def __init__(self, port_data=PORT_DATA, port_ctrl=PORT_CTRL,
port_time=PORT_TIME):
# Unique object ID:
self.id = uid()
# Set logger name:
LoggerMixin.__init__(self, 'man %s' % self.id)
self.port_data = port_data
self.port_ctrl = port_ctrl
self.port_time = port_time
# Set up a router socket to communicate with other topology
# components; linger period is set to 0 to prevent hanging on
# unsent messages when shutting down:
self.zmq_ctx = zmq.Context()
self.sock_ctrl = self.zmq_ctx.socket(zmq.ROUTER)
self.sock_ctrl.setsockopt(zmq.LINGER, LINGER_TIME)
self.sock_ctrl.bind("tcp://*:%i" % self.port_ctrl)
# Data structures for instances of objects that correspond to processes
# keyed on object IDs (bidicts are used to enable retrieval of
# broker/module IDs from object instances):
self.brokers = bidict.bidict()
self.modules = bidict.bidict()
# Set up a dynamic table to contain the routing table:
self.routing_table = RoutingTable()
# Number of emulation steps to run:
self.max_steps = float('inf')
# Set up process to handle time data:
self.time_listener = TimeListener(self.port_ctrl, self.port_time)
def __init__(self):
LoggerMixin.__init__(self, 'man')
set_excepthook(self.logger, True)
self._targets = {}
self._args = {}
self._kwargs = {}
self._intercomm = MPI.COMM_NULL
self._rank = 0
def __init__(self, port_ctrl, port_time, ids=set()):
super(TimeListener, self).__init__(port_ctrl, uid())
# Reformat logger name:
LoggerMixin.__init__(self, 'lis %s' % self.id)
# Time port:
if port_time == port_ctrl:
raise ValueError('time and control ports must differ')
self.port_time = port_time
# IDs of modules from which to collect timing data:
assert isinstance(ids, set)
self.ids = ids
# Queue for returning timing results to parent process:
self.queue = mp.Queue()
def __init__(self, port_data=PORT_DATA, port_ctrl=PORT_CTRL,
routing_table=None):
super(Broker, self).__init__(port_ctrl, uid())
# Reformat logger name:
LoggerMixin.__init__(self, 'brk %s' % self.id)
# Data port:
if port_data == port_ctrl:
raise ValueError('data and control ports must differ')
self.port_data = port_data
# Routing table:
self.routing_table = routing_table
# Buffers used to accumulate data to route:
self._data_to_route = []
def __init__(self, sel, sel_in, sel_out,
sel_gpot, sel_spike, data_gpot, data_spike,
columns=['interface', 'io', 'type'],
ctrl_tag=CTRL_TAG, gpot_tag=GPOT_TAG, spike_tag=SPIKE_TAG,
id=None, device=None,
routing_table=None, rank_to_id=None,
debug=False, time_sync=False):
super(Module, self).__init__(ctrl_tag)
self.debug = debug
self.time_sync = time_sync
self.device = device
self._gpot_tag = gpot_tag
self._spike_tag = spike_tag
# Require several necessary attribute columns:
if 'interface' not in columns:
raise ValueError('interface column required')
if 'io' not in columns:
raise ValueError('io column required')
if 'type' not in columns:
raise ValueError('type column required')
# Manually register the file close method associated with MPIOutput
# so that it is called by atexit before MPI.Finalize() (if the file is
# closed after MPI.Finalize() is called, an error will occur):
for k, v in twiggy.emitters.iteritems():
if isinstance(v._output, MPIOutput):
atexit.register(v._output.close)
# Ensure that the input and output port selectors respectively
# select mutually exclusive subsets of the set of all ports exposed by
# the module:
if not SelectorMethods.is_in(sel_in, sel):
raise ValueError('input port selector not in selector of all ports')
if not SelectorMethods.is_in(sel_out, sel):
raise ValueError('output port selector not in selector of all ports')
if not SelectorMethods.are_disjoint(sel_in, sel_out):
raise ValueError('input and output port selectors not disjoint')
