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NeuroML / pyNeuroML

A single package in Python unifying scripts and modules for reading, writing, simulating and analysing NeuroML2/LEMS models.
https://docs.neuroml.org/Userdocs/Software/pyNeuroML.html
GNU Lesser General Public License v3.0
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[Bug] Cannot create spike output file for class cell2CaPools #198

Closed harshagurnani closed 4 months ago

harshagurnani commented 1 year ago

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.

Error: execute_command_in_dir returned with output: None

An exception has occurred, use %tb to see the full traceback.
SystemExit: -1
c:\users\harsha\anaconda3\envs\nmlpy2\lib\site-packages\IPython\core\interactiveshell.py:2886: UserWarning: To exit: use 'exit', 'quit', or Ctrl-D.
  warn("To exit: use 'exit', 'quit', or Ctrl-D.", stacklevel=1)

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.

sanjayankur31 commented 1 year 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
harshagurnani commented 1 year ago

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

harshagurnani commented 1 year ago

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

sanjayankur31 commented 1 year ago

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)
sanjayankur31 commented 1 year ago

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)
pgleeson commented 1 year ago

Yes, something deep in the Java to resolve... Looking into it..

pgleeson commented 1 year ago

Fixed with this: https://github.com/NeuroML/org.neuroml.export/commit/e1065f4de64647009ad737524260fde7f5ae48cf#diff-0f77fe1e8ceeff29783e20d8ca662840486970e25cbef6feee283a45c683d623

Will be a day or two before a new release of pynml though...

sanjayankur31 commented 4 months ago

Should be fixed in recent jNeuroML releases. Will check again and re-open if not.

https://github.com/NeuroML/jNeuroML/releases