Source code for brian2genn.device

'''
Module implementing the bulk of the brian2genn interface by defining the "genn" device.
'''

import os
import platform
import re
import shutil
import sys

from pkg_resources import parse_version
from subprocess import call, check_call, CalledProcessError
import inspect
from builtins import map, range
from collections import defaultdict
from six import iteritems, iterkeys, itervalues
import tempfile
import itertools
import numpy
import numbers
from collections import Counter

from brian2.codegen.cpp_prefs import get_msvc_env
from brian2.codegen.translation import make_statements
from brian2.input.poissoninput import PoissonInput
from brian2.spatialneuron.spatialneuron import (SpatialNeuron,
                                                SpatialStateUpdater)
from brian2.units import second
from brian2.codegen.generators.cpp_generator import (c_data_type,
                                                     CPPCodeGenerator)
from brian2.codegen.templates import MultiTemplate
from brian2.core.clocks import defaultclock
from brian2.core.variables import *
from brian2.core.functions import Function
from brian2.core.network import Network
from brian2.devices.device import all_devices
from brian2.devices.cpp_standalone.device import CPPStandaloneDevice
from brian2.parsing.rendering import CPPNodeRenderer
from brian2.synapses.synapses import Synapses, SynapticPathway
from brian2.monitors.spikemonitor import SpikeMonitor
from brian2.monitors.ratemonitor import PopulationRateMonitor
from brian2.monitors.statemonitor import StateMonitor
from brian2.utils.filetools import copy_directory, ensure_directory
from brian2.utils.stringtools import word_substitute, get_identifiers
from brian2.groups.group import Group, CodeRunner
from brian2.groups.neurongroup import (NeuronGroup, StateUpdater, Resetter,
                                       Thresholder, SubexpressionUpdater)
from brian2.groups.subgroup import Subgroup
from brian2.input.poissongroup import PoissonGroup
from brian2.input.spikegeneratorgroup import *
from brian2.synapses.synapses import StateUpdater as SynapsesStateUpdater
from brian2.utils.logger import get_logger, std_silent
from brian2.devices.cpp_standalone.codeobject import CPPStandaloneCodeObject
from brian2.devices.cpp_standalone.device import CPPWriter
from brian2 import prefs
from .codeobject import GeNNCodeObject, GeNNUserCodeObject
from .genn_generator import get_var_ndim, GeNNCodeGenerator

__all__ = ['GeNNDevice']

logger = get_logger('brian2.devices.genn')


[docs]def stringify(code): ''' Helper function to prepare multiline strings (potentially including quotation marks) to be included in strings. Parameters ---------- code : str The code to convert. ''' code = code.replace('\n', '\\n\\\n') code = code.replace('"', '\\"') return code
[docs]def freeze(code, ns): ''' Support function for substituting constant values. ''' # this is a bit of a hack, it should be passed to the template somehow for k, v in iteritems(ns): if (isinstance(v, Variable) and v.scalar and v.constant and v.read_only): try: v = v.get_value() except NotImplementedError: continue if isinstance(v, str): code = word_substitute(code, {k: v}) elif isinstance(v, numbers.Number): # Use a renderer to correctly transform constants such as True or inf renderer = CPPNodeRenderer() string_value = renderer.render_expr(repr(v)) if v < 0: string_value = '(%s)' % string_value code = word_substitute(code, {k: string_value}) else: pass # don't deal with this object return code
[docs]def get_gcc_compile_args(): ''' Get the compile args for GCC based on the users preferences. Uses Brian's preferences for the C++ compilation (either `codegen.cpp.extra_compile_args` or `codegen.cpp.extra_compile_args_gcc`). Returns ------- (compile_args_gcc, compile_args_msvc, compile_args_nvcc) : (str, str, str) Tuple with the respective compiler arguments (as strings). ''' if prefs.codegen.cpp.extra_compile_args is not None: args = ' '.join(prefs.codegen.cpp.extra_compile_args) compile_args_gcc = args else: compile_args_gcc = ' '.join(prefs.codegen.cpp.extra_compile_args_gcc) return compile_args_gcc
[docs]def decorate(code, variables, shared_variables, parameters, do_final=True): ''' Support function for inserting GeNN-specific "decorations" for variables and parameters, such as $(.). ''' # this is a bit of a hack, it should be part of the language probably for v in itertools.chain(variables, shared_variables, parameters): code = word_substitute(code, {v: '$(' + v + ')'}) code = word_substitute(code, {'dt': 'DT'}).strip() if do_final: code = stringify(code) code = re.sub(r'addtoinSyn\s*=\s*(.*);', r'$(addToInSyn,\1);', code) code = word_substitute(code, {'_hidden_weightmatrix': '$(_hidden_weightmatrix)'}) return code
[docs]def extract_source_variables(variables, varname, smvariables): '''Support function to extract the "atomic" variables used in a variable that is of instance `Subexpression`. ''' identifiers = get_identifiers(variables[varname].expr) for vnm, var in iteritems(variables): if vnm in identifiers: if var in defaultclock.variables.values(): raise NotImplementedError('Recording an expression that depends on ' 'the time t or the timestep dt is ' 'currently not supported in Brian2GeNN') elif isinstance(var, ArrayVariable): smvariables.append(vnm) elif isinstance(var, Subexpression): smvariables = extract_source_variables(variables, vnm, smvariables) return smvariables
[docs]def find_executable(executable): """Tries to find 'executable' in the path Modified version of distutils.spawn.find_executable as this has stupid rules for extensions on Windows. Returns the complete filename or None if not found. """ path = os.environ.get('PATH', os.defpath) paths = path.split(os.pathsep) for p in paths: f = os.path.join(p, executable) if os.path.isfile(f): # the file exists, we have a shot at spawn working return f return None
[docs]class DelayedCodeObject(object): ''' Dummy class used for delaying the CodeObject creation of stateupdater, thresholder, and resetter of a NeuronGroup (which will all be merged into a single code object). ''' def __init__(self, owner, name, abstract_code, variables, variable_indices, override_conditional_write): self.owner = owner self.name = name self.abstract_code = abstract_code self.variables = variables self.variable_indices = variable_indices self.override_conditional_write = override_conditional_write
[docs] def before_run(self): pass
[docs] def after_run(self): pass
[docs]class neuronModel(object): ''' Class that contains all relevant information of a neuron model. ''' def __init__(self): self.name = '' self.clock = None self.N = 0 self.variables = [] self.variabletypes = [] self.variablescope = dict() self.shared_variables = [] self.shared_variabletypes = [] self.parameters = [] self.pvalue = [] self.code_lines = [] self.thresh_cond_lines = [] self.reset_code_lines = [] self.support_code_lines = []
[docs]class spikegeneratorModel(object): ''' Class that contains all relevant information of a spike generator group. ''' def __init__(self): self.name = '' self.codeobject_name = '' self.N = 0
[docs]class synapseModel(object): ''' Class that contains all relevant information about a synapse model. ''' def __init__(self): self.name = '' self.srcname = '' self.srcN = 0 self.trgname = '' self.trgN = 0 self.N = 0 self.variables = [] self.variabletypes = [] self.shared_variables = [] self.shared_variabletypes = [] self.variablescope = dict() self.external_variables = [] self.parameters = [] self.pvalue = [] self.postSyntoCurrent = [] # The following dictionaries contain keys "pre"/"post" for the pre- # and post-synaptic pathway and "dynamics" for the synaptic dynamics self.main_code_lines = defaultdict(str) self.support_code_lines = defaultdict(str) self.connectivity = '' self.delay = 0 self.summed_variables= None
[docs]class spikeMonitorModel(object): ''' Class the contains all relevant information about a spike monitor. ''' def __init__(self): self.name = '' self.codeobject_name = '' self.neuronGroup = '' self.notSpikeGeneratorGroup = True