# Ensure that the graded potential and spiking port selectors
# respectively select mutually exclusive subsets of the set of all ports
# exposed by the module:
if not SelectorMethods.is_in(sel_gpot, sel):
raise ValueError('gpot port selector not in selector of all ports')
if not SelectorMethods.is_in(sel_spike, sel):
raise ValueError('spike port selector not in selector of all ports')
if not SelectorMethods.are_disjoint(sel_gpot, sel_spike):
raise ValueError('gpot and spike port selectors not disjoint')
# Save routing table and mapping between MPI ranks and module IDs:
self.routing_table = routing_table
self.rank_to_id = rank_to_id
# Generate a unique ID if none is specified:
if id is None:
self.id = uid()
else:
# If a unique ID was specified and the routing table is not empty
# (i.e., there are connections between multiple modules),
# the id must be a node in the table:
if routing_table is not None and len(routing_table.ids) and \
not routing_table.has_node(id):
raise ValueError('routing table must contain specified module ID')
self.id = id
# Reformat logger name:
LoggerMixin.__init__(self, 'mod %s' % self.id)
# Create module interface given the specified ports:
self.interface = Interface(sel, columns)
# Set the interface ID to 0; we assume that a module only has one interface:
self.interface[sel, 'interface'] = 0
# Set the port attributes:
self.interface[sel_in, 'io'] = 'in'
self.interface[sel_out, 'io'] = 'out'
self.interface[sel_gpot, 'type'] = 'gpot'
self.interface[sel_spike, 'type'] = 'spike'
# Find the input and output ports:
self.in_ports = self.interface.in_ports().to_tuples()
self.out_ports = self.interface.out_ports().to_tuples()
# Find the graded potential and spiking ports:
self.gpot_ports = self.interface.gpot_ports().to_tuples()
self.spike_ports = self.interface.spike_ports().to_tuples()
self.in_gpot_ports = self.interface.in_ports().gpot_ports().to_tuples()
self.in_spike_ports = self.interface.in_ports().spike_ports().to_tuples()
self.out_gpot_ports = self.interface.out_ports().gpot_ports().to_tuples()
self.out_spike_ports = self.interface.out_ports().spike_ports().to_tuples()
# Set up mapper between port identifiers and their associated data:
if len(data_gpot) != len(self.gpot_ports):
raise ValueError('incompatible gpot port data array length')
if len(data_spike) != len(self.spike_ports):
raise ValueError('incompatible spike port data array length')
self.data = {}
self.data['gpot'] = data_gpot
self.data['spike'] = data_spike
self.pm = {}
self.pm['gpot'] = PortMapper(sel_gpot, self.data['gpot'])
self.pm['spike'] = PortMapper(sel_spike, self.data['spike'])
def __init__(self,
sel,
sel_in,
sel_out,
sel_gpot,
sel_spike,
data_gpot,
data_spike,
columns=['interface', 'io', 'type'],
ctrl_tag=CTRL_TAG,
gpot_tag=GPOT_TAG,
spike_tag=SPIKE_TAG,
id=None,
device=None,
routing_table=None,
rank_to_id=None,
pm_all=None,
debug=False,
time_sync=False):
# Call super for BaseModule rather than Module because most of the
# functionality of the former's constructor must be overridden in any case:
super(BaseModule, self).__init__(ctrl_tag)
self.debug = debug
self.time_sync = time_sync
self.device = device
self._gpot_tag = gpot_tag
self._spike_tag = spike_tag
# Require several necessary attribute columns:
assert 'interface' in columns
assert 'io' in columns
assert 'type' in columns
self._init_gpu()
# This is needed to ensure that MPI_Finalize is called before PyCUDA
# attempts to clean up; see
# https://groups.google.com/forum/#!topic/mpi4py/by0Rd5q0Ayw
atexit.register(MPI.Finalize)
# Manually register the file close method associated with MPIOutput
# so that it is called by atexit before MPI.Finalize() (if the file is
# closed after MPI.Finalize() is called, an error will occur):
for k, v in twiggy.emitters.iteritems():
if isinstance(v._output, MPIOutput):
atexit.register(v._output.close)
# Ensure that the input and output port selectors respectively
# select mutually exclusive subsets of the set of all ports exposed by
# the module:
assert SelectorMethods.is_in(sel_in, sel)
assert SelectorMethods.is_in(sel_out, sel)
assert SelectorMethods.are_disjoint(sel_in, sel_out)
# Ensure that the graded potential and spiking port selectors
# respectively select mutually exclusive subsets of the set of all ports
# exposed by the module:
assert SelectorMethods.is_in(sel_gpot, sel)
assert SelectorMethods.is_in(sel_spike, sel)
assert SelectorMethods.are_disjoint(sel_gpot, sel_spike)
# Save routing table and mapping between MPI ranks and module IDs:
self.routing_table = routing_table
self.rank_to_id = rank_to_id
# Save module interface data (stored in a dict of BasePortMapper instances):
self.pm_all = pm_all
# Generate a unique ID if none is specified:
if id is None:
self.id = uid()
else:
# Save routing table; if a unique ID was specified, it must be a node in
# the routing table:
if routing_table is not None and not routing_table.has_node(id):
raise ValueError(
'routing table must contain specified module ID')
self.id = id
# Reformat logger name:
LoggerMixin.__init__(self, 'mod %s' % self.id)
# Create module interface given the specified ports:
self.interface = Interface(sel, columns)
# Set the interface ID to 0; we assume that a module only has one interface:
self.interface[sel, 'interface'] = 0
# Set the port attributes:
self.interface[sel_in, 'io'] = 'in'
self.interface[sel_out, 'io'] = 'out'
self.interface[sel_gpot, 'type'] = 'gpot'
self.interface[sel_spike, 'type'] = 'spike'
# Find the input and output ports:
self.in_ports = self.interface.in_ports().to_tuples()
self.out_ports = self.interface.out_ports().to_tuples()
# Find the graded potential and spiking ports:
self.gpot_ports = self.interface.gpot_ports().to_tuples()
self.spike_ports = self.interface.spike_ports().to_tuples()
self.in_gpot_ports = self.interface.in_ports().gpot_ports().to_tuples()
self.in_spike_ports = self.interface.in_ports().spike_ports(
).to_tuples()
self.out_gpot_ports = self.interface.out_ports().gpot_ports(
).to_tuples()
self.out_spike_ports = self.interface.out_ports().spike_ports(
).to_tuples()
# Set up mapper between port identifiers and their associated data:
assert len(data_gpot) == len(self.gpot_ports)
assert len(data_spike) == len(self.spike_ports)
self.data = {}
self.data['gpot'] = gpuarray.to_gpu(data_gpot)
self.data['spike'] = gpuarray.to_gpu(data_spike)
self.pm = {}
self.pm['gpot'] = GPUPortMapper(sel_gpot,
self.data['gpot'],
make_copy=False)
self.pm['spike'] = GPUPortMapper(sel_spike,
self.data['spike'],
make_copy=False)
def __init__(self, sel, sel_in, sel_out,
sel_gpot, sel_spike,
data_gpot, data_spike,
columns=['interface', 'io', 'type'],
port_data=PORT_DATA, port_ctrl=PORT_CTRL, port_time=PORT_TIME,
id=None, device=None, debug=False, time_sync=False):
self.debug = debug
self.time_sync = time_sync
self.device = device
# Require several necessary attribute columns:
assert 'interface' in columns
assert 'io' in columns
assert 'type' in columns
# Generate a unique ID if none is specified:
if id is None:
id = uid()
# Call super for BaseModule rather than Module because most of the
# functionality of the former's constructor must be overridden in any case:
super(BaseModule, self).__init__(port_ctrl, id)
# Reformat logger name:
LoggerMixin.__init__(self, 'mod %s' % self.id)
# Data port:
if port_data == port_ctrl:
raise ValueError('data and control ports must differ')
self.port_data = port_data
if port_time == port_ctrl or port_time == port_data:
raise ValueError('time port must differ from data and control ports')
self.port_time = port_time
# Initial network connectivity:
self.net = 'none'
