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 0.001198/0.001198, allocations: 111.3 kB / 15.23 MB, free: 0.6406 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001283/0.001284, allocations: 195.3 kB / 16.14 MB, free: 6.688 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.275/1.275, allocations: 222.9 MB / 239.8 MB, free: 4.605 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.157/0.157, allocations: 12.27 MB / 302.2 MB, free: 1.344 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.00116/0.00116, allocations: 63.88 kB / 365.2 MB, free: 10.14 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.08487/0.08604, allocations: 52.07 MB / 417.3 MB, free: 5.953 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.1534/0.2395, allocations: 8.604 MB / 425.9 MB, free: 36.21 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.001398/0.2409, allocations: 0.8177 MB / 426.7 MB, free: 36.15 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0005779/0.2415, allocations: 43.31 kB / 426.7 MB, free: 36.15 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0003675/0.2419, allocations: 107.3 kB / 426.8 MB, free: 36.15 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0004937/0.2424, allocations: 165.6 kB / 427 MB, free: 36.15 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0003632/0.2428, allocations: 170.3 kB / 427.2 MB, free: 36.15 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0005008/0.2433, allocations: 0.7824 MB / 427.9 MB, free: 36.04 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.000548/0.2438, allocations: 479.5 kB / 428.4 MB, free: 35.98 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001883/0.244, allocations: 325.8 kB / 428.7 MB, free: 35.91 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.000255/0.2443, allocations: 409.1 kB / 429.1 MB, free: 35.8 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 8.253e-05/0.2444, allocations: 72.69 kB / 429.2 MB, free: 35.8 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001006/0.2445, allocations: 75.19 kB / 429.3 MB, free: 35.8 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 8.112e-05/0.2446, allocations: 180 kB / 429.5 MB, free: 35.77 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0002223/0.2448, allocations: 440.6 kB / 429.9 MB, free: 35.63 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0005386/0.2454, allocations: 1.11 MB / 431 MB, free: 35.29 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 3.346e-06/0.2454, allocations: 0.6562 kB / 431 MB, free: 35.29 MB / 350.1 MB
Notification: Performance of FrontEnd: time 7.52e-07/0.2454, allocations: 0 / 431 MB, free: 35.29 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 9.898e-06/0.2454, allocations: 1.281 kB / 431 MB, free: 35.29 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 0.001255/0.2466, allocations: 1.123 MB / 432.1 MB, free: 34.52 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.775e-05/0.2467, allocations: 6.969 kB / 432.1 MB, free: 34.52 MB / 350.1 MB
Notification: Performance of preOpt introduceOutputAliases (simulation): time 0.0001201/0.2468, allocations: 154 kB / 432.3 MB, free: 34.42 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.000105/0.2469, allocations: 94.69 kB / 432.4 MB, free: 34.38 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001669/0.2471, allocations: 307.3 kB / 432.7 MB, free: 34.09 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 4.14e-05/0.2472, allocations: 76.88 kB / 432.7 MB, free: 34.05 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 9.566e-05/0.2473, allocations: 105.8 kB / 432.8 MB, free: 34.02 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001062/0.2483, allocations: 0.8743 MB / 433.7 MB, free: 33.64 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.463e-05/0.2484, allocations: 16.03 kB / 433.7 MB, free: 33.63 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 5.808e-05/0.2484, allocations: 38.5 kB / 433.8 MB, free: 33.6 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.467e-05/0.2484, allocations: 26.62 kB / 433.8 MB, free: 33.6 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0008522/0.2493, allocations: 0.6216 MB / 434.4 MB, free: 33.38 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.003226/0.2525, allocations: 2.856 MB / 437.3 MB, free: 31.88 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0008064/0.2534, allocations: 0.5223 MB / 437.8 MB, free: 31.64 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003213/0.2537, allocations: 315 kB / 438.1 MB, free: 31.5 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.9e-05/0.2537, allocations: 9.625 kB / 438.1 MB, free: 31.5 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.424e-05/0.2537, allocations: 39.28 kB / 438.2 MB, free: 31.45 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=50): time 2.815e-06/0.2538, allocations: 1.125 kB / 438.2 MB, free: 31.45 MB / 350.1 MB
