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 0.001016/0.001016, allocations: 103.4 kB / 15.33 MB, free: 0.5039 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001062/0.001062, allocations: 196.2 kB / 16.25 MB, free: 6.621 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.249/1.249, allocations: 222.9 MB / 239.9 MB, free: 4.57 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 1.658/1.658, allocations: 12.26 MB / 302.4 MB, free: 1.344 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001068/0.001068, allocations: 59.91 kB / 365.4 MB, free: 10.05 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1102/0.1112, allocations: 52.08 MB / 417.5 MB, free: 5.859 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.2479/0.3592, allocations: 8.607 MB / 426.1 MB, free: 36.2 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.001899/0.3611, allocations: 0.8196 MB / 426.9 MB, free: 36.14 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.000393/0.3615, allocations: 41.31 kB / 426.9 MB, free: 36.14 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0003246/0.3618, allocations: 108 kB / 427 MB, free: 36.14 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0004986/0.3624, allocations: 166.6 kB / 427.2 MB, free: 36.14 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0003813/0.3628, allocations: 167.5 kB / 427.4 MB, free: 36.14 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0006133/0.3634, allocations: 0.8336 MB / 428.2 MB, free: 36.02 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0006722/0.3641, allocations: 0.5348 MB / 428.7 MB, free: 35.96 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002846/0.3644, allocations: 368.7 kB / 429.1 MB, free: 35.89 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0003274/0.3647, allocations: 431.3 kB / 429.5 MB, free: 35.79 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001164/0.3648, allocations: 121.6 kB / 429.6 MB, free: 35.79 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001213/0.365, allocations: 115 kB / 429.7 MB, free: 35.79 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001305/0.3651, allocations: 220.9 kB / 429.9 MB, free: 35.75 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0002946/0.3654, allocations: 487 kB / 430.4 MB, free: 35.48 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0007674/0.3662, allocations: 1.145 MB / 431.6 MB, free: 35.03 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 4.298e-06/0.3662, allocations: 0 / 431.6 MB, free: 35.03 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.363e-06/0.3662, allocations: 0 / 431.6 MB, free: 35.03 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 1.113e-05/0.3662, allocations: 1.125 kB / 431.6 MB, free: 35.03 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 0.001369/0.3676, allocations: 1.122 MB / 432.7 MB, free: 34.27 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.069e-05/0.3676, allocations: 12.66 kB / 432.7 MB, free: 34.27 MB / 350.1 MB
Notification: Performance of preOpt introduceOutputAliases (simulation): time 0.000136/0.3678, allocations: 154.6 kB / 432.9 MB, free: 34.16 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001182/0.3679, allocations: 94.84 kB / 432.9 MB, free: 34.12 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002042/0.3681, allocations: 312.2 kB / 433.3 MB, free: 33.82 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 4.834e-05/0.3682, allocations: 73.06 kB / 433.3 MB, free: 33.79 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001029/0.3683, allocations: 95.34 kB / 433.4 MB, free: 33.76 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001178/0.3695, allocations: 0.8785 MB / 434.3 MB, free: 33.38 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.901e-05/0.3695, allocations: 11.97 kB / 434.3 MB, free: 33.38 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 6.219e-05/0.3696, allocations: 38.44 kB / 434.3 MB, free: 33.34 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.648e-05/0.3696, allocations: 30.88 kB / 434.4 MB, free: 33.34 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0008595/0.3705, allocations: 0.6186 MB / 435 MB, free: 33.12 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.003572/0.374, allocations: 2.859 MB / 437.9 MB, free: 31.57 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0009029/0.375, allocations: 0.5196 MB / 438.4 MB, free: 31.34 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003625/0.3753, allocations: 315.9 kB / 438.7 MB, free: 31.2 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 3.229e-05/0.3754, allocations: 4.875 kB / 438.7 MB, free: 31.2 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.086e-05/0.3754, allocations: 39.28 kB / 438.7 MB, free: 31.16 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=50): time 3.557e-06/0.3754, allocations: 5.062 kB / 438.7 MB, free: 31.15 MB / 350.1 MB
Notification: Performance of matching and sorting (n=59): time 0.004637/0.3801, allocations: 2.179 MB / 440.9 MB, free: 30.14 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.705e-05/0.3801, allocations: 84.02 kB / 441 MB, free: 30.05 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.000318/0.3804, allocations: 357.5 kB / 441.3 MB, free: 29.87 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 3.032e-05/0.3805, allocations: 33.7 kB / 441.4 MB, free: 29.83 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0002204/0.3807, allocations: 458.1 kB / 441.8 MB, free: 29.47 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001249/0.3808, allocations: 218.4 kB / 442 MB, free: 29.3 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001696/0.381, allocations: 134.2 kB / 442.2 MB, free: 29.23 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 8.976e-05/0.3811, allocations: 365.4 kB / 442.5 MB, free: 28.89 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003142/0.3814, allocations: 246.6 kB / 442.8 MB, free: 28.79 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0004562/0.3819, allocations: 483.9 kB / 443.2 MB, free: 28.37 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.005328/0.3872, allocations: 1.713 MB / 444.9 MB, free: 27.55 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.559e-06/0.3873, allocations: 6.906 kB / 445 MB, free: 27.55 MB / 350.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.0009942/0.3883, allocations: 0.7985 MB / 445.8 MB, free: 27.19 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.922e-05/0.3883, allocations: 9.688 kB / 445.8 MB, free: 27.19 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.127e-05/0.3883, allocations: 6.438 kB / 445.8 MB, free: 27.19 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.373e-05/0.3883, allocations: 14.41 kB / 445.8 MB, free: 27.19 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006016/0.3889, allocations: 190 kB / 446 MB, free: 27.17 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.695e-05/0.389, allocations: 16.59 kB / 446 MB, free: 27.17 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.00038/0.3893, allocations: 47.34 kB / 446 MB, free: 27.14 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 3.901e-05/0.3894, allocations: 33.25 kB / 446.1 MB, free: 27.14 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 0.0004526/0.3899, allocations: 289.1 kB / 446.3 MB, free: 26.92 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 8.538e-05/0.3899, allocations: 44.88 kB / 446.4 MB, free: 26.9 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001136/0.3901, allocations: 73.16 kB / 446.5 MB, free: 26.84 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.669e-06/0.3901, allocations: 6.656 kB / 446.5 MB, free: 26.84 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.436e-05/0.3901, allocations: 5.641 kB / 446.5 MB, free: 26.84 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.642e-06/0.3901, allocations: 3.797 kB / 446.5 MB, free: 26.84 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.00093/0.391, allocations: 0.7558 MB / 447.2 MB, free: 26.42 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.096e-06/0.3911, allocations: 3.094 kB / 447.2 MB, free: 26.42 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005229/0.3916, allocations: 111.2 kB / 447.3 MB, free: 26.41 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 4.519e-06/0.3916, allocations: 3.094 kB / 447.3 MB, free: 26.41 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.755e-05/0.3916, allocations: 22.38 kB / 447.4 MB, free: 26.39 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.785e-06/0.3917, allocations: 0 / 447.4 MB, free: 26.39 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.092e-06/0.3917, allocations: 3.125 kB / 447.4 MB, free: 26.39 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0009894/0.3927, allocations: 0.9301 MB / 448.3 MB, free: 25.86 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 7.295e-05/0.3927, allocations: 120 kB / 448.4 MB, free: 25.75 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.844e-05/0.3928, allocations: 18.97 kB / 448.4 MB, free: 25.73 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0003085/0.3931, allocations: 28.02 kB / 448.5 MB, free: 25.72 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.325e-05/0.3932, allocations: 36.36 kB / 448.5 MB, free: 25.71 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.627e-05/0.3932, allocations: 20.11 kB / 448.5 MB, free: 25.71 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 0.0001886/0.3934, allocations: 240.8 kB / 448.8 MB, free: 25.58 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.1e-07/0.3934, allocations: 4 kB / 448.8 MB, free: 25.58 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0005785/0.394, allocations: 157.3 kB / 448.9 MB, free: 25.56 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 0.001175/0.3952, allocations: 1.488 MB / 450.4 MB, free: 24.48 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.001008/0.3962, allocations: 0.6171 MB / 451 MB, free: 24.24 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 1.993e-06/0.3962, allocations: 0 / 451 MB, free: 24.24 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0003028/0.3965, allocations: 266.6 kB / 451.3 MB, free: 24.14 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004962/0.397, allocations: 65.02 kB / 451.3 MB, free: 24.11 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.006803/0.4038, allocations: 6.32 MB / 457.7 MB, free: 19.71 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0004065/0.4043, allocations: 0.9445 MB / 458.6 MB, free: 19 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 0.0002915/0.4046, allocations: 57.92 kB / 458.7 MB, free: 18.99 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.000326/0.4049, allocations: 281 kB / 458.9 MB, free: 18.77 MB / 350.1 MB
Notification: Performance of SimCode: time 8.71e-07/0.4049, allocations: 1.406 kB / 458.9 MB, free: 18.77 MB / 350.1 MB
Notification: Performance of buildModelFMU: Generate the FMI files: time 0.0261/0.431, allocations: 10.55 MB / 469.5 MB, free: 17.97 MB / 350.1 MB
Notification: Performance of buildModelFMU: configured platform static using cached values: time 0.0001433/0.4312, allocations: 182.3 kB / 469.7 MB, free: 17.72 MB / 350.1 MB
Notification: Performance of buildModelFMU: Generate platform static: time 2.022/2.454, allocations: 5.344 kB / 469.7 MB, free: 17.72 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)