Closed harshagurnani closed 4 months ago
I just tried to reproduce this, but it looks like it works with the latest NeuroML software stack. I ran 2to3
to just update all the code to make it py3 compatible, and then black
to format it. Does this look like it ran fine, @harshagurnani ?
(ins)(neuroml-stable)[asinha@raam Network(feat/py3 *%)]$ python simulate_one_cell.py
pyNeuroML >>> INFO - Loading NeuroML2 file: ../Cells/Golgi/GoC.cell.nml
Writing files...
pyNeuroML >>> INFO - Executing: (java -Xmx400M -jar "/home/asinha/.local/share/virtualenvs/neuroml-stable/lib/python3.10/site-packages/pyneuroml/lib/jNeuroML-0.12.0-jar-with-dependencies.jar" -validate "OneGoC_GoC.net.nml" ) in directory: .
pyNeuroML >>> INFO - Command completed. Output:
jNeuroML >> jNeuroML v0.12.0
jNeuroML >> Validating: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/OneGoC_GoC.net.nml
jNeuroML >> Valid against schema and all tests
jNeuroML >> No warnings
jNeuroML >>
jNeuroML >> Validated 1 files: All valid and no warnings
jNeuroML >>
jNeuroML >>
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/OneGoC_GoC.net.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Cells/Golgi/GoC.cell.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_Na.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_NaR.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_NaP.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_KA.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_SK2.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_KM.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_KV.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_BK.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_CaHVA.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_CaLVA.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_HCN1f.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_HCN1s.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_HCN2f.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_HCN2s.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_lkg.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_CALC.nml
pyNeuroML >>> INFO - Loading LEMS file: LEMS_sim_OneGoC_GoC.xml and running with jNeuroML_NEURON
pyNeuroML >>> INFO - Executing: (java -Xmx2G -Djava.awt.headless=true -jar "/home/asinha/.local/share/virtualenvs/neuroml-stable/lib/python3.10/site-packages/pyneuroml/lib/jNeuroML-0.12.0-jar-with-dependencies.jar" "LEMS_sim_OneGoC_GoC.xml" -neuron -nogui -I '') in directory: .
pyNeuroML >>> INFO - Command completed. Output:
jNeuroML >> jNeuroML v0.12.0
jNeuroML >> (INFO) Reading from: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/LEMS_sim_OneGoC_GoC.xml
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c1_c2 type=forwardTransition): XMLAttribute(from, c1) at: org.lemsml.jlems.core.type.Component.resolve(Component.java:540)
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c1_c2 type=forwardTransition): XMLAttribute(to, c2) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c1_c2 type=reverseTransition): XMLAttribute(from, c1) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c1_c2 type=reverseTransition): XMLAttribute(to, c2) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c2_c3 type=forwardTransition): XMLAttribute(from, c2) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c2_c3 type=forwardTransition): XMLAttribute(to, c3) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c2_c3 type=reverseTransition): XMLAttribute(from, c2) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c2_c3 type=reverseTransition): XMLAttribute(to, c3) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c3_c4 type=forwardTransition): XMLAttribute(from, c3) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c3_c4 type=forwardTransition): XMLAttribute(to, c4) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c3_c4 type=reverseTransition): XMLAttribute(from, c3) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c3_c4 type=reverseTransition): XMLAttribute(to, c4) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c3_o1 type=forwardTransition): XMLAttribute(from, c3) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c3_o1 type=forwardTransition): XMLAttribute(to, o1) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c3_o1 type=reverseTransition): XMLAttribute(from, c3) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c3_o1 type=reverseTransition): XMLAttribute(to, o1) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c4_o2 type=forwardTransition): XMLAttribute(from, c4) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c4_o2 type=forwardTransition): XMLAttribute(to, o2) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c4_o2 type=reverseTransition): XMLAttribute(from, c4) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c4_o2 type=reverseTransition): XMLAttribute(to, o2) at:
jNeuroML >> (INFO) Creating NeuronWriter to output files to /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network
jNeuroML >> (INFO) Adding simulation Component(id=sim_OneGoC_GoC type=Simulation) of network/component: OneGoC_GoC (Type: networkWithTemperature: temperature=296.15 (SI temperature))
jNeuroML >> (INFO) Adding population: GoClPop
jNeuroML >> (INFO) -- Writing to hoc: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GoCl.hoc
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/LeakConductance.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/LeakConductance.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNa.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNa.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNaP.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNaP.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNaR.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNaR.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKA.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKA.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKV.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKV.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKM.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKM.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiBK.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiBK.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiSK2.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiSK2.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN1f.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN1f.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN1s.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN1s.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN2f.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN2f.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN2s.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN2s.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiCaHVA.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiCaHVA.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiCaLVA.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiCaLVA.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/Golgi_CALC.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/Golgi_CALC.mod exists and is identical
jNeuroML >> (INFO) Adding projections/connections...
jNeuroML >>
True
(ins)(neuroml-stable)[asinha@raam Network(feat/py3 *%)]$ python simulate_one_cell_write_spike.py
pyNeuroML >>> INFO - Loading NeuroML2 file: ../Cells/Golgi/GoC.cell.nml
Writing files...
pyNeuroML >>> INFO - Executing: (java -Xmx400M -jar "/home/asinha/.local/share/virtualenvs/neuroml-stable/lib/python3.10/site-packages/pyneuroml/lib/jNeuroML-0.12.0-jar-with-dependencies.jar" -validate "OneGoC_GoC.net.nml" ) in directory: .
pyNeuroML >>> INFO - Command completed. Output:
jNeuroML >> jNeuroML v0.12.0
jNeuroML >> Validating: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/OneGoC_GoC.net.nml
jNeuroML >> Valid against schema and all tests
jNeuroML >> No warnings
jNeuroML >>
jNeuroML >> Validated 1 files: All valid and no warnings
jNeuroML >>
jNeuroML >>
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/OneGoC_GoC.net.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Cells/Golgi/GoC.cell.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_Na.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_NaR.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_NaP.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_KA.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_SK2.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_KM.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_KV.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_BK.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_CaHVA.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_CaLVA.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_HCN1f.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_HCN1s.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_HCN2f.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_HCN2s.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_lkg.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_CALC.nml
pyNeuroML >>> INFO - Loading LEMS file: LEMS_sim_V2_OneGoC_GoC.xml and running with jNeuroML_NEURON
pyNeuroML >>> INFO - Executing: (java -Xmx2G -Djava.awt.headless=true -jar "/home/asinha/.local/share/virtualenvs/neuroml-stable/lib/python3.10/site-packages/pyneuroml/lib/jNeuroML-0.12.0-jar-with-dependencies.jar" "LEMS_sim_V2_OneGoC_GoC.xml" -neuron -nogui -I '') in directory: .
pyNeuroML >>> INFO - Command completed. Output:
jNeuroML >> jNeuroML v0.12.0
jNeuroML >> (INFO) Reading from: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/LEMS_sim_V2_OneGoC_GoC.xml
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c1_c2 type=forwardTransition): XMLAttribute(from, c1) at: org.lemsml.jlems.core.type.Component.resolve(Component.java:540)
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c1_c2 type=forwardTransition): XMLAttribute(to, c2) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c1_c2 type=reverseTransition): XMLAttribute(from, c1) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c1_c2 type=reverseTransition): XMLAttribute(to, c2) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c2_c3 type=forwardTransition): XMLAttribute(from, c2) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c2_c3 type=forwardTransition): XMLAttribute(to, c3) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c2_c3 type=reverseTransition): XMLAttribute(from, c2) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c2_c3 type=reverseTransition): XMLAttribute(to, c3) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c3_c4 type=forwardTransition): XMLAttribute(from, c3) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c3_c4 type=forwardTransition): XMLAttribute(to, c4) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c3_c4 type=reverseTransition): XMLAttribute(from, c3) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c3_c4 type=reverseTransition): XMLAttribute(to, c4) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c3_o1 type=forwardTransition): XMLAttribute(from, c3) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c3_o1 type=forwardTransition): XMLAttribute(to, o1) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c3_o1 type=reverseTransition): XMLAttribute(from, c3) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c3_o1 type=reverseTransition): XMLAttribute(to, o1) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c4_o2 type=forwardTransition): XMLAttribute(from, c4) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c4_o2 type=forwardTransition): XMLAttribute(to, o2) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c4_o2 type=reverseTransition): XMLAttribute(from, c4) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c4_o2 type=reverseTransition): XMLAttribute(to, o2) at:
jNeuroML >> (INFO) Creating NeuronWriter to output files to /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network
jNeuroML >> (INFO) Adding simulation Component(id=sim_V2_OneGoC_GoC type=Simulation) of network/component: OneGoC_GoC (Type: networkWithTemperature: temperature=296.15 (SI temperature))
jNeuroML >> (INFO) Adding population: GoClPop
jNeuroML >> (INFO) -- Writing to hoc: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GoCl.hoc
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/LeakConductance.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/LeakConductance.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNa.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNa.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNaP.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNaP.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNaR.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNaR.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKA.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKA.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKV.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKV.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKM.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKM.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiBK.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiBK.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiSK2.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiSK2.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN1f.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN1f.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN1s.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN1s.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN2f.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN2f.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN2s.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN2s.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiCaHVA.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiCaHVA.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiCaLVA.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiCaLVA.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/Golgi_CALC.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/Golgi_CALC.mod exists and is identical
jNeuroML >> (INFO) Adding projections/connections...
jNeuroML >>
True
System information:
pyNeuroML v0.7.2 (libNeuroML v0.4.1, jNeuroML v0.12.0)
Python 3.10.7
Running the sim by setting run=True
in simulate_one_cell_write_spike.py
gives me these spikes
(ins)(neuroml-stable)[asinha@raam Network(feat/py3 *%)]$ cat ../Data_OneGoC/sim_V2_OneGoC_GoC.spikes.dat
0 0.04352500000010134
0 0.2046500000000508
0 0.3710999999998994
0 0.5378499999998653
0 0.7047250000004724
0 0.8716250000010796
0 1.0385500000016867
0 1.205450000002294
0 1.372325000002901
0 1.5392000000035082
0 1.7060500000041152
0 1.872875000004722
Ah wwait - I realised you used the default cell modell GoC.cell.nml - that's of class Cell. Did you try giving the argument goc_file='Golgi_reduced_twoCaPools'? And you will need to add argument has2Pools=True
I have changed the defaults. You can try this again: https://github.com/harshagurnani/GoCModel_Basic/blob/main/Network/simulate_one_cell_write_spike.py
Yeh, I can reproduce the unsuccessful case from your notebook, though, so there's certainly an issue somewhere. I'll go test your script with the new defaults too:
import simulate_one_cell_write_spike as so2
goc_path = '../Cells/Golgi/'
goc_file='GoC_2Pools'
has2Pools = True
dur = 1000 #ms
dt=0.0025
so2.create_LEMS_sim(duration=dur,dt=dt, goc_path=goc_path, goc_file=goc_file, has2Pools=has2Pools)
gives:
$ python test.py
pyNeuroML >>> INFO - Loading NeuroML2 file: ../Cells/Golgi/GoC_2Pools.cell.nml
Writing files...
pyNeuroML >>> INFO - Executing: (java -Xmx400M -jar "/home/asinha/.local/share/virtualenvs/neuroml-stable/lib/python3.10/site-packages/pyneuroml/lib/jNeuroML-0.12.0-jar-with-dependencies.jar" -validate "OneGoC_GoC_2Pools_2CaPools.net.nml" ) in directory: .
pyNeuroML >>> INFO - Command completed. Output:
jNeuroML >> jNeuroML v0.12.0
jNeuroML >> Validating: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/OneGoC_GoC_2Pools_2CaPools.net.nml
jNeuroML >> Valid against schema and all tests
jNeuroML >> No warnings
jNeuroML >>
jNeuroML >> Validated 1 files: All valid and no warnings
jNeuroML >>
jNeuroML >>
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/OneGoC_GoC_2Pools_2CaPools.net.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Cells/Golgi/GoC_2Pools.cell.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_Na.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_NaR.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_NaP.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_KA.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_SK2.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_KM.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_KV.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_BK.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_CaHVA.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_CaLVA.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_HCN1f.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_HCN1s.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_HCN2f.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_HCN2s.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/GIRK.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_lkg.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_CALC.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_CALC2.nml
pyNeuroML >>> INFO - Loading LEMS file: LEMS_sim_V2_OneGoC_GoC_2Pools_2CaPools.xml and running with jNeuroML_NEURON
pyNeuroML >>> INFO - Executing: (java -Xmx2G -Djava.awt.headless=true -jar "/home/asinha/.local/share/virtualenvs/neuroml-stable/lib/python3.10/site-packages/pyneuroml/lib/jNeuroML-0.12.0-jar-with-dependencies.jar" "LEMS_sim_V2_OneGoC_GoC_2Pools_2CaPools.xml" -neuron -nogui -I '') in directory: .
pyNeuroML >>> CRITICAL - *** Problem running command:
Command 'java -Xmx2G -Djava.awt.headless=true -jar "/home/asinha/.local/share/virtualenvs/neuroml-stable/lib/python3.10/site-packages/pyneuroml/lib/jNeuroML-0.12.0-jar-with-dependencies.jar" "LEMS_sim_V2_OneGoC_GoC_2Pools_2CaPools.xml" -neuron -nogui -I ''' returned non-zero exit status 1.
pyNeuroML >>> CRITICAL - jNeuroML >> jNeuroML v0.12.0
jNeuroML >> (INFO) Reading from: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/LEMS_sim_V2_OneGoC_GoC_2Pools_2CaPools.xml
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c1_c2 type=forwardTransition): XMLAttribute(from, c1) at: org.lemsml.jlems.core.type.Component.resolve(Component.java:540)
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c1_c2 type=forwardTransition): XMLAttribute(to, c2) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c1_c2 type=reverseTransition): XMLAttribute(from, c1) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c1_c2 type=reverseTransition): XMLAttribute(to, c2) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c2_c3 type=forwardTransition): XMLAttribute(from, c2) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c2_c3 type=forwardTransition): XMLAttribute(to, c3) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c2_c3 type=reverseTransition): XMLAttribute(from, c2) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c2_c3 type=reverseTransition): XMLAttribute(to, c3) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c3_c4 type=forwardTransition): XMLAttribute(from, c3) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c3_c4 type=forwardTransition): XMLAttribute(to, c4) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c3_c4 type=reverseTransition): XMLAttribute(from, c3) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c3_c4 type=reverseTransition): XMLAttribute(to, c4) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c3_o1 type=forwardTransition): XMLAttribute(from, c3) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c3_o1 type=forwardTransition): XMLAttribute(to, o1) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c3_o1 type=reverseTransition): XMLAttribute(from, c3) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c3_o1 type=reverseTransition): XMLAttribute(to, o1) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c4_o2 type=forwardTransition): XMLAttribute(from, c4) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c4_o2 type=forwardTransition): XMLAttribute(to, o2) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c4_o2 type=reverseTransition): XMLAttribute(from, c4) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c4_o2 type=reverseTransition): XMLAttribute(to, o2) at:
jNeuroML >> (INFO) Creating NeuronWriter to output files to /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network
jNeuroML >> (INFO) Adding simulation Component(id=sim_V2_OneGoC_GoC_2Pools_2CaPools type=Simulation) of network/component: OneGoC_GoC_2Pools_2CaPools (Type: networkWithTemperature: temperature=296.15 (SI temperature))
jNeuroML >> (INFO) Adding population: GoCl_2PoolsPop
jNeuroML >> (INFO) -- Writing to hoc: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GoCl_2Pools.hoc
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/LeakConductance.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/LeakConductance.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNa.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNa.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNaP.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNaP.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNaR.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNaR.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKA.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKA.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKV.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKV.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKM.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKM.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiBK.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiBK.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiSK2.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiSK2.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN1f.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN1f.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN1s.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN1s.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN2f.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN2f.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN2s.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN2s.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiCaHVA.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiCaHVA.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiCaLVA.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiCaLVA.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GIRK.mod
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/Golgi_CALC.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/Golgi_CALC.mod exists and is identical
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/Golgi_CALC2.mod
jNeuroML >> (INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/Golgi_CALC2.mod exists and is identical
jNeuroML >> (INFO) Adding projections/connections...
jNeuroML >> Exception in thread "main" java.lang.NullPointerException: Cannot invoke "org.neuroml.model.BiophysicalProperties.getMembraneProperties()" because the return value of "org.neuroml.model.Cell.getBiophysicalProperties()" is null
jNeuroML >> at org.neuroml.export.neuron.NeuronWriter.getMainScript(NeuronWriter.java:1499)
jNeuroML >> at org.neuroml.export.neuron.NeuronWriter.generateMainScriptAndMods(NeuronWriter.java:277)
jNeuroML >> at org.neuroml.export.neuron.NeuronWriter.generateAndRun(NeuronWriter.java:155)
jNeuroML >> at org.neuroml.JNeuroML.main(JNeuroML.java:525)
jNeuroML >>
pyNeuroML >>> ERROR - execute_command_in_dir returned with output: jNeuroML v0.12.0
(INFO) Reading from: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/LEMS_sim_V2_OneGoC_GoC_2Pools_2CaPools.xml
(WARNING) Unused attribute in Component(id=alpha_c1_c2 type=forwardTransition): XMLAttribute(from, c1) at: org.lemsml.jlems.core.type.Component.resolve(Component.java:540)
(WARNING) Unused attribute in Component(id=alpha_c1_c2 type=forwardTransition): XMLAttribute(to, c2) at:
(WARNING) Unused attribute in Component(id=beta_c1_c2 type=reverseTransition): XMLAttribute(from, c1) at:
(WARNING) Unused attribute in Component(id=beta_c1_c2 type=reverseTransition): XMLAttribute(to, c2) at:
(WARNING) Unused attribute in Component(id=alpha_c2_c3 type=forwardTransition): XMLAttribute(from, c2) at:
(WARNING) Unused attribute in Component(id=alpha_c2_c3 type=forwardTransition): XMLAttribute(to, c3) at:
(WARNING) Unused attribute in Component(id=beta_c2_c3 type=reverseTransition): XMLAttribute(from, c2) at:
(WARNING) Unused attribute in Component(id=beta_c2_c3 type=reverseTransition): XMLAttribute(to, c3) at:
(WARNING) Unused attribute in Component(id=alpha_c3_c4 type=forwardTransition): XMLAttribute(from, c3) at:
(WARNING) Unused attribute in Component(id=alpha_c3_c4 type=forwardTransition): XMLAttribute(to, c4) at:
(WARNING) Unused attribute in Component(id=beta_c3_c4 type=reverseTransition): XMLAttribute(from, c3) at:
(WARNING) Unused attribute in Component(id=beta_c3_c4 type=reverseTransition): XMLAttribute(to, c4) at:
(WARNING) Unused attribute in Component(id=alpha_c3_o1 type=forwardTransition): XMLAttribute(from, c3) at:
(WARNING) Unused attribute in Component(id=alpha_c3_o1 type=forwardTransition): XMLAttribute(to, o1) at:
(WARNING) Unused attribute in Component(id=beta_c3_o1 type=reverseTransition): XMLAttribute(from, c3) at:
(WARNING) Unused attribute in Component(id=beta_c3_o1 type=reverseTransition): XMLAttribute(to, o1) at:
(WARNING) Unused attribute in Component(id=alpha_c4_o2 type=forwardTransition): XMLAttribute(from, c4) at:
(WARNING) Unused attribute in Component(id=alpha_c4_o2 type=forwardTransition): XMLAttribute(to, o2) at:
(WARNING) Unused attribute in Component(id=beta_c4_o2 type=reverseTransition): XMLAttribute(from, c4) at:
(WARNING) Unused attribute in Component(id=beta_c4_o2 type=reverseTransition): XMLAttribute(to, o2) at:
(INFO) Creating NeuronWriter to output files to /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network
(INFO) Adding simulation Component(id=sim_V2_OneGoC_GoC_2Pools_2CaPools type=Simulation) of network/component: OneGoC_GoC_2Pools_2CaPools (Type: networkWithTemperature: temperature=296.15 (SI temperature))
(INFO) Adding population: GoCl_2PoolsPop
(INFO) -- Writing to hoc: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GoCl_2Pools.hoc
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/LeakConductance.mod
(INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/LeakConductance.mod exists and is identical
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNa.mod
(INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNa.mod exists and is identical
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNaP.mod
(INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNaP.mod exists and is identical
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNaR.mod
(INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNaR.mod exists and is identical
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKA.mod
(INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKA.mod exists and is identical
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKV.mod
(INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKV.mod exists and is identical
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKM.mod
(INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKM.mod exists and is identical
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiBK.mod
(INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiBK.mod exists and is identical
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiSK2.mod
(INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiSK2.mod exists and is identical
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN1f.mod
(INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN1f.mod exists and is identical
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN1s.mod
(INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN1s.mod exists and is identical
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN2f.mod
(INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN2f.mod exists and is identical
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN2s.mod
(INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN2s.mod exists and is identical
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiCaHVA.mod
(INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiCaHVA.mod exists and is identical
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiCaLVA.mod
(INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiCaLVA.mod exists and is identical
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GIRK.mod
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/Golgi_CALC.mod
(INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/Golgi_CALC.mod exists and is identical
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/Golgi_CALC2.mod
(INFO) File /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/Golgi_CALC2.mod exists and is identical
(INFO) Adding projections/connections...
Exception in thread "main" java.lang.NullPointerException: Cannot invoke "org.neuroml.model.BiophysicalProperties.getMembraneProperties()" because the return value of "org.neuroml.model.Cell.getBiophysicalProperties()" is null
at org.neuroml.export.neuron.NeuronWriter.getMainScript(NeuronWriter.java:1499)
at org.neuroml.export.neuron.NeuronWriter.generateMainScriptAndMods(NeuronWriter.java:277)
at org.neuroml.export.neuron.NeuronWriter.generateAndRun(NeuronWriter.java:155)
at org.neuroml.JNeuroML.main(JNeuroML.java:525)
Here we go, same error:
(ins)(neuroml-stable)[asinha@raam Network(main *=)]$ python simulate_one_cell_write_spike.py
pyNeuroML >>> INFO - Loading NeuroML2 file: ../Cells/Golgi/Golgi_reduced_twoCaPools.cell.nml
Writing files...
pyNeuroML >>> INFO - Executing: (java -Xmx400M -jar "/home/asinha/.local/share/virtualenvs/neuroml-stable/lib/python3.10/site-packages/pyneuroml/lib/jNeuroML-0.12.0-jar-with-dependencies.jar" -validate "OneGoC_Golgi_reduced_twoCaPools_2CaPools.net.nml" ) in directory: .
pyNeuroML >>> INFO - Command completed. Output:
jNeuroML >> jNeuroML v0.12.0
jNeuroML >> Validating: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/OneGoC_Golgi_reduced_twoCaPools_2CaPools.net.nml
jNeuroML >> Valid against schema and all tests
jNeuroML >> No warnings
jNeuroML >>
jNeuroML >> Validated 1 files: All valid and no warnings
jNeuroML >>
jNeuroML >>
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/OneGoC_Golgi_reduced_twoCaPools_2CaPools.net.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Cells/Golgi/Golgi_reduced_twoCaPools.cell.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_Na.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_NaR.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_NaP.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_KA.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_SK2.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_KM.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_KV.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_BK.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_CaHVA.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_CaLVA.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_HCN1f.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_HCN1s.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_HCN2f.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_HCN2s.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_lkg.channel.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_CALC.nml
pyNeuroML >>> INFO - Loading NeuroML2 file: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Mechanisms/Golgi_CALC2.nml
pyNeuroML >>> INFO - Loading LEMS file: LEMS_sim_V2_OneGoC_Golgi_reduced_twoCaPools_2CaPools.xml and running with jNeuroML_NEURON
pyNeuroML >>> INFO - Executing: (java -Xmx2G -Djava.awt.headless=true -jar "/home/asinha/.local/share/virtualenvs/neuroml-stable/lib/python3.10/site-packages/pyneuroml/lib/jNeuroML-0.12.0-jar-with-dependencies.jar" "LEMS_sim_V2_OneGoC_Golgi_reduced_twoCaPools_2CaPools.xml" -neuron -nogui -I '') in directory: .
pyNeuroML >>> CRITICAL - *** Problem running command:
Command 'java -Xmx2G -Djava.awt.headless=true -jar "/home/asinha/.local/share/virtualenvs/neuroml-stable/lib/python3.10/site-packages/pyneuroml/lib/jNeuroML-0.12.0-jar-with-dependencies.jar" "LEMS_sim_V2_OneGoC_Golgi_reduced_twoCaPools_2CaPools.xml" -neuron -nogui -I ''' returned non-zero exit status 1.
pyNeuroML >>> CRITICAL - jNeuroML >> jNeuroML v0.12.0
jNeuroML >> (INFO) Reading from: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/LEMS_sim_V2_OneGoC_Golgi_reduced_twoCaPools_2CaPools.xml
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c1_c2 type=forwardTransition): XMLAttribute(from, c1) at: org.lemsml.jlems.core.type.Component.resolve(Component.java:540)
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c1_c2 type=forwardTransition): XMLAttribute(to, c2) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c1_c2 type=reverseTransition): XMLAttribute(from, c1) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c1_c2 type=reverseTransition): XMLAttribute(to, c2) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c2_c3 type=forwardTransition): XMLAttribute(from, c2) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c2_c3 type=forwardTransition): XMLAttribute(to, c3) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c2_c3 type=reverseTransition): XMLAttribute(from, c2) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c2_c3 type=reverseTransition): XMLAttribute(to, c3) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c3_c4 type=forwardTransition): XMLAttribute(from, c3) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c3_c4 type=forwardTransition): XMLAttribute(to, c4) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c3_c4 type=reverseTransition): XMLAttribute(from, c3) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c3_c4 type=reverseTransition): XMLAttribute(to, c4) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c3_o1 type=forwardTransition): XMLAttribute(from, c3) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c3_o1 type=forwardTransition): XMLAttribute(to, o1) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c3_o1 type=reverseTransition): XMLAttribute(from, c3) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c3_o1 type=reverseTransition): XMLAttribute(to, o1) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c4_o2 type=forwardTransition): XMLAttribute(from, c4) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=alpha_c4_o2 type=forwardTransition): XMLAttribute(to, o2) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c4_o2 type=reverseTransition): XMLAttribute(from, c4) at:
jNeuroML >> (WARNING) Unused attribute in Component(id=beta_c4_o2 type=reverseTransition): XMLAttribute(to, o2) at:
jNeuroML >> (INFO) Creating NeuronWriter to output files to /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network
jNeuroML >> (INFO) Adding simulation Component(id=sim_V2_OneGoC_Golgi_reduced_twoCaPools_2CaPools type=Simulation) of network/component: OneGoC_Golgi_reduced_twoCaPools_2CaPools (Type: networkWithTemperature: temperature=296.15 (SI temperature))
jNeuroML >> (INFO) Adding population: Golgi_10comp_all_channels_twoCaPoolsPop
jNeuroML >> (INFO) -- Writing to hoc: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/Golgi_10comp_all_channels_twoCaPools.hoc
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/LeakConductance.mod
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN1f.mod
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN1s.mod
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN2f.mod
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN2s.mod
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKA.mod
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiBK.mod
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKM.mod
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiSK2.mod
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKV.mod
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNaP.mod
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNaR.mod
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNa.mod
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiCaHVA.mod
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiCaLVA.mod
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/Golgi_CALC.mod
jNeuroML >> (INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/Golgi_CALC2.mod
jNeuroML >> (INFO) Adding projections/connections...
jNeuroML >> Exception in thread "main" java.lang.NullPointerException: Cannot invoke "org.neuroml.model.BiophysicalProperties.getMembraneProperties()" because the return value of "org.neuroml.model.Cell.getBiophysicalProperties()" is null
jNeuroML >> at org.neuroml.export.neuron.NeuronWriter.getMainScript(NeuronWriter.java:1499)
jNeuroML >> at org.neuroml.export.neuron.NeuronWriter.generateMainScriptAndMods(NeuronWriter.java:277)
jNeuroML >> at org.neuroml.export.neuron.NeuronWriter.generateAndRun(NeuronWriter.java:155)
jNeuroML >> at org.neuroml.JNeuroML.main(JNeuroML.java:525)
jNeuroML >>
pyNeuroML >>> ERROR - execute_command_in_dir returned with output: jNeuroML v0.12.0
(INFO) Reading from: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/LEMS_sim_V2_OneGoC_Golgi_reduced_twoCaPools_2CaPools.xml
(WARNING) Unused attribute in Component(id=alpha_c1_c2 type=forwardTransition): XMLAttribute(from, c1) at: org.lemsml.jlems.core.type.Component.resolve(Component.java:540)
(WARNING) Unused attribute in Component(id=alpha_c1_c2 type=forwardTransition): XMLAttribute(to, c2) at:
(WARNING) Unused attribute in Component(id=beta_c1_c2 type=reverseTransition): XMLAttribute(from, c1) at:
(WARNING) Unused attribute in Component(id=beta_c1_c2 type=reverseTransition): XMLAttribute(to, c2) at:
(WARNING) Unused attribute in Component(id=alpha_c2_c3 type=forwardTransition): XMLAttribute(from, c2) at:
(WARNING) Unused attribute in Component(id=alpha_c2_c3 type=forwardTransition): XMLAttribute(to, c3) at:
(WARNING) Unused attribute in Component(id=beta_c2_c3 type=reverseTransition): XMLAttribute(from, c2) at:
(WARNING) Unused attribute in Component(id=beta_c2_c3 type=reverseTransition): XMLAttribute(to, c3) at:
(WARNING) Unused attribute in Component(id=alpha_c3_c4 type=forwardTransition): XMLAttribute(from, c3) at:
(WARNING) Unused attribute in Component(id=alpha_c3_c4 type=forwardTransition): XMLAttribute(to, c4) at:
(WARNING) Unused attribute in Component(id=beta_c3_c4 type=reverseTransition): XMLAttribute(from, c3) at:
(WARNING) Unused attribute in Component(id=beta_c3_c4 type=reverseTransition): XMLAttribute(to, c4) at:
(WARNING) Unused attribute in Component(id=alpha_c3_o1 type=forwardTransition): XMLAttribute(from, c3) at:
(WARNING) Unused attribute in Component(id=alpha_c3_o1 type=forwardTransition): XMLAttribute(to, o1) at:
(WARNING) Unused attribute in Component(id=beta_c3_o1 type=reverseTransition): XMLAttribute(from, c3) at:
(WARNING) Unused attribute in Component(id=beta_c3_o1 type=reverseTransition): XMLAttribute(to, o1) at:
(WARNING) Unused attribute in Component(id=alpha_c4_o2 type=forwardTransition): XMLAttribute(from, c4) at:
(WARNING) Unused attribute in Component(id=alpha_c4_o2 type=forwardTransition): XMLAttribute(to, o2) at:
(WARNING) Unused attribute in Component(id=beta_c4_o2 type=reverseTransition): XMLAttribute(from, c4) at:
(WARNING) Unused attribute in Component(id=beta_c4_o2 type=reverseTransition): XMLAttribute(to, o2) at:
(INFO) Creating NeuronWriter to output files to /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network
(INFO) Adding simulation Component(id=sim_V2_OneGoC_Golgi_reduced_twoCaPools_2CaPools type=Simulation) of network/component: OneGoC_Golgi_reduced_twoCaPools_2CaPools (Type: networkWithTemperature: temperature=296.15 (SI temperature))
(INFO) Adding population: Golgi_10comp_all_channels_twoCaPoolsPop
(INFO) -- Writing to hoc: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/Golgi_10comp_all_channels_twoCaPools.hoc
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/LeakConductance.mod
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN1f.mod
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN1s.mod
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN2f.mod
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiHCN2s.mod
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKA.mod
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiBK.mod
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKM.mod
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiSK2.mod
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiKV.mod
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNaP.mod
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNaR.mod
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiNa.mod
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiCaHVA.mod
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/GolgiCaLVA.mod
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/Golgi_CALC.mod
(INFO) -- Writing to mod: /home/asinha/Documents/02_Code/00_mine/models/GoCModel_Basic/Network/Golgi_CALC2.mod
(INFO) Adding projections/connections...
Exception in thread "main" java.lang.NullPointerException: Cannot invoke "org.neuroml.model.BiophysicalProperties.getMembraneProperties()" because the return value of "org.neuroml.model.Cell.getBiophysicalProperties()" is null
at org.neuroml.export.neuron.NeuronWriter.getMainScript(NeuronWriter.java:1499)
at org.neuroml.export.neuron.NeuronWriter.generateMainScriptAndMods(NeuronWriter.java:277)
at org.neuroml.export.neuron.NeuronWriter.generateAndRun(NeuronWriter.java:155)
at org.neuroml.JNeuroML.main(JNeuroML.java:525)
Yes, something deep in the Java to resolve... Looking into it..
Will be a day or two before a new release of pynml though...
Should be fixed in recent jNeuroML releases. Will check again and re-open if not.
I was trying to simulate a network with a single cell. The model neuron is of class Cell2CaPools. However, I fail to create the neuron simulation from the corresponding LEMS simulation (XML).
I traced down the error to the creation of the output file that accesses the 'spike' event port. @pgleeson
There is no such issue if I instead use a model neuron from class Cell. Similarly, there is no error in reading the voltage variable from the class Cell2CaPools.
To Reproduce
The relevant files are at: https://github.com/harshagurnani/GoCModel_Basic/tree/main/Network
The functions to construct network, and the simulation files are simulate_one_cell.py and simulate_one_cell_write_spike.py, where the latter just uncomments lines 77-79 (creation of spikes output file).
Example usage is in the following notebook, with example successful and failed cases
The corresponding LEMS simulation files are:
Neuron models are in ../Cells/Golgi, where GoC is of class Cell, and Goc_2Pools and Golgi_reduced_twoCaPools are of class Cell2CaPools
Error message
No detailed error is given.
System information:
Additional context
As these are multicompartmental models, if you need to simulate, you will need to regenerate the hoc and mod files, and then compile the mod files. However the issue is generating the neuron sim files anyway.