Main Neurospaces logo neurospaces 0.1675 Thu, 27 Dec 2007 15:58:18 -0600 hugo

Index of group ./specifications/simple_run

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simple simulations of models, checking and resetting a simulation

1. Commands for a single passive compartment created from the shell
2. Commands to run the purkinje cell from an ndf file
3. Running, checking, saving, loading and resetting a simulation

1. Commands for a single passive compartment created from the shell

Startup command : bin/genesis-g3

(No model has been loaded for the following set of commands.)

1.1. Is startup successful ?

1. Expected output 
GENESIS 3 shell

1.2. Can we create a cell ?

1. Executed command
create cell /c
2. Expected output 







1.3. Can we create a segment ?





1. Executed command
create segment /c/s




2. Expected output 







1.4. Can we set parameter CM of the segment ?





1. Executed command
model_parameter_add /c/s CM 0.0164




2. Expected output 







1.5. Can we set parameter Vm_init of the segment ?





1. Executed command
model_parameter_add /c/s Vm_init -0.0680




2. Expected output 







1.6. Can we set parameter RM of the segment ?





1. Executed command
model_parameter_add /c/s RM 1.000




2. Expected output 







1.7. Can we set parameter RA of the segment ?





1. Executed command
model_parameter_add /c/s RA 2.50




2. Expected output 







1.8. Can we set parameter ELEAK of the segment ?





1. Executed command
model_parameter_add /c/s ELEAK -0.080




2. Expected output 







1.9. Can we set parameter DIA of the segment ?





1. Executed command
model_parameter_add /c/s DIA 2e-05




2. Expected output 







1.10. Can we set parameter LENGTH of the segment ?





1. Executed command
model_parameter_add /c/s LENGTH 4.47e-05




2. Expected output 







1.11. Can we define the output ?





1. Executed command
output_add /c/s Vm




2. Expected output 







1.12. Can we check the simulation ?





1. Executed command
check /c




2. Expected output 







1.13. Can we run the simulation ?





1. Executed command
run /c 0.001




2. Expected output 







1.14. Can we find the output ?





1. Executed command
sh cat /tmp/output




2. Expected output 

0.001 -0.0687098





3. Comment
only testing the last line of output







2. Commands to run the purkinje cell from an ndf file
Startup command : bin/genesis-g3
(No model has been loaded for the following set of commands.)
2.1. Is startup successful ?





1. Expected output 
GENESIS 3 shell







2.2. Can we load the purkinje cell model ?





1. Executed command
ndf_load cells/purkinje/edsjb1994.ndf




2. Expected output 







2.3. Can we check the simulation ?





1. Executed command
check /Purkinje




2. Expected output 







2.4. Can we run the simulation ?





1. Executed command
run /Purkinje 0.001




2. Expected output 







2.5. Can we find the output ?





1. Executed command
sh cat /tmp/output




2. Expected output 

0.001 -0.0678441





3. Comment
only testing the last line of output







3. Running, checking, saving, loading and resetting a simulation
Startup command : bin/genesis-g3
(No model has been loaded for the following set of commands.)
3.1. Is startup successful ?





1. Expected output 
GENESIS 3 shell







3.2. Can we load a single passive compartment model ?





1. Executed command
ndf_load tests/cells/singlep.ndf




2. Expected output 







3.3. Can we save the simulation ?





1. Executed command
ssp_save /singlep /tmp/singlep.ssp




2. Expected output 







3.4. Has the simulation been saved correctly ?





1. Executed command
sh cat /tmp/singlep.ssp




2. Expected output 

apply:
  analyzers:
    - method: analyze
  initializers:
    - method: compile
    - method: instantiate_inputs
    - method: instantiate_outputs
    - method: connect
    - method: initiate
    - method: optimize
  services:
    - method: instantiate_services
  simulation:
    - arguments: &2
        - 0
      method: advance
    - method: pause
history:
  - arguments: []
    method: instantiate_services
  - arguments: []
    method: compile
  - arguments: []
    method: instantiate_inputs
  - arguments: []
    method: instantiate_outputs
  - arguments: []
    method: connect
  - arguments: []
    method: initiate
  - arguments: []
    method: optimize
  - arguments: []
    method: analyze
  - arguments: *2
    method: advance
  - arguments: []
    method: pause
models:
  - modelname: /singlep
    solverclass: heccer
name: 'GENESIS3 SSP schedule initiated for /singlep, 0'
optimize: 'by default turned on, ignored when running in verbose mode'
outputclasses:
  double_2_ascii:
    module_name: Experiment
    options: &3
      filename: /tmp/output
      format: ''
      output_mode: ''
      resolution: ''
    package: Experiment::Output
    ssp_outputclass: &4 !!perl/hash:SSP::Output
      backend: !!perl/hash:Experiment::Output
        backend: !!perl/hash:SwiggableExperiment::OutputGenerator {}
        filename: /tmp/output
        format: ''
        module_name: Experiment
        name: double_2_ascii
        options: *3
        output_mode: ''
        package: Experiment::Output
        resolution: ''
        scheduler: *1
      module_name: Experiment
      name: double_2_ascii
      options: *3
      package: Experiment::Output
      scheduler: *1
outputs:
  - component_name: /singlep/segments/soma
    field: Vm
    outputclass: double_2_ascii
    warn_only: the default output (/singlep/segments/soma) was generated automatically and is not always available
schedule:
  - !!perl/hash:SSP::Engine
    backend: !!perl/hash:Heccer
      heccer: !!perl/hash:SwiggableHeccer::simobj_Heccer {}
      model_source:
        modelname: /singlep
        service_backend: &5 !!perl/hash:Neurospaces
          neurospaces: !!perl/hash:SwiggableNeurospaces::Neurospaces {}
        service_name: model_container
    compilation_priority: numerical
    constructor_settings: &6
      dStep: 2e-05
    modelname: /singlep
    module_name: Heccer
    name: /singlep
    scheduler: *1
    service: &7
      backend: *5
      ssp_service: !!perl/hash:SSP::Service
        backend: *5
        scheduler: *1
    service_name: model_container
    solverclass: heccer
  - *4
services:
  model_container: *7
simulation_time:
  steps: 0
  time: 0
solverclasses:
  heccer:
    compilation_priority: numerical
    constructor_settings: *6
    module_name: Heccer
    service_name: model_container








3.5. Can we reload the saved simulation ?





1. Executed command
ssp_load /singlep /tmp/singlep.ssp




2. Expected output 




3. This test is currently not executed
(disabled is 'ssp_load works, but "run /singlep 1" fails because Heccer is not initialized correctly (must be recompiled from the model)')







3.6. Can we check the simulation ?





1. Executed command
check /singlep




2. Expected output 







3.7. Can we run the simulation ?





1. Executed command
run /singlep 0.001




2. Expected output 







3.8. Can we determine the size of the output ?





1. Executed command
sh wc -l /tmp/output




2. Expected output 
50 /tmp/output





3. Comment
note that the expected output is badly anchored, so the test can possibly succeed in circumstances were we would really like it to fail







3.9. Can we find the output ?





1. Executed command
sh cat /tmp/output




2. Expected output 

0.001 -0.0687098





3. Comment
only testing the last line of output







3.10. Can we check the simulation again ?





1. Executed command
check /singlep




2. Expected output 







3.11. Can we reset the simulation ?





1. Executed command
reset /singlep




2. Expected output 







3.12. Is the output file empty ?





1. Executed command
sh wc -l /tmp/output




2. Expected output 
0 /tmp/output








3.13. Can we rerun the simulation ?





1. Executed command
run /singlep 0.001




2. Expected output 







3.14. Has output been reproduced again?





1. Executed command
sh wc -l /tmp/output




2. Expected output 
50 /tmp/output





3. Comment
note that the expected output is badly anchored, so the test can possibly succeed in circumstances were we would really like it to fail







3.15. Do we find the same output ?





1. Executed command
sh cat /tmp/output




2. Expected output 

0.001 -0.0687098





3. Comment
only testing the last line of output







3.16. Can we check the simulation once more ?





1. Executed command
check /singlep




2. Expected output 







3.17. Can we reset the simulation once more ?





1. Executed command
reset /singlep




2. Expected output 







3.18. Is the output file again empty ?





1. Executed command
sh wc -l /tmp/output




2. Expected output 
0 /tmp/output





3. Comment
note that the expected output is badly anchored, so the test can possibly succeed in circumstances were we would really like it to fail