[docs]class rateMonitorModel(object): ''' CLass that contains all relevant information about a rate monitor. ''' def __init__(self): self.name = '' self.codeobject_name = '' self.neuronGroup = '' self.notSpikeGeneratorGroup = True
[docs]class stateMonitorModel(object): ''' Class that contains all relvant information about a state monitor. ''' def __init__(self): self.name = '' self.codeobject_name = '' self.order = 0 self.monitored = '' self.src = None self.isSynaptic = False self.variables = [] self.srcN = 0 self.trgN = 0 self.when = '' self.connectivity = ''
# ------------------------------------------------------------------------------ # Start of GeNNDevice # ------------------------------------------------------------------------------
[docs]class GeNNDevice(CPPStandaloneDevice): ''' The main "genn" device. This does most of the translation work from Brian 2 generated code to functional GeNN code, assisted by the "GeNN language". ''' def __init__(self): super(GeNNDevice, self).__init__() # Remember whether we have already passed the "run" statement self.run_statement_used = False self.network_schedule = ['start', 'synapses', 'groups', 'thresholds', 'resets', 'end'] self.neuron_models = [] self.spikegenerator_models = [] self.synapse_models = [] self.max_row_length_include= [] self.max_row_length_run_calls= [] self.max_row_length_synapses= set() self.max_row_length_code_objects= {} self.delays = {} self.spike_monitor_models = [] self.rate_monitor_models = [] self.state_monitor_models = [] self.run_regularly_read_write = {} self.run_duration = None self.net = None self.simple_code_objects = {} self.report_func = '' self.src_counts= dict() self.trg_counts= dict() #: Set of all source and header files (to be included in runner) self.source_files = set() self.header_files = set() self.connectivityDict = dict() self.groupDict = dict() # Overwrite the code slots defined in standard C++ standalone self.code_lines = {'before_start': [], 'after_start': [], 'before_run': [], 'after_run': [], 'before_end': [], 'after_end': []}
[docs] def insert_code(self, slot, code): ''' Insert custom C++ code directly into ``main.cpp``. The available slots are: ``before_start`` / ``after_start`` Before/after allocating memory for the arrays and loading arrays from disk. ``before_run`` / ``after_run`` Before/after calling GeNN's ``run`` function. ``before_end`` / ``after_end`` Before/after writing results to disk and deallocating memory. Parameters ---------- slot : str The name of the slot where the code will be placed (see above for list of available slots). code : str The C++ code that should be inserted. ''' # Only overwritten so that we can have custom documentation super(GeNNDevice, self).insert_code(slot, code)
[docs] def activate(self, build_on_run=True, **kwargs): new_prefs = {'codegen.generators.cpp.restrict_keyword': '__restrict', 'codegen.loop_invariant_optimisations': False, 'core.network.default_schedule': ['start', 'synapses', 'groups', 'thresholds', 'resets', 'end']} changed = [] for new_pref, new_value in iteritems(new_prefs): if prefs[new_pref] != new_value: changed.append(new_pref) prefs[new_pref] = new_value if changed: logger.info('The following preferences have been changed for ' 'Brian2GeNN, reset them manually if you use a ' 'different device later in the same script: ' '{}'.format(', '.join(changed)), once=True) prefs._backup() super(GeNNDevice, self).activate(build_on_run, **kwargs)
[docs] def code_object_class(self, codeobj_class=None, *args, **kwds): if codeobj_class is None: codeobj_class = GeNNUserCodeObject return codeobj_class
[docs] def code_object(self, owner, name, abstract_code, variables, template_name, variable_indices, codeobj_class=None, template_kwds=None, override_conditional_write=None, **kwds): ''' Processes abstract code into code objects and stores them in different arrays for `GeNNCodeObjects` and `GeNNUserCodeObjects`. ''' if '_run_regularly_' in name: variables['N'] = owner.variables['N'] # Add an extra code object that executes the scalar code of # the run_regularly operation (will be directly called from # engine.cpp) codeobj = super(GeNNDevice, self).code_object(owner, name, abstract_code, variables, 'stateupdate', variable_indices, codeobj_class=CPPStandaloneCodeObject, template_kwds=template_kwds, override_conditional_write=override_conditional_write, ) # FIXME: The following is redundant with what is done during # the code object creation above. At the moment, the code # object does not allow us to access the information we # need (variables that are read/written by the run_regularly # code), though. generator = CPPCodeGenerator(variables, variable_indices, owner=owner, iterate_all=False, codeobj_class=GeNNUserCodeObject, name=name, template_name='run_regularly_scalar_code', override_conditional_write=override_conditional_write, allows_scalar_write=True) scalar_statements, vector_statements = make_statements(abstract_code[None], variables, numpy.float64) read_sc, write_sc, _ = generator.array_read_write(scalar_statements) read_ve, write_ve, _ = generator.array_read_write(vector_statements) # We do not need to copy over constant values from the GPU read = {r for r in (read_sc | read_ve) if not variables[r].constant} self.run_regularly_read_write[codeobj.name] = {'read': read, 'write': write_sc | write_ve} elif ((template_name in ['stateupdate', 'threshold', 'reset'] and isinstance(owner, NeuronGroup)) or (template_name in ['summed_variable'] and isinstance(owner, Synapses))): # Delay the code generation process, we want to merge them into one # code object later codeobj = DelayedCodeObject(owner=owner, name=name, abstract_code=abstract_code, variables=variables, variable_indices=variable_indices, override_conditional_write=override_conditional_write) # We need to clear the array cache for these at some point (normally # would be done in cpp_standalone.device.code_object() # I will do it here but not sure this is the best place # I am also not sure whether "written_readonly_vars" apply here # I WILL ASSUME NOT for var in codeobj.variables.values(): if (isinstance(var, ArrayVariable) and not var.read_only): self.array_cache[var] = None self.simple_code_objects[name] = codeobj elif template_name in ['reset', 'synapses', 'stateupdate', 'threshold']: codeobj_class = GeNNCodeObject codeobj = super(GeNNDevice, self).code_object(owner, name, abstract_code, variables, template_name, variable_indices, codeobj_class=codeobj_class, template_kwds=template_kwds, override_conditional_write=override_conditional_write, ) self.simple_code_objects[codeobj.name] = codeobj else: codeobj_class = GeNNUserCodeObject if ('_synapses_create_generator_' in name) or ('_synapses_create_array_' in name): # Here we process max_row_length for synapses # the strategy is to do a dry run of connection generationin in the model definition # function that has the same random numbers and just counts synaptic connections # rather than generating them for real generator= '_synapses_create_generator_' in name mrl_name= '%s_max_row_length' % owner.name i= 1 while mrl_name in self.max_row_length_code_objects: mrl_name= '%s_max_row_length_%d' % (owner.name, i) i= i+1 if generator: mrl_template_name= 'max_row_length_generator' else: mrl_template_name='max_row_length_array' codeobj = super(GeNNDevice, self).code_object(owner, mrl_name, abstract_code, variables, mrl_template_name, variable_indices, codeobj_class=codeobj_class, template_kwds=template_kwds, override_conditional_write=override_conditional_write, ) #self.code_objects['%s_max_row_length' % owner.name] = codeobj self.code_objects.pop(mrl_name, None) # remove this from the normal list of code objects self.max_row_length_code_objects[mrl_name]= codeobj # add to this dict instead self.max_row_length_synapses.add(owner.name) self.max_row_length_include.append('#include "code_objects/%s.cpp"' % codeobj.name) self.max_row_length_run_calls.append('_run_%s();' % mrl_name) codeobj = super(GeNNDevice, self).code_object(owner, name, abstract_code, variables, template_name, variable_indices, codeobj_class=codeobj_class, template_kwds=template_kwds, override_conditional_write=override_conditional_write, ) # FIXME: is this actually necessary or is it already added by the super? self.code_objects[codeobj.name] = codeobj return codeobj
# The following two methods are only overwritten to catch assignments to the # delay variable -- GeNN does not support heterogeneous delays
[docs] def fill_with_array(self, var, arr): if isinstance(var.owner, Synapses) and var.name == 'delay': # Assigning is only allowed if the variable has been declared in the # Synapse constructor and is therefore scalar if not var.scalar: raise NotImplementedError( 'GeNN does not support assigning to the ' 'delay variable -- set the delay for all' 'synapses (heterogeneous delays are not ' 'supported) as an argument to the ' 'Synapses initializer.') else: # We store the delay so that we can later access it self.delays[var.owner.name] = numpy.asarray(arr).item() elif isinstance(var.owner, NeuronGroup) and var.name == 'lastspike': # Workaround for versions of Brian 2 <= 2.1.3.1 which initialize # a NeuronGroup's lastspike variable to -inf, no longer supported # by the new implementation of the timestep function if arr == -numpy.inf: logger.warn('Initializing the lastspike variable with -10000s ' 'instead of -inf to copy the behaviour of Brian 2 ' 'for versions >= 2.2 -- upgrade Brian 2 to remove ' 'this warning', name_suffix='lastspike_inf', once=True) arr = numpy.array(-1e4) super(GeNNDevice, self).fill_with_array(var, arr)
[docs] def variableview_set_with_index_array(self, variableview, item, value, check_units): var = variableview.variable if isinstance(var.owner, Synapses) and var.name == 'delay': raise NotImplementedError('GeNN does not support assigning to the ' 'delay variable -- set the delay for all ' 'synapses (heterogeneous delays are not ' 'supported) as an argument to the ' 'Synapses initializer.') super(GeNNDevice, self).variableview_set_with_index_array(variableview, item, value, check_units)
[docs] def variableview_set_with_expression(self, variableview, item, code, run_namespace, check_units=True): var = variableview.variable if isinstance(var.owner, Synapses) and var.name == 'delay': raise NotImplementedError('GeNN does not support assigning to the ' 'delay variable -- set the delay for all ' 'synapses (heterogeneous delays are not ' 'supported) as an argument to the ' 'Synapses initializer.') variableview.set_with_expression.original_function(variableview, item, code, run_namespace, check_units)
[docs] def variableview_set_with_expression_conditional(self, variableview, cond, code, run_namespace, check_units=True): var = variableview.variable if isinstance(var.owner, Synapses) and var.name == 'delay': raise NotImplementedError('GeNN does not support assigning to the ' 'delay variable -- set the delay for all ' 'synapses (heterogeneous delays are not ' 'supported) as an argument to the ' 'Synapses initializer.') variableview.set_with_expression_conditional.original_function(variableview, cond, code, run_namespace, check_units)
# --------------------------------------------------------------------------
[docs] def make_main_lines(self): ''' Generates the code lines that handle initialisation of Brian 2 cpp_standalone type arrays. These are then translated into the appropriate GeNN data structures in separately generated code. ''' main_lines = [] procedures = [('', main_lines)] runfuncs = {} for func, args in self.main_queue: # explicitly exclude spike queue related code objects here: if (func.endswith('run_code_object') and (args[0].name.endswith('_initialise_queue') or args[0].name.endswith('_push_spikes'))): continue if func == 'run_code_object': codeobj, = args if self.run_statement_used: raise NotImplementedError('Cannot execute code after the ' 'run statement ' '(CodeObject: %s)' % codeobj.name) main_lines.append('_run_%s();' % codeobj.name) elif func == 'before_run_code_object': codeobj, = args main_lines.append('_before_run_%s();' % codeobj.name) elif func == 'after_run_code_object': codeobj, = args main_lines.append('_after_run_%s();' % codeobj.name) elif func == 'run_network': net, netcode = args # do nothing elif func == 'set_by_constant': arrayname, value, is_dynamic = args size_str = arrayname + '.size()' if is_dynamic else '_num_' + arrayname code = ''' for(int i=0; i<{size_str}; i++) {{ {arrayname}[i] = {value}; }} '''.format(arrayname=arrayname, size_str=size_str, value=CPPNodeRenderer().render_expr(repr(value))) main_lines.extend(code.split('\n')) elif func == 'set_by_array': arrayname, staticarrayname, is_dynamic = args size_str = arrayname + '.size()' if is_dynamic else '_num_' + arrayname code = ''' for(int i=0; i<{size_str}; i++) {{ {arrayname}[i] = {staticarrayname}[i]; }} '''.format(arrayname=arrayname, size_str=size_str, staticarrayname=staticarrayname) main_lines.extend(code.split('\n')) elif func == 'set_by_single_value': arrayname, item, value = args code = '{arrayname}[{item}] = {value};'.format( arrayname=arrayname, item=item, value=value) main_lines.extend([code]) elif func == 'set_array_by_array': arrayname, staticarrayname_index, staticarrayname_value = args code = ''' for(int i=0; i<_num_{staticarrayname_index}; i++) {{ {arrayname}[{staticarrayname_index}[i]] = {staticarrayname_value}[i]; }} '''.format(arrayname=arrayname, staticarrayname_index=staticarrayname_index, staticarrayname_value=staticarrayname_value) main_lines.extend(code.split('\n')) elif func == 'resize_array': array_name, new_size = args main_lines.append("{array_name}.resize({new_size});".format( array_name=array_name, new_size=new_size)) elif func == 'insert_code': main_lines.append(args) elif func == 'start_run_func': name, include_in_parent = args if include_in_parent: main_lines.append('%s();' % name) main_lines = [] procedures.append((name, main_lines)) elif func == 'end_run_func': name, include_in_parent = args name, main_lines = procedures.pop(-1) runfuncs[name] = main_lines name, main_lines = procedures[-1] elif func == 'seed': raise NotImplementedError('Setting a seed is currently ' 'not supported') else: raise TypeError("Unknown main queue function type " + func) # generate the finalisations for codeobj in itervalues(self.code_objects): if hasattr(codeobj.code, 'main_finalise'): main_lines.append(codeobj.code.main_finalise) return main_lines
[docs] def fix_random_generators(self, model, code): ''' Translates cpp_standalone style random number generator calls into GeNN- compatible calls by replacing the cpp_standalone `_vectorisation_idx` argument with the GeNN `_seed` argument. ''' # TODO: In principle, _vectorisation_idx is an argument to any # function that does not take any arguments -- in practice, random # number generators are the only argument-less functions that are # commonly used. We cannot check for explicit names `_rand`, etc., # since multiple uses of binomial or PoissonInput will need to names # that we cannot easily predict (poissoninput_binomial_2, etc.) if '_vectorisation_idx)' in code: code = code.replace('_vectorisation_idx)', '_seed)') if not '_seed' in model.variables: model.variables.append('_seed') model.variabletypes.append('uint64_t') model.variablescope['_seed'] = 'genn' return code
# --------------------------------------------------------------------------
[docs] def build(self, directory='GeNNworkspace', compile=True, run=True, use_GPU=True, debug=False, with_output=True, direct_call=True): ''' This function does the main post-translation work for the genn device. It uses the code generated during/before run() and extracts information about neuron groups, synapse groups, monitors, etc. that is then formatted for use in GeNN-specific templates. The overarching strategy of the brian2genn interface is to use cpp_standalone code generation and templates for most of the "user-side code" (in the meaning defined in GeNN) and have GeNN-specific templates for the model definition and the main code for the executable that pulls everything together (in main.cpp and engine.cpp templates). The handling of input/output arrays for everything is lent from cpp_standalone and the cpp_standalone arrays are then translated into GeNN-suitable data structures using the static (not code-generated) b2glib library functions. This means that the GeNN specific cod only has to be concerned about executing the correct model and feeding back results into the appropriate cpp_standalone data structures. ''' print('building genn executable ...') if directory is None: # used during testing directory = tempfile.mkdtemp() # Start building the project self.project_dir = directory ensure_directory(directory) for d in ['code_objects', 'results', 'static_arrays']: ensure_directory(os.path.join(directory, d)) writer = CPPWriter(directory) logger.debug( "Writing GeNN project to directory " + os.path.normpath(directory)) # FIXME: This is only needed to keep Brian2GeNN compatible with Brian2 2.0.1 and earlier if isinstance(self.arange_arrays, dict): arange_arrays = sorted([(var, start) for var, start in iteritems(self.arange_arrays)], key=lambda var_start: var_start[0].name) else: arange_arrays = self.arange_arrays # write the static arrays for code_object in itervalues(self.code_objects): for var in itervalues(code_object.variables): if isinstance(var, Function): self._insert_func_namespace(var, code_object, self.static_arrays) logger.debug("static arrays: " + str(sorted(self.static_arrays.keys()))) static_array_specs = [] for name, arr in sorted(self.static_arrays.items()): arr.tofile(os.path.join(directory, 'static_arrays', name)) static_array_specs.append( (name, c_data_type(arr.dtype), arr.size, name)) try: # Brian versions > 2.2.2.1 do not save the "contained objects" in # net.objects anymore from brian2.core.network import _get_all_objects net_objects = _get_all_objects(self.net.objects) except ImportError: net_objects = self.net.objects main_lines = self.make_main_lines() # assemble the model descriptions: objects = dict((obj.name, obj) for obj in net_objects) neuron_groups = [obj for obj in net_objects if isinstance(obj, NeuronGroup)] poisson_groups = [obj for obj in net_objects if isinstance(obj, PoissonGroup)] spikegenerator_groups = [obj for obj in net_objects if isinstance(obj, SpikeGeneratorGroup)] synapse_groups = [obj for obj in net_objects if isinstance(obj, Synapses)] spike_monitors = [obj for obj in net_objects if isinstance(obj, SpikeMonitor)] rate_monitors = [obj for obj in net_objects if isinstance(obj, PopulationRateMonitor)] state_monitors = [obj for obj in net_objects if isinstance(obj, StateMonitor)] for obj in net_objects: if isinstance(obj, (SpatialNeuron, SpatialStateUpdater)): raise NotImplementedError( 'Brian2GeNN does not support multicompartmental neurons') if not isinstance(obj, ( NeuronGroup, PoissonGroup, SpikeGeneratorGroup, Synapses, SpikeMonitor, PopulationRateMonitor, StateMonitor, StateUpdater, SynapsesStateUpdater, Resetter, Thresholder, SynapticPathway, CodeRunner)): raise NotImplementedError( "Brian2GeNN does not support objects of type " "'%s'" % obj.__class__.__name__) # We only support run_regularly and "constant over dt" # subexpressions for neurons if (isinstance(obj, SubexpressionUpdater) and not isinstance(obj.group, NeuronGroup)): raise NotImplementedError( 'Subexpressions with the flag "constant over dt" are only ' 'supported for NeuronGroup (not for objects of type ' '"%s").' % obj.group.__class__.__name__ ) self.dtDef = 'model.setDT(' + repr(float(defaultclock.dt)) + ');' # Process groups self.process_neuron_groups(neuron_groups, objects) self.process_poisson_groups(objects, poisson_groups) self.process_spikegenerators(spikegenerator_groups) self.process_synapses(synapse_groups, objects) # Process monitors self.process_spike_monitors(spike_monitors) self.process_rate_monitors(rate_monitors) self.process_state_monitors(directory, state_monitors, writer) # Turn anonymous namespaces into named namespaces to avoid # issues when cpp files are included for code_object in itertools.chain(self.code_objects.values(), self.max_row_length_code_objects.values()): cpp_code = getattr(code_object.code, 'cpp_file', code_object.code) if 'namespace {' in cpp_code: cpp_code = cpp_code.replace('namespace {', 'namespace {} {{'.format(code_object.name)) cpp_code = cpp_code.replace('using namespace brian;', 'using namespace brian;\nusing namespace {};'.format(code_object.name)) if hasattr(code_object.code, 'cpp_file'): code_object.code.cpp_file = cpp_code else: code_object.code = cpp_code # Write files from templates # Create an empty network.h file, this allows us to use Brian2's # objects.cpp template unchanged writer.write('network.*', GeNNUserCodeObject.templater.network(None, None)) self.header_files.add('network.h') self.generate_objects_source(arange_arrays, self.net, static_array_specs, synapse_groups, writer) self.copy_source_files(writer, directory) # Rename randomkit.c so that it gets compiled by an explicit rule in # GeNN's makefile template, otherwise optimization flags will not be # used. randomkit_dir = os.path.join(directory, 'brianlib', 'randomkit') shutil.move(os.path.join(randomkit_dir, 'randomkit.c'), os.path.join(randomkit_dir, 'randomkit.cc')) self.generate_code_objects(writer) self.generate_max_row_length_code_objects(writer) self.generate_model_source(writer, main_lines, use_GPU) self.generate_main_source(writer, main_lines) self.generate_engine_source(writer, objects) self.generate_makefile(directory, use_GPU) # Compile and run if compile: try: self.compile_source(debug, directory, use_GPU) except CalledProcessError as ex: raise RuntimeError(('Project compilation failed (Command {cmd} ' 'failed with error code {returncode}).\n' 'See the output above (if any) for more ' 'details.').format(cmd=ex.cmd, returncode=ex.returncode) ) if run: try: self.run(directory, use_GPU, with_output) except CalledProcessError as ex: if ex.returncode == 222: raise NotImplementedError('GeNN does not support multiple ' 'synapses per neuron pair (use ' 'multiple Synapses objects).') else: raise RuntimeError(('Project run failed (Command {cmd} ' 'failed with error code {returncode}).\n' 'See the output above (if any) for more ' 'details.').format(cmd=ex.cmd, returncode=ex.returncode) )
[docs] def generate_code_objects(self, writer): # Generate data for non-constant values code_object_defs = defaultdict(list) for codeobj in itervalues(self.code_objects): lines = [] for k, v in iteritems(codeobj.variables): if isinstance(v, ArrayVariable): try: if isinstance(v, DynamicArrayVariable): if get_var_ndim(v) == 1: dyn_array_name = self.dynamic_arrays[v] array_name = self.arrays[v] line = '{c_type}* const {array_name} = &{dyn_array_name}[0];' line = line.format(c_type=c_data_type(v.dtype), array_name=array_name, dyn_array_name=dyn_array_name) lines.append(line) line = 'const int _num{k} = {dyn_array_name}.size();' line = line.format(k=k, dyn_array_name=dyn_array_name) lines.append(line) else: lines.append('const int _num%s = %s;' % (k, v.size)) except TypeError: pass for line in lines: # Sometimes an array is referred to by to different keys in our # dictionary -- make sure to never add a line twice if not line in code_object_defs[codeobj.name]: code_object_defs[codeobj.name].append(line) # Generate the code objects for codeobj in itervalues(self.code_objects): ns = codeobj.variables # TODO: fix these freeze/CONSTANTS hacks somehow - they work but not elegant. if ((codeobj.template_name not in ['stateupdate', 'threshold', 'reset', 'synapses']) or ('_run_regularly_' in codeobj.name)): if isinstance(codeobj.code, MultiTemplate): code = freeze(codeobj.code.cpp_file, ns) code = code.replace('%CONSTANTS%', '\n'.join( code_object_defs[codeobj.name])) code = '#include "objects.h"\n' + code writer.write('code_objects/' + codeobj.name + '.cpp', code) self.source_files.add( 'code_objects/' + codeobj.name + '.cpp') writer.write('code_objects/' + codeobj.name + '.h', codeobj.code.h_file) self.header_files.add( 'code_objects/' + codeobj.name + '.h')
