Brian Object Exception error

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Dominic Burrows

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Sep 10, 2020, 11:15:37 AM9/10/20

to Brian

Hi there,

I keep on coming across the same error - weirdly I can run the below code for 2-3 times in my jupyter notebook without any error. And then the error appears. Also the specific object in my code that the error refers to seems to change arbitrarily when the code is identical - i.e. sometimes it is Poisson input, sometime state updater, sometime spike monitor.

My code (A and W refer to my own objects which I am using to generate network types):

N_extern=1000 #number of presynaptic excitatory poisson neurons - if None, computed as N_Excit*connection prob

w0= 0.1 * b2.mV #synaptic strength J

g= 4 #relative importance of inhibition

synaptic_delay= 1.5 * b2.ms #delay between presynaptic spike and postsynaptic increase

poisson_input_rate= 10. * b2.Hz #poisson rate of external population

w_external=0.1 * b2.mV #synaptic weight of excitatory external possion neurons onto all neurons - if None w_external set to w_0

v_rest=0. * b2.mV #Resting potential

v_reset= 10. * b2.mV #Reset potential

firing_threshold= +20. * b2.mV #Spike threshold

membrane_time_scale= 20. * b2.ms #tau

abs_refractory_period= 2.0 * b2.ms #absolute refractory period

monitored_subet_size=100 #n neurons for which a VOltageMonitor is recording Vm

random_vm_init=False #if true, membrane voltage of each neuron is random at start (uniform)

sim_time=100 #simulation time

s = 1

k = 5

A = netfn.ba_netsim(dist).adjmat_generate(s, k, divisor, soften).A

W = adjmat_generate(A, s, k, divisor, soften)

# record

b2.start_scope()

J_excit = w0

# define dynamics for each cell

lif_dynamics = """

dv/dt = -(v-v_rest) / membrane_time_scale : volt (unless refractory)"""

#Build neuron group

N = nodes.shape[0]

network = b2.NeuronGroup(

N, model=lif_dynamics,

threshold="v>firing_threshold", reset="v=v_reset", refractory=abs_refractory_period,

method="linear")

network.v = v_rest

#Build synapses

S = b2.Synapses(network, network, 'w:1', on_pre="v += J_excit", delay=synaptic_delay)

rows, cols = np.nonzero(A)

S.connect(i = rows, j = cols)

#Add weights

S.w = W[rows, cols]

external_poisson_input = b2.PoissonInput(target=network, target_var="v", N=N_extern,

rate=poisson_input_rate, weight=w_external)

spike_monitor = b2.SpikeMonitor(network)

b2.run(sim_time*b2.ms)

Dominic Burrows

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Sep 10, 2020, 11:16:32 AM9/10/20

to Brian

Error message:

libc++abi.dylib: terminating with uncaught exception of type std::runtime_error: Couldn't close file

---------------------------------------------------------------------------

DistutilsExecError Traceback (most recent call last)

~/Applications/anaconda3/lib/python3.7/distutils/unixccompiler.py in link(self, target_desc, objects, output_filename, output_dir, libraries, library_dirs, runtime_library_dirs, export_symbols, debug, extra_preargs, extra_postargs, build_temp, target_lang)

204

--> 205 self.spawn(linker + ld_args)

206 except DistutilsExecError as msg:

~/Applications/anaconda3/lib/python3.7/distutils/ccompiler.py in spawn(self, cmd)

908 def spawn(self, cmd):

--> 909 spawn(cmd, dry_run=self.dry_run)

910

~/Applications/anaconda3/lib/python3.7/distutils/spawn.py in spawn(cmd, search_path, verbose, dry_run)

35 if os.name == 'posix':

---> 36 _spawn_posix(cmd, search_path, dry_run=dry_run)

37 elif os.name == 'nt':

~/Applications/anaconda3/lib/python3.7/distutils/spawn.py in _spawn_posix(cmd, search_path, verbose, dry_run)

148 "command %r terminated by signal %d"

--> 149 % (cmd, os.WTERMSIG(status)))

