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")
[<interactive>:1:1-1:32:writable] Error: Class GC_set_max_heap_size not found in scope <global scope> (looking for a function or record).
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo): time 0.06516/0.06516, allocations: 15.26 MB / 22.54 MB, free: 1.109 MB / 18.57 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.0008734/0.0008734, allocations: 187.5 kB / 27.31 MB, free: 0 / 18.57 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.107/1.107, allocations: 221.4 MB / 253.3 MB, free: 10.67 MB / 202.7 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.0008776/0.0008776, allocations: 95.73 kB / 308.4 MB, free: 10.7 MB / 250.7 MB
Warning: Ignoring unknown experiment annotation option: __Dymola_Algorithm = "Dassl"
Notification: Performance of FrontEnd - loaded program: time 5.841e-06/5.861e-06, allocations: 1.281 kB / 369 MB, free: 5.816 MB / 298.7 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.07927/0.07929, allocations: 54.65 MB / 423.7 MB, free: 15.05 MB / 346.7 MB
Notification: Performance of FrontEnd - scodeFlatten: time 0.1024/0.1817, allocations: 99.39 MB / 0.5108 GB, free: 11.51 MB / 442.7 MB
Notification: Performance of FrontEnd - mkProgramGraph: time 0.0001529/0.1819, allocations: 67.97 kB / 0.5109 GB, free: 11.45 MB / 442.7 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: time 0.2541/0.436, allocations: 56.76 MB / 0.5663 GB, free: 112.6 MB / 442.7 MB
Notification: Performance of Transformations before backend: time 0.0001002/0.4362, allocations: 28.44 kB / 0.5663 GB, free: 112.6 MB / 442.7 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 0.004185/0.4404, allocations: 1.881 MB / 0.5682 GB, free: 111.4 MB / 442.7 MB
Notification: Performance of prepare preOptimizeDAE: time 3.185e-05/0.4404, allocations: 6.469 kB / 0.5682 GB, free: 111.4 MB / 442.7 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.001526/0.4419, allocations: 433.3 kB / 0.5686 GB, free: 111.2 MB / 442.7 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.002208/0.4442, allocations: 1.109 MB / 0.5697 GB, free: 110.4 MB / 442.7 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001064/0.4443, allocations: 110.8 kB / 0.5698 GB, free: 110.3 MB / 442.7 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0003519/0.4447, allocations: 79.64 kB / 0.5698 GB, free: 110.3 MB / 442.7 MB
Notification: Performance of preOpt removeEqualFunctionCalls (simulation): time 0.004061/0.4488, allocations: 3.607 MB / 0.5734 GB, free: 108.6 MB / 442.7 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002469/0.4512, allocations: 2.028 MB / 0.5753 GB, free: 107.4 MB / 442.7 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.699e-05/0.4513, allocations: 4 kB / 0.5753 GB, free: 107.4 MB / 442.7 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001008/0.4514, allocations: 0 / 0.5753 GB, free: 107.4 MB / 442.7 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.426e-05/0.4514, allocations: 33.03 kB / 0.5754 GB, free: 107.4 MB / 442.7 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.009679/0.4611, allocations: 7.719 MB / 0.5829 GB, free: 99.96 MB / 442.7 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.002474/0.4636, allocations: 2.868 MB / 0.5857 GB, free: 97.11 MB / 442.7 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.001162/0.4648, allocations: 1.367 MB / 0.5871 GB, free: 95.74 MB / 442.7 MB
Notification: Performance of preOpt evalFunc (simulation): time 0.0004366/0.4652, allocations: 414.7 kB / 0.5875 GB, free: 95.34 MB / 442.7 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.292e-05/0.4652, allocations: 51.88 kB / 0.5875 GB, free: 95.28 MB / 442.7 MB
Notification: Performance of pre-optimization done (n=163): time 3.537e-06/0.4653, allocations: 0 / 0.5875 GB, free: 95.28 MB / 442.7 MB
Notification: Performance of matching and sorting (n=214): time 0.03247/0.4977, allocations: 11.17 MB / 0.5984 GB, free: 84.11 MB / 442.7 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.454e-05/0.4978, allocations: 73.41 kB / 0.5985 GB, free: 84.02 MB / 442.7 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0007542/0.4985, allocations: 0.7315 MB / 0.5992 GB, free: 83.29 MB / 442.7 MB
Notification: Performance of collectPreVariables (initialization): time 0.0001039/0.4987, allocations: 25.7 kB / 0.5992 GB, free: 83.26 MB / 442.7 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001391/0.4988, allocations: 413.4 kB / 0.5996 GB, free: 82.84 MB / 442.7 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0003972/0.4992, allocations: 0.681 MB / 0.6003 GB, free: 82.15 MB / 442.7 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.000109/0.4993, allocations: 0 / 0.6003 GB, free: 82.15 MB / 442.7 MB
Notification: Performance of setup shared object (initialization): time 8.479e-05/0.4994, allocations: 381.9 kB / 0.6006 GB, free: 81.77 MB / 442.7 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.001521/0.5009, allocations: 1.538 MB / 0.6021 GB, free: 80.23 MB / 442.7 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.001577/0.5025, allocations: 1.75 MB / 0.6038 GB, free: 78.43 MB / 442.7 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.003566/0.5061, allocations: 1.987 MB / 0.6058 GB, free: 76.45 MB / 442.7 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.368e-06/0.5061, allocations: 0 / 0.6058 GB, free: 76.45 MB / 442.7 MB
