Running command: translateModel(BioChem.Examples.CaOscillations.Cytosol,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CaOscillations.Cytosol") Notification: Performance of loadModel(BioChem): time 2.003/2.003, allocations: 217.9 MB / 230 MB, free: 14.31 MB / 202.7 MB Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl" Notification: Performance of FrontEnd - loaded program: time 3.316e-05/3.324e-05, allocations: 4 kB / 283.4 MB, free: 9.629 MB / 234.7 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.09764/0.0977, allocations: 50.41 MB / 333.8 MB, free: 7.121 MB / 282.7 MB Notification: Performance of FrontEnd - scodeFlatten: time 0.4431/0.5408, allocations: 86.32 MB / 420.1 MB, free: 9.273 MB / 346.7 MB Notification: Performance of FrontEnd - mkProgramGraph: time 0.0002369/0.5411, allocations: 55.72 kB / 420.2 MB, free: 9.246 MB / 346.7 MB [/var/lib/jenkins/ws/OpenModelicaLibraryTestingWork/OpenModelica/OMCompiler/build/lib/omlibrary/BioChem 1.0.2/Examples/package.mo:2608:7-2609:166:writable] Warning: Connecting two signal sources while connecting Ca_Cyt.n1.V to endoplasmicReticulum.Ca_Cyt_node.V. Notification: Performance of FrontEnd - DAE generated: time 0.02832/0.5695, allocations: 4.748 MB / 424.9 MB, free: 5.211 MB / 346.7 MB Notification: Performance of FrontEnd: time 3.248e-06/0.5695, allocations: 0 / 424.9 MB, free: 5.211 MB / 346.7 MB Notification: Performance of Transformations before backend: time 2.482e-05/0.5696, allocations: 4 kB / 424.9 MB, free: 5.207 MB / 346.7 MB Notification: Model statistics after passing the front-end and creating the data structures used by the back-end: * Number of equations: 60 * Number of variables: 60 Notification: Performance of Generate backend data structure: time 0.001285/0.5709, allocations: 459.7 kB / 425.4 MB, free: 4.727 MB / 346.7 MB Notification: Performance of prepare preOptimizeDAE: time 7.691e-05/0.571, allocations: 8.031 kB / 425.4 MB, free: 4.719 MB / 346.7 MB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001525/0.5712, allocations: 23.72 kB / 425.4 MB, free: 4.695 MB / 346.7 MB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0003239/0.5715, allocations: 182.8 kB / 425.6 MB, free: 4.477 MB / 346.7 MB Notification: Performance of preOpt simplifyIfEquations (simulation): time 6.336e-05/0.5716, allocations: 26.52 kB / 425.6 MB, free: 4.457 MB / 346.7 MB Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001196/0.5717, allocations: 22.38 kB / 425.6 MB, free: 4.441 MB / 346.7 MB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0009732/0.5727, allocations: 197.8 kB / 425.8 MB, free: 4.297 MB / 346.7 MB Notification: Performance of preOpt findStateOrder (simulation): time 3.322e-05/0.5728, allocations: 0 / 425.8 MB, free: 4.297 MB / 346.7 MB Notification: Performance of preOpt replaceEdgeChange (simulation): time 6.701e-05/0.5729, allocations: 10.88 kB / 425.8 MB, free: 4.293 MB / 346.7 MB Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.765e-05/0.5729, allocations: 4 kB / 425.8 MB, free: 4.289 MB / 346.7 MB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0007773/0.5737, allocations: 128.7 kB / 426 MB, free: 4.207 MB / 346.7 MB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.003661/0.5774, allocations: 0.7699 MB / 426.7 MB, free: 3.52 MB / 346.7 MB Notification: Performance of preOpt comSubExp (simulation): time 0.0004856/0.5779, allocations: 104.1 kB / 426.8 MB, free: 3.438 MB / 346.7 MB Notification: Performance of preOpt resolveLoops (simulation): time 0.0006209/0.5786, allocations: 97.98 kB / 426.9 MB, free: 3.359 MB / 346.7 MB Notification: Performance of preOpt evalFunc (simulation): time 3.712e-05/0.5787, allocations: 4 kB / 426.9 MB, free: 3.355 MB / 346.7 MB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 5.807e-05/0.5787, allocations: 42.11 kB / 427 MB, free: 3.309 MB / 346.7 MB Notification: Performance of pre-optimization done (n=15): time 5.052e-06/0.5788, allocations: 0 / 427 MB, free: 3.309 MB / 346.7 MB Notification: Performance of matching and sorting (n=17): time 0.003082/0.5819, allocations: 0.5284 MB / 427.5 MB, free: 2.797 MB / 346.7 MB Notification: Performance of inlineWhenForInitialization (initialization): time 8.408e-05/0.582, allocations: 59.34 kB / 427.6 MB, free: 2.727 MB / 346.7 MB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003114/0.5823, allocations: 136.6 kB / 427.7 MB, free: 2.598 MB / 346.7 MB Notification: Performance of collectPreVariables (initialization): time 5.264e-05/0.5824, allocations: 25.7 kB / 427.7 MB, free: 2.566 MB / 346.7 MB Notification: Performance of collectInitialEqns (initialization): time 0.0002223/0.5827, allocations: 159.2 kB / 427.9 MB, free: 2.422 MB / 346.7 MB Notification: Performance of collectInitialBindings (initialization): time 0.0001372/0.5828, allocations: 62.34 kB / 427.9 MB, free: 2.367 MB / 346.7 MB Notification: Performance of simplifyInitialFunctions (initialization): time 2.624e-05/0.5829, allocations: 3.812 kB / 427.9 MB, free: 2.367 MB / 346.7 MB Notification: Performance of setup shared object (initialization): time 0.0002895/0.5832, allocations: 326.6 kB / 428.3 MB, free: 2.047 MB / 346.7 MB Notification: Performance of preBalanceInitialSystem (initialization): time 0.000266/0.5835, allocations: 51.53 kB / 428.3 MB, free: 2.012 MB / 346.7 MB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003437/0.5838, allocations: 84.86 kB / 428.4 MB, free: 1.926 MB / 346.7 MB Notification: Performance of analyzeInitialSystem (initialization): time 0.000354/0.5842, allocations: 67.64 kB / 428.5 MB, free: 1.879 MB / 346.7 MB Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.774e-06/0.5843, allocations: 0 / 428.5 MB, free: 1.879 MB / 346.7 MB Notification: Performance of matching and sorting (n=28) (initialization): time 0.000995/0.5853, allocations: 197.2 kB / 428.6 MB, free: 1.723 MB / 346.7 MB Notification: Performance of prepare postOptimizeDAE: time 3.087e-05/0.5853, allocations: 4 kB / 428.6 MB, free: 1.719 MB / 346.7 MB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.868e-05/0.5854, allocations: 8 kB / 428.7 MB, free: 1.711 MB / 346.7 MB Notification: Performance of postOpt tearingSystem (initialization): time 2.935e-05/0.5854, allocations: 4 kB / 428.7 MB, free: 1.707 MB / 346.7 MB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0005985/0.586, allocations: 51.97 kB / 428.7 MB, free: 1.66 MB / 346.7 MB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 2.854e-05/0.5861, allocations: 8 kB / 428.7 MB, free: 1.652 MB / 346.7 MB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003064/0.5864, allocations: 11.88 kB / 428.7 MB, free: 1.645 MB / 346.7 MB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 5.364e-05/0.5865, allocations: 8 kB / 428.7 MB, free: 1.637 MB / 346.7 MB Warning: Assuming fixed start value for the following 5 variables: p3_sbml:VARIABLE(start = 0.95 ) type: Real Ca_Cyt.n:VARIABLE(min = 0.0 unit = "mol" stateSelect=StateSelect.prefer ) "Number of moles of substance in pool (mol)" type: Real V:VARIABLE(start = 1.0 unit = "l" stateSelect=StateSelect.prefer ) "Compartment volume" type: Real endoplasmicReticulum.V:VARIABLE(start = 1.0 unit = "l" stateSelect=StateSelect.prefer ) "Compartment volume" type: Real endoplasmicReticulum.CaER.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: 7 * Number of states: 0 () * Number of discrete variables: 0 () * Number of discrete states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for initialization (28): * Single equations (assignments): 28 * 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 0.0003323/0.5869, allocations: 134.9 kB / 428.9 MB, free: 1.504 MB / 346.7 MB Notification: Performance of postOpt lateInlineFunction (simulation): time 8.256e-05/0.587, allocations: 15.81 kB / 428.9 MB, free: 1.488 MB / 346.7 MB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0008262/0.5878, allocations: 166.6 kB / 429 MB, free: 1.371 MB / 346.7 MB Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.229e-05/0.5878, allocations: 4 kB / 429.1 MB, free: 1.367 MB / 346.7 MB Notification: Performance of postOpt constantLinearSystem (simulation): time 1.336e-05/0.5879, allocations: 3.984 kB / 429.1 MB, free: 1.363 MB / 346.7 MB Notification: Performance of postOpt simplifysemiLinear (simulation): time 9.627e-06/0.5879, allocations: 0 / 429.1 MB, free: 1.363 MB / 346.7 MB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.002119/0.59, allocations: 0.5013 MB / 429.6 MB, free: 0.8828 MB / 346.7 MB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 6.471e-06/0.5901, allocations: 0 / 429.6 MB, free: 0.8828 MB / 346.7 MB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0006042/0.5907, allocations: 43.66 kB / 429.6 MB, free: 0.8438 MB / 346.7 MB Notification: Performance of postOpt tearingSystem (simulation): time 1.506e-05/0.5908, allocations: 4 kB / 429.6 MB, free: 0.8398 MB / 346.7 MB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 4.071e-05/0.5908, allocations: 0 / 429.6 MB, free: 0.8398 MB / 346.7 MB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 6.298e-06/0.5908, allocations: 0 / 429.6 MB, free: 0.8398 MB / 346.7 MB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.343e-06/0.5909, allocations: 0 / 429.6 MB, free: 0.8398 MB / 346.7 MB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001126/0.592, allocations: 306.4 kB / 429.9 MB, free: 0.582 MB / 346.7 MB Notification: Performance of postOpt removeConstants (simulation): time 0.0001347/0.5922, allocations: 88.92 kB / 430 MB, free: 488 kB / 346.7 MB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 7.415e-05/0.5923, allocations: 4 kB / 430 MB, free: 484 kB / 346.7 MB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0003801/0.5927, allocations: 11.88 kB / 430 MB, free: 476 kB / 346.7 MB Notification: Performance of postOpt findZeroCrossings (simulation): time 6.531e-05/0.5928, allocations: 11.97 kB / 430 MB, free: 464 kB / 346.7 MB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 4.162e-05/0.5928, allocations: 11.73 kB / 430 MB, free: 456 kB / 346.7 MB Notification: Performance of sorting global known variables: time 0.0002115/0.5931, allocations: 106.7 kB / 430.1 MB, free: 356 kB / 346.7 MB Notification: Performance of sort global known variables: time 1.33e-06/0.5931, allocations: 0 / 430.1 MB, free: 356 kB / 346.7 MB Notification: Performance of remove unused functions: time 0.001016/0.5941, allocations: 47.86 kB / 430.2 MB, free: 316 kB / 346.7 MB Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 1 * Number of states: 5 (V,endoplasmicReticulum.V,endoplasmicReticulum.CaER.n,Ca_Cyt.n,p3_sbml) * Number of discrete variables: 0 () * Number of discrete states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for simulation (18): * Single equations (assignments): 18 * 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 0.0002693/0.5944, allocations: 103.2 kB / 430.3 MB, free: 200 kB / 346.7 MB Notification: Performance of simCode: created initialization part: time 0.0006875/0.5951, allocations: 137.4 kB / 430.4 MB, free: 100 kB / 346.7 MB Notification: Performance of simCode: created event and clocks part: time 6.059e-06/0.5952, allocations: 3.938 kB / 430.4 MB, free: 100 kB / 346.7 MB Notification: Performance of simCode: created simulation system equations: time 0.0002819/0.5955, allocations: 59 kB / 430.5 MB, free: 56 kB / 346.7 MB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005201/0.596, allocations: 12.88 kB / 430.5 MB, free: 48 kB / 346.7 MB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002327/0.5984, allocations: 0.4998 MB / 431 MB, free: 15.55 MB / 362.7 MB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.000806/0.5992, allocations: 0.7478 MB / 431.7 MB, free: 14.78 MB / 362.7 MB Notification: Performance of simCode: alias equations: time 0.000262/0.5995, allocations: 17.2 kB / 431.8 MB, free: 14.76 MB / 362.7 MB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001452/0.5997, allocations: 15.44 kB / 431.8 MB, free: 14.74 MB / 362.7 MB Notification: Performance of SimCode: time 2.564e-06/0.5997, allocations: 0 / 431.8 MB, free: 14.74 MB / 362.7 MB Notification: Performance of Templates: time 0.01035/0.6101, allocations: 1.264 MB / 433 MB, free: 13.49 MB / 362.7 MB