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: translateModel(BioChem.Examples.CircadianOscillator.Container,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CircadianOscillator.Container")
translateModel(BioChem.Examples.CircadianOscillator.Container,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CircadianOscillator.Container")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.009169/0.009169, allocations: 100.2 kB / 15.87 MB, free: 6.297 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.00217/0.00217, allocations: 201.3 kB / 16.79 MB, free: 6.223 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.819/1.819, allocations: 222.9 MB / 240.5 MB, free: 4.594 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.2365/0.2365, allocations: 12.27 MB / 302.9 MB, free: 1.367 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.002058/0.002058, allocations: 56.12 kB / 365.7 MB, free: 10.23 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1543/0.1564, allocations: 52.08 MB / 417.8 MB, free: 6.039 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.3174/0.4738, allocations: 8.602 MB / 426.4 MB, free: 36.14 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.002692/0.4766, allocations: 0.814 MB / 427.2 MB, free: 36.07 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.001066/0.4777, allocations: 43.97 kB / 427.3 MB, free: 36.07 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.000824/0.4786, allocations: 106.5 kB / 427.4 MB, free: 36.07 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.001415/0.48, allocations: 164 kB / 427.5 MB, free: 36.07 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0008583/0.4809, allocations: 172.1 kB / 427.7 MB, free: 36.07 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.001313/0.4822, allocations: 0.7885 MB / 428.5 MB, free: 35.96 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.001043/0.4833, allocations: 483 kB / 429 MB, free: 35.91 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0004954/0.4838, allocations: 321.9 kB / 429.3 MB, free: 35.84 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.0004728/0.4843, allocations: 406.9 kB / 429.7 MB, free: 35.73 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 0.0001343/0.4845, allocations: 72.91 kB / 429.8 MB, free: 35.73 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001611/0.4846, allocations: 74.84 kB / 429.8 MB, free: 35.73 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 0.0001544/0.4848, allocations: 182.1 kB / 430 MB, free: 35.69 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0004511/0.4853, allocations: 447.3 kB / 430.4 MB, free: 35.55 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.000865/0.4861, allocations: 0.9027 MB / 431.3 MB, free: 35.35 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 7.745e-06/0.4862, allocations: 1.656 kB / 431.3 MB, free: 35.35 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.693e-06/0.4862, allocations: 0.75 kB / 431.3 MB, free: 35.35 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 2.357e-05/0.4862, allocations: 4.062 kB / 431.4 MB, free: 35.35 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 0.002414/0.4887, allocations: 1.12 MB / 432.5 MB, free: 34.59 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 5.643e-05/0.4887, allocations: 6.531 kB / 432.5 MB, free: 34.59 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0002259/0.489, allocations: 101.1 kB / 432.6 MB, free: 34.54 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0003377/0.4893, allocations: 308.1 kB / 432.9 MB, free: 34.26 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 6.271e-05/0.4894, allocations: 74 kB / 432.9 MB, free: 34.22 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001755/0.4896, allocations: 97.78 kB / 433 MB, free: 34.19 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002041/0.4916, allocations: 0.8801 MB / 433.9 MB, free: 33.82 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 4.807e-05/0.4917, allocations: 8.031 kB / 433.9 MB, free: 33.81 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001031/0.4918, allocations: 49.31 kB / 434 MB, free: 33.77 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.524e-05/0.4919, allocations: 24.09 kB / 434 MB, free: 33.77 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001647/0.4935, allocations: 0.6175 MB / 434.6 MB, free: 33.55 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.006457/0.5, allocations: 2.858 MB / 437.5 MB, free: 32.05 MB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.001456/0.5015, allocations: 0.5223 MB / 438 MB, free: 31.81 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0006159/0.5021, allocations: 315.2 kB / 438.3 MB, free: 31.68 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 4.41e-05/0.5022, allocations: 3.75 kB / 438.3 MB, free: 31.68 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.928e-05/0.5022, allocations: 39.41 kB / 438.4 MB, free: 31.63 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=50): time 4.339e-06/0.5023, allocations: 0 / 438.4 MB, free: 31.63 MB / 350.1 MB
Notification: Performance of matching and sorting (n=59): time 0.008174/0.5104, allocations: 2.175 MB / 440.5 MB, free: 30.63 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.388e-05/0.5105, allocations: 84.64 kB / 440.6 MB, free: 30.54 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0005545/0.5111, allocations: 359.7 kB / 441 MB, free: 30.35 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 5.365e-05/0.5112, allocations: 32.92 kB / 441 MB, free: 30.32 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 0.0003131/0.5115, allocations: 457.1 kB / 441.4 MB, free: 29.96 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 0.0001861/0.5117, allocations: 223.6 kB / 441.7 MB, free: 29.79 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002923/0.512, allocations: 138.9 kB / 441.8 MB, free: 29.71 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 0.0001268/0.5122, allocations: 354.7 kB / 442.1 MB, free: 29.38 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0005832/0.5128, allocations: 253 kB / 442.4 MB, free: 29.28 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0007398/0.5135, allocations: 482.6 kB / 442.9 MB, free: 28.86 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.009267/0.5228, allocations: 1.706 MB / 444.6 MB, free: 28.06 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 9.958e-06/0.5229, allocations: 3.031 kB / 444.6 MB, free: 28.06 MB / 350.1 MB
Notification: Performance of matching and sorting (n=107) (initialization): time 0.00203/0.5249, allocations: 0.8031 MB / 445.4 MB, free: 27.69 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 3.312e-05/0.525, allocations: 9.438 kB / 445.4 MB, free: 27.69 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 2.046e-05/0.525, allocations: 9.312 kB / 445.4 MB, free: 27.69 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 4.052e-05/0.5251, allocations: 14 kB / 445.4 MB, free: 27.69 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001144/0.5262, allocations: 182.5 kB / 445.6 MB, free: 27.68 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 3.161e-05/0.5263, allocations: 24.44 kB / 445.6 MB, free: 27.67 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0007895/0.5271, allocations: 42.12 kB / 445.6 MB, free: 27.65 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 7.653e-05/0.5272, allocations: 35.41 kB / 445.7 MB, free: 27.64 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 0.0008505/0.528, allocations: 286.8 kB / 446 MB, free: 27.43 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001792/0.5282, allocations: 44.41 kB / 446 MB, free: 27.4 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001897/0.5284, allocations: 70.19 kB / 446.1 MB, free: 27.35 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.047e-05/0.5284, allocations: 10.3 kB / 446.1 MB, free: 27.35 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.794e-05/0.5285, allocations: 3.156 kB / 446.1 MB, free: 27.35 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 8.396e-06/0.5285, allocations: 0 / 446.1 MB, free: 27.35 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001677/0.5302, allocations: 0.7705 MB / 446.9 MB, free: 26.93 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 7.434e-06/0.5302, allocations: 0 / 446.9 MB, free: 26.93 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0009945/0.5312, allocations: 111.2 kB / 447 MB, free: 26.92 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 1.061e-05/0.5312, allocations: 0 / 447 MB, free: 26.92 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 6.44e-05/0.5313, allocations: 14.25 kB / 447 MB, free: 26.91 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 9.749e-06/0.5313, allocations: 12.81 kB / 447 MB, free: 26.91 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.386e-06/0.5314, allocations: 0 / 447 MB, free: 26.91 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001799/0.5332, allocations: 0.9272 MB / 447.9 MB, free: 26.38 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 0.0001567/0.5333, allocations: 120.3 kB / 448 MB, free: 26.26 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001032/0.5335, allocations: 19.19 kB / 448.1 MB, free: 26.25 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0005647/0.534, allocations: 31.72 kB / 448.1 MB, free: 26.23 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001066/0.5342, allocations: 38.95 kB / 448.1 MB, free: 26.23 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 4.953e-05/0.5342, allocations: 13.12 kB / 448.1 MB, free: 26.22 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 0.0003597/0.5346, allocations: 239 kB / 448.4 MB, free: 26.09 MB / 350.1 MB
Notification: Performance of sort global known variables: time 3.21e-07/0.5346, allocations: 0 / 448.4 MB, free: 26.09 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.001185/0.5358, allocations: 159.9 kB / 448.5 MB, free: 26.07 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 0.000171/0.536, allocations: 117.1 kB / 448.6 MB, free: 25.96 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.001406/0.5374, allocations: 0.5896 MB / 449.2 MB, free: 25.75 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 3.947e-06/0.5374, allocations: 0 / 449.2 MB, free: 25.75 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0005382/0.538, allocations: 262.5 kB / 449.5 MB, free: 25.65 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0009304/0.5389, allocations: 67.5 kB / 449.6 MB, free: 25.61 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.004998/0.5439, allocations: 2.219 MB / 451.8 MB, free: 24.09 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0005108/0.5445, allocations: 0.9394 MB / 452.7 MB, free: 23.37 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003436/0.5449, allocations: 48.84 kB / 452.8 MB, free: 23.36 MB / 350.1 MB
Notification: Performance of SimCode: time 8.72e-07/0.5449, allocations: 3.094 kB / 452.8 MB, free: 23.36 MB / 350.1 MB
Notification: Performance of Templates: time 0.01642/0.5613, allocations: 7.412 MB / 460.2 MB, free: 22.53 MB / 350.1 MB
make -j1 -f BioChem_BioChem.Examples.CircadianOscillator.Container.makefile
(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 & ./BioChem_BioChem.Examples.CircadianOscillator.Container  -abortSlowSimulation -alarm=480 -lv LOG_STATS > BioChem_BioChem.Examples.CircadianOscillator.Container.pipe 2>&1)