jonrkarr
commented
2 years ago There's no problem here. I wasn't paying careful attention to the meaning of the LEMS steps (size) parameter. I was thinking of other languages which focus on the number of steps rather than their size.
Describe the bug As described in #136, time courses with Brian2 and NetPyNe are short. So I tried compensating by incrementing the step by 1 in the LEMS file. This caused the simulation to fail.
Brian2:
self = <brian2.codegen.runtime.numpy_rt.numpy_rt.NumpyCodeObject object at 0x7f890b5d05e0>, block = 'run' def run_block(self, block): compiled_code = self.compiled_code[block] if not compiled_code: return try: > exec(compiled_code, self.namespace) /usr/local/lib/python3.9/dist-packages/brian2/codegen/runtime/numpy_rt/numpy_rt.py:248: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? (string):26: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ t = 0.0 def unitless_timed_array_func(t): timestep = np.clip(np.int_(np.round(t/epsilon) / K), 0, n_values-1) > return values[timestep] E IndexError: index -1 is out of bounds for axis 0 with size 0 /usr/local/lib/python3.9/dist-packages/brian2/input/timedarray.py:246: IndexError The above exception was the direct cause of the following exception: self = <test_core_main.CoreCliTestCase testMethod=test_exec_sed_task_brian2> def test_exec_sed_task_brian2(self): task, variables = self._get_simulation() log = TaskLog() > results, log = core.exec_sed_task(task, variables, log=log, simulator=Simulator.brian2) /home/jonrkarr/Documents/biosimulations/Biosimulators_pyNeuroML/tests/test_core_main.py:87: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ /home/jonrkarr/Documents/biosimulations/Biosimulators_pyNeuroML/biosimulators_pyneuroml/core.py:155: in exec_sed_task lems_results = run_lems_xml( /home/jonrkarr/Documents/biosimulations/Biosimulators_pyNeuroML/biosimulators_pyneuroml/utils.py:224: in run_lems_xml result = run_lems_method(os.path.relpath(temp_filename, working_dirname), **options.to_kw_args(simulator)) /usr/local/lib/python3.9/dist-packages/pyneuroml/pynml.py:1592: in run_lems_with_jneuroml_brian2 exec("import %s" % brian2_py_name) <string>:1: in <module> ??? /home/jonrkarr/Documents/biosimulations/Biosimulators_pyNeuroML/tests/fixtures/tmp1wo0zeuo_brian2.py:234: in <module> run(duration) /usr/local/lib/python3.9/dist-packages/brian2/units/fundamentalunits.py:2434: in new_f result = f(*args, **kwds) /usr/local/lib/python3.9/dist-packages/brian2/core/magic.py:373: in run return magic_network.run(duration, report=report, report_period=report_period, /usr/local/lib/python3.9/dist-packages/brian2/core/magic.py:231: in run Network.run(self, duration, report=report, report_period=report_period, /usr/local/lib/python3.9/dist-packages/brian2/core/base.py:278: in device_override_decorated_function return func(*args, **kwds) /usr/local/lib/python3.9/dist-packages/brian2/units/fundamentalunits.py:2434: in new_f result = f(*args, **kwds) /usr/local/lib/python3.9/dist-packages/brian2/core/network.py:1076: in run obj.run() /usr/local/lib/python3.9/dist-packages/brian2/core/base.py:181: in run codeobj() /usr/local/lib/python3.9/dist-packages/brian2/codegen/codeobject.py:107: in __call__ return self.run() /usr/local/lib/python3.9/dist-packages/brian2/codegen/codeobject.py:135: in run return self.run_block('run') _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <brian2.codegen.runtime.numpy_rt.numpy_rt.NumpyCodeObject object at 0x7f890b5d05e0>, block = 'run' def run_block(self, block): compiled_code = self.compiled_code[block] if not compiled_code: return try: exec(compiled_code, self.namespace) except Exception as exc: code = getattr(self.code, block) message = ('An exception occured during the execution of the {} ' 'block of code object {}.\n').format(block, self.name) lines = code.split('\n') message += 'The error was raised in the following line:\n' _, _, tb = sys.exc_info() tb = tb.tb_next # Line in the code object's code message += lines[tb.tb_lineno - 1] + '\n' > raise BrianObjectException(message, self.owner) from exc E brian2.core.base.BrianObjectException: Error encountered with object named "neurongroup". E Object was created here (most recent call only, full details in debug log): E File "/home/jonrkarr/Documents/biosimulations/Biosimulators_pyNeuroML/tests/fixtures/tmp1wo0zeuo_brian2.py", line 185, in <module> E hhpop = NeuronGroup(1, model=hhcell_eqs, threshold = 'v > thresh and spiking < 0.5', reset = """spiking = 1""") E E An exception occured during the execution of the run block of code object neurongroup_stateupdater_codeobject. E The error was raised in the following line: E _lio_19 = hhpop_iSyn(t) E (See above for original error message and traceback.) /usr/local/lib/python3.9/dist-packages/brian2/codegen/runtime/numpy_rt/numpy_rt.py:258: BrianObjectExceptionNetPyNe:
System information:
python --version): 3.9.5pynml --help): pyneuroml 0.5.18, brian: 2.4.2, NetPyNe: 1.0.0.2