Notification: Performance of matching and sorting (n=59): time 0.004273/0.258, allocations: 2.174 MB / 440.3 MB, free: 30.45 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.718e-05/0.2581, allocations: 83.83 kB / 440.4 MB, free: 30.36 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002509/0.2583, allocations: 362.8 kB / 440.8 MB, free: 30.18 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 2.546e-05/0.2584, allocations: 33.7 kB / 440.8 MB, free: 30.14 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001408/0.2585, allocations: 453.4 kB / 441.2 MB, free: 29.79 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 9.069e-05/0.2586, allocations: 219.5 kB / 441.5 MB, free: 29.62 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001422/0.2588, allocations: 139.9 kB / 441.6 MB, free: 29.54 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 5.445e-05/0.2588, allocations: 359.3 kB / 441.9 MB, free: 29.21 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002951/0.2591, allocations: 251.8 kB / 442.2 MB, free: 29.1 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003399/0.2595, allocations: 484.6 kB / 442.7 MB, free: 28.68 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.005201/0.2647, allocations: 1.708 MB / 444.4 MB, free: 27.87 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.749e-06/0.2647, allocations: 7.094 kB / 444.4 MB, free: 27.87 MB / 350.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.0009153/0.2656, allocations: 0.7941 MB / 445.2 MB, free: 27.51 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.626e-05/0.2656, allocations: 11 kB / 445.2 MB, free: 27.51 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 9.388e-06/0.2656, allocations: 9.562 kB / 445.2 MB, free: 27.51 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 1.884e-05/0.2657, allocations: 16.62 kB / 445.2 MB, free: 27.51 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0005955/0.2663, allocations: 188.5 kB / 445.4 MB, free: 27.48 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.454e-05/0.2663, allocations: 21.08 kB / 445.4 MB, free: 27.48 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003337/0.2666, allocations: 38.78 kB / 445.5 MB, free: 27.46 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 3.832e-05/0.2667, allocations: 37.06 kB / 445.5 MB, free: 27.46 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 0.0003608/0.267, allocations: 284.6 kB / 445.8 MB, free: 27.24 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 8.177e-05/0.2671, allocations: 48.72 kB / 445.8 MB, free: 27.21 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.000108/0.2672, allocations: 69.02 kB / 445.9 MB, free: 27.16 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.149e-06/0.2673, allocations: 7.531 kB / 445.9 MB, free: 27.16 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 8.326e-06/0.2673, allocations: 4 kB / 445.9 MB, free: 27.16 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.59e-06/0.2673, allocations: 3.797 kB / 445.9 MB, free: 27.16 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0008304/0.2681, allocations: 0.7612 MB / 446.7 MB, free: 26.74 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.995e-06/0.2681, allocations: 3.234 kB / 446.7 MB, free: 26.74 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005145/0.2686, allocations: 105.2 kB / 446.8 MB, free: 26.73 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 3.366e-06/0.2687, allocations: 3.281 kB / 446.8 MB, free: 26.73 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.544e-05/0.2687, allocations: 17.95 kB / 446.8 MB, free: 26.72 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.505e-06/0.2687, allocations: 0 / 446.8 MB, free: 26.72 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.763e-06/0.2687, allocations: 3.188 kB / 446.8 MB, free: 26.72 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0009012/0.2696, allocations: 0.9371 MB / 447.7 MB, free: 26.18 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 5.374e-05/0.2697, allocations: 120.8 kB / 447.8 MB, free: 26.06 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.694e-05/0.2697, allocations: 11.16 kB / 447.9 MB, free: 26.05 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0003/0.27, allocations: 34.56 kB / 447.9 MB, free: 26.04 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.292e-05/0.2701, allocations: 37.95 kB / 447.9 MB, free: 26.03 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.577e-05/0.2701, allocations: 16.61 kB / 447.9 MB, free: 26.03 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 0.0001597/0.2703, allocations: 239.9 kB / 448.2 MB, free: 25.9 MB / 350.1 MB
Notification: Performance of sort global known variables: time 2e-07/0.2703, allocations: 0 / 448.2 MB, free: 25.9 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0005153/0.2708, allocations: 155.8 kB / 448.3 MB, free: 25.88 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 0.001028/0.2719, allocations: 1.491 MB / 449.8 MB, free: 24.8 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0006757/0.2726, allocations: 0.5947 MB / 450.4 MB, free: 24.58 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 1.663e-06/0.2726, allocations: 0 / 450.4 MB, free: 24.58 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0002679/0.2728, allocations: 261.5 kB / 450.7 MB, free: 24.48 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004618/0.2733, allocations: 57.92 kB / 450.7 MB, free: 24.46 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.005588/0.2789, allocations: 6.329 MB / 457.1 MB, free: 20.05 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0002778/0.2792, allocations: 0.9423 MB / 458 MB, free: 19.34 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 0.0002571/0.2795, allocations: 63.72 kB / 458.1 MB, free: 19.32 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0002808/0.2797, allocations: 280.6 kB / 458.3 MB, free: 19.11 MB / 350.1 MB
Notification: Performance of SimCode: time 4.31e-07/0.2797, allocations: 0 / 458.3 MB, free: 19.11 MB / 350.1 MB
Notification: Performance of buildModelFMU: Generate the FMI files: time 0.03327/0.313, allocations: 10.27 MB / 468.6 MB, free: 18.33 MB / 350.1 MB
Notification: Performance of buildModelFMU: configured platform static using cached values: time 0.0001398/0.3132, allocations: 201.7 kB / 468.8 MB, free: 18.07 MB / 350.1 MB
Notification: Performance of buildModelFMU: Generate platform static: time 1.873/2.186, allocations: 0 / 468.8 MB, free: 18.07 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)