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 0.001611/0.00161, allocations: 108 kB / 15.6 MB, free: 132 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.002126/0.002126, allocations: 195.1 kB / 16.53 MB, free: 6.391 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.704/1.704, allocations: 222.9 MB / 240.2 MB, free: 4.387 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.2581/0.2581, allocations: 12.27 MB / 302.7 MB, free: 1.297 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.001692/0.001693, allocations: 59.91 kB / 365.9 MB, free: 9.719 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.181/0.1827, allocations: 52.08 MB / 417.9 MB, free: 5.551 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.4073/0.59, allocations: 8.473 MB / 426.4 MB, free: 36.39 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.001938/0.592, allocations: 0.8137 MB / 427.2 MB, free: 36.29 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003643/0.5924, allocations: 38.81 kB / 427.3 MB, free: 36.29 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0003305/0.5928, allocations: 148.3 kB / 427.4 MB, free: 36.29 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0004794/0.5933, allocations: 198.1 kB / 427.6 MB, free: 36.25 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0004469/0.5938, allocations: 200.3 kB / 427.8 MB, free: 36.25 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0008027/0.5946, allocations: 0.8442 MB / 428.6 MB, free: 36.05 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0008229/0.5954, allocations: 0.5254 MB / 429.2 MB, free: 35.98 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0003221/0.5958, allocations: 370.2 kB / 429.5 MB, free: 35.9 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0004203/0.5962, allocations: 432.8 kB / 430 MB, free: 35.8 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001419/0.5963, allocations: 119.7 kB / 430.1 MB, free: 35.8 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001556/0.5965, allocations: 115.4 kB / 430.2 MB, free: 35.8 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001723/0.5967, allocations: 227.6 kB / 430.4 MB, free: 35.76 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0003729/0.5971, allocations: 485 kB / 430.9 MB, free: 35.45 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0009348/0.598, allocations: 1.144 MB / 432 MB, free: 34.97 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 8.205e-06/0.598, allocations: 0 / 432 MB, free: 34.97 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.973e-06/0.598, allocations: 0 / 432 MB, free: 34.97 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 2.543e-05/0.5981, allocations: 0 / 432 MB, free: 34.97 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 0.001964/0.6, allocations: 1.125 MB / 433.2 MB, free: 34.21 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 7.803e-05/0.6001, allocations: 8.594 kB / 433.2 MB, free: 34.21 MB / 350.1 MB
Notification: Performance of preOpt introduceOutputAliases (simulation): time 0.0001867/0.6003, allocations: 157 kB / 433.3 MB, free: 34.11 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001732/0.6005, allocations: 97.56 kB / 433.4 MB, free: 34.06 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0003537/0.6008, allocations: 302.7 kB / 433.7 MB, free: 33.77 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 7.733e-05/0.6009, allocations: 75.81 kB / 433.8 MB, free: 33.74 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001618/0.6011, allocations: 98.92 kB / 433.9 MB, free: 33.71 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.00144/0.6026, allocations: 0.8819 MB / 434.8 MB, free: 33.32 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 3.339e-05/0.6026, allocations: 7.844 kB / 434.8 MB, free: 33.32 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 8.278e-05/0.6027, allocations: 43.88 kB / 434.8 MB, free: 33.29 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.896e-05/0.6027, allocations: 24.75 kB / 434.8 MB, free: 33.29 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001048/0.6038, allocations: 0.6171 MB / 435.4 MB, free: 33.06 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.004333/0.6081, allocations: 2.873 MB / 438.3 MB, free: 31.52 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0009315/0.6091, allocations: 0.5207 MB / 438.8 MB, free: 31.28 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0004065/0.6095, allocations: 316.6 kB / 439.1 MB, free: 31.14 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 2.835e-05/0.6095, allocations: 7.094 kB / 439.2 MB, free: 31.14 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.707e-05/0.6096, allocations: 43.06 kB / 439.2 MB, free: 31.1 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=50): time 2.064e-06/0.6096, allocations: 0 / 439.2 MB, free: 31.1 MB / 350.1 MB
Notification: Performance of matching and sorting (n=59): time 0.005014/0.6146, allocations: 2.177 MB / 441.4 MB, free: 30.1 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.327e-05/0.6147, allocations: 84.23 kB / 441.5 MB, free: 30 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.000421/0.6151, allocations: 358.8 kB / 441.8 MB, free: 29.82 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 3.949e-05/0.6152, allocations: 32.45 kB / 441.8 MB, free: 29.79 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.000307/0.6155, allocations: 452.4 kB / 442.3 MB, free: 29.43 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001913/0.6157, allocations: 219.2 kB / 442.5 MB, free: 29.26 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002163/0.6159, allocations: 136.2 kB / 442.6 MB, free: 29.18 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001532/0.6161, allocations: 363 kB / 443 MB, free: 28.85 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003917/0.6165, allocations: 253.6 kB / 443.2 MB, free: 28.74 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0004862/0.617, allocations: 477.2 kB / 443.7 MB, free: 28.32 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.005532/0.6225, allocations: 1.724 MB / 445.4 MB, free: 27.5 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.082e-05/0.6225, allocations: 8.5 kB / 445.4 MB, free: 27.49 MB / 350.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.001317/0.6238, allocations: 0.7941 MB / 446.2 MB, free: 27.14 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 2.955e-05/0.6239, allocations: 11.16 kB / 446.2 MB, free: 27.13 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.718e-05/0.6239, allocations: 9.812 kB / 446.2 MB, free: 27.13 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 3.78e-05/0.624, allocations: 13.03 kB / 446.3 MB, free: 27.13 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006635/0.6246, allocations: 189.3 kB / 446.4 MB, free: 27.11 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 2.518e-05/0.6247, allocations: 20.31 kB / 446.5 MB, free: 27.11 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003003/0.625, allocations: 29 kB / 446.5 MB, free: 27.09 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 5.344e-05/0.625, allocations: 33.22 kB / 446.5 MB, free: 27.09 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 0.000674/0.6257, allocations: 282 kB / 446.8 MB, free: 26.87 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001198/0.6258, allocations: 46.31 kB / 446.8 MB, free: 26.84 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.000161/0.626, allocations: 76.66 kB / 446.9 MB, free: 26.79 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 8.015e-06/0.626, allocations: 3.281 kB / 446.9 MB, free: 26.79 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.408e-05/0.6261, allocations: 3.156 kB / 446.9 MB, free: 26.79 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.017e-05/0.6261, allocations: 3.328 kB / 446.9 MB, free: 26.79 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001254/0.6273, allocations: 0.7577 MB / 447.7 MB, free: 26.37 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.509e-06/0.6273, allocations: 3.188 kB / 447.7 MB, free: 26.37 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005563/0.6279, allocations: 115.2 kB / 447.8 MB, free: 26.35 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 4.819e-06/0.6279, allocations: 3.031 kB / 447.8 MB, free: 26.35 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 4.118e-05/0.628, allocations: 11.22 kB / 447.8 MB, free: 26.34 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 5.119e-06/0.628, allocations: 3.031 kB / 447.8 MB, free: 26.34 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.198e-06/0.628, allocations: 3.938 kB / 447.8 MB, free: 26.34 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.00137/0.6294, allocations: 0.9341 MB / 448.8 MB, free: 25.81 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 9.686e-05/0.6295, allocations: 116.9 kB / 448.9 MB, free: 25.69 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.824e-05/0.6295, allocations: 18.22 kB / 448.9 MB, free: 25.68 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002646/0.6298, allocations: 8 kB / 448.9 MB, free: 25.67 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 8.075e-05/0.6299, allocations: 41.23 kB / 448.9 MB, free: 25.66 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.286e-05/0.6299, allocations: 19 kB / 449 MB, free: 25.66 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 0.0002277/0.6302, allocations: 234.2 kB / 449.2 MB, free: 25.54 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1e-07/0.6302, allocations: 0 / 449.2 MB, free: 25.54 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0006292/0.6308, allocations: 161.2 kB / 449.3 MB, free: 25.51 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 0.001554/0.6324, allocations: 1.488 MB / 450.8 MB, free: 24.44 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.001175/0.6336, allocations: 0.6244 MB / 451.5 MB, free: 24.2 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 3.055e-06/0.6336, allocations: 1.812 kB / 451.5 MB, free: 24.2 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0003459/0.6339, allocations: 256.1 kB / 451.7 MB, free: 24.1 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005352/0.6345, allocations: 70.66 kB / 451.8 MB, free: 24.07 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.007734/0.6422, allocations: 5.941 MB / 457.7 MB, free: 20.05 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0005832/0.6428, allocations: 0.9408 MB / 458.7 MB, free: 19.34 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 0.0003104/0.6431, allocations: 59.73 kB / 458.7 MB, free: 19.33 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003872/0.6435, allocations: 282.1 kB / 459 MB, free: 19.12 MB / 350.1 MB
Notification: Performance of SimCode: time 6.41e-07/0.6435, allocations: 0 / 459 MB, free: 19.12 MB / 350.1 MB
Notification: Performance of buildModelFMU: Generate the FMI files: time 0.04229/0.6858, allocations: 10.64 MB / 469.6 MB, free: 18.2 MB / 350.1 MB
Notification: Performance of buildModelFMU: Generate platform static: time 9.725/10.41, allocations: 3.031 kB / 469.6 MB, free: 18.2 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)