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 0.001076/0.001076, allocations: 86.25 kB / 15.06 MB, free: 1.09 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001322/0.001322, allocations: 168.7 kB / 15.95 MB, free: 204 kB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.37/1.37, allocations: 223.2 MB / 240 MB, free: 5.312 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2/package.mo): time 0.1731/0.1731, allocations: 12.21 MB / 303.3 MB, free: 1.918 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.0004746/0.0004748, allocations: 8 kB / 367 MB, free: 9.551 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1136/0.1141, allocations: 53.08 MB / 420.1 MB, free: 4.383 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.194/0.3081, allocations: 7.67 MB / 427.7 MB, free: 35.02 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.001475/0.3096, allocations: 0.813 MB / 428.5 MB, free: 34.84 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0002419/0.3099, allocations: 40.62 kB / 428.6 MB, free: 34.84 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0001552/0.3101, allocations: 108.5 kB / 428.7 MB, free: 34.8 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0003658/0.3104, allocations: 166.6 kB / 428.8 MB, free: 34.73 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0004102/0.3109, allocations: 127.1 kB / 429 MB, free: 34.73 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0006713/0.3116, allocations: 0.7629 MB / 429.7 MB, free: 34.54 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0005689/0.3121, allocations: 407.4 kB / 430.1 MB, free: 34.5 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001803/0.3123, allocations: 254.9 kB / 430.4 MB, free: 34.43 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002606/0.3126, allocations: 314.8 kB / 430.7 MB, free: 34.34 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 6.135e-05/0.3127, allocations: 41.03 kB / 430.7 MB, free: 34.34 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 7.682e-05/0.3127, allocations: 40.06 kB / 430.8 MB, free: 34.34 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 8.268e-05/0.3128, allocations: 131.4 kB / 430.9 MB, free: 34.31 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 9.666e-05/0.3129, allocations: 179.9 kB / 431.1 MB, free: 34.25 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0006711/0.3136, allocations: 0.8759 MB / 431.9 MB, free: 34.2 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 6.583e-06/0.3136, allocations: 3.328 kB / 431.9 MB, free: 34.2 MB / 350.1 MB
Notification: Performance of FrontEnd: time 2.004e-06/0.3136, allocations: 1.062 kB / 431.9 MB, free: 34.2 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 9.969e-06/0.3137, allocations: 0 / 431.9 MB, free: 34.2 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 0.001113/0.3148, allocations: 0.9521 MB / 432.9 MB, free: 33.61 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 3.561e-05/0.3148, allocations: 11.88 kB / 432.9 MB, free: 33.61 MB / 350.1 MB
Notification: Performance of preOpt introduceOutputAliases (simulation): time 0.0001179/0.3149, allocations: 155.5 kB / 433.1 MB, free: 33.57 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001025/0.3151, allocations: 93.47 kB / 433.2 MB, free: 33.52 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0003006/0.3154, allocations: 297.6 kB / 433.4 MB, free: 33.25 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 4.544e-05/0.3154, allocations: 74.62 kB / 433.5 MB, free: 33.25 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.000104/0.3155, allocations: 98.81 kB / 433.6 MB, free: 33.24 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001138/0.3167, allocations: 0.8718 MB / 434.5 MB, free: 33.16 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 2.439e-05/0.3167, allocations: 1.125 kB / 434.5 MB, free: 33.16 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 6.069e-05/0.3168, allocations: 42.09 kB / 434.5 MB, free: 33.16 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.528e-05/0.3168, allocations: 26.27 kB / 434.6 MB, free: 33.16 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0009884/0.3178, allocations: 0.6134 MB / 435.2 MB, free: 33.15 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.003584/0.3214, allocations: 2.843 MB / 438 MB, free: 32.04 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.0007816/0.3222, allocations: 0.5142 MB / 438.5 MB, free: 31.8 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0003678/0.3226, allocations: 323.7 kB / 438.8 MB, free: 31.66 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 3.158e-05/0.3226, allocations: 6.875 kB / 438.8 MB, free: 31.66 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.238e-05/0.3227, allocations: 46.89 kB / 438.9 MB, free: 31.61 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=50): time 1.904e-06/0.3227, allocations: 3.125 kB / 438.9 MB, free: 31.61 MB / 350.1 MB
