Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries/ --ompython_omhome=/usr Chemical_Chemical.Examples.AcidBase.Dev.RedCellMembrane.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo", uses=false)
Using package ModelicaServices with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo)
Using package Modelica with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo)
Using package Complex with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo)
Using package Chemical with version 1.4.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo)
Running command: translateModel(Chemical.Examples.AcidBase.Dev.RedCellMembrane,tolerance=1e-06,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.AcidBase.Dev.RedCellMembrane")
translateModel(Chemical.Examples.AcidBase.Dev.RedCellMembrane,tolerance=1e-06,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.AcidBase.Dev.RedCellMembrane")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo): time 0.1063/0.1063, allocations: 15.26 MB / 22.74 MB, free: 0.9727 MB / 18.57 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001033/0.001033, allocations: 185 kB / 27.52 MB, free: 6.117 MB / 24.77 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.449/1.449, allocations: 221.5 MB / 253.7 MB, free: 10.42 MB / 202.7 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.000842/0.0008422, allocations: 94.27 kB / 308.8 MB, free: 10.45 MB / 250.7 MB
Notification: Performance of FrontEnd - loaded program: time 1.652e-05/1.654e-05, allocations: 2.969 kB / 369.6 MB, free: 53.98 MB / 298.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.09297/0.093, allocations: 54.64 MB / 424.2 MB, free: 13.82 MB / 298.7 MB
Notification: Performance of FrontEnd - scodeFlatten: time 0.3476/0.4406, allocations: 102.8 MB / 0.5147 GB, free: 12.27 MB / 362.7 MB
Notification: Performance of FrontEnd - mkProgramGraph: time 0.0001498/0.4408, allocations: 70.98 kB / 0.5148 GB, free: 12.27 MB / 362.7 MB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:4721:7-4721:66:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System blood_erythrocytes.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Solution$blood_erythrocytes.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:4721:7-4721:66:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System blood_plasma.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Solution.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System HCO3.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$HCO3.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System H2O.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$H2O.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System HCO3_E.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$HCO3_E.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System H2O_E.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$H2O_E.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System Cl_E.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$Cl_E.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System Cl.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$Cl.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System albumin.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$albumin.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System permeableUncharged.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$permeableUncharged.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System permeableUncharged_E.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$permeableUncharged_E.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System chargedImpermeable_E.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$chargedImpermeable_E.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System Lac_E.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$Lac_E.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System Lac.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$Lac.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System H_E.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$H_E.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System H.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$H.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System CO2.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$CO2.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System CO2_E.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$CO2_E.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System O2.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$O2.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System O2_E.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$O2_E.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System K.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$K.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System Na.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$Na.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System Na_E.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$Na_E.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System K_E.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$K_E.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System H2PO4_E.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$H2PO4_E.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System ADP_E.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$ADP_E.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System ATP_E.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$ATP_E.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System HPO4_E.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$HPO4_E.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System globulins.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$globulins.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System Ca.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$Ca.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System Mg.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$Mg.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System DPG.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$DPG.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System GSH.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$GSH.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System Hemoglobin.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Sources.Buffer$Hemoglobin.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
Notification: Performance of FrontEnd - DAE generated: time 1.068/1.509, allocations: 336.6 MB / 0.8435 GB, free: 10.8 MB / 490.7 MB
Notification: Performance of FrontEnd: time 1.302e-06/1.509, allocations: 0 / 0.8435 GB, free: 10.8 MB / 490.7 MB
Notification: Performance of Transformations before backend: time 0.0006739/1.51, allocations: 163.9 kB / 0.8437 GB, free: 10.64 MB / 490.7 MB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 1818
 * Number of variables: 1818
Notification: Performance of Generate backend data structure: time 0.02566/1.535, allocations: 8.887 MB / 0.8523 GB, free: 1.676 MB / 490.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.444e-05/1.535, allocations: 12.02 kB / 0.8523 GB, free: 1.664 MB / 490.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.3368/1.872, allocations: 2.398 MB / 0.8547 GB, free: 19.13 MB / 490.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.01365/1.886, allocations: 5.294 MB / 0.8599 GB, free: 18.55 MB / 490.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0004757/1.886, allocations: 325.3 kB / 0.8602 GB, free: 18.5 MB / 490.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.002631/1.889, allocations: 462.7 kB / 0.8606 GB, free: 18.48 MB / 490.7 MB
Notification: Performance of preOpt removeEqualFunctionCalls (simulation): time 0.0293/1.918, allocations: 21.22 MB / 0.8813 GB, free: 18.45 MB / 490.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.01911/1.938, allocations: 10.96 MB / 0.892 GB, free: 17.95 MB / 490.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 0.000146/1.938, allocations: 6.344 kB / 0.892 GB, free: 17.95 MB / 490.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0006885/1.938, allocations: 3.5 kB / 0.892 GB, free: 17.95 MB / 490.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.79e-05/1.939, allocations: 172 kB / 0.8922 GB, free: 17.95 MB / 490.7 MB
Warning: The model contains alias variables with conflicting start and/or nominal values. It is recommended to resolve the conflicts, because otherwise the system could be hard to solve. To print the conflicting alias sets and the chosen candidates please use -d=aliasConflicts.
