Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries/ --ompython_omhome=/usr Chemical_Chemical.Examples.EnzymeKinetics.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.EnzymeKinetics,tolerance=1e-06,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.EnzymeKinetics")
translateModel(Chemical.Examples.EnzymeKinetics,tolerance=1e-06,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.EnzymeKinetics")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo): time 0.1075/0.1075, 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 0.001093/0.001093, 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 1.543/1.543, allocations: 221.5 MB / 253.7 MB, free: 10.36 MB / 202.7 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.0008924/0.0008923, allocations: 91.88 kB / 308.7 MB, free: 10.46 MB / 250.7 MB
Warning: Ignoring unknown experiment annotation option: __Dymola_Algorithm = "Dassl"
Notification: Performance of FrontEnd - loaded program: time 2.537e-05/2.554e-05, allocations: 3 kB / 369.6 MB, free: 53.9 MB / 298.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1063/0.1064, allocations: 54.64 MB / 424.2 MB, free: 13.84 MB / 298.7 MB
Notification: Performance of FrontEnd - scodeFlatten: time 0.4308/0.5372, allocations: 99.45 MB / 0.5114 GB, free: 12.27 MB / 362.7 MB
Notification: Performance of FrontEnd - mkProgramGraph: time 0.0001783/0.5374, allocations: 70.88 kB / 0.5115 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 solution.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 P.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$P.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System S.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$S.
  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 liquidWater.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$liquidWater.
  Check if you have not misspelled the 'outer' component name.
  Please declare an 'inner' component with the same name in the top scope.
  Continuing flattening by only considering the 'outer' component declaration.
[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:3011:6-3011:65:writable] Warning: No corresponding 'inner' declaration found for component .Modelica.Fluid.System E.system declared as 'outer '.
  The existing 'inner' components are:
    There are no 'inner' components defined in the model in any of the parent scopes of 'outer' component's scope: Chemical.Components.Substance$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 ES.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$ES.
  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 0.1267/0.6641, allocations: 56.74 MB / 0.5669 GB, free: 9.395 MB / 378.7 MB
Notification: Performance of FrontEnd: time 1.272e-06/0.6641, allocations: 0 / 0.5669 GB, free: 9.395 MB / 378.7 MB
Notification: Performance of Transformations before backend: time 6.568e-05/0.6642, allocations: 40 kB / 0.5669 GB, free: 9.355 MB / 378.7 MB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 337
 * Number of variables: 337
Notification: Performance of Generate backend data structure: time 0.00404/0.6682, allocations: 1.825 MB / 0.5687 GB, free: 7.488 MB / 378.7 MB
Notification: Performance of prepare preOptimizeDAE: time 4.468e-05/0.6683, allocations: 16.02 kB / 0.5687 GB, free: 7.473 MB / 378.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001466/0.6698, allocations: 421 kB / 0.5691 GB, free: 7.059 MB / 378.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.002031/0.6718, allocations: 1.103 MB / 0.5702 GB, free: 5.934 MB / 378.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001279/0.672, allocations: 110.1 kB / 0.5703 GB, free: 5.812 MB / 378.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0002087/0.6722, allocations: 84 kB / 0.5704 GB, free: 5.73 MB / 378.7 MB
Notification: Performance of preOpt removeEqualFunctionCalls (simulation): time 0.004372/0.6766, allocations: 3.589 MB / 0.5739 GB, free: 2.137 MB / 378.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002814/0.6794, allocations: 2.028 MB / 0.5758 GB, free: 72 kB / 378.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.527e-05/0.6794, allocations: 0 / 0.5758 GB, free: 72 kB / 378.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001049/0.6795, allocations: 0 / 0.5758 GB, free: 72 kB / 378.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.831e-05/0.6796, allocations: 32 kB / 0.5759 GB, free: 40 kB / 378.7 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 0.01204/0.6916, allocations: 7.607 MB / 0.5833 GB, free: 8.305 MB / 394.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.005587/0.6972, allocations: 4.067 MB / 0.5873 GB, free: 4.141 MB / 394.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.001559/0.6988, allocations: 1.367 MB / 0.5886 GB, free: 2.777 MB / 394.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.0006088/0.6994, allocations: 423.1 kB / 0.589 GB, free: 2.375 MB / 394.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.137e-05/0.6995, allocations: 43.88 kB / 0.5891 GB, free: 2.32 MB / 394.7 MB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.001015/0.7005, allocations: 138.5 kB / 0.5892 GB, free: 2.188 MB / 394.7 MB
Notification: Performance of pre-optimization done (n=163): time 3.606e-06/0.7005, allocations: 0 / 0.5892 GB, free: 2.188 MB / 394.7 MB
Notification: Performance of matching and sorting (n=214): time 0.03677/0.7373, allocations: 11.03 MB / 0.6 GB, free: 7.141 MB / 410.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 7.023e-05/0.7374, allocations: 73.41 kB / 0.6 GB, free: 7.055 MB / 410.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.001523/0.739, allocations: 0.7314 MB / 0.6007 GB, free: 6.32 MB / 410.7 MB
Notification: Performance of collectPreVariables (initialization): time 0.0003688/0.7394, allocations: 25.7 kB / 0.6008 GB, free: 6.289 MB / 410.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0004867/0.7399, allocations: 0.5483 MB / 0.6013 GB, free: 5.73 MB / 410.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0009626/0.7408, allocations: 0.6849 MB / 0.602 GB, free: 5.035 MB / 410.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002289/0.7411, allocations: 0 / 0.602 GB, free: 5.035 MB / 410.7 MB
Notification: Performance of setup shared object (initialization): time 0.0002297/0.7413, allocations: 381.9 kB / 0.6023 GB, free: 4.656 MB / 410.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.002193/0.7435, allocations: 1.519 MB / 0.6038 GB, free: 3.137 MB / 410.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.002316/0.7458, allocations: 1.728 MB / 0.6055 GB, free: 1.355 MB / 410.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.004544/0.7504, allocations: 1.955 MB / 0.6074 GB, free: 15.4 MB / 426.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 7.023e-06/0.7504, allocations: 0 / 0.6074 GB, free: 15.4 MB / 426.7 MB
Notification: Performance of matching and sorting (n=247) (initialization): time 0.01097/0.7614, allocations: 4.42 MB / 0.6117 GB, free: 10.95 MB / 426.7 MB
Notification: Performance of prepare postOptimizeDAE: time 3.656e-05/0.7615, allocations: 8 kB / 0.6117 GB, free: 10.95 MB / 426.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 2.102e-05/0.7615, allocations: 4.562 kB / 0.6117 GB, free: 10.94 MB / 426.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.003306/0.7648, allocations: 0.6469 MB / 0.6124 GB, free: 10.29 MB / 426.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.002259/0.7671, allocations: 423.3 kB / 0.6128 GB, free: 9.871 MB / 426.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.006629/0.7738, allocations: 4.309 MB / 0.617 GB, free: 5.305 MB / 426.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.003461/0.7773, allocations: 207.5 kB / 0.6172 GB, free: 5.102 MB / 426.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0008832/0.7782, allocations: 95.89 kB / 0.6173 GB, free: 5.008 MB / 426.7 MB
Warning: Iteration variables with default zero start attribute in torn nonlinear equation system:
         E.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:
         E.solution.I:VARIABLE(flow=false min = 0.0 max = 0.0 unit = "1" )  "Mole fraction based ionic strength of the solution" type: Real
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 19
 * Number of states: 0 ()
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (220):
 * Single equations (assignments): 214
 * Array equations: 2
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (linear and non-linear blocks): 1
 * Torn equation systems: 3
 * Mixed (continuous/discrete) equation systems: 0
Notification: Equation system details:
 * Constant Jacobian: 0
 * Linear Jacobian (size,density): 1 {(2,100.0%)}
 * Non-linear Jacobian: 0
 * Without analytic Jacobian: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems: 1 {(1,100.0%) 3}
 * Non-linear torn systems: 2 {1 10,1 3}
Notification: Performance of prepare postOptimizeDAE: time 0.001105/0.7793, allocations: 155.3 kB / 0.6174 GB, free: 4.852 MB / 426.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0007518/0.7801, allocations: 142.2 kB / 0.6176 GB, free: 4.711 MB / 426.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.01578/0.7958, allocations: 5.081 MB / 0.6225 GB, free: 15.6 MB / 442.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.01393/0.8098, allocations: 4.599 MB / 0.627 GB, free: 10.98 MB / 442.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.829e-05/0.8099, allocations: 4 kB / 0.627 GB, free: 10.98 MB / 442.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.532e-05/0.81, allocations: 11.95 kB / 0.627 GB, free: 10.96 MB / 442.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.02164/0.8316, allocations: 10.35 MB / 0.6371 GB, free: 492 kB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.321e-05/0.8317, allocations: 8 kB / 0.6371 GB, free: 484 kB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001609/0.8333, allocations: 391.4 kB / 0.6375 GB, free: 92 kB / 442.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.006104/0.8394, allocations: 1.32 MB / 0.6388 GB, free: 14.76 MB / 458.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0002786/0.8397, allocations: 51.86 kB / 0.6389 GB, free: 14.71 MB / 458.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.01168/0.8514, allocations: 7.325 MB / 0.646 GB, free: 7.125 MB / 458.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 0.005817/0.8573, allocations: 2.462 MB / 0.6484 GB, free: 4.539 MB / 458.7 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.01645/0.8737, allocations: 7.554 MB / 0.6558 GB, free: 12.59 MB / 474.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.001354/0.8751, allocations: 454.9 kB / 0.6562 GB, free: 12.13 MB / 474.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0004903/0.8756, allocations: 19.98 kB / 0.6562 GB, free: 12.11 MB / 474.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.00196/0.8776, allocations: 115.7 kB / 0.6564 GB, free: 12 MB / 474.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0004992/0.8781, allocations: 217.5 kB / 0.6566 GB, free: 11.78 MB / 474.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0002418/0.8784, allocations: 95.92 kB / 0.6567 GB, free: 11.69 MB / 474.7 MB
Notification: Performance of sorting global known variables: time 0.001049/0.8794, allocations: 0.5655 MB / 0.6572 GB, free: 11.12 MB / 474.7 MB
Notification: Performance of sort global known variables: time 1.41e-07/0.8795, allocations: 0 / 0.6572 GB, free: 11.12 MB / 474.7 MB
Notification: Performance of remove unused functions: time 0.004835/0.8843, allocations: 1.269 MB / 0.6584 GB, free: 9.855 MB / 474.7 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 40
 * Number of states: 6 ($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 (210):
 * Single equations (assignments): 206
 * Array equations: 0
 * Algorithm blocks: 0
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (linear and non-linear blocks): 1
 * Torn equation systems: 3
 * Mixed (continuous/discrete) equation systems: 0
Notification: Equation system details:
 * Constant Jacobian: 0
 * Linear Jacobian (size,density): 1 {(2,100.0%)}
 * Non-linear Jacobian: 0
 * Without analytic Jacobian: 0
Notification: Torn system details for strict tearing set:
 * Linear torn systems: 1 {(1,100.0%) 3}
 * Non-linear torn systems: 2 {1 10,7 10}
Notification: Performance of Backend phase and start with SimCode phase: time 0.00265/0.887, allocations: 1.049 MB / 0.6595 GB, free: 8.852 MB / 474.7 MB
Notification: Performance of simCode: created initialization part: time 0.006115/0.8931, allocations: 3.783 MB / 0.6632 GB, free: 5.027 MB / 474.7 MB
Notification: Performance of simCode: created event and clocks part: time 1.028e-05/0.8931, allocations: 4 kB / 0.6632 GB, free: 5.023 MB / 474.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.004588/0.8977, allocations: 2.431 MB / 0.6655 GB, free: 2.559 MB / 474.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.003626/0.9014, allocations: 420.8 kB / 0.6659 GB, free: 2.148 MB / 474.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.262/1.163, allocations: 3.405 MB / 0.6693 GB, free: 123.4 MB / 474.7 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.001257/1.165, allocations: 1.355 MB / 0.6706 GB, free: 122.7 MB / 474.7 MB
Notification: Performance of simCode: alias equations: time 0.00203/1.167, allocations: 333.2 kB / 0.6709 GB, free: 122.6 MB / 474.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.000721/1.168, allocations: 188 kB / 0.6711 GB, free: 122.6 MB / 474.7 MB
Notification: Performance of SimCode: time 1.432e-06/1.168, allocations: 0 / 0.6711 GB, free: 122.6 MB / 474.7 MB
Notification: Performance of Templates: time 0.05828/1.226, allocations: 42.94 MB / 0.713 GB, free: 119.8 MB / 474.7 MB
make -j1 -f Chemical_Chemical.Examples.EnzymeKinetics.makefile
(rm -f Chemical_Chemical.Examples.EnzymeKinetics.pipe ; mkfifo Chemical_Chemical.Examples.EnzymeKinetics.pipe ; head -c 1048576 < Chemical_Chemical.Examples.EnzymeKinetics.pipe >> ../files/Chemical_Chemical.Examples.EnzymeKinetics.sim & ./Chemical_Chemical.Examples.EnzymeKinetics  -abortSlowSimulation -alarm=480 -lv LOG_STATS > Chemical_Chemical.Examples.EnzymeKinetics.pipe 2>&1)