Notification: Performance of matching and sorting (n=59): time 0.004202/0.3269, allocations: 2.161 MB / 441.1 MB, free: 30.62 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.148e-05/0.3269, allocations: 91.41 kB / 441.1 MB, free: 30.52 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002549/0.3272, allocations: 366.3 kB / 441.5 MB, free: 30.33 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 2.522e-05/0.3272, allocations: 33.7 kB / 441.5 MB, free: 30.29 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0001448/0.3274, allocations: 445.6 kB / 442 MB, free: 29.95 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 9.537e-05/0.3275, allocations: 217.3 kB / 442.2 MB, free: 29.78 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 2.524e-05/0.3275, allocations: 16.72 kB / 442.2 MB, free: 29.77 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 6.588e-05/0.3276, allocations: 364.4 kB / 442.6 MB, free: 29.43 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.000356/0.3279, allocations: 245.5 kB / 442.8 MB, free: 29.33 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003497/0.3283, allocations: 483.3 kB / 443.3 MB, free: 28.9 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0003653/0.3287, allocations: 303.5 kB / 443.6 MB, free: 28.74 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.677e-06/0.3287, allocations: 3.719 kB / 443.6 MB, free: 28.74 MB / 350.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.0009393/0.3296, allocations: 0.7942 MB / 444.4 MB, free: 28.37 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 1.827e-05/0.3297, allocations: 9.688 kB / 444.4 MB, free: 28.37 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.116e-05/0.3297, allocations: 8.5 kB / 444.4 MB, free: 28.37 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 4.237e-05/0.3297, allocations: 16.25 kB / 444.4 MB, free: 28.37 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006585/0.3304, allocations: 187.5 kB / 444.6 MB, free: 28.35 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 2.059e-05/0.3304, allocations: 19.34 kB / 444.6 MB, free: 28.34 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0002982/0.3307, allocations: 49.84 kB / 444.6 MB, free: 28.32 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 3.961e-05/0.3308, allocations: 38.81 kB / 444.7 MB, free: 28.31 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 0.0003493/0.3311, allocations: 278.4 kB / 445 MB, free: 28.1 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 7.607e-05/0.3312, allocations: 47.97 kB / 445 MB, free: 28.08 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.000141/0.3314, allocations: 69.19 kB / 445.1 MB, free: 28.02 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.348e-06/0.3314, allocations: 6.188 kB / 445.1 MB, free: 28.02 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 7.394e-06/0.3314, allocations: 0 / 445.1 MB, free: 28.02 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.863e-06/0.3314, allocations: 10.66 kB / 445.1 MB, free: 28.02 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0009093/0.3323, allocations: 0.7631 MB / 445.9 MB, free: 27.61 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.535e-06/0.3323, allocations: 4 kB / 445.9 MB, free: 27.6 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0004932/0.3328, allocations: 106.4 kB / 446 MB, free: 27.59 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 5.34e-06/0.3328, allocations: 3.344 kB / 446 MB, free: 27.59 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.461e-05/0.3329, allocations: 18.48 kB / 446 MB, free: 27.58 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.388e-06/0.3329, allocations: 5.344 kB / 446 MB, free: 27.58 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.142e-06/0.3329, allocations: 0 / 446 MB, free: 27.58 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0009805/0.3339, allocations: 0.9319 MB / 446.9 MB, free: 27.05 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 5.25e-05/0.334, allocations: 122.2 kB / 447 MB, free: 26.93 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.464e-05/0.334, allocations: 14 kB / 447.1 MB, free: 26.92 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002748/0.3343, allocations: 27.45 kB / 447.1 MB, free: 26.91 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.033e-05/0.3344, allocations: 34.47 kB / 447.1 MB, free: 26.91 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.463e-05/0.3344, allocations: 20.72 kB / 447.1 MB, free: 26.9 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 0.0001636/0.3346, allocations: 241 kB / 447.4 MB, free: 26.77 MB / 350.1 MB
Notification: Performance of sort global known variables: time 1.31e-07/0.3346, allocations: 0 / 447.4 MB, free: 26.77 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0005163/0.3351, allocations: 154.8 kB / 447.5 MB, free: 26.75 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 0.00116/0.3363, allocations: 1.487 MB / 449 MB, free: 25.67 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0006716/0.3369, allocations: 0.5913 MB / 449.6 MB, free: 25.46 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.645e-06/0.337, allocations: 0.6875 kB / 449.6 MB, free: 25.46 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0002777/0.3372, allocations: 267.8 kB / 449.9 MB, free: 25.35 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004571/0.3377, allocations: 66.22 kB / 449.9 MB, free: 25.31 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.004793/0.3425, allocations: 4.203 MB / 454.1 MB, free: 22.68 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0002909/0.3428, allocations: 0.9362 MB / 455.1 MB, free: 21.97 MB / 350.1 MB
Notification: Performance of simCode: alias equations: time 0.0002567/0.3431, allocations: 68.16 kB / 455.1 MB, free: 21.95 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003023/0.3434, allocations: 276.9 kB / 455.4 MB, free: 21.73 MB / 350.1 MB
Notification: Performance of SimCode: time 6.21e-07/0.3434, allocations: 0 / 455.4 MB, free: 21.73 MB / 350.1 MB
Notification: Performance of buildModelFMU: Generate the FMI files: time 0.02173/0.3651, allocations: 9.918 MB / 465.3 MB, free: 21.1 MB / 350.1 MB
Notification: Performance of buildModelFMU: configured platform static using cached values: time 0.0001223/0.3653, allocations: 173.6 kB / 465.5 MB, free: 20.86 MB / 350.1 MB
Notification: Performance of buildModelFMU: Generate platform static: time 2.018/2.383, allocations: 11.88 kB / 465.5 MB, free: 20.85 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: