Running command: translateModel(BioChem.Examples.CircadianOscillator.Container,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CircadianOscillator.Container") Notification: Performance of loadModel(BioChem): time 1.924/1.924, allocations: 217.9 MB / 230.1 MB, free: 14.3 MB / 202.7 MB Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl" Notification: Performance of FrontEnd - loaded program: time 3.397e-05/3.409e-05, allocations: 0 / 283.4 MB, free: 9.637 MB / 234.7 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.08768/0.08774, allocations: 50.42 MB / 333.8 MB, free: 7.125 MB / 282.7 MB Notification: Performance of FrontEnd - scodeFlatten: time 0.37/0.4578, allocations: 89.8 MB / 423.6 MB, free: 5.789 MB / 346.7 MB Notification: Performance of FrontEnd - mkProgramGraph: time 0.0001623/0.458, allocations: 59.28 kB / 423.7 MB, free: 5.762 MB / 346.7 MB [/var/lib/jenkins/ws/OpenModelicaLibraryTestingWork/OpenModelica/OMCompiler/build/lib/omlibrary/BioChem 1.0.2/Examples/package.mo:1332:7-1333:85:writable] Warning: Connecting two signal sources while connecting cytoplasm.y5_node.V to nucleus.y5_node.V. [/var/lib/jenkins/ws/OpenModelicaLibraryTestingWork/OpenModelica/OMCompiler/build/lib/omlibrary/BioChem 1.0.2/Examples/package.mo:1334:7-1335:84:writable] Warning: Connecting two signal sources while connecting nucleus.y6_node.V to cytoplasm.y6_node.V. [/var/lib/jenkins/ws/OpenModelicaLibraryTestingWork/OpenModelica/OMCompiler/build/lib/omlibrary/BioChem 1.0.2/Examples/package.mo:1336:7-1337:84:writable] Warning: Connecting two signal sources while connecting cytoplasm.y2_node.V to nucleus.y2_node.V. [/var/lib/jenkins/ws/OpenModelicaLibraryTestingWork/OpenModelica/OMCompiler/build/lib/omlibrary/BioChem 1.0.2/Examples/package.mo:1338:7-1339:85:writable] Warning: Connecting two signal sources while connecting nucleus.y3_node.V to cytoplasm.y3_node.V. Notification: Performance of FrontEnd - DAE generated: time 0.08935/0.5474, allocations: 25.14 MB / 448.8 MB, free: 1.25 MB / 362.7 MB Notification: Performance of FrontEnd: time 2.44e-06/0.5474, allocations: 3.938 kB / 448.8 MB, free: 1.246 MB / 362.7 MB Notification: Performance of Transformations before backend: time 2.857e-05/0.5475, allocations: 16 kB / 448.8 MB, free: 1.23 MB / 362.7 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 0.001718/0.5492, allocations: 0.9047 MB / 449.7 MB, free: 340 kB / 362.7 MB Notification: Performance of prepare preOptimizeDAE: time 4.365e-05/0.5493, allocations: 12.03 kB / 449.7 MB, free: 328 kB / 362.7 MB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0002343/0.5495, allocations: 98.78 kB / 449.8 MB, free: 228 kB / 362.7 MB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0004078/0.5499, allocations: 293.4 kB / 450.1 MB, free: 15.9 MB / 378.7 MB Notification: Performance of preOpt simplifyIfEquations (simulation): time 7.39e-05/0.55, allocations: 73.88 kB / 450.2 MB, free: 15.86 MB / 378.7 MB Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001823/0.5502, allocations: 108 kB / 450.3 MB, free: 15.79 MB / 378.7 MB Notification: Performance of preOpt clockPartitioning (simulation): time 0.001902/0.5521, allocations: 0.8282 MB / 451.1 MB, free: 15.24 MB / 378.7 MB Notification: Performance of preOpt findStateOrder (simulation): time 3.812e-05/0.5522, allocations: 0 / 451.1 MB, free: 15.24 MB / 378.7 MB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001039/0.5523, allocations: 44.78 kB / 451.2 MB, free: 15.23 MB / 378.7 MB Notification: Performance of preOpt inlineArrayEqn (simulation): time 3.108e-05/0.5524, allocations: 24 kB / 451.2 MB, free: 15.2 MB / 378.7 MB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.00157/0.5539, allocations: 0.5851 MB / 451.8 MB, free: 14.7 MB / 378.7 MB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.006523/0.5605, allocations: 2.838 MB / 454.6 MB, free: 11.77 MB / 378.7 MB Notification: Performance of preOpt comSubExp (simulation): time 0.0013/0.5618, allocations: 0.5096 MB / 455.1 MB, free: 11.25 MB / 378.7 MB Notification: Performance of preOpt resolveLoops (simulation): time 0.0006084/0.5624, allocations: 323 kB / 455.4 MB, free: 10.93 MB / 378.7 MB Notification: Performance of preOpt evalFunc (simulation): time 4.084e-05/0.5625, allocations: 8.375 kB / 455.4 MB, free: 10.92 MB / 378.7 MB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.445e-05/0.5626, allocations: 39 kB / 455.5 MB, free: 10.87 MB / 378.7 MB Notification: Performance of pre-optimization done (n=50): time 4.137e-06/0.5626, allocations: 0 / 455.5 MB, free: 10.87 MB / 378.7 MB Notification: Performance of matching and sorting (n=59): time 0.006455/0.569, allocations: 2.002 MB / 457.5 MB, free: 8.824 MB / 378.7 MB Notification: Performance of inlineWhenForInitialization (initialization): time 6.236e-05/0.5691, allocations: 89.7 kB / 457.6 MB, free: 8.719 MB / 378.7 MB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0004864/0.5696, allocations: 315.4 kB / 457.9 MB, free: 8.406 MB / 378.7 MB Notification: Performance of collectPreVariables (initialization): time 5.555e-05/0.5697, allocations: 33.7 kB / 457.9 MB, free: 8.367 MB / 378.7 MB Notification: Performance of collectInitialEqns (initialization): time 0.0003541/0.5701, allocations: 446.2 kB / 458.4 MB, free: 7.922 MB / 378.7 MB Notification: Performance of collectInitialBindings (initialization): time 0.0002246/0.5703, allocations: 224.8 kB / 458.6 MB, free: 7.699 MB / 378.7 MB Notification: Performance of simplifyInitialFunctions (initialization): time 4.574e-05/0.5704, allocations: 12 kB / 458.6 MB, free: 7.688 MB / 378.7 MB Notification: Performance of setup shared object (initialization): time 0.0002055/0.5706, allocations: 358.8 kB / 458.9 MB, free: 7.328 MB / 378.7 MB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0005401/0.5711, allocations: 234.6 kB / 459.2 MB, free: 7.098 MB / 378.7 MB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0007137/0.5719, allocations: 466.5 kB / 459.6 MB, free: 6.512 MB / 378.7 MB Notification: Performance of analyzeInitialSystem (initialization): time 0.0006536/0.5725, allocations: 297.3 kB / 459.9 MB, free: 6.223 MB / 378.7 MB Notification: Performance of solveInitialSystemEqSystem (initialization): time 8.534e-06/0.5726, allocations: 4 kB / 459.9 MB, free: 6.219 MB / 378.7 MB Notification: Performance of matching and sorting (n=107) (initialization): time 0.001712/0.5743, allocations: 0.7605 MB / 460.7 MB, free: 5.453 MB / 378.7 MB Notification: Performance of prepare postOptimizeDAE: time 2.306e-05/0.5743, allocations: 12.25 kB / 460.7 MB, free: 5.441 MB / 378.7 MB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.801e-05/0.5743, allocations: 15.95 kB / 460.7 MB, free: 5.426 MB / 378.7 MB Notification: Performance of postOpt tearingSystem (initialization): time 3.08e-05/0.5744, allocations: 12 kB / 460.7 MB, free: 5.414 MB / 378.7 MB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0008928/0.5753, allocations: 191.7 kB / 460.9 MB, free: 5.227 MB / 378.7 MB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 3.048e-05/0.5753, allocations: 19.94 kB / 460.9 MB, free: 5.207 MB / 378.7 MB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0005335/0.5759, allocations: 43.83 kB / 461 MB, free: 5.164 MB / 378.7 MB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 7.681e-05/0.576, allocations: 40 kB / 461 MB, free: 5.125 MB / 378.7 MB Warning: Assuming fixed start value for the following 12 variables: V:VARIABLE(start = 1.0 unit = "l" stateSelect=StateSelect.prefer ) "Compartment volume" type: Real cytoplasm.ambientSubstance.n:VARIABLE(min = 0.0 unit = "mol" stateSelect=StateSelect.prefer ) "Number of moles of substance in pool (mol)" type: Real cytoplasm.y5.n:VARIABLE(min = 0.0 unit = "mol" stateSelect=StateSelect.prefer ) "Number of moles of substance in pool (mol)" type: Real cytoplasm.y4.n:VARIABLE(min = 0.0 unit = "mol" stateSelect=StateSelect.prefer ) "Number of moles of substance in pool (mol)" type: Real cytoplasm.y2.n:VARIABLE(min = 0.0 unit = "mol" stateSelect=StateSelect.prefer ) "Number of moles of substance in pool (mol)" type: Real nucleus.V:VARIABLE(start = 1.0 unit = "l" stateSelect=StateSelect.prefer ) "Compartment volume" type: Real nucleus.y3.n:VARIABLE(min = 0.0 unit = "mol" stateSelect=StateSelect.prefer ) "Number of moles of substance in pool (mol)" type: Real nucleus.y6.n:VARIABLE(min = 0.0 unit = "mol" stateSelect=StateSelect.prefer ) "Number of moles of substance in pool (mol)" type: Real nucleus.y7.n:VARIABLE(min = 0.0 unit = "mol" stateSelect=StateSelect.prefer ) "Number of moles of substance in pool (mol)" type: Real nucleus.ambientSubstance.n:VARIABLE(min = 0.0 unit = "mol" stateSelect=StateSelect.prefer ) "Number of moles of substance in pool (mol)" type: Real cytoplasm.V:VARIABLE(start = 1.0 unit = "l" stateSelect=StateSelect.prefer ) "Compartment volume" type: Real cytoplasm.y1.n:VARIABLE(min = 0.0 unit = "mol" 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 () * 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 0.0003222/0.5763, allocations: 189.2 kB / 461.2 MB, free: 4.941 MB / 378.7 MB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001464/0.5765, allocations: 51.36 kB / 461.2 MB, free: 4.891 MB / 378.7 MB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001758/0.5767, allocations: 72.89 kB / 461.3 MB, free: 4.816 MB / 378.7 MB Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.03e-05/0.5767, allocations: 7.953 kB / 461.3 MB, free: 4.809 MB / 378.7 MB Notification: Performance of postOpt constantLinearSystem (simulation): time 7.842e-06/0.5767, allocations: 0 / 461.3 MB, free: 4.809 MB / 378.7 MB Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.004e-05/0.5767, allocations: 7.984 kB / 461.3 MB, free: 4.801 MB / 378.7 MB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001638/0.5784, allocations: 0.7477 MB / 462.1 MB, free: 4 MB / 378.7 MB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 7.3e-06/0.5784, allocations: 7.984 kB / 462.1 MB, free: 3.992 MB / 378.7 MB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0007677/0.5792, allocations: 111.8 kB / 462.2 MB, free: 3.883 MB / 378.7 MB Notification: Performance of postOpt tearingSystem (simulation): time 8.59e-06/0.5792, allocations: 0 / 462.2 MB, free: 3.883 MB / 378.7 MB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 5.955e-05/0.5793, allocations: 16 kB / 462.2 MB, free: 3.867 MB / 378.7 MB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.217e-05/0.5793, allocations: 11.94 kB / 462.2 MB, free: 3.855 MB / 378.7 MB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.209e-06/0.5793, allocations: 0 / 462.2 MB, free: 3.855 MB / 378.7 MB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001733/0.5811, allocations: 0.9339 MB / 463.1 MB, free: 2.902 MB / 378.7 MB Notification: Performance of postOpt removeConstants (simulation): time 0.0001565/0.5812, allocations: 120.6 kB / 463.3 MB, free: 2.766 MB / 378.7 MB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 9.004e-05/0.5813, allocations: 19.94 kB / 463.3 MB, free: 2.746 MB / 378.7 MB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0004246/0.5818, allocations: 23.98 kB / 463.3 MB, free: 2.723 MB / 378.7 MB Notification: Performance of postOpt findZeroCrossings (simulation): time 8.334e-05/0.5819, allocations: 32.52 kB / 463.3 MB, free: 2.691 MB / 378.7 MB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 4.994e-05/0.5819, allocations: 23.92 kB / 463.4 MB, free: 2.668 MB / 378.7 MB Notification: Performance of sorting global known variables: time 0.0003403/0.5823, allocations: 230.2 kB / 463.6 MB, free: 2.441 MB / 378.7 MB Notification: Performance of sort global known variables: time 7.54e-07/0.5823, allocations: 0 / 463.6 MB, free: 2.441 MB / 378.7 MB Notification: Performance of remove unused functions: time 0.0008984/0.5832, allocations: 172 kB / 463.8 MB, free: 2.273 MB / 378.7 MB Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 2 * Number of states: 12 (V,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) * Number of discrete variables: 0 () * Number of discrete 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 0.0001877/0.5834, allocations: 119.1 kB / 463.9 MB, free: 2.148 MB / 378.7 MB Notification: Performance of simCode: created initialization part: time 0.001236/0.5847, allocations: 0.5646 MB / 464.4 MB, free: 1.586 MB / 378.7 MB Notification: Performance of simCode: created event and clocks part: time 2.824e-06/0.5847, allocations: 0 / 464.4 MB, free: 1.586 MB / 378.7 MB Notification: Performance of simCode: created simulation system equations: time 0.0005065/0.5852, allocations: 254 kB / 464.7 MB, free: 1.34 MB / 378.7 MB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004496/0.5857, allocations: 50.77 kB / 464.7 MB, free: 1.293 MB / 378.7 MB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.004074/0.5897, allocations: 1.701 MB / 466.4 MB, free: 15.56 MB / 394.7 MB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.000775/0.5906, allocations: 0.9568 MB / 467.4 MB, free: 14.58 MB / 394.7 MB Notification: Performance of simCode: alias equations: time 0.0004722/0.591, allocations: 64.58 kB / 467.5 MB, free: 14.51 MB / 394.7 MB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001994/0.5913, allocations: 43.42 kB / 467.5 MB, free: 14.47 MB / 394.7 MB Notification: Performance of SimCode: time 1.754e-06/0.5913, allocations: 0 / 467.5 MB, free: 14.47 MB / 394.7 MB Notification: Performance of Templates: time 0.01553/0.6068, allocations: 4.913 MB / 472.4 MB, free: 9.574 MB / 394.7 MB