf_vertex, vertex),
vertex.result_partition_name)
if (model.cholesky):
# Create a Cholesky vertex
cholesky_vertex = MCMCCholeskyVertex(vertex, model)
n_cholesky += 1
g.add_machine_vertex_instance(cholesky_vertex)
# put it on the same chip as the standard mcmc vertex?
# no - put it on a "nearby" chip, however that works
cholesky_vertex.add_constraint(
ChipAndCoreConstraint(chip.x, chip.y))
# Add an edge from mcmc vertex to Cholesky vertex,
# to "send" the data - need to work this out
g.add_machine_edge_instance(
MachineEdge(vertex, cholesky_vertex),
vertex.cholesky_partition_name)
# Add edge from Cholesky vertex back to mcmc vertex
# to send acknowledgement / result - need to work this out
g.add_machine_edge_instance(
MachineEdge(cholesky_vertex, vertex),
vertex.cholesky_result_partition_name)
start_computing_time = time.time()
logger.info("n_chips_on_machine {}".format(n_chips_on_machine))
logger.info("Running {} worker cores".format(n_workers))
if (model.root_finder):
logger.info("Running {} root finder cores".format(n_root_finders))
if (model.cholesky):
logger.info("Running {} Cholesky cores".format(n_cholesky))
# Run the simulation
g.run_until_complete()
mid_computing_time = time.time()
# Wait for the application to finish
txrx = g.transceiver()
app_id = globals_variables.get_simulator()._app_id
logger.info("Running {} worker cores".format(n_workers))
if (model.root_finder):
logger.info("Running {} root finder cores".format(n_root_finders))
if (model.cholesky):
logger.info("Running {} Cholesky cores".format(n_cholesky))
logger.info("Waiting for application to finish...")
running = txrx.get_core_state_count(app_id, CPUState.RUNNING)
# there are now cores doing extra_monitor etc.
non_worker_cores = n_chips_on_machine + (2 * len(boards))
while running > non_worker_cores:
time.sleep(0.5)
error = txrx.get_core_state_count(app_id, CPUState.RUN_TIME_EXCEPTION)
watchdog = txrx.get_core_state_count(app_id, CPUState.WATCHDOG)
if error > 0 or watchdog > 0:
error_msg = "Some cores have failed ({} RTE, {} WDOG)".format(
error, watchdog)
raise Exception(error_msg)
running = txrx.get_core_state_count(app_id, CPUState.RUNNING)
print('running: ', running)
finish_computing_time = time.time()
# Get the data back
samples = dict()
for coord, coordinator in iteritems(coordinators):
samples[coord[0],
coord[1]] = coordinator.read_samples(g.buffer_manager())
# Close the machine
g.stop()
finish_time = time.time()
# Note: this timing appears to be incorrect now; needs looking at
print("Overhead time is %s seconds" % (start_computing_time - start_time))
print("Computing time is %s seconds" %
(finish_computing_time - start_computing_time))
print("run_until_complete takes %s seconds" %
(mid_computing_time - start_computing_time))
print("Data collecting time is %s seconds" %
(finish_time - finish_computing_time))
print("Overall running time is %s seconds" % (finish_time - start_time))
return samples
def run_model(data, n_chips=None, n_ihcan=0, fs=44100, resample_factor=1):
# Set up the simulation
g.setup(n_chips_required=n_chips, model_binary_module=model_binaries)
# Get the number of cores available for use
n_cores = 0
machine = g.machine()
# Create a OME for each chip
boards = dict()
#changed to lists to ensure data is read back in the same order that verticies are instantiated
ihcans = list()
cf_index = 0
count = 0
for chip in machine.chips:
if count >= n_chips:
break
else:
boards[chip.x, chip.y] = chip.ip_address
for j in range(n_ihcan):
ihcan = IHCANVertex(data[j][:], fs, resample_factor)
g.add_machine_vertex_instance(ihcan)
# constrain placement to local chip
ihcan.add_constraint(ChipAndCoreConstraint(chip.x, chip.y))
#ihcans[chip.x, chip.y,j] = ihcan
ihcans.append(ihcan)
count = count + 1
# Run the simulation
g.run(None)
# Wait for the application to finish
txrx = g.transceiver()
app_id = globals_variables.get_simulator()._app_id
#logger.info("Running {} worker cores".format(n_workers))
logger.info("Waiting for application to finish...")
