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/package.mo", uses=false)
Using package BioChem with version 1.1.2 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2/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 0.0008933/0.0008927, allocations: 100.8 kB / 15.06 MB, free: 1.094 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001033/0.001033, allocations: 177.3 kB / 15.95 MB, free: 208 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.31/1.31, allocations: 223.2 MB / 239.9 MB, free: 5.465 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2/package.mo): time 0.1892/0.1892, allocations: 12.19 MB / 303.2 MB, free: 1.875 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0003245/0.0003246, allocations: 8 kB / 366.9 MB, free: 9.586 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1115/0.1119, allocations: 53.08 MB / 419.9 MB, free: 4.418 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.2112/0.3231, allocations: 7.253 MB / 427.2 MB, free: 34.86 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.001712/0.3248, allocations: 0.8587 MB / 428 MB, free: 34.68 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003211/0.3252, allocations: 43.16 kB / 428.1 MB, free: 34.68 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0001994/0.3254, allocations: 113.4 kB / 428.2 MB, free: 34.64 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0003602/0.3257, allocations: 196.2 kB / 428.4 MB, free: 34.63 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0002781/0.326, allocations: 114.2 kB / 428.5 MB, free: 34.63 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.000551/0.3266, allocations: 0.5431 MB / 429 MB, free: 34.6 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.000532/0.3271, allocations: 413.1 kB / 429.4 MB, free: 34.56 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002107/0.3273, allocations: 241.7 kB / 429.7 MB, free: 34.5 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002644/0.3276, allocations: 311.3 kB / 430 MB, free: 34.42 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 6.747e-05/0.3277, allocations: 43.17 kB / 430 MB, free: 34.42 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 8.056e-05/0.3278, allocations: 46 kB / 430.1 MB, free: 34.41 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 8.214e-05/0.3279, allocations: 136.5 kB / 430.2 MB, free: 34.38 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0001161/0.328, allocations: 180.5 kB / 430.4 MB, free: 34.32 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0006246/0.3286, allocations: 0.8719 MB / 431.3 MB, free: 34.27 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 2.725e-06/0.3286, allocations: 1.75 kB / 431.3 MB, free: 34.27 MB / 350.1 MB
Notification: Performance of FrontEnd: time 2.244e-06/0.3286, allocations: 0.5312 kB / 431.3 MB, free: 34.27 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 1.02e-05/0.3287, allocations: 0.9062 kB / 431.3 MB, free: 34.27 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 0.001201/0.3299, allocations: 0.9514 MB / 432.2 MB, free: 33.68 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 4.821e-05/0.3299, allocations: 9.75 kB / 432.2 MB, free: 33.68 MB / 350.1 MB
Notification: Performance of preOpt introduceOutputAliases (simulation): time 0.0001597/0.3301, allocations: 149.2 kB / 432.4 MB, free: 33.64 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001254/0.3302, allocations: 99.16 kB / 432.5 MB, free: 33.59 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002552/0.3305, allocations: 298.2 kB / 432.8 MB, free: 33.32 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 5.15e-05/0.3305, allocations: 71.53 kB / 432.8 MB, free: 33.32 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001153/0.3307, allocations: 102.9 kB / 432.9 MB, free: 33.31 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001199/0.3319, allocations: 0.8611 MB / 433.8 MB, free: 33.24 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.579e-05/0.3319, allocations: 2.125 kB / 433.8 MB, free: 33.24 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 7.006e-05/0.332, allocations: 42.34 kB / 433.8 MB, free: 33.24 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.623e-05/0.332, allocations: 25.73 kB / 433.9 MB, free: 33.23 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0008963/0.3329, allocations: 0.6207 MB / 434.5 MB, free: 33.22 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.00356/0.3365, allocations: 2.839 MB / 437.3 MB, free: 32.14 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0007713/0.3373, allocations: 0.5129 MB / 437.8 MB, free: 31.91 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.686e-05/0.3373, allocations: 3.781 kB / 437.8 MB, free: 31.91 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.655e-05/0.3373, allocations: 44.8 kB / 437.9 MB, free: 31.86 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=50): time 1.883e-06/0.3373, allocations: 1.5 kB / 437.9 MB, free: 31.86 MB / 350.1 MB
Notification: Performance of matching and sorting (n=59): time 0.00432/0.3417, allocations: 2.168 MB / 440 MB, free: 30.88 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.343e-05/0.3417, allocations: 83.95 kB / 440.1 MB, free: 30.79 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002969/0.342, allocations: 367.6 kB / 440.5 MB, free: 30.59 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 3.094e-05/0.3421, allocations: 37.02 kB / 440.5 MB, free: 30.55 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001676/0.3422, allocations: 441.2 kB / 441 MB, free: 30.21 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001113/0.3423, allocations: 220.9 kB / 441.2 MB, free: 30.04 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 2.468e-05/0.3424, allocations: 15.69 kB / 441.2 MB, free: 30.03 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 7.441e-05/0.3425, allocations: 363.1 kB / 441.5 MB, free: 29.69 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002913/0.3428, allocations: 248.7 kB / 441.8 MB, free: 29.59 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003435/0.3431, allocations: 479.5 kB / 442.2 MB, free: 29.16 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0003489/0.3435, allocations: 304.9 kB / 442.5 MB, free: 29 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.577e-06/0.3435, allocations: 7.438 kB / 442.6 MB, free: 29 MB / 350.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.0009006/0.3444, allocations: 0.7986 MB / 443.4 MB, free: 28.62 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.905e-05/0.3444, allocations: 10.19 kB / 443.4 MB, free: 28.62 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.129e-05/0.3444, allocations: 9.781 kB / 443.4 MB, free: 28.62 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 2.163e-05/0.3445, allocations: 12.44 kB / 443.4 MB, free: 28.62 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006055/0.3451, allocations: 183.5 kB / 443.6 MB, free: 28.61 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.788e-05/0.3451, allocations: 21.8 kB / 443.6 MB, free: 28.61 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003455/0.3454, allocations: 50.73 kB / 443.6 MB, free: 28.58 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.1e-05/0.3455, allocations: 39.41 kB / 443.7 MB, free: 28.57 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 0.0004176/0.3459, allocations: 278.9 kB / 443.9 MB, free: 28.36 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 8.024e-05/0.346, allocations: 46.88 kB / 444 MB, free: 28.33 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001146/0.3461, allocations: 71.72 kB / 444.1 MB, free: 28.27 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.422e-06/0.3461, allocations: 6.406 kB / 444.1 MB, free: 28.27 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.352e-05/0.3462, allocations: 0 / 444.1 MB, free: 28.27 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.923e-06/0.3462, allocations: 3.938 kB / 444.1 MB, free: 28.27 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0008786/0.3471, allocations: 0.761 MB / 444.8 MB, free: 27.87 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.875e-06/0.3471, allocations: 0 / 444.8 MB, free: 27.87 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0004917/0.3476, allocations: 108.9 kB / 444.9 MB, free: 27.86 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 4.238e-06/0.3476, allocations: 3.062 kB / 444.9 MB, free: 27.86 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.174e-05/0.3476, allocations: 21.48 kB / 445 MB, free: 27.84 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.338e-06/0.3476, allocations: 5.25 kB / 445 MB, free: 27.84 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.202e-06/0.3476, allocations: 0 / 445 MB, free: 27.84 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0008805/0.3485, allocations: 0.9444 MB / 445.9 MB, free: 27.29 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 6.526e-05/0.3486, allocations: 120.7 kB / 446 MB, free: 27.17 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.686e-05/0.3486, allocations: 16.67 kB / 446 MB, free: 27.16 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002848/0.3489, allocations: 32.22 kB / 446.1 MB, free: 27.14 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.268e-05/0.349, allocations: 38.41 kB / 446.1 MB, free: 27.14 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.425e-05/0.349, allocations: 17.78 kB / 446.1 MB, free: 27.13 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 0.0001573/0.3492, allocations: 233.9 kB / 446.4 MB, free: 27 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.1e-07/0.3492, allocations: 0 / 446.4 MB, free: 27 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0005302/0.3497, allocations: 161.9 kB / 446.5 MB, free: 26.98 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 0.001019/0.3508, allocations: 1.566 MB / 448.1 MB, free: 25.82 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0006615/0.3514, allocations: 0.593 MB / 448.7 MB, free: 25.6 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.545e-06/0.3514, allocations: 0 / 448.7 MB, free: 25.6 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0002572/0.3517, allocations: 264.6 kB / 448.9 MB, free: 25.5 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.000312/0.352, allocations: 55.88 kB / 449 MB, free: 25.48 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.005718/0.3578, allocations: 9.916 MB / 458.9 MB, free: 17.1 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0003405/0.3581, allocations: 0.957 MB / 459.9 MB, free: 16.38 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 0.0002636/0.3584, allocations: 70.28 kB / 459.9 MB, free: 16.36 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0002798/0.3587, allocations: 278.8 kB / 460.2 MB, free: 16.15 MB / 350.1 MB
Notification: Performance of SimCode: time 4.6e-07/0.3587, allocations: 3.938 kB / 460.2 MB, free: 16.15 MB / 350.1 MB
Notification: Performance of buildModelFMU: Generate the FMI files: time 0.01896/0.3777, allocations: 9.887 MB / 470.1 MB, free: 15.51 MB / 350.1 MB
Notification: Performance of buildModelFMU: configured platform static using cached values: time 0.0001716/0.3779, allocations: 170.9 kB / 470.3 MB, free: 15.27 MB / 350.1 MB
Notification: Performance of buildModelFMU: Generate platform static: time 1.763/2.141, allocations: 0 / 470.3 MB, free: 15.27 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/linux/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)
Environment - environmentSimulation: