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jasonxanthakis / NeuroML-Thesis

Repository to research and practice software for Uni Year 3 Thesis
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Problem with setting baseline currents to 0.0nA #11

Closed jasonxanthakis closed 5 months ago

jasonxanthakis commented 6 months ago

@pgleeson @sanjayankur31 pyNeuroML >>> CRITICAL - * Problem running command: Command 'java -Xmx2000M -Djava.awt.headless=true -jar "/home/ixanthakis/wsl_repos/Dissertation_Repos/nsimenv3/lib/python3.10/site-packages/pyneuroml/lib/jNeuroML-0.13.0-jar-with-dependencies.jar" /home/ixanthakis/wsl_repos/PyNeuroMLTutorials/ClonedNeuroMLRepositories/del-Molino2017/NeuroML/ParamSweep_SimdelMolinoEtAl_low_baseline_Tue_Feb_20_15.58.37_2024/RUN20_SimdelMolinoEtAl_low_baselineglobal_offset_current0.1nA/LEMS_SimdelMolinoEtAl_low_baseline_RUN20_SimdelMolinoEtAl_low_baselineglobal_offset_current0.1nA.xml -nogui -I ''' returned non-zero exit status 1. pyNeuroML >>> CRITICAL - jNeuroML >> jNeuroML v0.13.0 jNeuroML >> Loading: /home/ixanthakis/wsl_repos/PyNeuroMLTutorials/ClonedNeuroMLRepositories/del-Molino2017/NeuroML/ParamSweep_SimdelMolinoEtAl_low_baseline_Tue_Feb_20_15.58.37_2024/RUN20_SimdelMolinoEtAl_low_baselineglobal_offset_current0.1nA/LEMS_SimdelMolinoEtAl_low_baseline_RUN20_SimdelMolinoEtAl_low_baselineglobal_offset_current0.1nA.xml with jLEMS, NO GUI mode... jNeuroML >> Feb 20, 2024 3:58:50 PM org.lemsml.jlems.io.logging.DefaultLogger msg jNeuroML >> SEVERE: (ERROR) org.lemsml.jlems.core.run.RuntimeError: jNeuroML >> Problem while trying to return a value for variable r: NaN jNeuroML >>
jNeuroML >> Current StateInstance: jNeuroML >> +--------------------------------------------------------------------------------------- jNeuroML >> | StateInstance: SST [StateType: abbottChance2005Cell, parent: 0] jNeuroML >> | Variables: {gl = 5.0E-9, f = NaN, tau = 0.016, Vth = -0.05, tau_r = 0.002, jNeuroML >> | iSyn = 1.0000000000000002E-10, r = NaN, t = 0.020000000000000316, v = 0.0, Vl = -0.07, jNeuroML >> | V = -0.05, Vscale = 0.001, Vr = -0.06, r0 = 3.0} jNeuroML >> | Exposures: {r = NaN, v = 0.0, V = -0.05, f = NaN, iSyn = 1.0000000000000002E-10} jNeuroML >> | | synapses[0] +-------------------------------------------------------------------- jNeuroML >> | | synapses[0] | StateInstance: baseline_exc_SST [StateType: pulseGenerator, parent: SST] jNeuroML >> | | synapses[0] | Variables: {duration = 2.0, amplitude = 0.0, delay = 0.02, t = 0.020000000000000316, i = 0.0, jNeuroML >> | | synapses[0] | weight = 1.0} jNeuroML >> | | synapses[0] | Exposures: {i = 0.0, weight = 1.0} jNeuroML >> | | synapses[0] +-------------------------------------------------------------------- jNeuroML >> | | synapses[1] +-------------------------------------------------------------------- jNeuroML >> | | synapses[1] | StateInstance: global_offset_curr_SST [StateType: pulseGenerator, parent: SST] jNeuroML >> | | synapses[1] | Variables: {duration = 2.0, amplitude = 1.0000000000000002E-10, delay = 0.02, t = 0.020000000000000316, i = 1.0000000000000002E-10, jNeuroML >> | | synapses[1] | weight = 1.0} jNeuroML >> | | synapses[1] | Exposures: {i = 1.0000000000000002E-10, weight = 1.0} jNeuroML >> | | synapses[1] +-------------------------------------------------------------------- jNeuroML >> | +--------------------------------------------------------------------------------------- jNeuroML >> +--------------------------------------------------------------------------------------- jNeuroML >>
jNeuroML >> Current StateInstance's parent: jNeuroML >> +--------------------------------------------------------------------------------------- jNeuroML >> | StateInstance: 0 [StateType: instance, parent: SST] jNeuroML >> | Variables: {t = 0.020000000000000316} jNeuroML >> | Exposures: {} jNeuroML >> | +---------------------------------------------------------------------------------- jNeuroML >> | | StateInstance: SST [StateType: abbottChance2005Cell, parent: 0] jNeuroML >> | | Variables: {gl = 5.0E-9, f = NaN, tau = 0.016, Vth = -0.05, tau_r = 0.002, jNeuroML >> | | iSyn = 1.0000000000000002E-10, r = NaN, t = 0.020000000000000316, v = 0.0, Vl = -0.07, jNeuroML >> | | V = -0.05, Vscale = 0.001, Vr = -0.06, r0 = 3.0} jNeuroML >> | | Exposures: {r = NaN, v = 0.0, V = -0.05, f = NaN, iSyn = 1.0000000000000002E-10} jNeuroML >> | | | synapses[0] +--------------------------------------------------------------- jNeuroML >> | | | synapses[0] | StateInstance: baseline_exc_SST [StateType: pulseGenerator, parent: SST] jNeuroML >> | | | synapses[0] | Variables: {duration = 2.0, amplitude = 0.0, delay = 0.02, t = 0.020000000000000316, i = 0.0, jNeuroML >> | | | synapses[0] | weight = 1.0} jNeuroML >> | | | synapses[0] | Exposures: {i = 0.0, weight = 1.0} jNeuroML >> | | | synapses[0] +--------------------------------------------------------------- jNeuroML >> | | | synapses[1] +--------------------------------------------------------------- jNeuroML >> | | | synapses[1] | StateInstance: global_offset_curr_SST [StateType: pulseGenerator, parent: SST] jNeuroML >> | | | synapses[1] | Variables: {duration = 2.0, amplitude = 1.0000000000000002E-10, delay = 0.02, t = 0.020000000000000316, i = 1.0000000000000002E-10, jNeuroML >> | | | synapses[1] | weight = 1.0} jNeuroML >> | | | synapses[1] | Exposures: {i = 1.0000000000000002E-10, weight = 1.0} jNeuroML >> | | | synapses[1] +--------------------------------------------------------------- jNeuroML >> | | +---------------------------------------------------------------------------------- jNeuroML >> | +---------------------------------------------------------------------------------- jNeuroML >> | +---------------------------------------------------------------------------------- jNeuroML >> | | StateInstance: null [StateType: location, parent: 0] jNeuroML >> | | Variables: {t = 0.020000000000000316, x = 67.1563481487985, y = 8.393822683708397, z = 7.664809327917963} jNeuroML >> | | Exposures: {} jNeuroML >> | +---------------------------------------------------------------------------------- jNeuroML >> +--------------------------------------------------------------------------------------- jNeuroML >> INFO Feb 20,2024 15:58 (INFO) Loading LEMS file from: /home/ixanthakis/wsl_repos/PyNeuroMLTutorials/ClonedNeuroMLRepositories/del-Molino2017/NeuroML/ParamSweep_SimdelMolinoEtAl_low_baseline_Tue_Feb_20_15.58.37_2024/RUN20_SimdelMolinoEtAl_low_baselineglobal_offset_current0.1nA/LEMS_SimdelMolinoEtAl_low_baseline_RUN20_SimdelMolinoEtAl_low_baselineglobal_offset_current0.1nA.xml jNeuroML >> INFO Feb 20,2024 15:58 (INFO) Reading from: /home/ixanthakis/wsl_repos/PyNeuroMLTutorials/ClonedNeuroMLRepositories/del-Molino2017/NeuroML/ParamSweep_SimdelMolinoEtAl_low_baseline_Tue_Feb_20_15.58.37_2024/RUN20_SimdelMolinoEtAl_low_baselineglobal_offset_current0.1nA/LEMS_SimdelMolinoEtAl_low_baseline_RUN20_SimdelMolinoEtAl_low_baselineglobal_offset_current0.1nA.xml jNeuroML >> INFO Feb 20,2024 15:58 (LOG) at org.lemsml.jlems.core.logging.E.multiError(E.java:251) jNeuroML >> INFO Feb 20,2024 15:58 (LOG) at org.lemsml.jlems.core.logging.E.error(E.java:217) jNeuroML >> INFO Feb 20,2024 15:58 (LOG) at org.lemsml.jlems.core.sim.Sim.run(Sim.java:319) jNeuroML >> INFO Feb 20,2024 15:58 (LOG) at org.lemsml.jlems.core.sim.Sim.run(Sim.java:154) jNeuroML >> INFO Feb 20,2024 15:58 (LOG) at org.lemsml.jlems.org.lemsml.jlems.core.run.RuntimeError: jNeuroML >> Problem while trying to return a value for variable r: NaN jNeuroML >>
jNeuroML >> Current StateInstance: jNeuroML >> +--------------------------------------------------------------------------------------- jNeuroML >> | StateInstance: SST [StateType: abbottChance2005Cell, parent: 0] jNeuroML >> | Variables: {gl = 5.0E-9, f = NaN, tau = 0.016, Vth = -0.05, tau_r = 0.002, jNeuroML >> | iSyn = 1.0000000000000002E-10, r = NaN, t = 0.020000000000000316, v = 0.0, Vl = -0.07, jNeuroML >> | V = -0.05, Vscale = 0.001, Vr = -0.06, r0 = 3.0} jNeuroML >> | Exposures: {r = NaN, v = 0.0, V = -0.05, f = NaN, iSyn = 1.0000000000000002E-10} jNeuroML >> | | synapses[0] +-------------------------------------------------------------------- jNeuroML >> | | synapses[0] | StateInstance: baseline_exc_SST [StateType: pulseGenerator, parent: SST] jNeuroML >> | | synapses[0] | Variables: {duration = 2.0, amplitude = 0.0, delay = 0.02, t = 0.020000000000000316, i = 0.0, jNeuroML >> | | synapses[0] | weight = 1.0} jNeuroML >> | | synapses[0] | Exposures: {i = 0.0, weight = 1.0} jNeuroML >> | | synapses[0] +-------------------------------------------------------------------- jNeuroML >> | | synapses[1] +-------------------------------------------------------------------- jNeuroML >> | | synapses[1] | StateInstance: global_offset_curr_SST [StateType: pulseGenerator, parent: SST] jNeuroML >> | | synapses[1] | Variables: {duration = 2.0, amplitude = 1.0000000000000002E-10, delay = 0.02, t = 0.020000000000000316, i = 1.0000000000000002E-10, jNeuroML >> | | synapses[1] | weight = 1.0} jNeuroML >> | | synapses[1] | Exposures: {i = 1.0000000000000002E-10, weight = 1.0} jNeuroML >> | | synapses[1] +-------------------------------------------------------------------- jNeuroML >> | +--------------------------------------------------------------------------------------- jNeuroML >> +--------------------------------------------------------------------------------------- jNeuroML >>
jNeuroML >> Current StateInstance's parent: jNeuroML >> +--------------------------------------------------------------------------------------- jNeuroML >> | StateInstance: 0 [StateType: instance, parent: SST] jNeuroML >> | Variables: {t = 0.020000000000000316} jNeuroML >> | Exposures: {} jNeuroML >> | +---------------------------------------------------------------------------------- jNeuroML >> | | StateInstance: SST [StateType: abbottChance2005Cell, parent: 0] jNeuroML >> | | Variables: {gl = 5.0E-9, f = NaN, tau = 0.016, Vth = -0.05, tau_r = 0.002, jNeuroML >> | | iSyn = 1.0000000000000002E-10, r = NaN, t = 0.020000000000000316, v = 0.0, Vl = -0.07, jNeuroML >> | | V = -0.05, Vscale = 0.001, Vr = -0.06, r0 = 3.0} jNeuroML >> | | Exposures: {r = NaN, v = 0.0, V = -0.05, f = NaN, iSyn = 1.0000000000000002E-10} jNeuroML >> | | | synapses[0] +--------------------------------------------------------------- jNeuroML >> | | | synapses[0] | StateInstance: baseline_exc_SST [StateType: pulseGenerator, parent: SST] jNeuroML >> | | | synapses[0] | Variables: {duration = 2.0, amplitude = 0.0, delay = 0.02, t = 0.020000000000000316, i = 0.0, jNeuroML >> | | | synapses[0] | weight = 1.0} jNeuroML >> | | | synapses[0] | Exposures: {i = 0.0, weight = 1.0} jNeuroML >> | | | synapses[0] +--------------------------------------------------------------- jNeuroML >> | | | synapses[1] +--------------------------------------------------------------- jNeuroML >> | | | synapses[1] | StateInstance: global_offset_curr_SST [StateType: pulseGenerator, parent: SST] jNeuroML >> | | | synapses[1] | Variables: {duration = 2.0, amplitude = 1.0000000000000002E-10, delay = 0.02, t = 0.020000000000000316, i = 1.0000000000000002E-10, jNeuroML >> | | | synapses[1] | weight = 1.0} jNeuroML >> | | | synapses[1] | Exposures: {i = 1.0000000000000002E-10, weight = 1.0} jNeuroML >> | | | synapses[1] +--------------------------------------------------------------- jNeuroML >> | | +---------------------------------------------------------------------------------- jNeuroML >> | +---------------------------------------------------------------------------------- jNeuroML >> | +---------------------------------------------------------------------------------- jNeuroML >> | | StateInstance: null [StateType: location, parent: 0] jNeuroML >> | | Variables: {t = 0.020000000000000316, x = 67.1563481487985, y = 8.393822683708397, z = 7.664809327917963} jNeuroML >> | | Exposures: {} jNeuroML >> | +---------------------------------------------------------------------------------- jNeuroML >> +--------------------------------------------------------------------------------------- jNeuroML >> at org.lemsml.jlems.core.run.StateInstance.checkReturn(StateInstance.java:596) jNeuroML >> at org.lemsml.jlems.core.run.StateInstance.getVariable(StateInstance.java:567) jNeuroML >> at org.lemsml.jlems.core.run.StateWrapper.getValue(StateWrapper.java:44) jNeuroML >> at org.lemsml.jlems.core.run.RuntimeRecorder.appendState(RuntimeRecorder.java:83) jNeuroML >> at org.lemsml.jlems.core.sim.Sim.run(Sim.java:301) jNeuroML >> at org.lemsml.jlems.core.sim.Sim.run(Sim.java:154) jNeuroML >> at org.lemsml.jlems.core.sim.Sim.run(Sim.java:145) jNeuroML >> at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:527) jNeuroML >> at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493) jNeuroML >> at org.neuroml.JNeuroML.main(JNeuroML.java:622) jNeuroML >> Feb 20, 2024 3:58:51 PM org.lemsml.jlems.io.logging.DefaultLogger msg jNeuroML >> SEVERE: (ERROR) jNeuroML >>
jNeuroML >> ***** jNeuroML >> jNeuroML >> Error occurred when running jLEMS! jNeuroML >>
jNeuroML >> Note: LEMS model description was successfully parsed, and simulation started (t = 0.02 sec) jNeuroML >> This error MAY be caused by too large a time step (dt = 2.5E-5 sec currently) jNeuroML >> Try reducing the 'step' attribute in the element jNeuroML >> * jNeuroML >> *** jNeuroML >>
jNeuroML >> core.sim.Sim.run(Sim.java:145) jNeuroML >> INFO Feb 20,2024 15:58 (LOG) at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:527) jNeuroML >> INFO Feb 20,2024 15:58 (LOG) at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493) jNeuroML >> INFO Feb 20,2024 15:58 (LOG) at org.neuroml.JNeuroML.main(JNeuroML.java:622) jNeuroML >> INFO Feb 20,2024 15:58 (LOG) at org.lemsml.jlems.core.logging.E.multiError(E.java:251) jNeuroML >> INFO Feb 20,2024 15:58 (LOG) at org.lemsml.jlems.core.logging.E.informativeError(E.java:226) jNeuroML >> INFO Feb 20,2024 15:58 (LOG) at org.lemsml.jlems.core.sim.Sim.run(Sim.java:328) jNeuroML >> INFO Feb 20,2024 15:58 (LOG) at org.lemsml.jlems.core.sim.Sim.run(Sim.java:154) jNeuroML >> INFO Feb 20,2024 15:58 (LOG) at org.lemsml.jlems.core.sim.Sim.run(Sim.java:145) jNeuroML >> INFO Feb 20,2024 15:58 (LOG) at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:527) jNeuroML >> INFO Feb 20,2024 15:58 (LOG) at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493) jNeuroML >> INFO Feb 20,2024 15:58 (LOG) at org.neuroml.JNeuroML.main(JNeuroML.java:622) jNeuroML >>
pyNeuroML >>> ERROR - execute_command_in_dir returned with output: jNeuroML v0.13.0 Loading: /home/ixanthakis/wsl_repos/PyNeuroMLTutorials/ClonedNeuroMLRepositories/del-Molino2017/NeuroML/ParamSweep_SimdelMolinoEtAl_low_baseline_Tue_Feb_20_15.58.37_2024/RUN20_SimdelMolinoEtAl_low_baseline__global_offset_current0.1nA/LEMS_SimdelMolinoEtAl_low_baseline_RUN20_SimdelMolinoEtAl_low_baseline__global_offset_current0.1nA.xml with jLEMS, NO GUI mode... Feb 20, 2024 3:58:50 PM org.lemsml.jlems.io.logging.DefaultLogger msg SEVERE: (ERROR) org.lemsml.jlems.core.run.RuntimeError: Problem while trying to return a value for variable r: NaN

Current StateInstance: +--------------------------------------------------------------------------------------- | StateInstance: SST [StateType: abbottChance2005Cell, parent: 0] | Variables: {gl = 5.0E-9, f = NaN, tau = 0.016, Vth = -0.05, tau_r = 0.002, | iSyn = 1.0000000000000002E-10, r = NaN, t = 0.020000000000000316, v = 0.0, Vl = -0.07, | V = -0.05, Vscale = 0.001, Vr = -0.06, r0 = 3.0} | Exposures: {r = NaN, v = 0.0, V = -0.05, f = NaN, iSyn = 1.0000000000000002E-10} | | synapses[0] +-------------------------------------------------------------------- | | synapses[0] | StateInstance: baseline_exc_SST [StateType: pulseGenerator, parent: SST] | | synapses[0] | Variables: {duration = 2.0, amplitude = 0.0, delay = 0.02, t = 0.020000000000000316, i = 0.0, | | synapses[0] | weight = 1.0} | | synapses[0] | Exposures: {i = 0.0, weight = 1.0} | | synapses[0] +-------------------------------------------------------------------- | | synapses[1] +-------------------------------------------------------------------- | | synapses[1] | StateInstance: global_offset_curr_SST [StateType: pulseGenerator, parent: SST] | | synapses[1] | Variables: {duration = 2.0, amplitude = 1.0000000000000002E-10, delay = 0.02, t = 0.020000000000000316, i = 1.0000000000000002E-10, | | synapses[1] | weight = 1.0} | | synapses[1] | Exposures: {i = 1.0000000000000002E-10, weight = 1.0} | | synapses[1] +-------------------------------------------------------------------- | +--------------------------------------------------------------------------------------- +---------------------------------------------------------------------------------------

Current StateInstance's parent: +--------------------------------------------------------------------------------------- | StateInstance: 0 [StateType: instance, parent: SST] | Variables: {t = 0.020000000000000316} | Exposures: {} | +---------------------------------------------------------------------------------- | | StateInstance: SST [StateType: abbottChance2005Cell, parent: 0] | | Variables: {gl = 5.0E-9, f = NaN, tau = 0.016, Vth = -0.05, tau_r = 0.002, | | iSyn = 1.0000000000000002E-10, r = NaN, t = 0.020000000000000316, v = 0.0, Vl = -0.07, | | V = -0.05, Vscale = 0.001, Vr = -0.06, r0 = 3.0} | | Exposures: {r = NaN, v = 0.0, V = -0.05, f = NaN, iSyn = 1.0000000000000002E-10} | | | synapses[0] +--------------------------------------------------------------- | | | synapses[0] | StateInstance: baseline_exc_SST [StateType: pulseGenerator, parent: SST] | | | synapses[0] | Variables: {duration = 2.0, amplitude = 0.0, delay = 0.02, t = 0.020000000000000316, i = 0.0, | | | synapses[0] | weight = 1.0} | | | synapses[0] | Exposures: {i = 0.0, weight = 1.0} | | | synapses[0] +--------------------------------------------------------------- | | | synapses[1] +--------------------------------------------------------------- | | | synapses[1] | StateInstance: global_offset_curr_SST [StateType: pulseGenerator, parent: SST] | | | synapses[1] | Variables: {duration = 2.0, amplitude = 1.0000000000000002E-10, delay = 0.02, t = 0.020000000000000316, i = 1.0000000000000002E-10, | | | synapses[1] | weight = 1.0} | | | synapses[1] | Exposures: {i = 1.0000000000000002E-10, weight = 1.0} | | | synapses[1] +--------------------------------------------------------------- | | +---------------------------------------------------------------------------------- | +---------------------------------------------------------------------------------- | +---------------------------------------------------------------------------------- | | StateInstance: null [StateType: location, parent: 0] | | Variables: {t = 0.020000000000000316, x = 67.1563481487985, y = 8.393822683708397, z = 7.664809327917963} | | Exposures: {} | +---------------------------------------------------------------------------------- +--------------------------------------------------------------------------------------- INFO Feb 20,2024 15:58 (INFO) Loading LEMS file from: /home/ixanthakis/wsl_repos/PyNeuroMLTutorials/ClonedNeuroMLRepositories/del-Molino2017/NeuroML/ParamSweep_SimdelMolinoEtAl_low_baseline_Tue_Feb_20_15.58.37_2024/RUN20_SimdelMolinoEtAl_low_baselineglobal_offset_current0.1nA/LEMS_SimdelMolinoEtAl_low_baseline_RUN20_SimdelMolinoEtAl_low_baselineglobal_offset_current0.1nA.xml INFO Feb 20,2024 15:58 (INFO) Reading from: /home/ixanthakis/wsl_repos/PyNeuroMLTutorials/ClonedNeuroMLRepositories/del-Molino2017/NeuroML/ParamSweep_SimdelMolinoEtAl_low_baseline_Tue_Feb_20_15.58.37_2024/RUN20_SimdelMolinoEtAl_low_baselineglobal_offset_current0.1nA/LEMS_SimdelMolinoEtAl_low_baseline_RUN20_SimdelMolinoEtAl_low_baselineglobal_offset_current0.1nA.xml INFO Feb 20,2024 15:58 (LOG) at org.lemsml.jlems.core.logging.E.multiError(E.java:251) INFO Feb 20,2024 15:58 (LOG) at org.lemsml.jlems.core.logging.E.error(E.java:217) INFO Feb 20,2024 15:58 (LOG) at org.lemsml.jlems.core.sim.Sim.run(Sim.java:319) INFO Feb 20,2024 15:58 (LOG) at org.lemsml.jlems.core.sim.Sim.run(Sim.java:154) INFO Feb 20,2024 15:58 (LOG) at org.lemsml.jlems.org.lemsml.jlems.core.run.RuntimeError: Problem while trying to return a value for variable r: NaN

Current StateInstance: +--------------------------------------------------------------------------------------- | StateInstance: SST [StateType: abbottChance2005Cell, parent: 0] | Variables: {gl = 5.0E-9, f = NaN, tau = 0.016, Vth = -0.05, tau_r = 0.002, | iSyn = 1.0000000000000002E-10, r = NaN, t = 0.020000000000000316, v = 0.0, Vl = -0.07, | V = -0.05, Vscale = 0.001, Vr = -0.06, r0 = 3.0} | Exposures: {r = NaN, v = 0.0, V = -0.05, f = NaN, iSyn = 1.0000000000000002E-10} | | synapses[0] +-------------------------------------------------------------------- | | synapses[0] | StateInstance: baseline_exc_SST [StateType: pulseGenerator, parent: SST] | | synapses[0] | Variables: {duration = 2.0, amplitude = 0.0, delay = 0.02, t = 0.020000000000000316, i = 0.0, | | synapses[0] | weight = 1.0} | | synapses[0] | Exposures: {i = 0.0, weight = 1.0} | | synapses[0] +-------------------------------------------------------------------- | | synapses[1] +-------------------------------------------------------------------- | | synapses[1] | StateInstance: global_offset_curr_SST [StateType: pulseGenerator, parent: SST] | | synapses[1] | Variables: {duration = 2.0, amplitude = 1.0000000000000002E-10, delay = 0.02, t = 0.020000000000000316, i = 1.0000000000000002E-10, | | synapses[1] | weight = 1.0} | | synapses[1] | Exposures: {i = 1.0000000000000002E-10, weight = 1.0} | | synapses[1] +-------------------------------------------------------------------- | +--------------------------------------------------------------------------------------- +---------------------------------------------------------------------------------------

Current StateInstance's parent: +--------------------------------------------------------------------------------------- | StateInstance: 0 [StateType: instance, parent: SST] | Variables: {t = 0.020000000000000316} | Exposures: {} | +---------------------------------------------------------------------------------- | | StateInstance: SST [StateType: abbottChance2005Cell, parent: 0] | | Variables: {gl = 5.0E-9, f = NaN, tau = 0.016, Vth = -0.05, tau_r = 0.002, | | iSyn = 1.0000000000000002E-10, r = NaN, t = 0.020000000000000316, v = 0.0, Vl = -0.07, | | V = -0.05, Vscale = 0.001, Vr = -0.06, r0 = 3.0} | | Exposures: {r = NaN, v = 0.0, V = -0.05, f = NaN, iSyn = 1.0000000000000002E-10} | | | synapses[0] +--------------------------------------------------------------- | | | synapses[0] | StateInstance: baseline_exc_SST [StateType: pulseGenerator, parent: SST] | | | synapses[0] | Variables: {duration = 2.0, amplitude = 0.0, delay = 0.02, t = 0.020000000000000316, i = 0.0, | | | synapses[0] | weight = 1.0} | | | synapses[0] | Exposures: {i = 0.0, weight = 1.0} | | | synapses[0] +--------------------------------------------------------------- | | | synapses[1] +--------------------------------------------------------------- | | | synapses[1] | StateInstance: global_offset_curr_SST [StateType: pulseGenerator, parent: SST] | | | synapses[1] | Variables: {duration = 2.0, amplitude = 1.0000000000000002E-10, delay = 0.02, t = 0.020000000000000316, i = 1.0000000000000002E-10, | | | synapses[1] | weight = 1.0} | | | synapses[1] | Exposures: {i = 1.0000000000000002E-10, weight = 1.0} | | | synapses[1] +--------------------------------------------------------------- | | +---------------------------------------------------------------------------------- | +---------------------------------------------------------------------------------- | +---------------------------------------------------------------------------------- | | StateInstance: null [StateType: location, parent: 0] | | Variables: {t = 0.020000000000000316, x = 67.1563481487985, y = 8.393822683708397, z = 7.664809327917963} | | Exposures: {} | +---------------------------------------------------------------------------------- +--------------------------------------------------------------------------------------- at org.lemsml.jlems.core.run.StateInstance.checkReturn(StateInstance.java:596) at org.lemsml.jlems.core.run.StateInstance.getVariable(StateInstance.java:567) at org.lemsml.jlems.core.run.StateWrapper.getValue(StateWrapper.java:44) at org.lemsml.jlems.core.run.RuntimeRecorder.appendState(RuntimeRecorder.java:83) at org.lemsml.jlems.core.sim.Sim.run(Sim.java:301) at org.lemsml.jlems.core.sim.Sim.run(Sim.java:154) at org.lemsml.jlems.core.sim.Sim.run(Sim.java:145) at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:527) at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493) at org.neuroml.JNeuroML.main(JNeuroML.java:622) Feb 20, 2024 3:58:51 PM org.lemsml.jlems.io.logging.DefaultLogger msg SEVERE: (ERROR)

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core.sim.Sim.run(Sim.java:145) INFO Feb 20,2024 15:58 (LOG) at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:527) INFO Feb 20,2024 15:58 (LOG) at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493) INFO Feb 20,2024 15:58 (LOG) at org.neuroml.JNeuroML.main(JNeuroML.java:622) INFO Feb 20,2024 15:58 (LOG) at org.lemsml.jlems.core.logging.E.multiError(E.java:251) INFO Feb 20,2024 15:58 (LOG) at org.lemsml.jlems.core.logging.E.informativeError(E.java:226) INFO Feb 20,2024 15:58 (LOG) at org.lemsml.jlems.core.sim.Sim.run(Sim.java:328) INFO Feb 20,2024 15:58 (LOG) at org.lemsml.jlems.core.sim.Sim.run(Sim.java:154) INFO Feb 20,2024 15:58 (LOG) at org.lemsml.jlems.core.sim.Sim.run(Sim.java:145) INFO Feb 20,2024 15:58 (LOG) at org.neuroml.export.utils.Utils.loadLemsFile(Utils.java:527) INFO Feb 20,2024 15:58 (LOG) at org.neuroml.export.utils.Utils.runLemsFile(Utils.java:493) INFO Feb 20,2024 15:58 (LOG) at org.neuroml.JNeuroML.main(JNeuroML.java:622)

An error has occured during the function execution Traceback (most recent call last): File "/home/ixanthakis/wsl_repos/Dissertation_Repos/nsimenv3/lib/python3.10/site-packages/ppft/main.py", line 99, in run result = f(*__args) File "", line 7, in run_instance File "/home/ixanthakis/wsl_repos/Dissertation_Repos/nsimenv3/lib/python3.10/site-packages/neuromllite/sweep/ParameterSweep.py", line 598, in run_once traces, events = generate_and_run( File "/home/ixanthakis/wsl_repos/Dissertation_Repos/nsimenv3/lib/python3.10/site-packages/neuromllite/NetworkGenerator.py", line 2153, in generate_and_run results = pynml.run_lems_with_jneuroml( File "/home/ixanthakis/wsl_repos/Dissertation_Repos/nsimenv3/lib/python3.10/site-packages/pyneuroml/pynml.py", line 1312, in run_lems_with_jneuroml success = run_jneuroml( File "/home/ixanthakis/wsl_repos/Dissertation_Repos/nsimenv3/lib/python3.10/site-packages/pyneuroml/pynml.py", line 2567, in run_jneuroml sys.exit(retcode) SystemExit: 1 Traceback (most recent call last): File "/home/ixanthakis/wsl_repos/PyNeuroMLTutorials/ClonedNeuroMLRepositories/del-Molino2017/NeuroML/Sweep.py", line 86, in report = ps.run() File "/home/ixanthakis/wsl_repos/Dissertation_Repos/nsimenv3/lib/python3.10/site-packages/neuromllite/sweep/ParameterSweep.py", line 334, in run self._run_all() File "/home/ixanthakis/wsl_repos/Dissertation_Repos/nsimenv3/lib/python3.10/site-packages/neuromllite/sweep/ParameterSweep.py", line 210, in _run_all traces, events = job() TypeError: cannot unpack non-iterable NoneType object