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Raise exception when the voltage becomes unrealistic during a neuron simulation #387

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Raise exception when the voltage becomes unrealistic during a neuron simulation #387

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5 changes: 4 additions & 1 deletion bluepyopt/ephys/protocols.py
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Original file line number Diff line number Diff line change
Expand Up @@ -171,7 +171,10 @@ def _run_func(self, cell_model, param_values, sim=None):
self.instantiate(sim=sim, icell=cell_model.icell)

try:
sim.run(self.total_duration, cvode_active=self.cvode_active)
sim.run(
self.total_duration,
cvode_active=self.cvode_active,
icell=cell_model.icell)
except (RuntimeError, simulators.NrnSimulatorException):
logger.debug(
'SweepProtocol: Running of parameter set {%s} generated '
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14 changes: 12 additions & 2 deletions bluepyopt/ephys/simulators.py
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Original file line number Diff line number Diff line change
Expand Up @@ -112,12 +112,19 @@ def neuron(self):

return neuron

def check_voltage_valid(self, icell, voltage_bound=200.):
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I find this dangerous though. Ideally NEURON should detect if it gets values that it can't handle. Do we know what the effect this has on optimizations? I wouldn't be surprised if a lot of initial solutions might be out of bounds here.

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Ok,I will open an issue in Neuron

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Any news?

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The engineer who was looking into it is just back from vacation. He will resume working on it.

"""Raises exception if voltage at soma is out of bound"""

if icell and abs(icell.soma[0](0.5).v) > voltage_bound:
raise NrnSimulatorException('Membrane potential is out of bound')

def run(
self,
tstop=None,
dt=None,
cvode_active=None,
random123_globalindex=None):
random123_globalindex=None,
icell=None):
"""Run protocol"""

self.neuron.h.tstop = tstop
Expand Down Expand Up @@ -163,7 +170,10 @@ def run(
rng.Random123_globalindex(random123_globalindex)

try:
self.neuron.h.run()
self.neuron.h.finitialize()
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Are we sure this 'exactly' replicates the 'run()' behavior of Neuron? We don't want to change results if not necessary.

while self.neuron.h.t < self.neuron.h.tstop:
self.neuron.h.fadvance()
self.check_voltage_valid(icell)
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We also need to check how this affects the simulation time.

except Exception as e:
raise NrnSimulatorException('Neuron simulator error', e)

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