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Generic simulation bundle for Geppetto
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"Error with LEMS content" while Running Experiment #111

Closed jrmartin closed 7 years ago

jrmartin commented 8 years ago

While running hhcell experiment I get "Error with LEMS content" exception. I ran it with the following recorded variables

hhcell.hhpop[0].v hhcell.hhpop[0].bioPhys1.membraneProperties.naChans.na.m.q hhcell.hhpop[0].bioPhys1.membraneProperties.naChans.na.h.q hhcell.hhpop[0].bioPhys1.membraneProperties.kChans.k.n.q hhcell.hhpop[0].bioPhys1.membraneProperties.kChans.k.n.fcond hhcell.hhpop[0].bioPhys1.membraneProperties.kChans.k.n.alpha hhcell.hhpop[0].bioPhys1.membraneProperties.kChans.k.n.beta hhcell.hhpop[0].iSyn hhcell.hhpop[0].caConc hhcell.hhpop[0].bioPhys1.membraneProperties.naChans.gDensity hhcell.hhpop[0].bioPhys1.membraneProperties.naChans.iDensity

`[2016-09-12 11:07:13.966] ERROR Thread-84 System.err java.lang.Exception [2016-09-12 11:07:13.970] ERROR Thread-84 System.err at org.lemsml.jlems.core.type.Component.getStringValue(Component.java:933) [2016-09-12 11:07:13.970] ERROR Thread-84 System.err at org.neuroml.export.neuron.LEMSQuantityPathNeuron.convertToNeuronVariable(LEMSQuantityPathNeuron.java:141) [2016-09-12 11:07:13.970] ERROR Thread-84 System.err at org.neuroml.export.neuron.LEMSQuantityPathNeuron.getNeuronVariableReference(LEMSQuantityPathNeuron.java:209) [2016-09-12 11:07:13.970] ERROR Thread-84 System.err at org.neuroml.export.neuron.NeuronWriter.getMainScript(NeuronWriter.java:1189) [2016-09-12 11:07:13.976] ERROR Thread-84 System.err at org.neuroml.export.neuron.NeuronWriter.generateMainScriptAndMods(NeuronWriter.java:191) [2016-09-12 11:07:13.976] ERROR Thread-84 System.err at org.neuroml.export.neuron.NeuronWriter.convert(NeuronWriter.java:3045) [2016-09-12 11:07:13.976] ERROR Thread-84 System.err at org.geppetto.model.neuroml.services.LEMSConversionService.convert(LEMSConversionService.java:254) [2016-09-12 11:07:13.976] ERROR Thread-84 System.err at org.geppetto.simulation.manager.ExperimentRunThread.init(ExperimentRunThread.java:230) [2016-09-12 11:07:13.976] ERROR Thread-84 System.err at org.geppetto.simulation.manager.ExperimentRunThread.run(ExperimentRunThread.java:278) [2016-09-12 11:07:13.976] ERROR Thread-84 System.err org.neuroml.export.exceptions.GenerationException: Error with LEMS content [2016-09-12 11:07:13.976] ERROR Thread-84 System.err at org.neuroml.export.neuron.NeuronWriter.getMainScript(NeuronWriter.java:1377) [2016-09-12 11:07:13.976] ERROR Thread-84 System.err at org.neuroml.export.neuron.NeuronWriter.generateMainScriptAndMods(NeuronWriter.java:191) [2016-09-12 11:07:13.976] ERROR Thread-84 System.err at org.neuroml.export.neuron.NeuronWriter.convert(NeuronWriter.java:3045) [2016-09-12 11:07:13.976] ERROR Thread-84 System.err at org.geppetto.model.neuroml.services.LEMSConversionService.convert(LEMSConversionService.java:254) [2016-09-12 11:07:13.976] ERROR Thread-84 System.err at org.geppetto.simulation.manager.ExperimentRunThread.init(ExperimentRunThread.java:230) [2016-09-12 11:07:13.976] ERROR Thread-84 System.err at org.geppetto.simulation.manager.ExperimentRunThread.run(ExperimentRunThread.java:278) [2016-09-12 11:07:13.977] ERROR Thread-84 System.err Caused by: org.lemsml.jlems.core.sim.ContentError: No such field 'ion' in Component(id=naChans type=channelDensity) [2016-09-12 11:07:13.977] ERROR Thread-84 System.err -- Component, id = naChans, type: channelDensity ---------- [2016-09-12 11:07:13.977] ERROR Thread-84 System.err Parameters: [2016-09-12 11:07:13.977] ERROR Thread-84 System.err erev = 0.05 (SI voltage) [2016-09-12 11:07:13.984] ERROR Thread-84 System.err condDensity = 1200.0 (SI conductanceDensity) [2016-09-12 11:07:13.985] ERROR Thread-84 System.err Refs: [2016-09-12 11:07:13.985] ERROR Thread-84 System.err --ionChannel-- [2016-09-12 11:07:13.985] ERROR Thread-84 System.err --> Component(id=na type=ionChannelHH) [2016-09-12 11:07:13.985] ERROR Thread-84 System.err --------------------------------------------- [2016-09-12 11:07:13.985] ERROR Thread-84 System.err at org.lemsml.jlems.core.type.Component.getStringValue(Component.java:934) [2016-09-12 11:07:13.985] ERROR Thread-84 System.err at org.neuroml.export.neuron.LEMSQuantityPathNeuron.convertToNeuronVariable(LEMSQuantityPathNeuron.java:141) [2016-09-12 11:07:13.985] ERROR Thread-84 System.err at org.neuroml.export.neuron.LEMSQuantityPathNeuron.getNeuronVariableReference(LEMSQuantityPathNeuron.java:209) [2016-09-12 11:07:13.985] ERROR Thread-84 System.err at org.neuroml.export.neuron.NeuronWriter.getMainScript(NeuronWriter.java:1189) [2016-09-12 11:07:13.985] ERROR Thread-84 System.err ... 5 more [2016-09-12 11:07:13.989] ERROR Thread-84 org.geppetto.frontend.controllers.ConnectionHandler Error running experiment with name: (New Experiment 5) and id: 26 org.geppetto.core.common.GeppettoInitializationException: org.geppetto.core.conversion.ConversionException: org.neuroml.export.exceptions.GenerationException: Error with LEMS content at org.geppetto.simulation.manager.ExperimentRunThread.init(ExperimentRunThread.java:265) at org.geppetto.simulation.manager.ExperimentRunThread.run(ExperimentRunThread.java:278) Caused by: org.geppetto.core.conversion.ConversionException: org.neuroml.export.exceptions.GenerationException: Error with LEMS content at org.geppetto.model.neuroml.services.LEMSConversionService.convert(LEMSConversionService.java:264) at org.geppetto.simulation.manager.ExperimentRunThread.init(ExperimentRunThread.java:230) ... 1 common frames omitted Caused by: org.neuroml.export.exceptions.GenerationException: Error with LEMS content at org.neuroml.export.neuron.NeuronWriter.getMainScript(NeuronWriter.java:1377) at org.neuroml.export.neuron.NeuronWriter.generateMainScriptAndMods(NeuronWriter.java:191) at org.neuroml.export.neuron.NeuronWriter.convert(NeuronWriter.java:3045) at org.geppetto.model.neuroml.services.LEMSConversionService.convert(LEMSConversionService.java:254) ... 2 common frames omitted Caused by: org.lemsml.jlems.core.sim.ContentError: No such field 'ion' in Component(id=naChans type=channelDensity) -- Component, id = naChans, type: channelDensity ---------- Parameters: erev = 0.05 (SI voltage) condDensity = 1200.0 (SI conductanceDensity) Refs: --ionChannel--

--> Component(id=na type=ionChannelHH)

at org.lemsml.jlems.core.type.Component.getStringValue(Component.java:934)
at org.neuroml.export.neuron.LEMSQuantityPathNeuron.convertToNeuronVariable(LEMSQuantityPathNeuron.java:141)
at org.neuroml.export.neuron.LEMSQuantityPathNeuron.getNeuronVariableReference(LEMSQuantityPathNeuron.java:209)
at org.neuroml.export.neuron.NeuronWriter.getMainScript(NeuronWriter.java:1189)
... 5 common frames omitted

[2016-09-12 11:07:14.028] ERROR Thread-84 org.geppetto.simulation.manager.ExperimentRunThread org.geppetto.core.common.GeppettoInitializationException: org.geppetto.core.conversion.ConversionException: org.neuroml.export.exceptions.GenerationException: Error with LEMS content `