running = txrx.get_core_state_count(app_id, CPUState.RUNNING)
while running > 0:
time.sleep(0.5)
error = txrx.get_core_state_count(app_id, CPUState.RUN_TIME_EXCEPTION)
watchdog = txrx.get_core_state_count(app_id, CPUState.WATCHDOG)
if error > 0 or watchdog > 0:
error_msg = "Some cores have failed ({} RTE, {} WDOG)".format(
error, watchdog)
raise Exception(error_msg)
running = txrx.get_core_state_count(app_id, CPUState.RUNNING)
# Get the data back
samples = list()
progress = ProgressBar(len(ihcans), "Reading results")
for ihcan in ihcans:
samples.append(ihcan.read_samples(g.buffer_manager()))
progress.update()
progress.end()
samples = numpy.hstack(samples)
# Close the machine
g.stop()
print "channels running: ", len(ihcans) / 5.0
print "output data: {} fibres with length {}".format(
len(ihcans) * 2, len(samples))
#if(len(samples) != len(ihcans)*2*numpy.floor(len(data[0][0])/100)*100*(1.0/resample_factor)):
if (len(samples) !=
len(ihcans) * 2 * numpy.floor(len(data[0][0]) / 96) * 96):
#print "samples length {} isn't expected size {}".format(len(samples),len(ihcans)*2*numpy.floor(len(data[0][0])/100)*100*(1.0/resample_factor))
print "samples length {} isn't expected size {}".format(
len(samples),
len(ihcans) * 2 * numpy.floor(len(data[0][0]) / 96) * 96)
return samples
def run_broken():
machine_time_step = 1000
time_scale_factor = 1
# machine_port = 11111
machine_receive_port = 22222
machine_host = "0.0.0.0"
live_gatherer_label = "LiveHeatGatherer"
notify_port = 19999
database_listen_port = 19998
# set up the front end and ask for the detected machines dimensions
front_end.setup(
graph_label="heat_demo_graph",
model_binary_module=sys.modules[__name__],
database_socket_addresses={SocketAddress(
"127.0.0.1", notify_port, database_listen_port)})
machine = front_end.machine()
# create a live gatherer vertex for each board
default_gatherer = None
live_gatherers = dict()
used_cores = set()
for chip in machine.ethernet_connected_chips:
# Try to use core 17 if one is available as it is outside the grid
processor = chip.get_processor_with_id(17)
if processor is None or processor.is_monitor:
processor = chip.get_first_none_monitor_processor()
if processor is not None:
live_gatherer = front_end.add_machine_vertex(
LivePacketGatherMachineVertex,
{
'label': live_gatherer_label,
'ip_address': machine_host,
'port': machine_receive_port,
'payload_as_time_stamps': False,
'use_payload_prefix': False,
'strip_sdp': True,
'message_type': EIEIOType.KEY_PAYLOAD_32_BIT
}
)
live_gatherers[chip.x, chip.y] = live_gatherer
used_cores.add((chip.x, chip.y, processor.processor_id))
if default_gatherer is None:
default_gatherer = live_gatherer
# Create a list of lists of vertices (x * 4) by (y * 4)
# (for 16 cores on a chip - missing cores will have missing vertices)
max_x_element_id = (machine.max_chip_x + 1) * 4
max_y_element_id = (machine.max_chip_y + 1) * 4
vertices = [
[None for _ in range(max_y_element_id)]
for _ in range(max_x_element_id)
]
receive_labels = list()
for x in range(0, max_x_element_id):
for y in range(0, max_y_element_id):
chip_x = x / 4
chip_y = y / 4
core_x = x % 4
core_y = y % 4
core_p = ((core_x * 4) + core_y) + 1
# Add an element if the chip and core exists
chip = machine.get_chip_at(chip_x, chip_y)
if chip is not None:
core = chip.get_processor_with_id(core_p)
if (core is not None and not core.is_monitor and
(chip_x, chip_y, core_p) not in used_cores):
element = front_end.add_machine_vertex(
HeatDemoVertex,
{
'machine_time_step': machine_time_step,
'time_scale_factor': time_scale_factor
},
label="Heat Element {}, {}".format(
x, y))
vertices[x][y] = element
vertices[x][y].add_constraint(
ChipAndCoreConstraint(chip_x, chip_y, core_p))
# add a link from the heat element to the live packet
# gatherer
live_gatherer = live_gatherers.get(
(chip.nearest_ethernet_x, chip.nearest_ethernet_y),
default_gatherer)
front_end.add_machine_edge(
MachineEdge,
{
'pre_vertex': vertices[x][y],
'post_vertex': live_gatherer
},
label="Live output from {}, {}".format(x, y),
semantic_label="TRANSMISSION")
receive_labels.append(vertices[x][y].label)
# build edges
for x in range(0, max_x_element_id):
for y in range(0, max_y_element_id):
if vertices[x][y] is not None:
# Add a north link if not at the top
if y+1 < max_y_element_id and vertices[x][y+1] is not None:
front_end.add_machine_edge(
HeatDemoEdge,
{
'pre_vertex': vertices[x][y],
'post_vertex': vertices[x][y + 1],
'direction': HeatDemoEdge.DIRECTIONS.SOUTH
},
label="North Edge from {}, {} to {}, {}".format(
x, y, x + 1, y),
semantic_label="TRANSMISSION")
# Add an east link if not at the right
if x+1 < max_y_element_id and vertices[x+1][y] is not None:
front_end.add_machine_edge(
HeatDemoEdge,
{
'pre_vertex': vertices[x][y],
'post_vertex': vertices[x + 1][y],
'direction': HeatDemoEdge.DIRECTIONS.WEST
},
label="East Edge from {}, {} to {}, {}".format(
x, y, x + 1, y),
semantic_label="TRANSMISSION")
# Add a south link if not at the bottom
if (y - 1) >= 0 and vertices[x][y - 1] is not None:
front_end.add_machine_edge(
HeatDemoEdge,
{
'pre_vertex': vertices[x][y],
'post_vertex': vertices[x][y - 1],
'direction': HeatDemoEdge.DIRECTIONS.NORTH
},
label="South Edge from {}, {} to {}, {}".format(
x, y, x, y - 1),
semantic_label="TRANSMISSION")
# check for the likely hood for a W link
if (x - 1) >= 0 and vertices[x - 1][y] is not None:
front_end.add_machine_edge(
HeatDemoEdge,
{
'pre_vertex': vertices[x][y],
'post_vertex': vertices[x - 1][y],
'direction': HeatDemoEdge.DIRECTIONS.EAST
},
label="West Edge from {}, {} to {}, {}".format(
x, y, x - 1, y),
semantic_label="TRANSMISSION")
# Set up the live connection for receiving heat elements
live_heat_connection = LiveEventConnection(
live_gatherer_label, receive_labels=receive_labels,
local_port=notify_port, machine_vertices=True)
heat_values = defaultdict(list)
condition = Condition()
def receive_heat(label, atom, value):
with condition:
print "{}: {}".format(label, value / 65536.0)
# Set up callbacks to occur when spikes are received
for label in receive_labels:
live_heat_connection.add_receive_callback(label, receive_heat)
front_end.run(1000)
front_end.stop()
for label in receive_labels:
print "{}: {}".format(
label, ["{:05.2f}".format(value) for value in heat_values[label]])