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.06823/2.007, allocations: 42.71 MB / 0.9339 GB, free: 9.461 MB / 490.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.03235/2.039, allocations: 21.79 MB / 0.9552 GB, free: 15.9 MB / 0.4948 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.01029/2.049, allocations: 8.084 MB / 0.9631 GB, free: 12.22 MB / 0.4948 GB
Notification: Performance of preOpt evalFunc (simulation): time 0.004737/2.054, allocations: 2.408 MB / 0.9654 GB, free: 11.55 MB / 0.4948 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001194/2.054, allocations: 129.7 kB / 0.9656 GB, free: 11.45 MB / 0.4948 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.004887/2.059, allocations: 0.5358 MB / 0.9661 GB, free: 11.27 MB / 0.4948 GB
Notification: Performance of pre-optimization done (n=925): time 1.784e-05/2.059, allocations: 0 / 0.9661 GB, free: 11.27 MB / 0.4948 GB
Notification: Performance of matching and sorting (n=1339): time 0.7071/2.766, allocations: 135.3 MB / 1.098 GB, free: 72.12 MB / 0.5417 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001137/2.767, allocations: 181.9 kB / 1.098 GB, free: 72.05 MB / 0.5417 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.006475/2.773, allocations: 3.813 MB / 1.102 GB, free: 71.76 MB / 0.5417 GB
Notification: Performance of collectPreVariables (initialization): time 0.002747/2.776, allocations: 29.48 kB / 1.102 GB, free: 71.73 MB / 0.5417 GB
Notification: Performance of collectInitialEqns (initialization): time 0.002063/2.778, allocations: 2.899 MB / 1.105 GB, free: 71.02 MB / 0.5417 GB
Notification: Performance of collectInitialBindings (initialization): time 0.008205/2.786, allocations: 4.333 MB / 1.109 GB, free: 68.37 MB / 0.5417 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.002344/2.789, allocations: 0 / 1.109 GB, free: 68.37 MB / 0.5417 GB
Notification: Performance of setup shared object (initialization): time 0.0006727/2.789, allocations: 0.7529 MB / 1.11 GB, free: 68.04 MB / 0.5417 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.02178/2.811, allocations: 14.97 MB / 1.125 GB, free: 68.01 MB / 0.5417 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.02264/2.834, allocations: 16.33 MB / 1.141 GB, free: 66.89 MB / 0.5417 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.03557/2.869, allocations: 17.62 MB / 1.158 GB, free: 66.53 MB / 0.5417 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0001137/2.869, allocations: 8.438 kB / 1.158 GB, free: 66.53 MB / 0.5417 GB
Notification: Performance of matching and sorting (n=1539) (initialization): time 0.07843/2.948, allocations: 38.09 MB / 1.195 GB, free: 52.61 MB / 0.5417 GB
Notification: Performance of prepare postOptimizeDAE: time 4.55e-05/2.948, allocations: 19.41 kB / 1.195 GB, free: 52.59 MB / 0.5417 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 4.751e-05/2.948, allocations: 28 kB / 1.195 GB, free: 52.56 MB / 0.5417 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.01282/2.961, allocations: 3.677 MB / 1.199 GB, free: 49.68 MB / 0.5417 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01615/2.977, allocations: 2.885 MB / 1.201 GB, free: 47.73 MB / 0.5417 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.02633/3.003, allocations: 18.88 MB / 1.22 GB, free: 29.98 MB / 0.5417 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.09592/3.099, allocations: 5.826 MB / 1.226 GB, free: 27.32 MB / 0.5417 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.005182/3.105, allocations: 1.04 MB / 1.227 GB, free: 26.89 MB / 0.5417 GB
