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 0.001152/0.001152, allocations: 100.1 kB / 15.88 MB, free: 12 kB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001176/0.001176, allocations: 197.4 kB / 16.79 MB, free: 6.809 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.329/1.329, allocations: 222.9 MB / 240.5 MB, free: 4.535 MB / 190.1 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.2649/0.2649, allocations: 15.32 MB / 305.9 MB, free: 15.31 MB / 254.1 MB Notification: Performance of FrontEnd - loaded program: time 0.001262/0.001262, allocations: 55.91 kB / 370.3 MB, free: 4.414 MB / 302.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.1209/0.1221, allocations: 53.61 MB / 423.9 MB, free: 14.75 MB / 366.1 MB [/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo:4740:7-4740:66: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:4740:7-4740:66: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 0.2639/0.3861, allocations: 44.24 MB / 468.2 MB, free: 35.4 MB / 366.1 MB Notification: Performance of NFInst.instExpressions: time 0.07898/0.4651, allocations: 72.56 MB / 0.528 GB, free: 9.785 MB / 398.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.007436/0.4726, allocations: 111.2 kB / 0.5282 GB, free: 9.676 MB / 398.1 MB Notification: Performance of NFTyping.typeComponents: time 0.00647/0.4791, allocations: 1.454 MB / 0.5296 GB, free: 8.57 MB / 398.1 MB Notification: Performance of NFTyping.typeBindings: time 0.0225/0.5017, allocations: 5.178 MB / 0.5346 GB, free: 4.27 MB / 398.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.03301/0.5347, allocations: 9.004 MB / 0.5434 GB, free: 11.66 MB / 414.1 MB Notification: Performance of NFFlatten.flatten: time 0.03492/0.5697, allocations: 25.66 MB / 0.5685 GB, free: 1.906 MB / 430.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.02677/0.5965, allocations: 17.92 MB / 0.586 GB, free: 15.87 MB / 462.1 MB Notification: Performance of NFEvalConstants.evaluate: time 0.5054/1.102, allocations: 16.16 MB / 0.6018 GB, free: 17.49 MB / 462.1 MB Notification: Performance of NFSimplifyModel.simplify: time 0.02588/1.128, allocations: 14.89 MB / 0.6163 GB, free: 17.09 MB / 462.1 MB Notification: Performance of NFPackage.collectConstants: time 0.01135/1.139, allocations: 1.686 MB / 0.618 GB, free: 17.09 MB / 462.1 MB Notification: Performance of NFFlatten.collectFunctions: time 0.05142/1.191, allocations: 9.277 MB / 0.627 GB, free: 17.09 MB / 462.1 MB Notification: Performance of NFScalarize.scalarize: time 0.01771/1.208, allocations: 5.39 MB / 0.6323 GB, free: 16.5 MB / 462.1 MB Notification: Performance of NFVerifyModel.verify: time 0.04282/1.251, allocations: 10.52 MB / 0.6426 GB, free: 14.12 MB / 462.1 MB Notification: Performance of NFConvertDAE.convert: time 0.05535/1.307, allocations: 33.2 MB / 0.675 GB, free: 6.738 MB / 462.1 MB Notification: Performance of FrontEnd - DAE generated: time 8.526e-06/1.307, allocations: 0 / 0.675 GB, free: 6.738 MB / 462.1 MB Notification: Performance of FrontEnd: time 1.844e-06/1.307, allocations: 0 / 0.675 GB, free: 6.738 MB / 462.1 MB Notification: Performance of Transformations before backend: time 0.001285/1.308, allocations: 0 / 0.675 GB, free: 6.738 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 0.1132/1.421, allocations: 24.76 MB / 0.6992 GB, free: 9.152 MB / 478.1 MB Notification: Performance of prepare preOptimizeDAE: time 6.045e-05/1.421, allocations: 12.53 kB / 0.6992 GB, free: 9.152 MB / 478.1 MB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.03103/1.452, allocations: 3.891 MB / 0.703 GB, free: 5.285 MB / 478.1 MB Notification: Performance of preOpt evaluateParameters (simulation): time 0.03405/1.487, allocations: 11.76 MB / 0.7145 GB, free: 9.934 MB / 494.1 MB Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.002551/1.489, allocations: 2.131 MB / 0.7165 GB, free: 7.586 MB / 494.1 MB Notification: Performance of preOpt expandDerOperator (simulation): time 0.01334/1.503, allocations: 1.537 MB / 0.718 GB, free: 6.051 MB / 494.1 MB Notification: Performance of preOpt clockPartitioning (simulation): time 0.1066/1.609, allocations: 34.79 MB / 0.752 GB, free: 