# Create module interface given the specified ports:
self.interface = Interface(sel, columns)
# Set the interface ID to 0
# we assume that a module only has one interface:
self.interface[sel, 'interface'] = 0
# Set port types:
assert SelectorMethods.is_in(sel_in, sel)
assert SelectorMethods.is_in(sel_out, sel)
assert SelectorMethods.are_disjoint(sel_in, sel_out)
self.interface[sel_in, 'io'] = 'in'
self.interface[sel_out, 'io'] = 'out'
assert SelectorMethods.is_in(sel_gpot, sel)
assert SelectorMethods.is_in(sel_spike, sel)
assert SelectorMethods.are_disjoint(sel_gpot, sel_spike)
self.interface[sel_gpot, 'type'] = 'gpot'
self.interface[sel_spike, 'type'] = 'spike'
# Set up mapper between port identifiers and their associated data:
assert len(data_gpot) == len(self.interface.gpot_ports())
assert len(data_spike) == len(self.interface.spike_ports())
self.data = {}
self.data['gpot'] = data_gpot
self.data['spike'] = data_spike
self.pm = {}
self.pm['gpot'] = PortMapper(sel_gpot, self.data['gpot'])
self.pm['spike'] = PortMapper(sel_spike, self.data['spike'])
# Patterns connecting this module instance with other modules instances.
# Keyed on the IDs of those modules:
self.patterns = {}
# Each entry in pat_ints is a tuple containing the identifiers of which
# of a pattern's identifiers are connected to the current module (first
# entry) and the modules to which it is connected (second entry).
# Keyed on the IDs of those modules:
self.pat_ints = {}
# Dict for storing incoming data; each entry (corresponding to each
# module that sends input to the current module) is a deque containing
# incoming data, which in turn contains transmitted data arrays. Deques
# are used here to accommodate situations when multiple data from a
# single source arrive:
self._in_data = {}
# List for storing outgoing data; each entry is a tuple whose first
# entry is the source or destination module ID and whose second entry is
# the data to transmit:
self._out_data = []
# Dictionaries containing ports of source modules that
# send output to this module. Must be initialized immediately before
# an emulation begins running. Keyed on source module ID:
self._in_port_dict = {}
self._in_port_dict_ids = {}
self._in_port_dict['gpot'] = {}
self._in_port_dict['spike'] = {}
# Dictionaries containing ports of destination modules that
# receive input from this module. Must be initialized immediately before
# an emulation begins running. Keyed on destination module ID:
self._out_port_dict = {}
self._out_port_dict_ids = {}
self._out_port_dict['gpot'] = {}
self._out_port_dict['spike'] = {}
self._out_ids = []
self._in_ids = []
def __init__(self, sel, sel_in, sel_out,
sel_gpot, sel_spike, data_gpot, data_spike,
columns=['interface', 'io', 'type'],
ctrl_tag=CTRL_TAG, gpot_tag=GPOT_TAG, spike_tag=SPIKE_TAG,
id=None, device=None,
routing_table=None, rank_to_id=None,
debug=False, time_sync=False):
super(Module, self).__init__(ctrl_tag)
self.debug = debug
self.time_sync = time_sync
self.device = device
self._gpot_tag = gpot_tag
self._spike_tag = spike_tag
# Require several necessary attribute columns:
if 'interface' not in columns:
raise ValueError('interface column required')
if 'io' not in columns:
raise ValueError('io column required')
if 'type' not in columns:
raise ValueError('type column required')
# Initialize GPU here so as to be able to initialize a port mapper
# containing GPU memory:
self._init_gpu()
# This is needed to ensure that MPI_Finalize is called before PyCUDA
# attempts to clean up; see
# https://groups.google.com/forum/#!topic/mpi4py/by0Rd5q0Ayw
atexit.register(MPI.Finalize)
# Manually register the file close method associated with MPIOutput
# so that it is called by atexit before MPI.Finalize() (if the file is
# closed after MPI.Finalize() is called, an error will occur):
for k, v in twiggy.emitters.iteritems():
if isinstance(v._output, MPIOutput):
atexit.register(v._output.close)
# Ensure that the input and output port selectors respectively
# select mutually exclusive subsets of the set of all ports exposed by
# the module:
if not SelectorMethods.is_in(sel_in, sel):
raise ValueError('input port selector not in selector of all ports')
if not SelectorMethods.is_in(sel_out, sel):
raise ValueError('output port selector not in selector of all ports')
if not SelectorMethods.are_disjoint(sel_in, sel_out):
raise ValueError('input and output port selectors not disjoint')
# Ensure that the graded potential and spiking port selectors
# respectively select mutually exclusive subsets of the set of all ports
# exposed by the module:
if not SelectorMethods.is_in(sel_gpot, sel):
raise ValueError('gpot port selector not in selector of all ports')
if not SelectorMethods.is_in(sel_spike, sel):
raise ValueError('spike port selector not in selector of all ports')
if not SelectorMethods.are_disjoint(sel_gpot, sel_spike):
raise ValueError('gpot and spike port selectors not disjoint')
# Save routing table and mapping between MPI ranks and module IDs:
self.routing_table = routing_table
self.rank_to_id = rank_to_id
# Generate a unique ID if none is specified:
if id is None:
self.id = uid()
else:
# If a unique ID was specified and the routing table is not empty
# (i.e., there are connections between multiple modules), the id
# must be a node in the routing table:
if routing_table is not None and len(routing_table.ids) and \
not routing_table.has_node(id):
raise ValueError('routing table must contain specified '
'module ID: {}'.format(id))
self.id = id
# Reformat logger name:
LoggerMixin.__init__(self, 'mod %s' % self.id)
# Create module interface given the specified ports:
self.interface = Interface(sel, columns)
# Set the interface ID to 0; we assume that a module only has one interface:
self.interface[sel, 'interface'] = 0
# Set the port attributes:
self.interface[sel_in, 'io'] = 'in'
self.interface[sel_out, 'io'] = 'out'
self.interface[sel_gpot, 'type'] = 'gpot'
self.interface[sel_spike, 'type'] = 'spike'
# Find the input and output ports:
self.in_ports = self.interface.in_ports().to_tuples()
self.out_ports = self.interface.out_ports().to_tuples()
# Find the graded potential and spiking ports:
self.gpot_ports = self.interface.gpot_ports().to_tuples()
self.spike_ports = self.interface.spike_ports().to_tuples()
self.in_gpot_ports = self.interface.in_ports().gpot_ports().to_tuples()
self.in_spike_ports = self.interface.in_ports().spike_ports().to_tuples()
self.out_gpot_ports = self.interface.out_ports().gpot_ports().to_tuples()
self.out_spike_ports = self.interface.out_ports().spike_ports().to_tuples()
# Set up mapper between port identifiers and their associated data:
if len(data_gpot) != len(self.gpot_ports):
raise ValueError('incompatible gpot port data array length')
if len(data_spike) != len(self.spike_ports):
raise ValueError('incompatible spike port data array length')
self.data = {}
self.data['gpot'] = gpuarray.to_gpu(data_gpot)
self.data['spike'] = gpuarray.to_gpu(data_spike)
self.pm = {}
self.pm['gpot'] = GPUPortMapper(sel_gpot, self.data['gpot'], make_copy=False)
self.pm['spike'] = GPUPortMapper(sel_spike, self.data['spike'], make_copy=False)
# MPI Request object for resolving asynchronous transfers:
self.req = MPI.Request()
def __init__(self, *args, **kwargs):
LoggerMixin.__init__(self, 'prc %s' % MPI.COMM_WORLD.Get_rank())
set_excepthook(self.logger, True)
self._args = args
self._kwargs = kwargs
def __init__(self, sel, sel_in, sel_out,
sel_gpot, sel_spike, data_gpot, data_spike,
columns=['interface', 'io', 'type'],
ctrl_tag=CTRL_TAG, gpot_tag=GPOT_TAG, spike_tag=SPIKE_TAG,
id=None, device=None,
routing_table=None, rank_to_id=None, pm_all=None,
debug=False, time_sync=False):
# Call super for BaseModule rather than Module because most of the
# functionality of the former's constructor must be overridden in any case:
super(BaseModule, self).__init__(ctrl_tag)
self.debug = debug
self.time_sync = time_sync
self.device = device
self._gpot_tag = gpot_tag
self._spike_tag = spike_tag
# Require several necessary attribute columns:
assert 'interface' in columns
assert 'io' in columns
assert 'type' in columns
self._init_gpu()
# This is needed to ensure that MPI_Finalize is called before PyCUDA
# attempts to clean up; see
# https://groups.google.com/forum/#!topic/mpi4py/by0Rd5q0Ayw
atexit.register(MPI.Finalize)
# Manually register the file close method associated with MPIOutput
# so that it is called by atexit before MPI.Finalize() (if the file is
# closed after MPI.Finalize() is called, an error will occur):
for k, v in twiggy.emitters.iteritems():
if isinstance(v._output, MPIOutput):
atexit.register(v._output.close)
# Ensure that the input and output port selectors respectively
# select mutually exclusive subsets of the set of all ports exposed by
# the module:
assert SelectorMethods.is_in(sel_in, sel)
assert SelectorMethods.is_in(sel_out, sel)
assert SelectorMethods.are_disjoint(sel_in, sel_out)
# Ensure that the graded potential and spiking port selectors
# respectively select mutually exclusive subsets of the set of all ports
# exposed by the module:
assert SelectorMethods.is_in(sel_gpot, sel)
assert SelectorMethods.is_in(sel_spike, sel)
assert SelectorMethods.are_disjoint(sel_gpot, sel_spike)
# Save routing table and mapping between MPI ranks and module IDs:
self.routing_table = routing_table
self.rank_to_id = rank_to_id
# Save module interface data (stored in a dict of BasePortMapper instances):
self.pm_all = pm_all
# Generate a unique ID if none is specified:
if id is None:
self.id = uid()
else:
# Save routing table; if a unique ID was specified, it must be a node in
# the routing table:
if routing_table is not None and not routing_table.has_node(id):
raise ValueError('routing table must contain specified module ID')
self.id = id
# Reformat logger name:
LoggerMixin.__init__(self, 'mod %s' % self.id)
# Create module interface given the specified ports:
self.interface = Interface(sel, columns)
# Set the interface ID to 0; we assume that a module only has one interface:
self.interface[sel, 'interface'] = 0
# Set the port attributes:
self.interface[sel_in, 'io'] = 'in'
self.interface[sel_out, 'io'] = 'out'
self.interface[sel_gpot, 'type'] = 'gpot'
self.interface[sel_spike, 'type'] = 'spike'
# Find the input and output ports:
self.in_ports = self.interface.in_ports().to_tuples()
self.out_ports = self.interface.out_ports().to_tuples()
# Find the graded potential and spiking ports:
self.gpot_ports = self.interface.gpot_ports().to_tuples()
self.spike_ports = self.interface.spike_ports().to_tuples()
self.in_gpot_ports = self.interface.in_ports().gpot_ports().to_tuples()
self.in_spike_ports = self.interface.in_ports().spike_ports().to_tuples()
self.out_gpot_ports = self.interface.out_ports().gpot_ports().to_tuples()
self.out_spike_ports = self.interface.out_ports().spike_ports().to_tuples()
# Set up mapper between port identifiers and their associated data:
assert len(data_gpot) == len(self.gpot_ports)
assert len(data_spike) == len(self.spike_ports)
self.data = {}
self.data['gpot'] = gpuarray.to_gpu(data_gpot)
self.data['spike'] = gpuarray.to_gpu(data_spike)
self.pm = {}
self.pm['gpot'] = GPUPortMapper(sel_gpot, self.data['gpot'], make_copy=False)
self.pm['spike'] = GPUPortMapper(sel_spike, self.data['spike'], make_copy=False)