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 0.001246/0.001246, allocations: 111.9 kB / 15.99 MB, free: 5.91 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001216/0.001216, allocations: 190.7 kB / 16.91 MB, free: 5.758 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.336/1.336, allocations: 222.9 MB / 240.6 MB, free: 15.45 MB / 206.1 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.07604/0.07604, allocations: 15.31 MB / 306 MB, free: 15.61 MB / 254.1 MB Notification: Performance of FrontEnd - loaded program: time 0.00128/0.00128, allocations: 63.14 kB / 370.5 MB, free: 51.02 MB / 302.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.1034/0.1047, allocations: 53.63 MB / 424.1 MB, free: 14.52 MB / 302.1 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 0.04946/0.1542, allocations: 44.24 MB / 468.3 MB, free: 2.32 MB / 334.1 MB Notification: Performance of NFInst.instExpressions: time 0.3122/0.4665, allocations: 71.77 MB / 0.5274 GB, free: 15.28 MB / 382.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.005612/0.4721, allocations: 105.7 kB / 0.5275 GB, free: 15.28 MB / 382.1 MB Notification: Performance of NFTyping.typeComponents: time 0.005576/0.4777, allocations: 1.452 MB / 0.529 GB, free: 15.27 MB / 382.1 MB Notification: Performance of NFTyping.typeBindings: time 0.01894/0.4967, allocations: 5.332 MB / 0.5342 GB, free: 15.02 MB / 382.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.02879/0.5255, allocations: 9.177 MB / 0.5431 GB, free: 12.51 MB / 382.1 MB Notification: Performance of NFFlatten.flatten: time 0.02605/0.5516, allocations: 26.69 MB / 0.5692 GB, free: 10.59 MB / 398.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.03022/0.5819, allocations: 21.86 MB / 0.5905 GB, free: 5.895 MB / 414.1 MB Notification: Performance of NFEvalConstants.evaluate: time 0.02969/0.6116, allocations: 18.76 MB / 0.6089 GB, free: 3.363 MB / 430.1 MB Notification: Performance of NFSimplifyModel.simplify: time 0.02848/0.6401, allocations: 16.52 MB / 0.625 GB, free: 3.281 MB / 446.1 MB Notification: Performance of NFPackage.collectConstants: time 0.01115/0.6513, allocations: 3.094 MB / 0.628 GB, free: 192 kB / 446.1 MB Notification: Performance of NFFlatten.collectFunctions: time 0.03844/0.6898, allocations: 10.89 MB / 0.6386 GB, free: 5.375 MB / 462.1 MB Notification: Performance of NFScalarize.scalarize: time 0.01327/0.7031, allocations: 7.076 MB / 0.6456 GB, free: 14.48 MB / 478.1 MB Notification: Performance of NFVerifyModel.verify: time 0.0265/0.7296, allocations: 12.27 MB / 0.6575 GB, free: 2.379 MB / 478.1 MB Notification: Performance of NFConvertDAE.convert: time 0.04362/0.7733, allocations: 33.64 MB / 0.6904 GB, free: 2.129 MB / 0.4981 GB Notification: Performance of FrontEnd - DAE generated: time 6.672e-06/0.7733, allocations: 4 kB / 0.6904 GB, free: 2.125 MB / 0.4981 GB Notification: Performance of FrontEnd: time 2.024e-06/0.7733, allocations: 0 / 0.6904 GB, free: 2.125 MB / 0.4981 GB Notification: Performance of Transformations before backend: time 0.0009858/0.7743, allocations: 0 / 0.6904 GB, free: 2.125 MB / 0.4981 GB 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 0.4218/1.196, allocations: 24.75 MB / 0.7146 GB, free: 161.5 MB / 0.4982 GB Notification: Performance of prepare preOptimizeDAE: time 4.221e-05/1.196, allocations: 11.84 kB / 0.7146 GB, free: 161.5 MB / 0.4982 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.02404/1.22, allocations: 3.89 MB / 0.7184 GB, free: 159.8 MB / 0.4982 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0249/1.245, allocations: 11.78 MB / 0.7299 GB, free: 153 MB / 0.4982 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.001825/1.247, allocations: 2.134 MB / 0.732 GB, free: 150.9 MB / 0.4982 GB Notification: Performance of preOpt expandDerOperator (simulation): time 0.008524/1.256, allocations: 1.523 MB / 0.7334 GB, free: 149.4 MB / 0.4982 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0782/1.334, allocations: 34.79 MB / 0.7674 GB, free: 114.4 MB / 0.4982 GB Notification: Performance of preOpt findStateOrder (simulation): time 0.0005557/1.334, allocations: 14.44 kB / 0.7674 GB, free: 114.4 MB / 0.4982 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.007476/1.342, allocations: 0.5906 MB / 0.768 GB, free: 113.8 MB / 0.4982 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0002371/1.342, allocations: 360 kB / 0.7684 GB, free: 113.4 MB / 0.4982 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.08206/1.424, allocations: 46.83 MB / 0.8141 GB, free: 66.55 MB / 0.4982 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 0.4699/1.894, allocations: 128.1 MB / 0.9392 GB, free: 104.4 MB / 0.4982 GB Notification: Performance of preOpt comSubExp (simulation): time 0.8493/2.744, allocations: 276 MB / 1.209 GB, free: 57.32 MB / 0.5138 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.03368/2.777, allocations: 19.81 MB / 1.228 GB, free: 37.47 MB / 0.5138 GB Notification: Performance of preOpt evalFunc (simulation): time 0.4297/3.207, allocations: 87.57 MB / 1.314 GB, free: 161.3 MB / 0.5294 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 9.237e-05/3.207, allocations: 129.4 kB / 1.314 GB, free: 161.1 MB / 0.5294 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.0248/3.232, allocations: 4.521 MB / 1.318 GB, free: 160.2 MB / 0.5294 GB Notification: Performance of pre-optimization done (n=995): time 9.364e-05/3.232, allocations: 0 / 1.318 GB, free: 160.2 MB / 0.5294 GB Notification: Performance of matching and sorting (n=1129): time 0.6501/3.882, allocations: 130.7 MB / 1.446 GB, free: 47.96 MB / 0.5294 GB Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001235/3.882, allocations: 168.2 kB / 1.446 GB, free: 47.78 MB / 0.5294 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.02039/3.903, allocations: 10.16 MB / 1.456 GB, free: 37.68 MB / 0.5294 GB Notification: Performance of collectPreVariables (initialization): time 0.00503/3.908, allocations: 209.7 kB / 1.456 GB, free: 37.47 MB / 0.5294 GB Notification: Performance of collectInitialEqns (initialization): time 0.005612/3.913, allocations: 6.883 MB / 1.463 GB, free: 30.57 MB / 0.5294 GB Notification: Performance of collectInitialBindings (initialization): time 0.008095/3.922, allocations: 3.912 MB / 1.467 GB, free: 26.69 MB / 0.5294 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.3023/4.224, allocations: 3.262 MB / 1.47 GB, free: 168.6 MB / 0.5294 GB Notification: Performance of setup shared object (initialization): time 7.902e-05/4.224, allocations: 301.1 kB / 1.47 GB, free: 168.3 MB / 0.5294 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.02537/4.249, allocations: 11.82 MB / 1.482 GB, free: 166 MB / 0.5294 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.02626/4.276, allocations: 16.56 MB / 1.498 GB, free: 155.8 MB / 0.5294 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0486/4.324, allocations: 29.73 MB / 1.527 GB, free: 139.5 MB / 0.5294 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0002507/4.325, allocations: 44.75 kB / 1.527 GB, free: 139.5 MB / 0.5294 GB Notification: Performance of matching and sorting (n=1889) (initialization): time 0.4159/4.741, allocations: 81.46 MB / 1.606 GB, free: 67.87 MB / 0.5294 GB Notification: Performance of prepare postOptimizeDAE: time 0.0003199/4.741, allocations: 68 kB / 1.607 GB, free: 67.8 MB / 0.5294 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0003806/4.741, allocations: 156 kB / 1.607 GB, free: 67.65 MB / 0.5294 GB Notification: Performance of postOpt tearingSystem (initialization): time 0.05956/4.801, allocations: 22.4 MB / 1.629 GB, free: 45.41 MB / 0.5294 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01723/4.818, allocations: 3.728 MB / 1.632 GB, free: 41.68 MB / 0.5294 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.4828/5.301, allocations: 93.97 MB / 1.724 GB, free: 127 MB / 0.5294 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.01996/5.321, allocations: 1.143 MB / 1.725 GB, free: 126.5 MB / 0.5294 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.005817/5.327, allocations: 0.9321 MB / 1.726 GB, free: 126.2 MB / 0.5294 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 0.01798/5.345, allocations: 5.38 MB / 1.731 GB, free: 123.2 MB / 0.5294 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.006602/5.351, allocations: 1.056 MB / 1.732 GB, free: 123.2 MB / 0.5294 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.2689/5.62, allocations: 48.63 MB / 1.78 GB, free: 80.45 MB / 0.5294 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.0001874/5.621, allocations: 120 kB / 1.78 GB, free: 80.33 MB / 0.5294 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 0.0001833/5.621, allocations: 23.69 kB / 1.78 GB, free: 80.31 MB / 0.5294 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0004992/5.621, allocations: 59.77 kB / 1.78 GB, free: 80.25 MB / 0.5294 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.5833/6.205, allocations: 73.04 MB / 1.851 GB, free: 133.9 MB / 0.5294 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 0.0001294/6.205, allocations: 5.375 kB / 1.851 GB, free: 133.9 MB / 0.5294 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.01417/6.219, allocations: 2.417 MB / 1.854 GB, free: 133.9 MB / 0.5294 GB Notification: Performance of postOpt tearingSystem (simulation): time 0.03316/6.252, allocations: 11.88 MB / 1.865 GB, free: 133.8 MB / 0.5294 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.00431/6.257, allocations: 476.5 kB / 1.866 GB, free: 133.8 MB / 0.5294 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.176/6.433, allocations: 46.96 MB / 1.912 GB, free: 119.1 MB / 0.5294 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.709e-06/6.433, allocations: 7.562 kB / 1.912 GB, free: 119.1 MB / 0.5294 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.2794/6.712, allocations: 62.73 MB / 1.973 GB, free: 80.02 MB / 0.5294 GB Notification: Performance of postOpt removeConstants (simulation): time 0.01131/6.723, allocations: 3.3 MB / 1.976 GB, free: 77.3 MB / 0.5294 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.006073/6.73, allocations: 298.3 kB / 1.976 GB, free: 77.02 MB / 0.5294 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.01553/6.745, allocations: 0.7898 MB / 1.977 GB, free: 76.26 MB / 0.5294 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.007509/6.753, allocations: 1.507 MB / 1.979 GB, free: 74.75 MB / 0.5294 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.003937/6.757, allocations: 471.6 kB / 1.979 GB, free: 74.29 MB / 0.5294 GB Notification: Performance of sorting global known variables: time 0.01201/6.769, allocations: 6.97 MB / 1.986 GB, free: 67.37 MB / 0.5294 GB Notification: Performance of sort global known variables: time 5.81e-07/6.769, allocations: 0 / 1.986 GB, free: 67.37 MB / 0.5294 GB Notification: Performance of remove unused functions: time 0.03487/6.804, allocations: 6.666 MB / 1.992 GB, free: 61.07 MB / 0.5294 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 0.01174/6.815, allocations: 3.532 MB / 1.996 GB, free: 58.02 MB / 0.5294 GB Notification: Performance of simCode: created initialization part: time 0.4934/7.309, allocations: 108.8 MB / 2.102 GB, free: 140.4 MB / 0.5294 GB Notification: Performance of simCode: created event and clocks part: time 9.908e-06/7.309, allocations: 0 / 2.102 GB, free: 140.4 MB / 0.5294 GB Notification: Performance of simCode: created simulation system equations: time 0.03887/7.348, allocations: 14.86 MB / 2.117 GB, free: 127.9 MB / 0.5294 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0194/7.367, allocations: 2.511 MB / 2.119 GB, free: 126.1 MB / 0.5294 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.08872/7.456, allocations: 44.18 MB / 2.162 GB, free: 87.11 MB / 0.5294 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0148/7.471, allocations: 9.634 MB / 2.172 GB, free: 78.75 MB / 0.5294 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.008088/7.479, allocations: 1.576 MB / 2.173 GB, free: 77.18 MB / 0.5294 GB Notification: Performance of SimCode: time 1.182e-06/7.479, allocations: 0 / 2.173 GB, free: 77.18 MB / 0.5294 GB Notification: Performance of Templates: time 1.231/8.71, allocations: 0.511 GB / 2.684 GB, free: 138.7 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)