Warning: Iteration variables with default zero start attribute in torn nonlinear equation system:
         CO2.solution.n:DUMMY_STATE(flow=false min = 0.0 max = 0.0 unit = "mol" )  "Amount of the solution" type: Real
Warning: Iteration variables with default zero start attribute in torn nonlinear equation system:
         CO2.solution.I:VARIABLE(flow=false min = 0.0 max = 0.0 unit = "1" )  "Mole fraction based ionic strength of the solution" type: Real
Warning: Iteration variables with default zero start attribute in torn nonlinear equation system:
         Hemoglobin.solution.n:DUMMY_STATE(flow=false min = 0.0 max = 0.0 unit = "mol" )  "Amount of the solution" type: Real
Warning: Iteration variables with default zero start attribute in torn nonlinear equation system:
         ADP_E.solution.I:VARIABLE(flow=false min = 0.0 max = 0.0 unit = "1" )  "Mole fraction based ionic strength of the solution" type: Real 
         ADP_E.solution.v:DUMMY_STATE(flow=false unit = "V" )  "Electric potential in the solution" type: Real
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 127
 * Number of states: 0 ()
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (1297):
 * Single equations (assignments): 1288
 * Array equations: 2
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (linear and non-linear blocks): 0
 * Torn equation systems: 7
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems: 3 {(2,100.0%) 36,(1,100.0%) 3,(1,100.0%) 3}
 * Non-linear torn systems: 4 {3 99,1 3,1 26,1 3}
Notification: Performance of prepare postOptimizeDAE: time 0.006301/3.111, allocations: 303.9 kB / 1.227 GB, free: 26.72 MB / 0.5417 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.004497/3.115, allocations: 0.7999 MB / 1.228 GB, free: 25.91 MB / 0.5417 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.07341/3.189, allocations: 36.21 MB / 1.263 GB, free: 11.82 MB / 0.5573 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.5249/3.714, allocations: 41.76 MB / 1.304 GB, free: 84.27 MB / 0.5573 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.419e-05/3.714, allocations: 8.406 kB / 1.304 GB, free: 84.27 MB / 0.5573 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0006188/3.715, allocations: 73.5 kB / 1.304 GB, free: 84.27 MB / 0.5573 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.7433/4.458, allocations: 213.4 MB / 1.512 GB, free: 83.13 MB / 0.5573 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 0.0002536/4.458, allocations: 75.41 kB / 1.512 GB, free: 83.13 MB / 0.5573 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.01281/4.471, allocations: 2.443 MB / 1.515 GB, free: 83.13 MB / 0.5573 GB
Notification: Performance of postOpt tearingSystem (simulation): time 0.1809/4.652, allocations: 49.46 MB / 1.563 GB, free: 82.16 MB / 0.5573 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.003867/4.656, allocations: 0.5194 MB / 1.563 GB, free: 82.16 MB / 0.5573 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.1069/4.763, allocations: 56.17 MB / 1.618 GB, free: 62.47 MB / 0.5573 GB
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:376:7-379:62:writable] Error: Model is structurally singular, error found sorting equations 
 231: H2O_E.SelfClustering_dG = $cse29 - blood_erythrocytes.temperature * $cse28;
262: H2O_E.amountOfBaseMolecules = exp(H2O_E.logn);
261: Cl_E.amountOfBaseMolecules = exp(Cl_E.logn);
259: HPO4_E.amountOfBaseMolecules = exp(HPO4_E.logn);
257: Lac_E.amountOfBaseMolecules = exp(Lac_E.logn);
256: O2_E.amountOfBaseMolecules = exp(O2_E.logn);
255: chargedImpermeable_E.amountOfBaseMolecules = exp(chargedImpermeable_E.logn);
254: Mg.amountOfBaseMolecules = exp(Mg.logn);
253: ATP_E.amountOfBaseMolecules = exp(ATP_E.logn);
250: permeableUncharged_E.amountOfBaseMolecules = exp(permeableUncharged_E.logn);
248: ADP_E.amountOfBaseMolecules = exp(ADP_E.logn);
247: DPG.amountOfBaseMolecules = exp(DPG.logn);
246: H2PO4_E.amountOfBaseMolecules = exp(H2PO4_E.logn);
241: H_E.amountOfBaseMolecules = exp(H_E.logn);
239: HCO3_E.amountOfBaseMolecules = exp(HCO3_E.logn);
238: Na_E.amountOfBaseMolecules = exp(Na_E.logn);
237: K_E.amountOfBaseMolecules = exp(K_E.logn);
234: GSH.amountOfBaseMolecules = exp(GSH.logn);
232: CO2_E.amountOfBaseMolecules = exp(CO2_E.logn);
109: HCO3_E.amountOfBaseMolecules + H2O_E.solution.nj + Cl_E.amountOfBaseMolecules + permeableUncharged_E.amountOfBaseMolecules + chargedImpermeable_E.amountOfBaseMolecules + Lac_E.amountOfBaseMolecules + H_E.amountOfBaseMolecules + CO2_E.amountOfBaseMolecules + O2_E.amountOfBaseMolecules + Na_E.amountOfBaseMolecules + K_E.amountOfBaseMolecules + H2PO4_E.amountOfBaseMolecules + ADP_E.amountOfBaseMolecules + ATP_E.amountOfBaseMolecules + HPO4_E.amountOfBaseMolecules + Mg.amountOfBaseMolecules + DPG.amountOfBaseMolecules + GSH.amountOfBaseMolecules - Hemoglobin.solution.n = 0.0;
230: H2O_E.SelfClustering_K = exp((-0.120272355042726) * H2O_E.SelfClustering_dG / blood_erythrocytes.temperature);
108: H2O_E.x = 0.5 * (2.0 * H2O_E.SelfClustering_K + Hemoglobin.solution.n / H2O_E.amountOfBaseMolecules - sqrt(4.0 * H2O_E.SelfClustering_K * Hemoglobin.solution.n / H2O_E.amountOfBaseMolecules + (Hemoglobin.solution.n / H2O_E.amountOfBaseMolecules) ^ 2.0)) / H2O_E.SelfClustering_K ^ 2.0;
267: $STATESET1.J[5] = H2O_E.x - H2O_E.amountOfFreeMolecule / Hemoglobin.solution.n;
106: H2O_E.solution.nj * (1.0 - H2O_E.SelfClustering_K * H2O_E.x) = H2O_E.amountOfFreeMolecule;
 for variables 
 H2O_E.SelfClustering_dG(36), $STATESET1.J[4](4), HPO4_E.amountOfBaseMolecules(8), Lac_E.amountOfBaseMolecules(10), O2_E.amountOfBaseMolecules(11), chargedImpermeable_E.amountOfBaseMolecules(12), Mg.amountOfBaseMolecules(13), ATP_E.amountOfBaseMolecules(14), permeableUncharged_E.amountOfBaseMolecules(17), ADP_E.amountOfBaseMolecules(19), DPG.amountOfBaseMolecules(20), H2PO4_E.amountOfBaseMolecules(21), H_E.amountOfBaseMolecules(26), HCO3_E.amountOfBaseMolecules(28), Na_E.amountOfBaseMolecules(29), K_E.amountOfBaseMolecules(30), GSH.amountOfBaseMolecules(33), CO2_E.amountOfBaseMolecules(35), Hemoglobin.solution.n(158), H2O_E.SelfClustering_K(37), H2O_E.x(159), $cse211(155), H2O_E.amountOfFreeMolecule(161), H_E.solution.Ij(106)
Error: Internal error Transformation Module PFPlusExt index Reduction Method Pantelides failed!
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 0.02005/4.783, allocations: 7.571 MB / 1.626 GB, free: 60.4 MB / 0.5573 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.5867/5.369, allocations: 74.4 MB / 1.698 GB, free: 74.96 MB / 0.5573 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.006191/5.376, allocations: 1.642 MB / 1.7 GB, free: 74.87 MB / 0.5573 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.006283/5.382, allocations: 123.1 kB / 1.7 GB, free: 74.87 MB / 0.5573 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.05541/5.437, allocations: 2.735 MB / 1.703 GB, free: 74.87 MB / 0.5573 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.00523/5.443, allocations: 1.392 MB / 1.704 GB, free: 74.85 MB / 0.5573 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.003909/5.447, allocations: 0.7834 MB / 1.705 GB, free: 74.85 MB / 0.5573 GB
Notification: Performance of sorting global known variables: time 0.004982/5.452, allocations: 2.851 MB / 1.708 GB, free: 74.67 MB / 0.5573 GB
Notification: Performance of sort global known variables: time 4.31e-07/5.452, allocations: 2.719 kB / 1.708 GB, free: 74.67 MB / 0.5573 GB
Notification: Performance of remove unused functions: time 0.06136/5.513, allocations: 24.06 MB / 1.731 GB, free: 74.67 MB / 0.5573 GB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 322
 * Number of states: 34 ($STATESET1.x[34],$STATESET1.x[33],$STATESET1.x[32],$STATESET1.x[31],$STATESET1.x[30],$STATESET1.x[29],$STATESET1.x[28],$STATESET1.x[27],$STATESET1.x[26],$STATESET1.x[25],$STATESET1.x[24],$STATESET1.x[23],$STATESET1.x[22],$STATESET1.x[21],$STATESET1.x[20],$STATESET1.x[19],$STATESET1.x[18],$STATESET1.x[17],$STATESET1.x[16],$STATESET1.x[15],$STATESET1.x[14],$STATESET1.x[13],$STATESET1.x[12],$STATESET1.x[11],$STATESET1.x[10],$STATESET1.x[9],$STATESET1.x[8],$STATESET1.x[7],$STATESET1.x[6],$STATESET1.x[5],$STATESET1.x[4],$STATESET1.x[3],$STATESET1.x[2],$STATESET1.x[1])
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (1193):
 * Single equations (assignments): 1189
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (linear and non-linear blocks): 0
 * Torn equation systems: 4
 * Mixed (continuous/discrete) equation systems: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems: 3 {(2,100.0%) 36,(1,100.0%) 3,(1,100.0%) 3}
 * Non-linear torn systems: 1 {42 259}
Notification: Performance of Backend phase and start with SimCode phase: time 0.01878/5.532, allocations: 6.09 MB / 1.737 GB, free: 74.02 MB / 0.5573 GB
Notification: Performance of simCode: created initialization part: time 0.05272/5.585, allocations: 34.37 MB / 1.771 GB, free: 73.25 MB / 0.5573 GB
Notification: Performance of simCode: created event and clocks part: time 6.143e-05/5.585, allocations: 12.72 kB / 1.771 GB, free: 73.25 MB / 0.5573 GB
Notification: Performance of simCode: created simulation system equations: time 0.08462/5.669, allocations: 42.82 MB / 1.813 GB, free: 63.12 MB / 0.5573 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.02671/5.696, allocations: 2.441 MB / 1.815 GB, free: 61.7 MB / 0.5573 GB
[/var/lib/jenkins/ws/OpenModelicaLibraryTestingWork/OMCompiler/Compiler/SimCode/SimCodeUtil.mo:3851:9-3851:59:writable] Error: Internal error function createStateSetsSets failed.
[/var/lib/jenkins/ws/OpenModelicaLibraryTestingWork/OMCompiler/Compiler/SimCode/SimCodeUtil.mo:637:5-637:146:writable] Error: Internal error function createSimCode failed [Transformation from optimised DAE to simulation code structure failed]