3.043 MB / 0.5138 GB Notification: Performance of preOpt findStateOrder (simulation): time 0.0008573/1.61, allocations: 10.75 kB / 0.752 GB, free: 3.039 MB / 0.5138 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.01393/1.624, allocations: 0.5869 MB / 0.7526 GB, free: 2.453 MB / 0.5138 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0003478/1.624, allocations: 362.7 kB / 0.7529 GB, free: 2.102 MB / 0.5138 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.1061/1.73, allocations: 46.83 MB / 0.7987 GB, free: 3.27 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 0.588/2.319, allocations: 128.1 MB / 0.9238 GB, free: 119.3 MB / 0.5607 GB Notification: Performance of preOpt comSubExp (simulation): time 0.8838/3.202, allocations: 276 MB / 1.193 GB, free: 90.49 MB / 0.5607 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.03462/3.237, allocations: 19.81 MB / 1.213 GB, free: 74.67 MB / 0.5607 GB Notification: Performance of preOpt evalFunc (simulation): time 0.4636/3.701, allocations: 87.58 MB / 1.298 GB, free: 176.1 MB / 0.5607 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.000131/3.701, allocations: 138 kB / 1.298 GB, free: 176.1 MB / 0.5607 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.0255/3.726, allocations: 4.43 MB / 1.303 GB, free: 176 MB / 0.5607 GB Notification: Performance of pre-optimization done (n=995): time 8.241e-05/3.727, allocations: 0 / 1.303 GB, free: 176 MB / 0.5607 GB Notification: Performance of matching and sorting (n=1129): time 0.6664/4.393, allocations: 130.7 MB / 1.43 GB, free: 103.6 MB / 0.5607 GB Notification: Performance of inlineWhenForInitialization (initialization): time 9.591e-05/4.393, allocations: 168.2 kB / 1.43 GB, free: 103.4 MB / 0.5607 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.01586/4.409, allocations: 10.16 MB / 1.44 GB, free: 93.29 MB / 0.5607 GB Notification: Performance of collectPreVariables (initialization): time 0.005198/4.414, allocations: 213.7 kB / 1.441 GB, free: 93.07 MB / 0.5607 GB Notification: Performance of collectInitialEqns (initialization): time 0.00499/4.419, allocations: 6.876 MB / 1.447 GB, free: 86.18 MB / 0.5607 GB Notification: Performance of collectInitialBindings (initialization): time 0.008191/4.427, allocations: 3.913 MB / 1.451 GB, free: 82.29 MB / 0.5607 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.01557/4.443, allocations: 3.256 MB / 1.454 GB, free: 79.02 MB / 0.5607 GB Notification: Performance of setup shared object (initialization): time 5.215e-05/4.443, allocations: 305.8 kB / 1.455 GB, free: 78.73 MB / 0.5607 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.02101/4.464, allocations: 11.82 MB / 1.466 GB, free: 66.89 MB / 0.5607 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.3233/4.787, allocations: 16.56 MB / 1.482 GB, free: 167.9 MB / 0.5607 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.05307/4.841, allocations: 29.73 MB / 1.511 GB, free: 157.4 MB / 0.5607 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0003244/4.841, allocations: 42.16 kB / 1.511 GB, free: 157.4 MB / 0.5607 GB Notification: Performance of matching and sorting (n=1889) (initialization): time 0.4412/5.282, allocations: 81.47 MB / 1.591 GB, free: 124.1 MB / 0.5607 GB Notification: Performance of prepare postOptimizeDAE: time 0.0001357/5.282, allocations: 76 kB / 1.591 GB, free: 124.1 MB / 0.5607 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0002397/5.283, allocations: 148 kB / 1.591 GB, free: 123.9 MB / 0.5607 GB Notification: Performance of postOpt tearingSystem (initialization): time 0.05678/5.339, allocations: 22.39 MB / 1.613 GB, free: 101.8 MB / 0.5607 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01765/5.357, allocations: 3.728 MB / 1.617 GB, free: 98.02 MB / 0.5607 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.4427/5.8, allocations: 88.28 MB / 1.703 GB, free: 151.1 MB / 0.5607 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.02263/5.822, allocations: 1.141 MB / 1.704 GB, free: 150.8 MB / 0.5607 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.00806/5.831, allocations: 0.9347 MB / 1.705 GB, free: 150.7 MB / 0.5607 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 0.02256/5.853, allocations: 5.375 MB / 1.71 GB, free: 148.7 MB / 0.5607 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.008575/5.862, allocations: 1.054 MB / 1.711 GB, free: 148.7 MB / 0.5607 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.2844/6.146, allocations: 48.63 MB / 1.759 GB, free: 132.6 MB / 0.5607 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.0001574/6.146, allocations: 118.6 kB / 1.759 GB, free: 132.6 MB / 0.5607 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 0.0001125/6.147, allocations: 20.5 kB / 1.759 GB, free: 132.6 MB / 0.5607 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0004136/6.147, allocations: 59.77 kB / 1.759 GB, free: 132.5 MB / 0.5607 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.323/6.47, allocations: 73.05 MB / 1.83 GB, free: 69.9 MB / 0.5607 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 0.0001397/6.47, allocations: 4 kB / 1.83 GB, free: 69.9 MB / 0.5607 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.01424/6.484, allocations: 2.421 MB / 1.833 GB, free: 67.59 MB / 0.5607 GB Notification: Performance of postOpt tearingSystem (simulation): time 0.03135/6.516, allocations: 11.88 MB / 1.844 GB, free: 55.92 MB / 0.5607 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.004581/6.52, allocations: 475.5 kB / 1.845 GB, free: 55.45 MB / 0.5607 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.3459/6.866, allocations: 42.17 MB / 1.886 GB, free: 157.5 MB / 0.5607 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 7.243e-06/6.866, allocations: 9.766 kB / 1.886 GB, free: 157.5 MB / 0.5607 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.2892/7.156, allocations: 62.73 MB / 1.947 GB, free: 139.8 MB / 0.5607 GB Notification: Performance of postOpt removeConstants (simulation): time 0.01091/7.167, allocations: 3.294 MB / 1.95 GB, free: 138.3 MB / 0.5607 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.006398/7.173, allocations: 296.5 kB / 1.951 GB, free: 138.1 MB / 0.5607 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.01441/7.187, allocations: 0.7928 MB / 1.951 GB, free: 137.7 MB / 0.5607 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.007676/7.195, allocations: 1.488 MB / 1.953 GB, free: 136.8 MB / 0.5607 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.003984/7.199, allocations: 475.8 kB / 1.953 GB, free: 136.7 MB / 0.5607 GB Notification: Performance of sorting global known variables: time 0.0135/7.213, allocations: 6.967 MB / 1.96 GB, free: 133.1 MB / 0.5607 GB Notification: Performance of sort global known variables: time 5.21e-07/7.213, allocations: 2.688 kB / 1.96 GB, free: 133.1 MB / 0.5607 GB Notification: Performance of remove unused functions: time 0.03569/7.248, allocations: 6.67 MB / 1.967 GB, free: 129.1 MB / 0.5607 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 0.01112/7.26, allocations: 3.54 MB / 1.97 GB, free: 126.6 MB / 0.5607 GB Notification: Performance of simCode: created initialization part: time 0.06876/7.328, allocations: 27.72 MB / 1.997 GB, free: 99.16 MB / 0.5607 GB Notification: Performance of simCode: created event and clocks part: time 1.15e-05/7.328, allocations: 0 / 1.997 GB, free: 99.16 MB / 0.5607 GB Notification: Performance of simCode: created simulation system equations: time 0.042/7.37, allocations: 14.86 MB / 2.012 GB, free: 84.27 MB / 0.5607 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0203/7.391, allocations: 2.34 MB / 2.014 GB, free: 82.13 MB / 0.5607 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.3161/7.707, allocations: 44.18 MB / 2.057 GB, free: 153.2 MB / 0.5607 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.01459/7.722, allocations: 9.636 MB / 2.066 GB, free: 152.2 MB / 0.5607 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.009424/7.731, allocations: 1.54 MB / 2.068 GB, free: 152.2 MB / 0.5607 GB Notification: Performance of SimCode: time 1.383e-06/7.731, allocations: 0 / 2.068 GB, free: 152.2 MB / 0.5607 GB Notification: Performance of Templates: time 1.085/8.816, allocations: 0.511 GB / 2.579 GB, free: 86.07 MB / 0.5607 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)