Running: ./testmodel.py --libraries=/var/lib/jenkins/ws/OpenModelicaLibraryTestingWork/OpenModelicaLibraryTesting/converted-libraries/.openmodelica/libraries/ --ompython_omhome=/usr BioChem_BioChem.Examples.CircadianOscillator.Container.conf.json loadFile("/var/lib/jenkins/ws/OpenModelicaLibraryTestingWork/OpenModelicaLibraryTesting/converted-libraries/.openmodelica/libraries/BioChem 1.1.2/package.mo", uses=false) loadFile("/var/lib/jenkins/ws/OpenModelicaLibraryTestingWork/OpenModelicaLibraryTesting/converted-libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo", uses=false) loadFile("/var/lib/jenkins/ws/OpenModelicaLibraryTestingWork/OpenModelicaLibraryTesting/converted-libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo", uses=false) loadFile("/var/lib/jenkins/ws/OpenModelicaLibraryTestingWork/OpenModelicaLibraryTesting/converted-libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo", uses=false) Using package ModelicaServices with version 4.0.0 (/var/lib/jenkins/ws/OpenModelicaLibraryTestingWork/OpenModelicaLibraryTesting/converted-libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo) Using package Modelica with version 4.0.0 (/var/lib/jenkins/ws/OpenModelicaLibraryTestingWork/OpenModelicaLibraryTesting/converted-libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo) Using package Complex with version 4.0.0 (/var/lib/jenkins/ws/OpenModelicaLibraryTestingWork/OpenModelicaLibraryTesting/converted-libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo) Using package BioChem with version 1.1.2 (/var/lib/jenkins/ws/OpenModelicaLibraryTestingWork/OpenModelicaLibraryTesting/converted-libraries/.openmodelica/libraries/BioChem 1.1.2/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(/var/lib/jenkins/ws/OpenModelicaLibraryTestingWork/OpenModelicaLibraryTesting/converted-libraries/.openmodelica/libraries/BioChem 1.1.2/package.mo): time 0.06225/0.06225, allocations: 12.66 MB / 27.91 MB, free: 0.8359 MB / 18.57 MB Notification: Performance of loadFile(/var/lib/jenkins/ws/OpenModelicaLibraryTestingWork/OpenModelicaLibraryTesting/converted-libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.0013/0.0013, allocations: 193 kB / 31.47 MB, free: 3.559 MB / 24.77 MB Notification: Performance of loadFile(/var/lib/jenkins/ws/OpenModelicaLibraryTestingWork/OpenModelicaLibraryTesting/converted-libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.446/1.446, allocations: 225.7 MB / 260.6 MB, free: 9.18 MB / 202.7 MB Notification: Performance of loadFile(/var/lib/jenkins/ws/OpenModelicaLibraryTestingWork/OpenModelicaLibraryTesting/converted-libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.0007209/0.0007212, allocations: 91.09 kB / 314.4 MB, free: 9.43 MB / 250.7 MB Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl" Notification: Performance of FrontEnd - loaded program: time 0.0002751/0.000275, allocations: 12.59 kB / 378.2 MB, free: 53.19 MB / 298.7 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.078/0.07828, allocations: 53.09 MB / 431.3 MB, free: 9.586 MB / 298.7 MB Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.008004/0.08634, allocations: 7.773 MB / 439.1 MB, free: 1.777 MB / 298.7 MB Notification: Performance of NFInst.instExpressions: time 0.001309/0.08768, allocations: 0.8145 MB / 439.9 MB, free: 0.9609 MB / 298.7 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.0004528/0.08815, allocations: 40 kB / 440 MB, free: 0.9219 MB / 298.7 MB Notification: Performance of NFTyping.typeComponents: time 0.0002308/0.08839, allocations: 107.4 kB / 440.1 MB, free: 0.8164 MB / 298.7 MB Notification: Performance of NFTyping.typeBindings: time 0.0003922/0.08879, allocations: 170.6 kB / 440.2 MB, free: 0.6484 MB / 298.7 MB Notification: Performance of NFTyping.typeClassSections: time 0.0003088/0.08911, allocations: 167.9 kB / 440.4 MB, free: 496 kB / 298.7 MB Notification: Performance of NFFlatten.flatten: time 0.0005283/0.08964, allocations: 0.783 MB / 441.2 MB, free: 15.7 MB / 314.7 MB Notification: Performance of NFFlatten.resolveConnections: time 0.0005897/0.09024, allocations: 479.7 kB / 441.7 MB, free: 15.21 MB / 314.7 MB Notification: Performance of NFEvalConstants.evaluate: time 0.0002089/0.09046, allocations: 258.7 kB / 441.9 MB, free: 14.95 MB / 314.7 MB Notification: Performance of NFSimplifyModel.simplify: time 0.0002987/0.09076, allocations: 326.1 kB / 442.2 MB, free: 14.63 MB / 314.7 MB Notification: Performance of NFPackage.collectConstants: time 7.179e-05/0.09084, allocations: 40 kB / 442.3 MB, free: 14.59 MB / 314.7 MB Notification: Performance of NFFlatten.collectFunctions: time 8.176e-05/0.09093, allocations: 47.94 kB / 442.3 MB, free: 14.55 MB / 314.7 MB Notification: Performance of NFScalarize.scalarize: time 0.0001013/0.09104, allocations: 139.3 kB / 442.4 MB, free: 14.41 MB / 314.7 MB Notification: Performance of NFVerifyModel.verify: time 0.0003143/0.09136, allocations: 411.4 kB / 442.8 MB, free: 14 MB / 314.7 MB Notification: Performance of NFConvertDAE.convert: time 0.0008254/0.09219, allocations: 1.051 MB / 443.9 MB, free: 12.95 MB / 314.7 MB Notification: Performance of FrontEnd - DAE generated: time 5.41e-06/0.09221, allocations: 4 kB / 443.9 MB, free: 12.94 MB / 314.7 MB Notification: Performance of FrontEnd: time 1.693e-06/0.09222, allocations: 0 / 443.9 MB, free: 12.94 MB / 314.7 MB Notification: Performance of Transformations before backend: time 1.183e-05/0.09224, allocations: 0 / 443.9 MB, free: 12.94 MB / 314.7 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 0.001287/0.09353, allocations: 0.9398 MB / 444.8 MB, free: 11.95 MB / 314.7 MB Notification: Performance of prepare preOptimizeDAE: time 3.801e-05/0.09357, allocations: 8.031 kB / 444.8 MB, free: 11.94 MB / 314.7 MB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.000133/0.09371, allocations: 95.81 kB / 444.9 MB, free: 11.85 MB / 314.7 MB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002506/0.09397, allocations: 310.7 kB / 445.2 MB, free: 11.5 MB / 314.7 MB Notification: Performance of preOpt simplifyIfEquations (simulation): time 6.389e-05/0.09404, allocations: 74.38 kB / 445.3 MB, free: 11.43 MB / 314.7 MB Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001278/0.09418, allocations: 100.4 kB / 445.4 MB, free: 11.33 MB / 314.7 MB Notification: Performance of preOpt clockPartitioning (simulation): time 0.001324/0.09551, allocations: 0.8724 MB / 446.3 MB, free: 10.45 MB / 314.7 MB Notification: Performance of preOpt findStateOrder (simulation): time 2.646e-05/0.09554, allocations: 8.094 kB / 446.3 MB, free: 10.44 MB / 314.7 MB Notification: Performance of preOpt replaceEdgeChange (simulation): time 6.626e-05/0.09562, allocations: 47.94 kB / 446.3 MB, free: 10.39 MB / 314.7 MB Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.866e-05/0.09564, allocations: 24 kB / 446.4 MB, free: 10.37 MB / 314.7 MB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001028/0.09667, allocations: 0.613 MB / 447 MB, free: 9.758 MB / 314.7 MB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.004118/0.1008, allocations: 2.839 MB / 449.8 MB, free: 6.832 MB / 314.7 MB Notification: Performance of preOpt comSubExp (simulation): time 0.001006/0.1018, allocations: 0.5182 MB / 450.3 MB, free: 6.297 MB / 314.7 MB Notification: Performance of preOpt resolveLoops (simulation): time 0.0004452/0.1023, allocations: 327 kB / 450.7 MB, free: 5.977 MB / 314.7 MB Notification: Performance of preOpt evalFunc (simulation): time 2.992e-05/0.1023, allocations: 4.438 kB / 450.7 MB, free: 5.973 MB / 314.7 MB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.829e-05/0.1024, allocations: 50.94 kB / 450.7 MB, free: 5.914 MB / 314.7 MB Notification: Performance of pre-optimization done (n=50): time 4.348e-06/0.1024, allocations: 0 / 450.7 MB, free: 5.914 MB / 314.7 MB Notification: Performance of matching and sorting (n=59): time 0.004865/0.1073, allocations: 2.172 MB / 452.9 MB, free: 3.695 MB / 314.7 MB Notification: Performance of inlineWhenForInitialization (initialization): time 4.841e-05/0.1073, allocations: 85.66 kB / 453 MB, free: 3.594 MB / 314.7 MB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003444/0.1077, allocations: 361.5 kB / 453.3 MB, free: 3.234 MB / 314.7 MB Notification: Performance of collectPreVariables (initialization): time 2.906e-05/0.1077, allocations: 29.7 kB / 453.3 MB, free: 3.199 MB / 314.7 MB Notification: Performance of collectInitialEqns (initialization): time 0.0002477/0.108, allocations: 454.1 kB / 453.8 MB, free: 2.746 MB / 314.7 MB Notification: Performance of collectInitialBindings (initialization): time 0.0001386/0.1081, allocations: 216.8 kB / 454 MB, free: 2.531 MB / 314.7 MB Notification: Performance of simplifyInitialFunctions (initialization): time 2.765e-05/0.1081, allocations: 16.03 kB / 454 MB, free: 2.516 MB / 314.7 MB Notification: Performance of setup shared object (initialization): time 0.0001255/0.1083, allocations: 362.8 kB / 454.4 MB, free: 2.152 MB / 314.7 MB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003532/0.1086, allocations: 250.7 kB / 454.6 MB, free: 1.902 MB / 314.7 MB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0005223/0.1092, allocations: 480.9 kB / 455.1 MB, free: 1.312 MB / 314.7 MB Notification: Performance of analyzeInitialSystem (initialization): time 0.005986/0.1152, allocations: 1.752 MB / 456.8 MB, free: 15.44 MB / 330.7 MB Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.691e-06/0.1152, allocations: 4 kB / 456.8 MB, free: 15.43 MB / 330.7 MB Notification: Performance of matching and sorting (n=107) (initialization): time 0.001121/0.1163, allocations: 0.7988 MB / 457.6 MB, free: 14.63 MB / 330.7 MB Notification: Performance of prepare postOptimizeDAE: time 2.354e-05/0.1163, allocations: 11.98 kB / 457.7 MB, free: 14.62 MB / 330.7 MB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.117e-05/0.1164, allocations: 8 kB / 457.7 MB, free: 14.61 MB / 330.7 MB Notification: Performance of postOpt tearingSystem (initialization): time 2.783e-05/0.1164, allocations: 12 kB / 457.7 MB, free: 14.6 MB / 330.7 MB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006605/0.1171, allocations: 188.4 kB / 457.9 MB, free: 14.41 MB / 330.7 MB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 2.264e-05/0.1171, allocations: 23.94 kB / 457.9 MB, free: 14.39 MB / 330.7 MB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003554/0.1175, allocations: 35.98 kB / 457.9 MB, free: 14.36 MB / 330.7 MB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.411e-05/0.1175, allocations: 36 kB / 458 MB, free: 14.32 MB / 330.7 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.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 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.y6.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.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 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.y5.n:VARIABLE(min = 0.0 unit = "mol" fixed = true stateSelect=StateSelect.prefer ) "Number of moles of substance in pool (mol)" 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 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 0.0004438/0.118, allocations: 289.9 kB / 458.2 MB, free: 14.03 MB / 330.7 MB Notification: Performance of postOpt lateInlineFunction (simulation): time 8.317e-05/0.118, allocations: 43.44 kB / 458.3 MB, free: 13.98 MB / 330.7 MB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001344/0.1182, allocations: 72.91 kB / 458.3 MB, free: 13.91 MB / 330.7 MB Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.74e-06/0.1182, allocations: 4 kB / 458.4 MB, free: 13.91 MB / 330.7 MB Notification: Performance of postOpt constantLinearSystem (simulation): time 7.865e-06/0.1182, allocations: 7.984 kB / 458.4 MB, free: 13.9 MB / 330.7 MB Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.871e-06/0.1182, allocations: 0 / 458.4 MB, free: 13.9 MB / 330.7 MB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001034/0.1193, allocations: 0.7553 MB / 459.1 MB, free: 13.1 MB / 330.7 MB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.649e-06/0.1193, allocations: 8 kB / 459.1 MB, free: 13.09 MB / 330.7 MB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005694/0.1199, allocations: 107.8 kB / 459.2 MB, free: 12.98 MB / 330.7 MB Notification: Performance of postOpt tearingSystem (simulation): time 3.807e-06/0.1199, allocations: 0 / 459.2 MB, free: 12.98 MB / 330.7 MB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 4.155e-05/0.1199, allocations: 27.98 kB / 459.3 MB, free: 12.95 MB / 330.7 MB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.745e-06/0.1199, allocations: 0 / 459.3 MB, free: 12.95 MB / 330.7 MB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.523e-06/0.1199, allocations: 0 / 459.3 MB, free: 12.95 MB / 330.7 MB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001095/0.121, allocations: 0.9322 MB / 460.2 MB, free: 12 MB / 330.7 MB Notification: Performance of postOpt removeConstants (simulation): time 8.243e-05/0.1211, allocations: 116.5 kB / 460.3 MB, free: 11.87 MB / 330.7 MB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.098e-05/0.1212, allocations: 23.92 kB / 460.3 MB, free: 11.84 MB / 330.7 MB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.000285/0.1215, allocations: 19.98 kB / 460.3 MB, free: 11.82 MB / 330.7 MB Notification: Performance of postOpt findZeroCrossings (simulation): time 6.244e-05/0.1216, allocations: 32.52 kB / 460.4 MB, free: 11.79 MB / 330.7 MB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.869e-05/0.1216, allocations: 19.98 kB / 460.4 MB, free: 11.77 MB / 330.7 MB Notification: Performance of sorting global known variables: time 0.0002178/0.1218, allocations: 239.2 kB / 460.6 MB, free: 11.54 MB / 330.7 MB Notification: Performance of sort global known variables: time 1.7e-07/0.1218, allocations: 0 / 460.6 MB, free: 11.54 MB / 330.7 MB Notification: Performance of remove unused functions: time 0.0005508/0.1224, allocations: 156 kB / 460.8 MB, free: 11.39 MB / 330.7 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 0.0001471/0.1225, allocations: 116.5 kB / 460.9 MB, free: 11.26 MB / 330.7 MB Notification: Performance of simCode: created initialization part: time 0.0009264/0.1235, allocations: 0.5978 MB / 461.5 MB, free: 10.66 MB / 330.7 MB Notification: Performance of simCode: created event and clocks part: time 2.905e-06/0.1235, allocations: 0 / 461.5 MB, free: 10.66 MB / 330.7 MB Notification: Performance of simCode: created simulation system equations: time 0.0003796/0.1239, allocations: 259.2 kB / 461.7 MB, free: 10.41 MB / 330.7 MB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.000509/0.1244, allocations: 74.95 kB / 461.8 MB, free: 10.34 MB / 330.7 MB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003471/0.1279, allocations: 2.337 MB / 464.2 MB, free: 7.969 MB / 330.7 MB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0005691/0.1285, allocations: 0.9352 MB / 465.1 MB, free: 7.004 MB / 330.7 MB Notification: Performance of simCode: alias equations: time 0.0003062/0.1288, allocations: 64.59 kB / 465.2 MB, free: 6.941 MB / 330.7 MB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001413/0.1289, allocations: 43.42 kB / 465.2 MB, free: 6.898 MB / 330.7 MB Notification: Performance of SimCode: time 8.92e-07/0.1289, allocations: 0 / 465.2 MB, free: 6.898 MB / 330.7 MB Notification: Performance of Templates: time 0.01021/0.1391, allocations: 5.056 MB / 470.3 MB, free: 1.852 MB / 330.7 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)