[docs] def generate_max_row_length_code_objects(self, writer): # Generate data for non-constant values code_object_defs = defaultdict(set) for codeobj in itervalues(self.max_row_length_code_objects): for k, v in iteritems(codeobj.variables): if isinstance(v, ArrayVariable): try: if isinstance(v, DynamicArrayVariable): if get_var_ndim(v) == 1: dyn_array_name = self.dynamic_arrays[v] array_name = self.arrays[v] # do the const stuff line = '{c_type}* const {array_name} = &{dyn_array_name}[0];' line = line.format(c_type=c_data_type(v.dtype), array_name=array_name, dyn_array_name=dyn_array_name) code_object_defs[codeobj.name].add(line) line = 'const int _num{k} = {dyn_array_name}.size();' line = line.format(k=k, dyn_array_name=dyn_array_name) code_object_defs[codeobj.name].add(line) else: array_name = self.arrays[v] line = '{c_type} {array_name}[{size}];' line = line.format(c_type=c_data_type(v.dtype), array_name=array_name, size=v.size) code_object_defs[codeobj.name].add('const int _num%s = %s;' % (k, v.size)) except TypeError: pass for codeobj in itervalues(self.max_row_length_code_objects): ns = codeobj.variables # TODO: fix these freeze/CONSTANTS hacks somehow - they work but not elegant. code = freeze(codeobj.code, ns) code = code.replace('%CONSTANTS%', '\n'.join( code_object_defs[codeobj.name])) writer.write('code_objects/' + codeobj.name + '.cpp', code)
[docs] def run(self, directory, use_GPU, with_output): gpu_arg = "1" if use_GPU else "0" if gpu_arg == "1": where = 'on GPU' else: where = 'on CPU' print('executing genn binary %s ...' % where) pref_vars = prefs['devices.cpp_standalone.run_environment_variables'] for key, value in itertools.chain(iteritems(pref_vars), iteritems(self.run_environment_variables)): if key in os.environ and os.environ[key] != value: logger.info('Overwriting environment variable ' '"{key}"'.format(key=key), name_suffix='overwritten_env_var', once=True) os.environ[key] = value with std_silent(with_output): if os.sys.platform == 'win32': cmd = directory + "\\main_Release.exe test " + str( self.run_duration) check_call(cmd, cwd=directory) else: # print ["./main", "test", str(self.run_duration), gpu_arg] check_call(["./main", "test", str(self.run_duration)], cwd=directory) self.has_been_run = True last_run_info = open( os.path.join(directory, 'results/last_run_info.txt'), 'r').read() self._last_run_time, self._last_run_completed_fraction = map(float, last_run_info.split()) # The following is a verbatim copy of the respective code in # CPPStandaloneDevice.run. In the long run, we can hopefully implement # this on the device-independent level, see #761 and discussion in # #750. # Make sure that integration did not create NaN or very large values owners = [var.owner for var in self.arrays] # We don't want to check the same owner twice but var.owner is a # weakproxy which we can't put into a set. We therefore store the name # of all objects we already checked. Furthermore, under some specific # instances a variable might have been created whose owner no longer # exists (e.g. a `_sub_idx` variable for a subgroup) -- we ignore the # resulting reference error. already_checked = set() for owner in owners: try: if owner.name in already_checked: continue if isinstance(owner, Group): owner._check_for_invalid_states() already_checked.add(owner.name) except ReferenceError: pass
[docs] def compile_source(self, debug, directory, use_GPU): if prefs.devices.genn.path is not None: genn_path = prefs.devices.genn.path logger.debug('Using GeNN path from preference: ' '"{}"'.format(genn_path)) elif 'GENN_PATH' in os.environ: genn_path = os.environ['GENN_PATH'] logger.debug('Using GeNN path from environment variable: ' '"{}"'.format(genn_path)) else: # Find genn-buildmodel genn_bin = (find_executable("genn-buildmodel.bat") if os.sys.platform == 'win32' else find_executable("genn-buildmodel.sh")) if genn_bin is None: raise RuntimeError('Add GeNN\'s bin directory to the path ' 'or set the devices.genn.path preference.') # Remove genn-buildmodel from path, navigate up a directory and normalize genn_path = os.path.normpath(os.path.join(os.path.dirname(genn_bin), "..")) logger.debug('Using GeNN path determined from path: ' '"{}"'.format(genn_path)) # Check for GeNN compatibility genn_version = None version_file = os.path.join(genn_path, 'version.txt') if os.path.exists(version_file): try: with open(version_file, 'r') as f: genn_version = parse_version(f.read().strip()) logger.debug('GeNN version: %s' % genn_version) except (OSError, IOError) as ex: logger.debug('Getting version from %s/version.txt ' 'failed: %s' % (genn_path, str(ex))) if genn_version is None or not genn_version >= parse_version('4.2.1'): raise RuntimeError('Brian2GeNN requires GeNN 4.2.1 or later. ' 'Please upgrade your GeNN version.') env = os.environ.copy() if use_GPU: if prefs.devices.genn.cuda_backend.cuda_path is not None: cuda_path = prefs.devices.genn.cuda_backend.cuda_path env['CUDA_PATH'] = cuda_path logger.debug('Using CUDA path from preference: ' '"{}"'.format(cuda_path)) elif 'CUDA_PATH' in env: cuda_path = env['CUDA_PATH'] logger.debug('Using CUDA path from environment variable: ' '"{}"'.format(cuda_path)) else: raise RuntimeError('Set the CUDA_PATH environment variable or ' 'the devices.genn.cuda_path preference.') with std_silent(debug): if os.sys.platform == 'win32': # Make sure that all environment variables are upper case env = {k.upper() : v for k, v in iteritems(env)} # If there is vcvars command to call, start cmd with that cmd = '' msvc_env, vcvars_cmd = get_msvc_env() if vcvars_cmd: cmd += vcvars_cmd + ' && ' # Otherwise, update environment, again ensuring # that all variables are upper case else: env.update({k.upper() : v for k, v in iteritems(msvc_env)}) # Add start of call to genn-buildmodel buildmodel_cmd = os.path.join(genn_path, 'bin', 'genn-buildmodel.bat') cmd += buildmodel_cmd + ' -s' # If we're not using CPU, add CPU option if not use_GPU: cmd += ' -c' # Add include directories # **NOTE** on windows semicolons are used to seperate multiple include paths # **HACK** argument list syntax to check_call doesn't support quoting arguments to batch # files so we have to build argument string manually(https://bugs.python.org/issue23862) wdir = os.getcwd() cmd += ' -i "%s;%s;%s"' % (wdir, os.path.join(wdir, directory), os.path.join(wdir, directory, 'brianlib','randomkit')) cmd += ' magicnetwork_model.cpp' # Add call to build generated code cmd += ' && msbuild /m /verbosity:minimal /p:Configuration=Release "' + os.path.join(wdir, directory, 'magicnetwork_model_CODE', 'runner.vcxproj') + '"' # Add call to build executable cmd += ' && msbuild /m /verbosity:minimal /p:Configuration=Release "' + os.path.join(wdir, directory, 'project.vcxproj') + '"' # Run combined command # **NOTE** because vcvars MODIFIED environment, # making seperate check_calls doesn't work check_call(cmd, cwd=directory, env=env) else: if prefs['codegen.cpp.extra_link_args']: # declare the link flags as an environment variable so that GeNN's # generateALL can pick it up env['LDFLAGS'] = ' '.join(prefs['codegen.cpp.extra_link_args']) buildmodel_cmd = os.path.join(genn_path, 'bin', 'genn-buildmodel.sh') args = [buildmodel_cmd] if not use_GPU: args += ['-c'] wdir= os.getcwd() inc_path= wdir; inc_path+= ':'+os.path.join(wdir, directory) inc_path+= ':'+os.path.join(wdir, directory, 'brianlib','randomkit') args += ['-i', inc_path] args += ['magicnetwork_model.cpp'] print(args) check_call(args, cwd=directory, env=env) call(["make", "clean"], cwd=directory, env=env) check_call(["make"], cwd=directory, env=env)
[docs] def add_parameter(self, model, varname, variable): model.parameters.append(varname) model.pvalue.append(CPPNodeRenderer().render_expr(repr(variable.value)))
[docs] def add_array_variable(self, model, varname, variable): if variable.scalar: model.shared_variables.append(varname) model.shared_variabletypes.append(c_data_type(variable.dtype)) else: model.variables.append(varname) model.variabletypes.append(c_data_type(variable.dtype)) model.variablescope[varname] = 'brian'
[docs] def add_array_variables(self, model, owner): for varname, variable in iteritems(owner.variables): if varname in ['_spikespace', 't', 'dt']: pass elif getattr(variable.owner, 'name', None) != owner.name: pass elif isinstance(variable, ArrayVariable): self.add_array_variable(model, varname, variable)
[docs] def process_poisson_groups(self, objects, poisson_groups): for obj in poisson_groups: # throw error if events other than spikes are used event_keys = list(iterkeys(obj.events)) if (len(event_keys) > 1 or (len(event_keys) == 1 and event_keys[0] != 'spike')): raise NotImplementedError( 'Brian2GeNN does not support events that are not spikes') # Extract the variables neuron_model = neuronModel() neuron_model.name = obj.name neuron_model.clock = obj.clock neuron_model.N = obj.N self.add_array_variables(neuron_model, obj) support_lines = [] suffix = '_thresholder'; lines = neuron_model.thresh_cond_lines; codeobj = objects[obj.name + suffix].codeobj for k, v in iteritems(codeobj.variables): if k != 'dt' and isinstance(v, Constant): if k not in neuron_model.parameters: self.add_parameter(neuron_model, k, v) code = codeobj.code.cpp_file code = self.fix_random_generators(neuron_model, code) code = decorate(code, neuron_model.variables, neuron_model.shared_variables, neuron_model.parameters).strip() lines.append(code) code = stringify(codeobj.code.h_file) support_lines.append(code) neuron_model.support_code_lines = support_lines self.neuron_models.append(neuron_model) self.groupDict[neuron_model.name] = neuron_model
[docs] def process_neuron_groups(self, neuron_groups, objects): for obj in neuron_groups: # throw error if events other than spikes are used event_keys = list(iterkeys(obj.events)) if len(event_keys) > 1 or (len(event_keys) == 1 and event_keys[0] != 'spike'): raise NotImplementedError( 'Brian2GeNN does not support events that are not spikes') # Extract the variables neuron_model = neuronModel() neuron_model.name = obj.name neuron_model.clock = obj.clock neuron_model.N = obj.N self.add_array_variables(neuron_model, obj) # We have previously only created "dummy code objects" for the # state update, threshold, and reset of a NeuronGroup. We will now # generate a single code object for all of them, adding the # threshold calculation code to the end of the state update. When # using subexpressions, the threshold condition code could consist # of multiple lines, and GeNN only supports a threshold condition # that is directly used as an if condition. We therefore store the # result in a boolean variable and only pass this variable as the # threshold condition to GeNN. # It is also important that stateupdate/threshold share the same # code object with the reset, as in GeNN both codes have the same # support code. If they used two separate code objects, adding the # two support codes might lead to duplicate definitions of # functions. combined_abstract_code = {'stateupdate': [], 'reset': [], 'subexpression_update': [], 'poisson_input': []} combined_variables = {} combined_variable_indices = defaultdict(lambda: '_idx') combined_override_conditional_write = set() thresholder_codeobj = getattr(objects.get(obj.name + '_thresholder', None), 'codeobj', None) if thresholder_codeobj is not None: neuron_model.thresh_cond_lines = '_cond' else: neuron_model.thresh_cond_lines = '0' for suffix, code_slot in [('_stateupdater', 'stateupdate'), ('_thresholder', 'stateupdate'), ('_resetter', 'reset'), ('_subexpression_update', 'subexpression_update')]: full_name = obj.name + suffix if full_name in objects and objects[full_name].codeobj is not None: codeobj = objects[full_name].codeobj combined_abstract_code[code_slot] += [codeobj.abstract_code[None]] combined_variables.update(codeobj.variables) combined_variable_indices.update(codeobj.variable_indices) # The resetter includes "not_refractory" as an override_conditional_write # variable, meaning that it removes the write-protection based on that # variable that would otherwise apply to "unless refractory" variables, # e.g. the membrane potential. This is not strictly necessary, it will just # introduce an unnecessary check, because a neuron that spiked is by # definition not in its refractory period. However, if we included it as # a override_conditional_write variable for the whole code object here, # this would apply also to the state updater, and therefore # remove the write-protection from "unless refractory" variables in the # state update code. if suffix != '_resetter': combined_override_conditional_write.update(codeobj.override_conditional_write) if obj._refractory is not False: combined_abstract_code['reset'] += ['lastspike = t', 'not_refractory = False'] # Find PoissonInputs targetting this NeuronGroup poisson_inputs = [o for o in itervalues(objects) if isinstance(o, PoissonInput) and o.group.name == obj.name] for poisson_input in poisson_inputs: if poisson_input.when != 'synapses': raise NotImplementedError('Brian2GeNN does not support ' 'changing the scheduling slot ' 'of PoissonInput objects.') codeobj = poisson_input.codeobj combined_abstract_code['poisson_input'] += [codeobj.abstract_code[None]] combined_variables.update(codeobj.variables) combined_variable_indices.update(codeobj.variable_indices) for code_block in iterkeys(combined_abstract_code): combined_abstract_code[code_block] = '\n'.join(combined_abstract_code[code_block]) if any(len(ac) for ac in itervalues(combined_abstract_code)): codeobj = super(GeNNDevice, self).code_object(obj, obj.name + '_stateupdater', combined_abstract_code, combined_variables.copy(), 'neuron_code', combined_variable_indices, codeobj_class=GeNNCodeObject, override_conditional_write=combined_override_conditional_write, ) # Remove the code object from the code_objects dictionary, we # take care of it manually and do not want it to be generated as # part of `generate_code_objects`. del self.code_objects[codeobj.name] for k, v in iteritems(codeobj.variables): if k != 'dt' and isinstance(v, Constant): if k not in neuron_model.parameters: self.add_parameter(neuron_model, k, v) update_code = codeobj.code.stateupdate_code reset_code = codeobj.code.reset_code for code, lines in [(update_code, neuron_model.code_lines), (reset_code, neuron_model.reset_code_lines)]: code = self.fix_random_generators(neuron_model, code) code = decorate(code, neuron_model.variables, neuron_model.shared_variables, neuron_model.parameters).strip() lines.append(code) support_code = stringify(codeobj.code.h_file) neuron_model.support_code_lines = support_code self.neuron_models.append(neuron_model) self.groupDict[neuron_model.name] = neuron_model
[docs] def process_spikegenerators(self, spikegenerator_groups): for obj in spikegenerator_groups: spikegenerator_model = spikegeneratorModel() spikegenerator_model.name = obj.name spikegenerator_model.codeobject_name = obj.codeobj.name spikegenerator_model.N = obj.N self.spikegenerator_models.append(spikegenerator_model)
[docs] def process_synapses(self, synapse_groups, objects): for obj in synapse_groups: synapse_model = synapseModel() synapse_model.name = obj.name if isinstance(obj.source, Subgroup): synapse_model.srcname = obj.source.source.name synapse_model.srcN = obj.source.source.variables['N'].get_value() else: synapse_model.srcname = obj.source.name synapse_model.srcN = obj.source.variables['N'].get_value() if isinstance(obj.target, Subgroup): synapse_model.trgname = obj.target.source.name synapse_model.trgN = obj.target.source.variables['N'].get_value() else: synapse_model.trgname = obj.target.name synapse_model.trgN = obj.target.variables['N'].get_value() synapse_model.connectivity = prefs.devices.genn.connectivity self.connectivityDict[obj.name] = synapse_model.connectivity for pathway in obj._synaptic_updaters: if pathway not in ['pre', 'post']: raise NotImplementedError("brian2genn only supports a " "single synaptic pre and post " "pathway, cannot use pathway " "'%s'." % pathway) for pathway in ['pre', 'post']: if hasattr(obj, pathway): codeobj = getattr(obj, pathway).codeobj # A little hack to support "write-protection" for refractory # variables -- brian2genn currently requires that # post-synaptic variables end with "_post" if pathway == 'pre' and 'not_refractory' in codeobj.variables: codeobj.variables['not_refractory_post'] = \ codeobj.variables['not_refractory'] codeobj.variable_indices['not_refractory_post'] = \ codeobj.variable_indices['not_refractory'] del codeobj.variables['not_refractory'] del codeobj.variable_indices['not_refractory'] self.collect_synapses_variables(synapse_model, pathway, codeobj) if pathway == 'pre': # Use the stored scalar delay (if any) for these synapses synapse_model.delay = int( self.delays.get(obj.name, 0.0) / defaultclock.dt_ + 0.5) code = codeobj.code.cpp_file code_lines = [line.strip() for line in code.split('\n')] new_code_lines = [] if pathway == 'pre': for line in code_lines: if line.startswith('addtoinSyn'): if synapse_model.connectivity == 'SPARSE': line = line.replace('_hidden_weightmatrix*', '') line = line.replace( '_hidden_weightmatrix *', '') new_code_lines.append(line) code = '\n'.join(new_code_lines) self.fix_synapses_code(synapse_model, pathway, codeobj, code) if obj.state_updater is not None: codeobj = obj.state_updater.codeobj code = codeobj.code.cpp_file self.collect_synapses_variables(synapse_model, 'dynamics', codeobj) self.fix_synapses_code(synapse_model, 'dynamics', codeobj, code) synapse_model.summed_variables = [ s for s in objects if s.startswith(obj.name+'_summed_variable')] if len(synapse_model.summed_variables) > 0 and hasattr(obj, '_genn_post_write_var'): raise NotImplementedError("brian2genn only supports a " "either a single synaptic output variable " "or a single summed variable per Synapses group.") if len(synapse_model.summed_variables) > 0 and isinstance(obj.target,Subgroup): raise NotImplementedError("brian2genn does not support summed variables " "when the target is a Subgroup.") if len(synapse_model.summed_variables) > 1: raise NotImplementedError("brian2genn only supports a " "single summed variable per Synapses group.") if hasattr(obj, '_genn_post_write_var'): synapse_model.postSyntoCurrent = '0; $(' + obj._genn_post_write_var.replace( '_post', '') + ') += $(inSyn); $(inSyn)= 0' else: if len(synapse_model.summed_variables) > 0: summed_variable_updater= objects.get(synapse_model.summed_variables[0], None) if obj.target != summed_variable_updater.target: raise NotImplementedError("brian2genn only supports summed " "variables that target the post-synaptic neuron group of the Synapses the variable is defined in.") synapse_model.postSyntoCurrent = '0; $(' + summed_variable_updater.target_var.name + ') = $(inSyn); $(inSyn)= 0' # also add the inSyn updating code to the synapse dynamics code addVar = summed_variable_updater.abstract_code.replace('_synaptic_var = ', '').replace('\n', '').replace(' ', '') codeobj = summed_variable_updater.codeobj code_generator = GeNNCodeGenerator(codeobj.variables, codeobj.variable_indices, codeobj.owner, None, GeNNCodeObject, codeobj.name, None) addVar = code_generator.translate_expression(addVar) kwds = code_generator.determine_keywords() identifiers = get_identifiers(addVar) for k, v in iteritems(codeobj.variables): if k in ['_spikespace', 't', 'dt'] or k not in identifiers: pass else: if '_pre' not in k and '_post' not in k: if isinstance(v, Constant): if k not in synapse_model.parameters: self.add_parameter(synapse_model, k, v) elif isinstance(v, ArrayVariable): if k not in synapse_model.variables: self.add_array_variable(synapse_model, k, v) addVar= addVar.replace(k,'$('+k+')') code= '\\n\\\n $(addToInSyn,'+addVar+');\\n' synapse_model.main_code_lines['dynamics'] += code synapse_model.support_code_lines['dynamics'] += stringify('\n'.join(kwds['support_code_lines'])) else: synapse_model.postSyntoCurrent = '0' self.synapse_models.append(synapse_model) self.groupDict[synapse_model.name] = synapse_model
[docs] def collect_synapses_variables(self, synapse_model, pathway, codeobj): identifiers = set() for code in itervalues(codeobj.code): identifiers |= get_identifiers(code) indices = codeobj.variable_indices for k, v in iteritems(codeobj.variables): if k in ['_spikespace', 't', 'dt'] or k not in identifiers: pass elif isinstance(v, Constant): if k not in synapse_model.parameters: self.add_parameter(synapse_model, k, v) elif isinstance(v, ArrayVariable): if indices[k] == '_idx': if k not in synapse_model.variables: self.add_array_variable(synapse_model, k, v) elif indices[k] == '0': if k not in synapse_model.shared_variables: self.add_array_variable(synapse_model, k, v) else: index = indices[k] if (pathway in ['pre', 'post'] and index == '_{}synaptic_idx'.format(pathway)): raise NotImplementedError('brian2genn does not support ' 'references to {pathway}-' 'synaptic variables in ' 'on_{pathway} ' 'statements.'.format( pathway=pathway)) if k not in synapse_model.external_variables: synapse_model.external_variables.append(k) elif isinstance(v, Subexpression): raise NotImplementedError( 'Brian2genn does not support the use of ' 'subexpressions in synaptic statements')
[docs] def fix_synapses_code(self, synapse_model, pathway, codeobj, code): if synapse_model.connectivity == 'DENSE': code = 'if (_hidden_weightmatrix != 0.0) {' + code + '}' code = self.fix_random_generators(synapse_model, code) thecode = decorate(code, synapse_model.variables, synapse_model.shared_variables, synapse_model.parameters, False).strip() thecode = decorate(thecode, synapse_model.external_variables, [], [], True).strip() synapse_model.main_code_lines[pathway] = thecode code = stringify(codeobj.code.h_file) synapse_model.support_code_lines[pathway] = code
[docs] def process_spike_monitors(self, spike_monitors): for obj in spike_monitors: if obj.event != 'spike': raise NotImplementedError( 'GeNN does not yet support event monitors for non-spike events.'); sm = spikeMonitorModel() sm.name = obj.name sm.codeobject_name = obj.codeobj.name if (hasattr(obj, 'when')): if (not obj.when in ['end', 'thresholds']): # GeNN always records in the end slot but this should # almost never make a difference and we therefore do not # raise a warning if the SpikeMonitor records in the default # thresholds slot. We do raise a NotImplementedError if the # user manually changed the time slot to something else -- # there was probably a reason for doing it. raise NotImplementedError( "Spike monitor {!s} has 'when' property '{!s}' which " "is not supported in GeNN, defaulting to 'end'.".format( sm.name, obj.when)) src = obj.source if isinstance(src, Subgroup): src = src.source sm.neuronGroup = src.name if isinstance(src, SpikeGeneratorGroup): sm.notSpikeGeneratorGroup = False self.spike_monitor_models.append(sm)
# ------------------------------------------------------------------------------ # Process rate monitors
[docs] def process_rate_monitors(self, rate_monitors): for obj in rate_monitors: sm = rateMonitorModel() sm.name = obj.name sm.codeobject_name = obj.codeobj.name if obj.when != 'end': logger.warn("Rate monitor {!s} has 'when' property '{!s}' which" "is not supported in GeNN, defaulting to" "'end'.".format(sm.name, obj.when)) src = obj.source if isinstance(src, Subgroup): src = src.source sm.neuronGroup = src.name if isinstance(src, SpikeGeneratorGroup): sm.notSpikeGeneratorGroup = False self.rate_monitor_models.append(sm)
[docs] def process_state_monitors(self, directory, state_monitors, writer): for obj in state_monitors: sm = stateMonitorModel() sm.name = obj.name sm.codeobject_name = obj.codeobj.name sm.order = obj.order src = obj.source if isinstance(src, Subgroup): src = src.source sm.monitored = src.name sm.src = src sm.when = obj.when if sm.when not in ['start', 'end']: logger.warn("State monitor {!s} has 'when' property '{!s}'" "which is not supported in GeNN, defaulting to" "'end'.".format(sm.name, sm.when)) sm.when = 'end' if isinstance(src, Synapses): sm.isSynaptic = True sm.srcN = src.source.variables['N'].get_value() sm.trgN = src.target.variables['N'].get_value() sm.connectivity = self.connectivityDict[src.name] else: sm.isSynaptic = False sm.N = src.variables['N'].get_value() for varname in obj.record_variables: if src.variables[varname] in itervalues(defaultclock.variables): raise NotImplementedError('Recording the time t or the ' 'timestep dt is currently not ' 'supported in Brian2GeNN') if isinstance(src.variables[varname], Subexpression): extract_source_variables(src.variables, varname, sm.variables) elif isinstance(src.variables[varname], Constant): logger.warn( "variable '%s' is a constant - not monitoring" % varname) elif varname not in self.groupDict[sm.monitored].variables: logger.warn( "variable '%s' is unused - not monitoring" % varname) else: sm.variables.append(varname) self.state_monitor_models.append(sm)
[docs] def generate_model_source(self, writer, main_lines, use_GPU): synapses_classes_tmp = CPPStandaloneCodeObject.templater.synapses_classes(None, None) writer.write('synapses_classes.*', synapses_classes_tmp) default_dtype = prefs.core.default_float_dtype if default_dtype == numpy.float32: precision = 'GENN_FLOAT' elif default_dtype == numpy.float64: precision = 'GENN_DOUBLE' else: raise NotImplementedError("GeNN does not support default dtype " "'{}'".format(default_dtype.__name__)) dry_main_lines= [] for line in main_lines: if ('_synapses_create_' not in line) and ('monitor' not in line): dry_main_lines.append(line) codeobj_inc= [] for codeobj in itervalues(self.code_objects): if ('group_variable' in codeobj.name): codeobj_inc.append('#include "code_objects/'+codeobj.name+'.cpp"') model_tmp = GeNNCodeObject.templater.model(None, None, use_GPU=use_GPU, code_lines=self.code_lines, neuron_models=self.neuron_models, spikegenerator_models=self.spikegenerator_models, synapse_models=self.synapse_models, main_lines=dry_main_lines, max_row_length_include= self.max_row_length_include, max_row_length_run_calls=self.max_row_length_run_calls, max_row_length_synapses=self.max_row_length_synapses, codeobj_inc=codeobj_inc, dtDef=self.dtDef, prefs=prefs, precision=precision ) writer.write('magicnetwork_model.cpp', model_tmp)
[docs] def generate_main_source(self, writer, main_lines): header_files = sorted(self.header_files) + prefs['codegen.cpp.headers'] runner_tmp = GeNNCodeObject.templater.main(None, None, code_lines=self.code_lines, neuron_models=self.neuron_models, synapse_models=self.synapse_models, main_lines=main_lines, header_files=header_files, source_files=sorted(self.source_files), prefs=prefs, ) writer.write('main.*', runner_tmp)
[docs] def generate_engine_source(self, writer, objects): maximum_run_time = self._maximum_run_time if maximum_run_time is not None: maximum_run_time = float(maximum_run_time) run_regularly_objects = [o for name, o in objects.items() if '_run_regularly' in name] run_regularly_operations = [] for run_reg in run_regularly_objects: # Figure out after how many steps the operation should be executed if run_reg.when != 'start': raise NotImplementedError( 'Brian2GeNN does not support changing ' 'the scheduling slot for "run_regularly" ' 'operations.') run_regularly_dt = run_reg.clock.dt_ group_dt = run_reg.group.dt_[:] if run_regularly_dt < group_dt: raise NotImplementedError( 'Brian2GeNN does not support run_regularly ' 'operations with a dt smaller than the dt ' 'used by the group.') dt_mismatch = abs(((run_regularly_dt + group_dt / 2) % group_dt) - group_dt / 2) if dt_mismatch > 1e-4 * group_dt: raise NotImplementedError( 'Brian2GeNN does not support run_regularly ' 'operations where the dt is not a multiple of ' 'the dt used by the group.') step_value = int(run_regularly_dt / group_dt + 0.5) codeobj_read_write = self.run_regularly_read_write[run_reg.codeobj.name] op = {'name': run_reg.name, 'order': run_reg.order, 'codeobj': run_reg.codeobj, 'owner': run_reg.group, 'read': codeobj_read_write['read'], 'write': codeobj_read_write['write'], 'step': step_value, 'isSynaptic': False} if isinstance(run_reg.group, Synapses): op['isSynaptic'] = True op['srcN'] = run_reg.group.source.variables['N'].get_value() op['trgN'] = run_reg.group.target.variables['N'].get_value() op['connectivity'] = self.connectivityDict[run_reg.group.name] run_regularly_operations.append(op) # StateMonitors and run_regularly operations are both executed in the "start" # slot. Their order of execution can matter, so we provide a list which sorts # them by their order attribute. For convenient use in the template, the list # stores tuples of a boolean and the object, where the boolean states whether # the object is a stateMonitorModel. run_reg_state_monitor_operations = ([(run_reg['order'], run_reg['name'], False, run_reg) for run_reg in run_regularly_operations] + [(sm.order, sm.name, True, sm) for sm in self.state_monitor_models] ) run_reg_state_monitor_operations = [(is_state_mon, obj) for _, _, is_state_mon, obj in sorted(run_reg_state_monitor_operations)] engine_tmp = GeNNCodeObject.templater.engine(None, None, neuron_models=self.neuron_models, spikegenerator_models=self.spikegenerator_models, synapse_models=self.synapse_models, spike_monitor_models=self.spike_monitor_models, rate_monitor_models=self.rate_monitor_models, state_monitor_models=self.state_monitor_models, run_regularly_operations=run_regularly_operations, maximum_run_time=maximum_run_time, run_reg_state_monitor_operations=run_reg_state_monitor_operations ) writer.write('engine.*', engine_tmp)
[docs] def generate_makefile(self, directory, use_GPU): if os.sys.platform == 'win32': project_tmp = GeNNCodeObject.templater.project_vcxproj(None, None, source_files=self.source_files) open(os.path.join(directory, 'project.vcxproj'), 'w').write( project_tmp) else: compile_args_gcc = get_gcc_compile_args() linker_flags = ' '.join(prefs.codegen.cpp.extra_link_args) makefile_tmp = GeNNCodeObject.templater.Makefile(None, None, source_files=self.source_files, compiler_flags=compile_args_gcc, linker_flags=linker_flags) open(os.path.join(directory, 'Makefile'), 'w').write(makefile_tmp)
[docs] def generate_objects_source(self, arange_arrays, net, static_array_specs, synapses, writer): # ------------------------------------------------------------------------------ # create the objects.cpp and objects.h code the_objects = list(itervalues(self.code_objects)) arr_tmp = GeNNUserCodeObject.templater.objects( None, None, array_specs=self.arrays, dynamic_array_specs=self.dynamic_arrays, dynamic_array_2d_specs=self.dynamic_arrays_2d, zero_arrays=self.zero_arrays, arange_arrays=arange_arrays, synapses=synapses, clocks=self.clocks, static_array_specs=static_array_specs, networks=[], # We don't want to create any networks get_array_filename=self.get_array_filename, get_array_name=self.get_array_name, code_objects=the_objects ) writer.write('objects.*', arr_tmp) self.header_files.add('objects.h') self.source_files.add('objects.cpp')
[docs] def copy_source_files(self, writer, directory): # Copies brianlib, spikequeue and randomkit super(GeNNDevice, self).copy_source_files(writer, directory) # Copy the b2glib directory b2glib_dir = os.path.join( os.path.split(inspect.getsourcefile(GeNNCodeObject))[0], 'b2glib') b2glib_files = copy_directory(b2glib_dir, os.path.join(directory, 'b2glib')) for file in b2glib_files: if file.lower().endswith('.cpp'): self.source_files.add('b2glib/' + file) elif file.lower().endswith('.h'): self.header_files.add('b2glib/' + file)
[docs] def network_run(self, net, duration, report=None, report_period=10 * second, namespace=None, profile=False, level=0, **kwds): if profile is True: raise NotImplementedError('Brian2GeNN does not yet support ' 'detailed profiling.') if kwds: logger.warn(('Unsupported keyword argument(s) provided for run: ' + '%s') % ', '.join(iterkeys(kwds))) if self.run_duration is not None: raise NotImplementedError( 'Only a single run statement is supported for the genn device.') self.run_duration = float(duration) for obj in net.objects: if obj.clock.name != 'defaultclock' and not (obj.__class__ == CodeRunner): raise NotImplementedError( 'Multiple clocks are not supported for the genn device') for obj in net.objects: if hasattr(obj, '_linked_variables'): if len(obj._linked_variables) > 0: raise NotImplementedError( 'The genn device does not support linked variables') print('running brian code generation ...') self.net = net super(GeNNDevice, self).network_run(net=net, duration=duration, report=report, report_period=report_period, namespace=namespace, level=level + 1) self.run_statement_used = True
# ------------------------------------------------------------------------------ # End of GeNNDevice # ------------------------------------------------------------------------------ genn_device = GeNNDevice() all_devices['genn'] = genn_device