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 0.001192/0.001192, allocations: 111.3 kB / 15.23 MB, free: 0.6602 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001133/0.001133, allocations: 190.2 kB / 16.13 MB, free: 6.66 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.288/1.288, allocations: 222.9 MB / 239.8 MB, free: 4.586 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.1799/0.1799, allocations: 12.26 MB / 302.2 MB, free: 1.336 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001135/0.001135, allocations: 55.91 kB / 365.1 MB, free: 10.28 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.0977/0.09885, allocations: 52.08 MB / 417.2 MB, free: 6.086 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.1715/0.2704, allocations: 8.599 MB / 425.8 MB, free: 36.11 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.001395/0.2718, allocations: 0.8194 MB / 426.6 MB, free: 36.05 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.000273/0.2721, allocations: 41.44 kB / 426.6 MB, free: 36.05 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0002303/0.2724, allocations: 108.3 kB / 426.7 MB, free: 36.05 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0003682/0.2728, allocations: 163.9 kB / 426.9 MB, free: 36.05 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0002927/0.2731, allocations: 172.2 kB / 427.1 MB, free: 36.05 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0004611/0.2735, allocations: 0.7823 MB / 427.9 MB, free: 35.95 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0005384/0.2741, allocations: 479.7 kB / 428.3 MB, free: 35.89 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001913/0.2743, allocations: 323.5 kB / 428.6 MB, free: 35.82 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002506/0.2745, allocations: 406.5 kB / 429 MB, free: 35.71 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 8.099e-05/0.2746, allocations: 76.34 kB / 429.1 MB, free: 35.71 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 9.676e-05/0.2747, allocations: 73.78 kB / 429.2 MB, free: 35.71 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001083/0.2748, allocations: 178.8 kB / 429.4 MB, free: 35.68 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.000244/0.2751, allocations: 441.6 kB / 429.8 MB, free: 35.54 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0005761/0.2757, allocations: 1.109 MB / 430.9 MB, free: 35.2 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 5.18e-06/0.2757, allocations: 2.688 kB / 430.9 MB, free: 35.2 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.222e-06/0.2757, allocations: 0 / 430.9 MB, free: 35.2 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 1.405e-05/0.2757, allocations: 0 / 430.9 MB, free: 35.2 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 0.001296/0.277, allocations: 1.122 MB / 432 MB, free: 34.44 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.502e-05/0.2771, allocations: 9.969 kB / 432 MB, free: 34.44 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001321/0.2772, allocations: 102 kB / 432.1 MB, free: 34.39 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002107/0.2774, allocations: 302.1 kB / 432.4 MB, free: 34.11 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.959e-05/0.2775, allocations: 76.41 kB / 432.5 MB, free: 34.07 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.000103/0.2776, allocations: 104.4 kB / 432.6 MB, free: 34.04 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001133/0.2787, allocations: 0.8743 MB / 433.5 MB, free: 33.66 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.718e-05/0.2788, allocations: 4.094 kB / 433.5 MB, free: 33.66 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 8.416e-05/0.2788, allocations: 49.94 kB / 433.5 MB, free: 33.62 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.96e-05/0.2789, allocations: 22.81 kB / 433.6 MB, free: 33.62 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0009122/0.2798, allocations: 0.6239 MB / 434.2 MB, free: 33.39 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.003506/0.2833, allocations: 2.861 MB / 437 MB, free: 31.89 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0008268/0.2841, allocations: 0.5216 MB / 437.6 MB, free: 31.66 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003345/0.2845, allocations: 315.8 kB / 437.9 MB, free: 31.52 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.756e-05/0.2845, allocations: 9.375 kB / 437.9 MB, free: 31.52 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.722e-05/0.2846, allocations: 38.31 kB / 437.9 MB, free: 31.48 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=50): time 2.886e-06/0.2846, allocations: 0 / 437.9 MB, free: 31.48 MB / 350.1 MB
Notification: Performance of matching and sorting (n=59): time 0.004426/0.289, allocations: 2.17 MB / 440.1 MB, free: 30.47 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.484e-05/0.2891, allocations: 84.14 kB / 440.2 MB, free: 30.38 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003077/0.2894, allocations: 365.1 kB / 440.5 MB, free: 30.2 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 2.839e-05/0.2894, allocations: 33.7 kB / 440.6 MB, free: 30.16 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001575/0.2896, allocations: 453.1 kB / 441 MB, free: 29.8 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001005/0.2897, allocations: 220 kB / 441.2 MB, free: 29.64 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.000154/0.2898, allocations: 135.4 kB / 441.3 MB, free: 29.56 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 7.443e-05/0.2899, allocations: 359.6 kB / 441.7 MB, free: 29.23 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003119/0.2902, allocations: 249.9 kB / 441.9 MB, free: 29.12 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0004149/0.2907, allocations: 487.4 kB / 442.4 MB, free: 28.7 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.005385/0.2961, allocations: 1.708 MB / 444.1 MB, free: 27.9 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 7.053e-06/0.2961, allocations: 5.094 kB / 444.1 MB, free: 27.9 MB / 350.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.0009959/0.2971, allocations: 0.8023 MB / 444.9 MB, free: 27.54 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.705e-05/0.2971, allocations: 6.688 kB / 444.9 MB, free: 27.54 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.083e-05/0.2971, allocations: 9.938 kB / 444.9 MB, free: 27.54 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.136e-05/0.2972, allocations: 13.97 kB / 445 MB, free: 27.54 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0005948/0.2978, allocations: 185.3 kB / 445.1 MB, free: 27.52 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.637e-05/0.2978, allocations: 17.16 kB / 445.2 MB, free: 27.51 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.000378/0.2982, allocations: 45.36 kB / 445.2 MB, free: 27.49 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.139e-05/0.2982, allocations: 37.25 kB / 445.2 MB, free: 27.48 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
         nucleus.V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  "Compartment volume" type: Real
         cytoplasm.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
         cytoplasm.y2.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" 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
         nucleus.ambientSubstance.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.y6.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer )  "Number of moles of substance in pool (mol)" 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
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 (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of prepare postOptimizeDAE: time 0.0005351/0.2988, allocations: 287.7 kB / 445.5 MB, free: 27.27 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.000101/0.2989, allocations: 46.28 kB / 445.6 MB, free: 27.24 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.000128/0.299, allocations: 65.98 kB / 445.6 MB, free: 27.19 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 8.646e-06/0.299, allocations: 6.125 kB / 445.6 MB, free: 27.19 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.551e-05/0.2991, allocations: 0 / 445.6 MB, free: 27.19 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 9.578e-06/0.2991, allocations: 9.469 kB / 445.6 MB, free: 27.19 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0009548/0.3, allocations: 0.7658 MB / 446.4 MB, free: 26.78 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.599e-06/0.3001, allocations: 2.938 kB / 446.4 MB, free: 26.78 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005231/0.3006, allocations: 104.7 kB / 446.5 MB, free: 26.77 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 4.178e-06/0.3006, allocations: 2.969 kB / 446.5 MB, free: 26.77 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.635e-05/0.3006, allocations: 20.75 kB / 446.5 MB, free: 26.76 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.627e-06/0.3006, allocations: 6.969 kB / 446.5 MB, free: 26.75 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.252e-06/0.3007, allocations: 0 / 446.5 MB, free: 26.75 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0009355/0.3016, allocations: 0.936 MB / 447.5 MB, free: 26.22 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 6.405e-05/0.3017, allocations: 112.4 kB / 447.6 MB, free: 26.1 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.834e-05/0.3017, allocations: 14.47 kB / 447.6 MB, free: 26.09 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0003035/0.302, allocations: 35.27 kB / 447.6 MB, free: 26.07 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.992e-05/0.3021, allocations: 36.62 kB / 447.7 MB, free: 26.07 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.767e-05/0.3021, allocations: 16.81 kB / 447.7 MB, free: 26.07 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 0.0001729/0.3023, allocations: 240 kB / 447.9 MB, free: 25.94 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.21e-07/0.3023, allocations: 0 / 447.9 MB, free: 25.94 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0005594/0.3029, allocations: 156 kB / 448.1 MB, free: 25.92 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 (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of Backend phase and start with SimCode phase: time 9.52e-05/0.303, allocations: 118.6 kB / 448.2 MB, free: 25.81 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0007192/0.3037, allocations: 0.5947 MB / 448.8 MB, free: 25.59 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 1.894e-06/0.3037, allocations: 0 / 448.8 MB, free: 25.59 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0002788/0.304, allocations: 263.1 kB / 449 MB, free: 25.49 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.000479/0.3045, allocations: 57.67 kB / 449.1 MB, free: 25.46 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002477/0.307, allocations: 2.185 MB / 451.3 MB, free: 23.97 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0002677/0.3073, allocations: 0.9451 MB / 452.2 MB, free: 23.25 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 0.0002615/0.3075, allocations: 64.56 kB / 452.3 MB, free: 23.24 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001364/0.3077, allocations: 46.89 kB / 452.3 MB, free: 23.23 MB / 350.1 MB
Notification: Performance of SimCode: time 3.01e-07/0.3077, allocations: 0 / 452.3 MB, free: 23.23 MB / 350.1 MB
Notification: Performance of Templates: time 0.007718/0.3154, allocations: 5.11 MB / 457.5 MB, free: 22.9 MB / 350.1 MB
make -j1 -f BioChem_BioChem.Examples.CircadianOscillator.Container.makefile
(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)