Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries/ --ompython_omhome=/usr BioChem_BioChem.Examples.CircadianOscillator.Container.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/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/BioChem 1.1.2-master/package.mo", uses=false)
Using package BioChem with version 1.1.2 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/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 ModelicaServices with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo)
Running command: translateModel(BioChem.Examples.CircadianOscillator.Container,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CircadianOscillator.Container")
translateModel(BioChem.Examples.CircadianOscillator.Container,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CircadianOscillator.Container")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.0009953/0.0009953, allocations: 99.86 kB / 15.05 MB, free: 1.105 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001192/0.001192, allocations: 177.3 kB / 15.95 MB, free: 216 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.572/1.572, allocations: 223.2 MB / 239.9 MB, free: 5.418 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.2437/0.2437, allocations: 12.23 MB / 303.2 MB, free: 2.074 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0003377/0.0003379, allocations: 8 kB / 366.8 MB, free: 9.809 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1286/0.1289, allocations: 53.08 MB / 419.9 MB, free: 4.621 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.2262/0.3552, allocations: 7.259 MB / 427.2 MB, free: 34.73 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.001436/0.3567, allocations: 0.8557 MB / 428 MB, free: 34.55 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0002588/0.3569, allocations: 40.88 kB / 428 MB, free: 34.55 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0001644/0.3571, allocations: 114.1 kB / 428.2 MB, free: 34.52 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0003482/0.3575, allocations: 200.1 kB / 428.4 MB, free: 34.51 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0002692/0.3577, allocations: 117.7 kB / 428.5 MB, free: 34.51 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0004884/0.3582, allocations: 0.5348 MB / 429 MB, free: 34.48 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0005771/0.3588, allocations: 404.2 kB / 429.4 MB, free: 34.45 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002144/0.359, allocations: 249.9 kB / 429.6 MB, free: 34.38 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002665/0.3593, allocations: 313 kB / 430 MB, free: 34.3 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 6.399e-05/0.3594, allocations: 42.3 kB / 430 MB, free: 34.3 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 7.551e-05/0.3595, allocations: 42.72 kB / 430 MB, free: 34.3 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 7.32e-05/0.3596, allocations: 128.1 kB / 430.2 MB, free: 34.27 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 9.607e-05/0.3597, allocations: 187.5 kB / 430.3 MB, free: 34.2 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0005097/0.3602, allocations: 0.8721 MB / 431.2 MB, free: 34.15 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 2.314e-06/0.3602, allocations: 0.5938 kB / 431.2 MB, free: 34.15 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.713e-06/0.3602, allocations: 2.094 kB / 431.2 MB, free: 34.15 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 1.06e-05/0.3602, allocations: 0 / 431.2 MB, free: 34.15 MB / 350.1 MB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 252
 * Number of variables: 252
Notification: Performance of Generate backend data structure: time 0.001176/0.3614, allocations: 0.9502 MB / 432.2 MB, free: 33.56 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.671e-05/0.3614, allocations: 5.938 kB / 432.2 MB, free: 33.56 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001129/0.3615, allocations: 98.42 kB / 432.3 MB, free: 33.52 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.000208/0.3618, allocations: 292.3 kB / 432.6 MB, free: 33.25 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 4.87e-05/0.3618, allocations: 76.22 kB / 432.6 MB, free: 33.24 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001074/0.3619, allocations: 105.4 kB / 432.7 MB, free: 33.24 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001198/0.3631, allocations: 0.8621 MB / 433.6 MB, free: 33.16 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.698e-05/0.3632, allocations: 0 / 433.6 MB, free: 33.16 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 6.547e-05/0.3632, allocations: 42.12 kB / 433.6 MB, free: 33.16 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.894e-05/0.3633, allocations: 29.92 kB / 433.7 MB, free: 33.16 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0009042/0.3642, allocations: 0.6146 MB / 434.3 MB, free: 33.15 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.003623/0.3678, allocations: 2.845 MB / 437.1 MB, free: 32.25 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0007985/0.3686, allocations: 0.5155 MB / 437.6 MB, free: 32.01 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.529e-05/0.3687, allocations: 6.781 kB / 437.6 MB, free: 32.01 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.522e-05/0.3687, allocations: 38.28 kB / 437.7 MB, free: 31.96 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=50): time 1.824e-06/0.3687, allocations: 1.219 kB / 437.7 MB, free: 31.96 MB / 350.1 MB
Notification: Performance of matching and sorting (n=59): time 0.004416/0.3731, allocations: 2.175 MB / 439.9 MB, free: 30.98 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.169e-05/0.3732, allocations: 85.86 kB / 439.9 MB, free: 30.88 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003338/0.3735, allocations: 369.5 kB / 440.3 MB, free: 30.68 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 3.049e-05/0.3736, allocations: 29.7 kB / 440.3 MB, free: 30.65 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001945/0.3738, allocations: 451.2 kB / 440.8 MB, free: 30.3 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001216/0.3739, allocations: 220.7 kB / 441 MB, free: 30.13 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 2.686e-05/0.3739, allocations: 15.16 kB / 441 MB, free: 30.12 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 9.822e-05/0.374, allocations: 358.6 kB / 441.4 MB, free: 29.79 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003027/0.3743, allocations: 243.3 kB / 441.6 MB, free: 29.69 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0004601/0.3748, allocations: 484.3 kB / 442.1 MB, free: 29.26 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0003865/0.3752, allocations: 304.3 kB / 442.4 MB, free: 29.1 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.955e-06/0.3752, allocations: 0 / 442.4 MB, free: 29.1 MB / 350.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.0009939/0.3762, allocations: 0.8036 MB / 443.2 MB, free: 28.73 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.077e-05/0.3762, allocations: 7.188 kB / 443.2 MB, free: 28.73 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.197e-05/0.3763, allocations: 11.56 kB / 443.2 MB, free: 28.73 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.614e-05/0.3763, allocations: 15.97 kB / 443.2 MB, free: 28.73 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006172/0.3769, allocations: 186.9 kB / 443.4 MB, free: 28.7 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.816e-05/0.3769, allocations: 22 kB / 443.4 MB, free: 28.7 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003444/0.3773, allocations: 43.02 kB / 443.4 MB, free: 28.68 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.432e-05/0.3773, allocations: 43.48 kB / 443.5 MB, free: 28.67 MB / 350.1 MB
Warning: Assuming fixed start value for the following 12 variables:
         V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  "Compartment volume" type: Real
         cytoplasm.ambientSubstance.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         cytoplasm.y5.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         cytoplasm.y4.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         nucleus.y6.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         nucleus.V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  "Compartment volume" type: Real
         nucleus.y3.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         nucleus.y7.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         nucleus.ambientSubstance.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         cytoplasm.V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  "Compartment volume" type: Real
         cytoplasm.y1.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
         cytoplasm.y2.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" type: Real
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 39
 * Number of states: 0 ()
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (107):
 * Single equations (assignments): 107
 * 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: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of prepare postOptimizeDAE: time 0.0004638/0.3778, allocations: 274.1 kB / 443.8 MB, free: 28.46 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 8.496e-05/0.3779, allocations: 48.88 kB / 443.8 MB, free: 28.43 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001323/0.378, allocations: 71.38 kB / 443.9 MB, free: 28.38 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 7.223e-06/0.378, allocations: 6.812 kB / 443.9 MB, free: 28.38 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.288e-05/0.3781, allocations: 1.078 kB / 443.9 MB, free: 28.38 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 7.995e-06/0.3781, allocations: 3.516 kB / 443.9 MB, free: 28.38 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.000988/0.3791, allocations: 0.7561 MB / 444.6 MB, free: 27.97 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.837e-06/0.3791, allocations: 2 kB / 444.6 MB, free: 27.97 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0004979/0.3796, allocations: 109.7 kB / 444.7 MB, free: 27.96 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 5.951e-06/0.3796, allocations: 3.219 kB / 444.8 MB, free: 27.96 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.374e-05/0.3796, allocations: 20.89 kB / 444.8 MB, free: 27.95 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.246e-06/0.3797, allocations: 0 / 444.8 MB, free: 27.95 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.015e-06/0.3797, allocations: 4.031 kB / 444.8 MB, free: 27.95 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0009605/0.3806, allocations: 0.9408 MB / 445.7 MB, free: 27.4 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 7.299e-05/0.3807, allocations: 116.8 kB / 445.8 MB, free: 27.28 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.587e-05/0.3808, allocations: 22.12 kB / 445.9 MB, free: 27.27 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002827/0.3811, allocations: 31.84 kB / 445.9 MB, free: 27.25 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.109e-05/0.3811, allocations: 36.7 kB / 445.9 MB, free: 27.24 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.435e-05/0.3812, allocations: 15.88 kB / 445.9 MB, free: 27.24 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 0.0001709/0.3813, allocations: 239.6 kB / 446.2 MB, free: 27.11 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.2e-07/0.3813, allocations: 0 / 446.2 MB, free: 27.11 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0005603/0.3819, allocations: 160.3 kB / 446.3 MB, free: 27.09 MB / 350.1 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 2
 * Number of states: 12 (nucleus.V,nucleus.y3.n,nucleus.y6.n,nucleus.y7.n,nucleus.ambientSubstance.n,cytoplasm.V,cytoplasm.y1.n,cytoplasm.y2.n,cytoplasm.y4.n,cytoplasm.y5.n,cytoplasm.ambientSubstance.n,V)
 * Number of discrete variables: 0 ()
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (59):
 * Single equations (assignments): 59
 * 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: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of Backend phase and start with SimCode phase: time 0.000108/0.382, allocations: 110.2 kB / 446.4 MB, free: 26.99 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0007073/0.3827, allocations: 0.5987 MB / 447 MB, free: 26.76 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.395e-06/0.3828, allocations: 0 / 447 MB, free: 26.76 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0002718/0.383, allocations: 256.7 kB / 447.3 MB, free: 26.67 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003148/0.3834, allocations: 55.62 kB / 447.3 MB, free: 26.64 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.00277/0.3861, allocations: 2.243 MB / 449.6 MB, free: 25.16 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0003585/0.3865, allocations: 0.9504 MB / 450.5 MB, free: 24.45 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 0.0002733/0.3868, allocations: 68.12 kB / 450.6 MB, free: 24.43 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001248/0.3869, allocations: 46.34 kB / 450.6 MB, free: 24.43 MB / 350.1 MB
Notification: Performance of SimCode: time 3.31e-07/0.3869, allocations: 0 / 450.6 MB, free: 24.43 MB / 350.1 MB
Notification: Performance of Templates: time 0.008536/0.3955, allocations: 4.879 MB / 455.5 MB, free: 24.11 MB / 350.1 MB
make -j1 -f BioChem_BioChem.Examples.CircadianOscillator.Container.makefile
Environment - environmentSimulation:
(rm -f BioChem_BioChem.Examples.CircadianOscillator.Container.pipe ; mkfifo BioChem_BioChem.Examples.CircadianOscillator.Container.pipe ; head -c 1048576 < BioChem_BioChem.Examples.CircadianOscillator.Container.pipe >> ../files/BioChem_BioChem.Examples.CircadianOscillator.Container.sim & ./BioChem_BioChem.Examples.CircadianOscillator.Container  -abortSlowSimulation -alarm=480 -lv LOG_STATS > BioChem_BioChem.Examples.CircadianOscillator.Container.pipe 2>&1)
Environment - environmentSimulation: