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: "" <> buildModelFMU(BioChem.Examples.CircadianOscillator.Container,fileNamePrefix="BioChem_BioChem_Examples_CircadianOscillator_Container",fmuType="me",version="2.0",platforms={"static"})
"" <> buildModelFMU(BioChem.Examples.CircadianOscillator.Container,fileNamePrefix="BioChem_BioChem_Examples_CircadianOscillator_Container",fmuType="me",version="2.0",platforms={"static"})
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.0008613/0.0008614, allocations: 91.84 kB / 15.36 MB, free: 0.7383 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.005241/0.005241, allocations: 169.9 kB / 16.26 MB, free: 6.613 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.226/1.226, allocations: 223.3 MB / 240.3 MB, free: 5.352 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.5014/0.5014, allocations: 12.25 MB / 303.7 MB, free: 2.027 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0002696/0.0002697, allocations: 8 kB / 367.6 MB, free: 9.367 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.08522/0.0855, allocations: 53.09 MB / 420.7 MB, free: 4.172 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.1729/0.2584, allocations: 8.034 MB / 428.8 MB, free: 34.54 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.001112/0.2595, allocations: 0.8107 MB / 429.6 MB, free: 34.36 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0002252/0.2598, allocations: 43.69 kB / 429.6 MB, free: 34.36 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0001491/0.2599, allocations: 105.5 kB / 429.7 MB, free: 34.33 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.00035/0.2603, allocations: 172.1 kB / 429.9 MB, free: 34.25 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0002894/0.2606, allocations: 166.7 kB / 430.1 MB, free: 34.25 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0005032/0.2611, allocations: 0.7829 MB / 430.8 MB, free: 34.06 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0006161/0.2617, allocations: 469.2 kB / 431.3 MB, free: 34 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001688/0.2619, allocations: 261.9 kB / 431.5 MB, free: 33.93 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002397/0.2621, allocations: 333.8 kB / 431.9 MB, free: 33.82 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 5.886e-05/0.2622, allocations: 42.16 kB / 431.9 MB, free: 33.82 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 6.929e-05/0.2623, allocations: 40.84 kB / 432 MB, free: 33.82 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 7.713e-05/0.2624, allocations: 131.4 kB / 432.1 MB, free: 33.79 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0002257/0.2626, allocations: 411.8 kB / 432.5 MB, free: 33.62 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0006633/0.2633, allocations: 1.062 MB / 433.5 MB, free: 33.47 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 3.587e-06/0.2633, allocations: 0 / 433.5 MB, free: 33.47 MB / 350.1 MB
Notification: Performance of FrontEnd: time 9.42e-07/0.2633, allocations: 0 / 433.5 MB, free: 33.47 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 9.908e-06/0.2633, allocations: 0 / 433.5 MB, free: 33.47 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 0.001134/0.2645, allocations: 0.9397 MB / 434.5 MB, free: 32.88 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.858e-05/0.2645, allocations: 10.62 kB / 434.5 MB, free: 32.88 MB / 350.1 MB
Notification: Performance of preOpt introduceOutputAliases (simulation): time 0.0001261/0.2646, allocations: 152.9 kB / 434.6 MB, free: 32.84 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001112/0.2647, allocations: 94.62 kB / 434.7 MB, free: 32.79 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002339/0.265, allocations: 311 kB / 435 MB, free: 32.5 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 5.27e-05/0.2651, allocations: 73.75 kB / 435.1 MB, free: 32.5 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001272/0.2652, allocations: 97.5 kB / 435.2 MB, free: 32.5 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.00115/0.2663, allocations: 0.8761 MB / 436.1 MB, free: 32.43 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.606e-05/0.2664, allocations: 7.875 kB / 436.1 MB, free: 32.42 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 6.386e-05/0.2665, allocations: 43.28 kB / 436.1 MB, free: 32.42 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.763e-05/0.2665, allocations: 27.25 kB / 436.2 MB, free: 32.42 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0009131/0.2674, allocations: 0.6229 MB / 436.8 MB, free: 32.41 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.003531/0.2709, allocations: 2.834 MB / 439.6 MB, free: 31.67 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0008333/0.2718, allocations: 0.5237 MB / 440.1 MB, free: 31.43 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003269/0.2721, allocations: 316.5 kB / 440.5 MB, free: 31.29 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 3.195e-05/0.2722, allocations: 3.594 kB / 440.5 MB, free: 31.29 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.754e-05/0.2722, allocations: 43.12 kB / 440.5 MB, free: 31.25 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=50): time 2.284e-06/0.2722, allocations: 1.781 kB / 440.5 MB, free: 31.25 MB / 350.1 MB
Notification: Performance of matching and sorting (n=59): time 0.004377/0.2766, allocations: 2.182 MB / 442.7 MB, free: 30.25 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.166e-05/0.2766, allocations: 80.89 kB / 442.8 MB, free: 30.15 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.000248/0.2769, allocations: 364.6 kB / 443.1 MB, free: 29.96 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 2.716e-05/0.2769, allocations: 39.92 kB / 443.2 MB, free: 29.93 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001365/0.2771, allocations: 453.5 kB / 443.6 MB, free: 29.57 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 9.072e-05/0.2772, allocations: 221.4 kB / 443.8 MB, free: 29.41 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 6.614e-05/0.2772, allocations: 68.77 kB / 443.9 MB, free: 29.37 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 5.968e-05/0.2773, allocations: 361.5 kB / 444.2 MB, free: 29.03 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002891/0.2776, allocations: 247.9 kB / 444.5 MB, free: 28.93 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003325/0.2779, allocations: 485.8 kB / 445 MB, free: 28.5 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.005585/0.2835, allocations: 1.753 MB / 446.7 MB, free: 27.7 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.957e-06/0.2835, allocations: 3.938 kB / 446.7 MB, free: 27.7 MB / 350.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.0009311/0.2845, allocations: 0.8078 MB / 447.5 MB, free: 27.33 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.538e-05/0.2845, allocations: 6.656 kB / 447.5 MB, free: 27.33 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.767e-06/0.2845, allocations: 13.55 kB / 447.5 MB, free: 27.33 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.989e-05/0.2845, allocations: 12.81 kB / 447.5 MB, free: 27.33 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0005969/0.2851, allocations: 186.1 kB / 447.7 MB, free: 27.31 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.32e-05/0.2852, allocations: 16.06 kB / 447.7 MB, free: 27.3 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003357/0.2855, allocations: 47.14 kB / 447.8 MB, free: 27.29 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 3.706e-05/0.2856, allocations: 36.91 kB / 447.8 MB, free: 27.28 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 0.0003625/0.2859, allocations: 273.7 kB / 448.1 MB, free: 27.07 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 7.869e-05/0.286, allocations: 53.52 kB / 448.1 MB, free: 27.04 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001424/0.2862, allocations: 69.78 kB / 448.2 MB, free: 26.98 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.899e-06/0.2862, allocations: 6.875 kB / 448.2 MB, free: 26.98 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 7.644e-06/0.2862, allocations: 0 / 448.2 MB, free: 26.98 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.881e-06/0.2862, allocations: 3.188 kB / 448.2 MB, free: 26.98 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0008231/0.287, allocations: 0.7683 MB / 449 MB, free: 26.57 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.465e-06/0.287, allocations: 0 / 449 MB, free: 26.57 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005095/0.2875, allocations: 105.9 kB / 449.1 MB, free: 26.56 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.526e-06/0.2876, allocations: 2.906 kB / 449.1 MB, free: 26.56 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.341e-05/0.2876, allocations: 18.44 kB / 449.1 MB, free: 26.55 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.247e-06/0.2876, allocations: 5.031 kB / 449.1 MB, free: 26.55 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.684e-06/0.2876, allocations: 9.469 kB / 449.1 MB, free: 26.55 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0008706/0.2885, allocations: 0.9327 MB / 450.1 MB, free: 26.01 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 5.238e-05/0.2885, allocations: 112.7 kB / 450.2 MB, free: 25.89 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.167e-05/0.2886, allocations: 18.06 kB / 450.2 MB, free: 25.88 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002856/0.2889, allocations: 27.19 kB / 450.2 MB, free: 25.88 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.875e-05/0.2889, allocations: 34.16 kB / 450.3 MB, free: 25.87 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.321e-05/0.289, allocations: 13.34 kB / 450.3 MB, free: 25.87 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 0.0001563/0.2891, allocations: 239.8 kB / 450.5 MB, free: 25.74 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.41e-07/0.2891, allocations: 0 / 450.5 MB, free: 25.74 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.000509/0.2897, allocations: 156.9 kB / 450.7 MB, free: 25.72 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 0.0009939/0.2907, allocations: 1.498 MB / 452.2 MB, free: 24.63 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0006446/0.2913, allocations: 0.5968 MB / 452.7 MB, free: 24.41 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.314e-06/0.2913, allocations: 0 / 452.7 MB, free: 24.41 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0002576/0.2916, allocations: 260.4 kB / 453 MB, free: 24.31 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004486/0.292, allocations: 66.12 kB / 453.1 MB, free: 24.28 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.005546/0.2976, allocations: 6.456 MB / 459.5 MB, free: 19.84 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0002786/0.2979, allocations: 0.9433 MB / 460.5 MB, free: 19.12 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 0.0002492/0.2981, allocations: 59.83 kB / 460.5 MB, free: 19.1 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0002838/0.2984, allocations: 281.9 kB / 460.8 MB, free: 18.89 MB / 350.1 MB
Notification: Performance of SimCode: time 3.31e-07/0.2984, allocations: 0 / 460.8 MB, free: 18.89 MB / 350.1 MB
Notification: Performance of buildModelFMU: Generate the FMI files: time 0.5855/0.884, allocations: 10.14 MB / 470.9 MB, free: 18.23 MB / 350.1 MB
Notification: Performance of buildModelFMU: configured platform static using cached values: time 0.0001484/0.8842, allocations: 191.3 kB / 471.1 MB, free: 17.97 MB / 350.1 MB
Notification: Performance of buildModelFMU: Generate platform static: time 1.836/2.72, allocations: 0 / 471.1 MB, free: 17.97 MB / 350.1 MB
(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 & /home/hudson/saved_omc/OMSimulator/install/bin/OMSimulator  --tempDir=temp_BioChem_BioChem_Examples_CircadianOscillator_Container_fmu --startTime=0 --stopTime=150 --timeout=50 --tolerance=1e-06 BioChem_BioChem_Examples_CircadianOscillator_Container.fmu > BioChem_BioChem.Examples.CircadianOscillator.Container.pipe 2>&1)