150 elif os.WIFEXITED(status):

DistutilsExecError: command 'g++' terminated by signal 6

During handling of the above exception, another exception occurred:

LinkError Traceback (most recent call last)

~/Applications/anaconda3/lib/python3.7/site-packages/brian2/core/network.py in before_run(self, run_namespace)

896 try:

--> 897 obj.before_run(run_namespace)

898 except Exception as ex:

~/Applications/anaconda3/lib/python3.7/site-packages/brian2/input/poissoninput.py in before_run(self, run_namespace)

114 'created.' % self.group.name)

--> 115 CodeRunner.before_run(self, run_namespace=run_namespace)

~/Applications/anaconda3/lib/python3.7/site-packages/brian2/groups/group.py in before_run(self, run_namespace)

1141 def before_run(self, run_namespace):

-> 1142 self.create_code_objects(run_namespace)

1143 super(CodeRunner, self).before_run(run_namespace)

~/Applications/anaconda3/lib/python3.7/site-packages/brian2/groups/group.py in create_code_objects(self, run_namespace)

1134 # Overwrite this function to use more than one.

-> 1135 code_object = self.create_default_code_object(run_namespace)

1136 if code_object:

~/Applications/anaconda3/lib/python3.7/site-packages/brian2/groups/group.py in create_default_code_object(self, run_namespace)

1127 override_conditional_write=self.override_conditional_write,

-> 1128 codeobj_class=self.codeobj_class

1129 )

~/Applications/anaconda3/lib/python3.7/site-packages/brian2/codegen/codeobject.py in create_runner_codeobj(group, code, template_name, run_namespace, user_code, variable_indices, name, check_units, needed_variables, additional_variables, template_kwds, override_conditional_write, codeobj_class)

449 override_conditional_write=override_conditional_write,

--> 450 compiler_kwds=compiler_kwds

451 )

~/Applications/anaconda3/lib/python3.7/site-packages/brian2/devices/device.py in code_object(self, owner, name, abstract_code, variables, template_name, variable_indices, codeobj_class, template_kwds, override_conditional_write, compiler_kwds)

326 name=name, compiler_kwds=compiler_kwds)

--> 327 codeobj.compile()

328 return codeobj

~/Applications/anaconda3/lib/python3.7/site-packages/brian2/codegen/codeobject.py in compile(self)

100 for block in ['before_run', 'run', 'after_run']:

--> 101 self.compiled_code[block] = self.compile_block(block)

102

~/Applications/anaconda3/lib/python3.7/site-packages/brian2/codegen/runtime/cython_rt/cython_rt.py in compile_block(self, block)

152 owner_name=self.owner.name+'_'+self.template_name,

--> 153 sources=self.sources

154 )

~/Applications/anaconda3/lib/python3.7/site-packages/brian2/codegen/runtime/cython_rt/extension_manager.py in create_extension(self, code, force, name, define_macros, include_dirs, library_dirs, runtime_library_dirs, extra_compile_args, extra_link_args, libraries, compiler, sources, owner_name)

125 key=key,

--> 126 sources=sources)

127 return module

~/Applications/anaconda3/lib/python3.7/site-packages/brian2/codegen/runtime/cython_rt/extension_manager.py in _load_module(self, module_path, define_macros, include_dirs, library_dirs, extra_compile_args, extra_link_args, libraries, code, lib_dir, module_name, runtime_library_dirs, compiler, key, sources)

261 build_extension.build_lib = lib_dir

--> 262 build_extension.run()

263 if prefs['codegen.runtime.cython.delete_source_files']:

~/Applications/anaconda3/lib/python3.7/distutils/command/build_ext.py in run(self)

339 # Now actually compile and link everything.

--> 340 self.build_extensions()

341

~/Applications/anaconda3/lib/python3.7/distutils/command/build_ext.py in build_extensions(self)

448 else:

--> 449 self._build_extensions_serial()

450

~/Applications/anaconda3/lib/python3.7/distutils/command/build_ext.py in _build_extensions_serial(self)

473 with self._filter_build_errors(ext):

--> 474 self.build_extension(ext)

475

~/Applications/anaconda3/lib/python3.7/distutils/command/build_ext.py in build_extension(self, ext)

558 build_temp=self.build_temp,

--> 559 target_lang=language)

560

~/Applications/anaconda3/lib/python3.7/distutils/ccompiler.py in link_shared_object(self, objects, output_filename, output_dir, libraries, library_dirs, runtime_library_dirs, export_symbols, debug, extra_preargs, extra_postargs, build_temp, target_lang)

716 export_symbols, debug,

--> 717 extra_preargs, extra_postargs, build_temp, target_lang)

718

206 except DistutilsExecError as msg:

--> 207 raise LinkError(msg)

208 else:

LinkError: command 'g++' terminated by signal 6

The above exception was the direct cause of the following exception:

BrianObjectException Traceback (most recent call last)

<ipython-input-10-d4bffc186c09> in <module>

37 spike_monitor = b2.SpikeMonitor(network)

---> 38 b2.run(sim_time*b2.ms)

~/Applications/anaconda3/lib/python3.7/site-packages/brian2/units/fundamentalunits.py in new_f(*args, **kwds)

2383 get_dimensions(newkeyset[k]))

2384

-> 2385 result = f(*args, **kwds)

2386 if 'result' in au:

2387 if au['result'] == bool:

~/Applications/anaconda3/lib/python3.7/site-packages/brian2/core/magic.py in run(duration, report, report_period, namespace, profile, level)

372 '''

373 return magic_network.run(duration, report=report, report_period=report_period,

--> 374 namespace=namespace, profile=profile, level=2+level)

375 run.__module__ = __name__

376

~/Applications/anaconda3/lib/python3.7/site-packages/brian2/core/magic.py in run(self, duration, report, report_period, namespace, profile, level)

230 self._update_magic_objects(level=level+1)

231 Network.run(self, duration, report=report, report_period=report_period,

--> 232 namespace=namespace, profile=profile, level=level+1)

233

234 def store(self, name='default', filename=None, level=0):

~/Applications/anaconda3/lib/python3.7/site-packages/brian2/core/base.py in device_override_decorated_function(*args, **kwds)

276 return getattr(curdev, name)(*args, **kwds)

277 else:

--> 278 return func(*args, **kwds)

279

280 device_override_decorated_function.__doc__ = func.__doc__

~/Applications/anaconda3/lib/python3.7/site-packages/brian2/units/fundamentalunits.py in new_f(*args, **kwds)

2383 get_dimensions(newkeyset[k]))

2384

-> 2385 result = f(*args, **kwds)

2386 if 'result' in au:

2387 if au['result'] == bool:

~/Applications/anaconda3/lib/python3.7/site-packages/brian2/core/network.py in run(self, duration, report, report_period, namespace, profile, level)

1006 namespace = get_local_namespace(level=level+3)

1007

-> 1008 self.before_run(namespace)

1009

1010 if len(all_objects) == 0:

~/Applications/anaconda3/lib/python3.7/site-packages/brian2/core/base.py in device_override_decorated_function(*args, **kwds)

276 return getattr(curdev, name)(*args, **kwds)

277 else:

--> 278 return func(*args, **kwds)

279

280 device_override_decorated_function.__doc__ = func.__doc__

~/Applications/anaconda3/lib/python3.7/site-packages/brian2/core/network.py in before_run(self, run_namespace)

897 obj.before_run(run_namespace)

898 except Exception as ex:

--> 899 raise BrianObjectException("An error occurred when preparing an object.", obj) from ex

900

901 # Check that no object has been run as part of another network before

BrianObjectException: Error encountered with object named "poissoninput".

Object was created here (most recent call only, full details in debug log):

File "<ipython-input-10-d4bffc186c09>", line 35, in <module>

rate=poisson_input_rate, weight=w_external)

An error occurred when preparing an object. (See above for original error message and traceback.)

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