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Upgrade RNG #144

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Upgrade RNG #144

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9e033c7
Fix device.py whitespace, courtesy of Atom IDE
kernfel Jan 18, 2022
e877ae8
Replaced bare _rand[n] calls with $(gennrand_*)
kernfel Jan 21, 2022
6740049
Added support for RNG seeding.
kernfel Jan 24, 2022
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59 changes: 35 additions & 24 deletions brian2genn/device.py
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Original file line number Diff line number Diff line change
Expand Up @@ -160,8 +160,8 @@ def extract_source_variables(variables, varname, smvariables):
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.
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)
Expand Down Expand Up @@ -199,7 +199,7 @@ def after_run(self):

class neuronModel(object):
'''
Class that contains all relevant information of a neuron model.
Class that contains all relevant information of a neuron model.
'''

def __init__(self):
Expand Down Expand Up @@ -335,6 +335,7 @@ def __init__(self):
#: Set of all source and header files (to be included in runner)
self.source_files = set()
self.header_files = set()
self._seed = 0

self.connectivityDict = dict()
self.groupDict = dict()
Expand Down Expand Up @@ -478,7 +479,7 @@ def code_object(self, owner, name, abstract_code, variables, template_name,
else:
codeobj_class = GeNNUserCodeObject
if ('_synapses_create_generator_' in name) or ('_synapses_create_array_' in name):
# Here we process max_row_length for synapses
# 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
Expand Down Expand Up @@ -685,8 +686,15 @@ def make_main_lines(self):
runfuncs[name] = main_lines
name, main_lines = procedures[-1]
elif func == 'seed':
raise NotImplementedError('Setting a seed is currently '
'not supported')
logger.warn('Setting a seed with Brian2GeNN is experimental.')
self._seed = 0 if args is None else int(args)
if args == 0:
logger.warn('In Brian2GeNN, seed(0) is equivalent to '
'seed() and sets a randomly chosen seed.')
if self._seed == 0:
main_lines.append('rk_randomseed(brian::_mersenne_twister_states[0]);')
else:
main_lines.append(f'rk_seed({self._seed}, brian::_mersenne_twister_states[0]);')
else:
raise TypeError("Unknown main queue function type " + func)

Expand All @@ -708,6 +716,8 @@ def fix_random_generators(self, model, code):
# 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.)
code = code.replace('_rand(_vectorisation_idx)', '$(gennrand_uniform)')
code = code.replace('_randn(_vectorisation_idx)', '$(gennrand_normal)')
if '_vectorisation_idx)' in code:
code = code.replace('_vectorisation_idx)',
'_seed)')
Expand Down Expand Up @@ -741,7 +751,7 @@ def build(self, directory='GeNNworkspace', compile=True, run=True,
'''

print('building genn executable ...')

if directory is None: # used during testing
directory = tempfile.mkdtemp()

Expand Down Expand Up @@ -980,7 +990,7 @@ def generate_max_row_length_code_objects(self, writer):
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.
Expand All @@ -989,8 +999,8 @@ def generate_max_row_length_code_objects(self, writer):
code_object_defs[codeobj.name]))
writer.write('code_objects/' + codeobj.name + '.cpp', code)



def run(self, directory, use_GPU, with_output):
gpu_arg = "1" if use_GPU else "0"
if gpu_arg == "1":
Expand Down Expand Up @@ -1061,7 +1071,7 @@ def compile_source(self, debug, directory, use_GPU):
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.')
Expand All @@ -1070,7 +1080,7 @@ def compile_source(self, debug, directory, use_GPU):
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')
Expand Down Expand Up @@ -1106,13 +1116,13 @@ def compile_source(self, debug, directory, use_GPU):
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
# Otherwise, update environment, again ensuring
# that all variables are upper case
else:
env.update({k.upper() : v for k, v in iteritems(msvc_env)})
Expand All @@ -1121,11 +1131,11 @@ def compile_source(self, debug, directory, use_GPU):
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
Expand All @@ -1134,23 +1144,23 @@ def compile_source(self, debug, directory, use_GPU):
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,
# **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:
Expand Down Expand Up @@ -1192,7 +1202,7 @@ 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
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')
Expand Down Expand Up @@ -1463,7 +1473,7 @@ def process_synapses(self, synapse_groups, objects):
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'
code= '\\n\\\n $(addToInSyn,'+addVar+');\\n'
synapse_model.main_code_lines['dynamics'] += code
#quick and dirty test to avoid adding the same support code twice
support_code = stringify('\n'.join(kwds['support_code_lines']))
Expand Down Expand Up @@ -1670,7 +1680,8 @@ def generate_model_source(self, writer, main_lines, use_GPU):
dtDef=self.dtDef,
prefs=prefs,
precision=precision,
header_files=prefs['codegen.cpp.headers']
header_files=prefs['codegen.cpp.headers'],
seed=self._seed,
)
writer.write('magicnetwork_model.cpp', model_tmp)

Expand Down
1 change: 1 addition & 0 deletions brian2genn/templates/model.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -225,6 +225,7 @@ void modelDefinition(NNmodel &model)
{% if prefs['devices.genn.kernel_timing'] %}
model.setTiming(true);
{% endif %}
model.setSeed({{seed}});
{% for neuron_model in neuron_models %}
model.addNeuronPopulation<{{neuron_model.name}}NEURON>("{{neuron_model.name}}", {{neuron_model.N}}, {{neuron_model.name}}_p, {{neuron_model.name}}_ini);
{% endfor %}
Expand Down