Notification: Performance of matching and sorting (n=247) (initialization): time 0.009468/0.5156, allocations: 4.529 MB / 0.6102 GB, free: 71.89 MB / 442.7 MB
Notification: Performance of prepare postOptimizeDAE: time 1.364e-05/0.5156, allocations: 8.562 kB / 0.6102 GB, free: 71.89 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.362e-05/0.5156, allocations: 8 kB / 0.6102 GB, free: 71.88 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (initialization): time 0.003319/0.519, allocations: 0.6398 MB / 0.6109 GB, free: 71.23 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001722/0.5207, allocations: 443.2 kB / 0.6113 GB, free: 70.8 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.004881/0.5256, allocations: 4.263 MB / 0.6154 GB, free: 66.28 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.002177/0.5278, allocations: 143.6 kB / 0.6156 GB, free: 66.14 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0002346/0.528, allocations: 110.9 kB / 0.6157 GB, free: 66.04 MB / 442.7 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 0.0003444/0.5284, allocations: 145.2 kB / 0.6158 GB, free: 65.89 MB / 442.7 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.00026/0.5287, allocations: 138.2 kB / 0.6159 GB, free: 65.75 MB / 442.7 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.01276/0.5414, allocations: 5.163 MB / 0.621 GB, free: 60.61 MB / 442.7 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.01155/0.553, allocations: 4.655 MB / 0.6255 GB, free: 55.94 MB / 442.7 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.04e-05/0.553, allocations: 8 kB / 0.6255 GB, free: 55.93 MB / 442.7 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.869e-05/0.553, allocations: 11.95 kB / 0.6256 GB, free: 55.92 MB / 442.7 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.01696/0.57, allocations: 10.35 MB / 0.6357 GB, free: 45.43 MB / 442.7 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.161e-05/0.57, allocations: 8 kB / 0.6357 GB, free: 45.43 MB / 442.7 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001448/0.5715, allocations: 395.4 kB / 0.636 GB, free: 45.04 MB / 442.7 MB
Notification: Performance of postOpt tearingSystem (simulation): time 0.006352/0.5778, allocations: 1.314 MB / 0.6373 GB, free: 43.71 MB / 442.7 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0001502/0.578, allocations: 49.48 kB / 0.6374 GB, free: 43.67 MB / 442.7 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.009648/0.5877, allocations: 7.2 MB / 0.6444 GB, free: 36.22 MB / 442.7 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 0.005492/0.5932, allocations: 2.398 MB / 0.6468 GB, free: 33.7 MB / 442.7 MB
Notification: Performance of postOpt detectJacobianSparsePattern (simulation): time 0.01315/0.6063, allocations: 7.629 MB / 0.6542 GB, free: 25.68 MB / 442.7 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0007909/0.6071, allocations: 448.2 kB / 0.6546 GB, free: 25.23 MB / 442.7 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.000299/0.6075, allocations: 19.98 kB / 0.6546 GB, free: 25.21 MB / 442.7 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.001494/0.609, allocations: 87.8 kB / 0.6547 GB, free: 25.12 MB / 442.7 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0002203/0.6092, allocations: 165.5 kB / 0.6549 GB, free: 24.96 MB / 442.7 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0001463/0.6093, allocations: 91.94 kB / 0.655 GB, free: 24.87 MB / 442.7 MB
Notification: Performance of sort global known variables: time 0.0005628/0.6099, allocations: 0.5616 MB / 0.6555 GB, free: 24.31 MB / 442.7 MB
Notification: Performance of remove unused functions: time 0.00277/0.6127, allocations: 1.268 MB / 0.6568 GB, free: 23.04 MB / 442.7 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 0.001654/0.6143, allocations: 1.052 MB / 0.6578 GB, free: 22.04 MB / 442.7 MB
Notification: Performance of simCode: created initialization part: time 0.004846/0.6192, allocations: 3.878 MB / 0.6616 GB, free: 18.12 MB / 442.7 MB
Notification: Performance of simCode: created event and clocks part: time 3.417e-06/0.6192, allocations: 4 kB / 0.6616 GB, free: 18.12 MB / 442.7 MB
Notification: Performance of simCode: created simulation system equations: time 0.002998/0.6222, allocations: 2.365 MB / 0.6639 GB, free: 15.72 MB / 442.7 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001681/0.6239, allocations: 404.4 kB / 0.6643 GB, free: 15.34 MB / 442.7 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.004796/0.6287, allocations: 3.502 MB / 0.6677 GB, free: 11.68 MB / 442.7 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001225/0.63, allocations: 1.555 MB / 0.6692 GB, free: 10.1 MB / 442.7 MB
Notification: Performance of SimCode: time 2.61e-07/0.63, allocations: 6.719 kB / 0.6692 GB, free: 10.09 MB / 442.7 MB
Notification: Performance of Templates: time 0.1671/0.7971, allocations: 45.92 MB / 0.7141 GB, free: 156.9 MB / 458.7 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)