Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries/ --ompython_omhome=/usr Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.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/Chemical 1.4.1-master/package.mo", uses=false) Using package Chemical with version 1.4.1 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-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(Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery,tolerance=1e-06,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery") translateModel(Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery,tolerance=1e-06,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery") Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.0009948/0.0009948, allocations: 92.16 kB / 16.02 MB, free: 80 kB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001342/0.001342, allocations: 173.2 kB / 16.92 MB, free: 6.652 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.365/1.365, allocations: 223.3 MB / 241 MB, free: 5.352 MB / 190.1 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.2189/0.2189, allocations: 15.27 MB / 307.4 MB, free: 15.71 MB / 254.1 MB Notification: Performance of FrontEnd - loaded program: time 0.0003259/0.0003259, allocations: 12 kB / 372.8 MB, free: 3.645 MB / 302.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.2849/0.2852, allocations: 54.62 MB / 427.4 MB, free: 40.34 MB / 350.1 MB [/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo:3019:6-3019:65:writable] Warning: An inner declaration for outer component system could not be found and was automatically generated. [/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo:3019:6-3019:65:writable] Notification: The diagnostics message for the missing inner is: Your model is using an outer "system" component but an inner "system" component is not defined. For simulation drag Modelica.Fluid.System into your model to specify system properties. Notification: Performance of NFInst.instantiate(Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery): time 0.0428/0.3281, allocations: 43.49 MB / 470.9 MB, free: 19.54 MB / 350.1 MB Notification: Performance of NFInst.instExpressions: time 0.07611/0.4042, allocations: 71.78 MB / 0.5299 GB, free: 2.637 MB / 398.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.006543/0.4108, allocations: 95.25 kB / 0.53 GB, free: 2.543 MB / 398.1 MB Notification: Performance of NFTyping.typeComponents: time 0.005377/0.4162, allocations: 1.463 MB / 0.5314 GB, free: 1.07 MB / 398.1 MB Notification: Performance of NFTyping.typeBindings: time 0.02039/0.4366, allocations: 5.17 MB / 0.5365 GB, free: 11.87 MB / 414.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.02928/0.4659, allocations: 9.001 MB / 0.5453 GB, free: 2.82 MB / 414.1 MB Notification: Performance of NFFlatten.flatten: time 0.02674/0.4927, allocations: 25.65 MB / 0.5703 GB, free: 9.074 MB / 446.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.2674/0.7601, allocations: 17.22 MB / 0.5872 GB, free: 11.94 MB / 446.1 MB Notification: Performance of NFEvalConstants.evaluate: time 0.02527/0.7855, allocations: 15.55 MB / 0.6023 GB, free: 11.49 MB / 446.1 MB Notification: Performance of NFSimplifyModel.simplify: time 0.03074/0.8162, allocations: 14.09 MB / 0.6161 GB, free: 9.723 MB / 446.1 MB Notification: Performance of NFPackage.collectConstants: time 0.01152/0.8278, allocations: 1.429 MB / 0.6175 GB, free: 9.719 MB / 446.1 MB Notification: Performance of NFFlatten.collectFunctions: time 0.03883/0.8666, allocations: 9.024 MB / 0.6263 GB, free: 9 MB / 446.1 MB Notification: Performance of NFScalarize.scalarize: time 0.01261/0.8793, allocations: 4.985 MB / 0.6312 GB, free: 7.18 MB / 446.1 MB Notification: Performance of NFVerifyModel.verify: time 0.02531/0.9046, allocations: 10.05 MB / 0.641 GB, free: 3.648 MB / 446.1 MB Notification: Performance of NFConvertDAE.convert: time 0.04543/0.9501, allocations: 32.5 MB / 0.6727 GB, free: 1.34 MB / 462.1 MB Notification: Performance of FrontEnd - DAE generated: time 5.681e-06/0.9501, allocations: 0 / 0.6727 GB, free: 1.34 MB / 462.1 MB Notification: Performance of FrontEnd: time 2.374e-06/0.9502, allocations: 0 / 0.6727 GB, free: 1.34 MB / 462.1 MB Notification: Performance of Transformations before backend: time 0.001362/0.9515, allocations: 0 / 0.6727 GB, free: 1.34 MB / 462.1 MB Notification: Model statistics after passing the front-end and creating the data structures used by the back-end: * Number of equations: 3808 * Number of variables: 3808 Notification: Performance of Generate backend data structure: time 0.07279/1.024, allocations: 20.17 MB / 0.6924 GB, free: 13.3 MB / 494.1 MB Notification: Performance of prepare preOptimizeDAE: time 4.961e-05/1.024, allocations: 10.72 kB / 0.6924 GB, free: 13.29 MB / 494.1 MB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.02548/1.05, allocations: 3.904 MB / 0.6962 GB, free: 9.375 MB / 494.1 MB Notification: Performance of preOpt evaluateParameters (simulation): time 0.03114/1.081, allocations: 11.46 MB / 0.7074 GB, free: 14.32 MB / 0.4981 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.002552/1.084, allocations: 2.131 MB / 0.7095 GB, free: 11.98 MB / 0.4981 GB Notification: Performance of preOpt expandDerOperator (simulation): time 0.01056/1.094, allocations: 1.533 MB / 0.711 GB, free: 10.45 MB / 0.4981 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.09648/1.191, allocations: 34.79 MB / 0.745 GB, free: 7.441 MB / 0.5294 GB Notification: Performance of preOpt findStateOrder (simulation): time 0.000691/1.191, allocations: 11.22 kB / 0.745 GB, free: 7.438 MB / 0.5294 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.01017/1.202, allocations: 0.5898 MB / 0.7456 GB, free: 6.848 MB / 0.5294 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0003422/1.202, allocations: 362.7 kB / 0.7459 GB, free: 6.496 MB / 0.5294 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.5873/1.789, allocations: 46.83 MB / 0.7917 GB, free: 189.9 MB / 0.5607 GB Warning: The model contains alias variables with redundant start and/or conflicting nominal values. It is recommended to resolve the conflicts, because otherwise the system could be hard to solve. To print the conflicting alias sets and the chosen candidates please use -d=aliasConflicts. Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.2607/2.05, allocations: 127.9 MB / 0.9165 GB, free: 110.4 MB / 0.5607 GB Notification: Performance of preOpt comSubExp (simulation): time 0.9844/3.035, allocations: 276.1 MB / 1.186 GB, free: 74.73 MB / 0.5608 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.03014/3.065, allocations: 19.82 MB / 1.205 GB, free: 55.05 MB / 0.5608 GB Notification: Performance of preOpt evalFunc (simulation): time 0.4606/3.525, allocations: 87.13 MB / 1.291 GB, free: 174.2 MB / 0.5608 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001969/3.526, allocations: 130.4 kB / 1.291 GB, free: 174 MB / 0.5608 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.02813/3.554, allocations: 4.437 MB / 1.295 GB, free: 172.9 MB / 0.5608 GB Notification: Performance of pre-optimization done (n=995): time 9.93e-05/3.554, allocations: 0 / 1.295 GB, free: 172.9 MB / 0.5608 GB Notification: Performance of matching and sorting (n=1129): time 0.7151/4.269, allocations: 131 MB / 1.423 GB, free: 78.66 MB / 0.5608 GB Notification: Performance of inlineWhenForInitialization (initialization): time 9.736e-05/4.269, allocations: 168.2 kB / 1.423 GB, free: 78.48 MB / 0.5608 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.01492/4.284, allocations: 10.16 MB / 1.433 GB, free: 68.39 MB / 0.5608 GB Notification: Performance of collectPreVariables (initialization): time 0.004924/4.289, allocations: 217.7 kB / 1.433 GB, free: 68.17 MB / 0.5608 GB Notification: Performance of collectInitialEqns (initialization): time 0.005303/4.294, allocations: 6.884 MB / 1.44 GB, free: 61.27 MB / 0.5608 GB Notification: Performance of collectInitialBindings (initialization): time 0.008353/4.303, allocations: 3.913 MB / 1.444 GB, free: 57.38 MB / 0.5608 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.007247/4.31, allocations: 1.156 MB / 1.445 GB, free: 56.22 MB / 0.5608 GB Notification: Performance of setup shared object (initialization): time 0.0001028/4.31, allocations: 301.1 kB / 1.445 GB, free: 55.92 MB / 0.5608 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.3417/4.652, allocations: 11.82 MB / 1.457 GB, free: 178.3 MB / 0.5608 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.02568/4.678, allocations: 16.55 MB / 1.473 GB, free: 170.4 MB / 0.5608 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.06712/4.745, allocations: 29.74 MB / 1.502 GB, free: 154.2 MB / 0.5608 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0002406/4.745, allocations: 42.31 kB / 1.502 GB, free: 154.2 MB / 0.5608 GB Notification: Performance of matching and sorting (n=1889) (initialization): time 0.4651/5.21, allocations: 81.56 MB / 1.582 GB, free: 102.4 MB / 0.5608 GB Notification: Performance of prepare postOptimizeDAE: time 0.0001282/5.21, allocations: 72 kB / 1.582 GB, free: 102.3 MB / 0.5608 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0002517/5.21, allocations: 148 kB / 1.582 GB, free: 102.1 MB / 0.5608 GB Notification: Performance of postOpt tearingSystem (initialization): time 0.06238/5.273, allocations: 22.54 MB / 1.604 GB, free: 79.8 MB / 0.5608 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01836/5.291, allocations: 3.726 MB / 1.608 GB, free: 76.07 MB / 0.5608 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.5108/5.802, allocations: 88.3 MB / 1.694 GB, free: 150.2 MB / 0.5608 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.02096/5.823, allocations: 1.15 MB / 1.695 GB, free: 150 MB / 0.5608 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.00567/5.829, allocations: 0.9338 MB / 1.696 GB, free: 149.9 MB / 0.5608 GB Notification: Model statistics after passing the back-end for initialization: * Number of independent subsystems: 677 * 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 (1841): * Single equations (assignments): 1838 * Array equations: 0 * Algorithm blocks: 0 * Record equations: 0 * When equations: 0 * If-equations: 0 * Equation systems (not torn): 0 * Torn equation systems: 3 * Mixed (continuous/discrete) equation systems: 0 Notification: Torn system details for strict tearing set: * Linear torn systems (#iteration vars, #inner vars, density): 2 systems {(1,3,100.0%), (33,10,82.4%)} * Non-linear torn systems (#iteration vars, #inner vars): 1 system {(1,3)} Notification: Performance of prepare postOptimizeDAE: time 0.0165/5.845, allocations: 5.38 MB / 1.701 GB, free: 147.9 MB / 0.5608 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.007866/5.853, allocations: 1.054 MB / 1.702 GB, free: 147.9 MB / 0.5608 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.2846/6.138, allocations: 48.56 MB / 1.749 GB, free: 123 MB / 0.5608 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.0001344/6.138, allocations: 124 kB / 1.75 GB, free: 122.8 MB / 0.5608 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 0.000166/6.138, allocations: 16 kB / 1.75 GB, free: 122.8 MB / 0.5608 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0004147/6.139, allocations: 59.77 kB / 1.75 GB, free: 122.8 MB / 0.5608 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.3269/6.465, allocations: 72.94 MB / 1.821 GB, free: 50.05 MB / 0.5608 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 0.0001139/6.466, allocations: 6.625 kB / 1.821 GB, free: 50.05 MB / 0.5608 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.01471/6.48, allocations: 2.415 MB / 1.823 GB, free: 47.63 MB / 0.5608 GB Notification: Performance of postOpt tearingSystem (simulation): time 0.2779/6.758, allocations: 11.74 MB / 1.835 GB, free: 159.9 MB / 0.5608 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.005628/6.764, allocations: 482.8 kB / 1.835 GB, free: 159.9 MB / 0.5608 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.1084/6.872, allocations: 42.2 MB / 1.876 GB, free: 149.4 MB / 0.5608 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 6.011e-06/6.872, allocations: 7.75 kB / 1.876 GB, free: 149.4 MB / 0.5608 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.2965/7.169, allocations: 62.67 MB / 1.938 GB, free: 127 MB / 0.5608 GB Notification: Performance of postOpt removeConstants (simulation): time 0.01102/7.18, allocations: 3.303 MB / 1.941 GB, free: 125.5 MB / 0.5608 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.005402/7.185, allocations: 293.8 kB / 1.941 GB, free: 125.3 MB / 0.5608 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.01471/7.2, allocations: 0.7922 MB / 1.942 GB, free: 124.8 MB / 0.5608 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.007152/7.207, allocations: 1.496 MB / 1.943 GB, free: 123.3 MB / 0.5608 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.003581/7.211, allocations: 475.2 kB / 1.944 GB, free: 122.8 MB / 0.5608 GB Notification: Performance of sorting global known variables: time 0.01203/7.223, allocations: 6.966 MB / 1.951 GB, free: 115.9 MB / 0.5608 GB Notification: Performance of sort global known variables: time 6.52e-07/7.223, allocations: 0 / 1.951 GB, free: 115.9 MB / 0.5608 GB Notification: Performance of remove unused functions: time 0.03222/7.255, allocations: 6.671 MB / 1.957 GB, free: 109.7 MB / 0.5608 GB Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 15 * Number of states: 60 (solution.temperature,O2_free.logn,H2O.logn,relaxed.OxyHm[1].logn,relaxed.OxyHm[2].logn,relaxed.OxyHm[3].logn,relaxed.OxyHm[4].logn,relaxed.DeoxyHm[1].logn,relaxed.DeoxyHm[2].logn,relaxed.DeoxyHm[3].logn,relaxed.DeoxyHm[4].logn,relaxed.HmAH[1].logn,relaxed.HmAH[2].logn,relaxed.HmAH[3].logn,relaxed.HmAH[4].logn,relaxed.HmA[1].logn,relaxed.HmA[2].logn,relaxed.HmA[3].logn,relaxed.HmA[4].logn,relaxed.HmNH3[1].logn,relaxed.HmNH3[2].logn,relaxed.HmNH3[3].logn,relaxed.HmNH3[4].logn,relaxed.HmNH2[1].logn,relaxed.HmNH2[2].logn,relaxed.HmNH2[3].logn,relaxed.HmNH2[4].logn,relaxed.HmNHCOO[1].logn,relaxed.HmNHCOO[2].logn,relaxed.HmNHCOO[3].logn,relaxed.HmNHCOO[4].logn,tensed.OxyHm[1].logn,tensed.OxyHm[2].logn,tensed.OxyHm[3].logn,tensed.OxyHm[4].logn,tensed.DeoxyHm[1].logn,tensed.DeoxyHm[2].logn,tensed.DeoxyHm[3].logn,tensed.DeoxyHm[4].logn,tensed.HmAH[1].logn,tensed.HmAH[2].logn,tensed.HmAH[3].logn,tensed.HmAH[4].logn,tensed.HmA[1].logn,tensed.HmA[2].logn,tensed.HmA[3].logn,tensed.HmA[4].logn,tensed.HmNH3[1].logn,tensed.HmNH3[2].logn,tensed.HmNH3[3].logn,tensed.HmNH3[4].logn,tensed.HmNH2[1].logn,tensed.HmNH2[2].logn,tensed.HmNH2[3].logn,tensed.HmNH2[4].logn,tensed.HmNHCOO[1].logn,tensed.HmNHCOO[2].logn,tensed.HmNHCOO[3].logn,tensed.HmNHCOO[4].logn,CO2_free.logn) * 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 (1234): * Single equations (assignments): 1231 * Array equations: 0 * Algorithm blocks: 0 * Record equations: 0 * When equations: 0 * If-equations: 0 * Equation systems (not torn): 0 * Torn equation systems: 3 * Mixed (continuous/discrete) equation systems: 0 Notification: Torn system details for strict tearing set: * Linear torn systems (#iteration vars, #inner vars, density): 2 systems {(1,3,100.0%), (33,10,82.4%)} * Non-linear torn systems (#iteration vars, #inner vars): 1 system {(1,3)} Notification: Performance of Backend phase and start with SimCode phase: time 0.0098/7.265, allocations: 3.516 MB / 1.961 GB, free: 107.2 MB / 0.5608 GB Notification: Performance of simCode: created initialization part: time 0.06843/7.334, allocations: 27.72 MB / 1.988 GB, free: 79.51 MB / 0.5608 GB Notification: Performance of simCode: created event and clocks part: time 9.899e-06/7.334, allocations: 4 kB / 1.988 GB, free: 79.5 MB / 0.5608 GB Notification: Performance of simCode: created simulation system equations: time 0.0401/7.374, allocations: 14.86 MB / 2.002 GB, free: 64.63 MB / 0.5608 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.02536/7.399, allocations: 2.335 MB / 2.004 GB, free: 62.49 MB / 0.5608 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.3191/7.718, allocations: 44.42 MB / 2.048 GB, free: 156 MB / 0.5608 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0166/7.735, allocations: 9.633 MB / 2.057 GB, free: 155 MB / 0.5608 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.009063/7.744, allocations: 1.541 MB / 2.059 GB, free: 155 MB / 0.5608 GB Notification: Performance of SimCode: time 1.072e-06/7.744, allocations: 1.312 kB / 2.059 GB, free: 155 MB / 0.5608 GB Notification: Performance of Templates: time 1.14/8.884, allocations: 0.5088 GB / 2.568 GB, free: 76.45 MB / 0.5608 GB make -j1 -f Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.makefile (rm -f Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.pipe ; mkfifo Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.pipe ; head -c 1048576 < Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.pipe >> ../files/Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.sim & ./Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery -abortSlowSimulation -alarm=480 -lv LOG_STATS > Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.pipe 2>&1)