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 0.0012/0.0012, allocations: 106.7 kB / 16.41 MB, free: 6.473 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001098/0.001098, allocations: 187 kB / 17.34 MB, free: 5.754 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.314/1.314, allocations: 222.9 MB / 241 MB, free: 15.14 MB / 206.1 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.08407/0.08407, allocations: 15.31 MB / 306.5 MB, free: 15.42 MB / 254.1 MB Notification: Performance of FrontEnd - loaded program: time 0.001235/0.001236, allocations: 59.91 kB / 425.9 MB, free: 11.45 MB / 302.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.1048/0.106, allocations: 53.62 MB / 479.5 MB, free: 5.777 MB / 350.1 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 0.4419/0.548, allocations: 41.61 MB / 0.5089 GB, free: 2.332 MB / 382.1 MB Notification: Performance of NFInst.instExpressions: time 0.074/0.622, allocations: 72.71 MB / 0.5799 GB, free: 5.145 MB / 430.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.004738/0.6268, allocations: 63.25 kB / 0.58 GB, free: 5.121 MB / 430.1 MB Notification: Performance of NFTyping.typeComponents: time 0.004985/0.6318, allocations: 1.62 MB / 0.5815 GB, free: 3.828 MB / 430.1 MB Notification: Performance of NFTyping.typeBindings: time 0.02023/0.6521, allocations: 5.919 MB / 0.5873 GB, free: 15.16 MB / 446.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.02795/0.6801, allocations: 10.21 MB / 0.5973 GB, free: 7.129 MB / 446.1 MB Notification: Performance of NFFlatten.flatten: time 0.02643/0.7065, allocations: 26.69 MB / 0.6234 GB, free: 15.57 MB / 478.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.02639/0.7329, allocations: 21.97 MB / 0.6448 GB, free: 9.492 MB / 494.1 MB Notification: Performance of NFEvalConstants.evaluate: time 0.02653/0.7595, allocations: 17.48 MB / 0.6619 GB, free: 7.98 MB / 0.4982 GB Notification: Performance of NFSimplifyModel.simplify: time 0.02883/0.7884, allocations: 16.2 MB / 0.6777 GB, free: 7.738 MB / 0.5138 GB Notification: Performance of NFPackage.collectConstants: time 0.01104/0.7995, allocations: 3.09 MB / 0.6807 GB, free: 4.648 MB / 0.5138 GB Notification: Performance of NFFlatten.collectFunctions: time 0.03673/0.8362, allocations: 10.71 MB / 0.6912 GB, free: 9.93 MB / 0.5294 GB Notification: Performance of NFScalarize.scalarize: time 0.01238/0.8487, allocations: 6.973 MB / 0.698 GB, free: 2.941 MB / 0.5294 GB Notification: Performance of NFVerifyModel.verify: time 0.0232/0.8719, allocations: 12.16 MB / 0.7098 GB, free: 6.738 MB / 0.545 GB Notification: Performance of NFConvertDAE.convert: time 0.3515/1.223, allocations: 42.22 MB / 0.7511 GB, free: 60.19 MB / 0.545 GB Notification: Performance of FrontEnd - DAE generated: time 7.394e-06/1.223, allocations: 0 / 0.7511 GB, free: 60.19 MB / 0.545 GB Notification: Performance of FrontEnd: time 2.144e-06/1.223, allocations: 0 / 0.7511 GB, free: 60.19 MB / 0.545 GB Notification: Performance of Transformations before backend: time 0.00126/1.225, allocations: 0 / 0.7511 GB, free: 60.19 MB / 0.545 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 0.09867/1.323, allocations: 24.72 MB / 0.7752 GB, free: 53.19 MB / 0.545 GB Notification: Performance of prepare preOptimizeDAE: time 4.134e-05/1.323, allocations: 7.906 kB / 0.7752 GB, free: 53.19 MB / 0.545 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.02859/1.352, allocations: 3.896 MB / 0.779 GB, free: 51.71 MB / 0.545 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.03057/1.383, allocations: 12 MB / 0.7908 GB, free: 48.29 MB / 0.545 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.002416/1.385, allocations: 2.133 MB / 0.7928 GB, free: 47.12 MB / 0.545 GB Notification: Performance of preOpt expandDerOperator (simulation): time 0.015/1.4, allocations: 1.528 MB / 0.7943 GB, free: 47.07 MB / 0.545 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.09024/1.49, allocations: 34.8 MB / 0.8283 GB, free: 15.41 MB / 0.545 GB Notification: Performance of preOpt findStateOrder (simulation): time 0.0006798/1.491, allocations: 8.969 kB / 0.8283 GB, free: 15.41 MB / 0.545 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.01071/1.502, allocations: 0.5859 MB / 0.8289 GB, free: 14.82 MB / 0.545 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0002194/1.502, allocations: 365 kB / 0.8292 GB, free: 14.47 MB / 0.545 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.09658/1.599, allocations: 46.83 MB / 0.875 GB, free: 15.64 MB / 0.5919 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 0.6093/2.208, allocations: 127.9 MB / 0.9999 GB, free: 215.5 MB / 0.6544 GB Notification: Performance of preOpt comSubExp (simulation): time 0.8597/3.068, allocations: 276 MB / 1.269 GB, free: 221.5 MB / 0.6544 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.042/3.11, allocations: 19.81 MB / 1.289 GB, free: 218.4 MB / 0.6544 GB Notification: Performance of preOpt evalFunc (simulation): time 0.172/3.282, allocations: 87.47 MB / 1.374 GB, free: 158.2 MB / 0.6544 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001477/3.282, allocations: 140.9 kB / 1.374 GB, free: 158.1 MB / 0.6544 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.02373/3.306, allocations: 4.51 MB / 1.379 GB, free: 153.7 MB / 0.6544 GB Notification: Performance of pre-optimization done (n=995): time 7.533e-05/3.306, allocations: 2.656 kB / 1.379 GB, free: 153.7 MB / 0.6544 GB Notification: Performance of matching and sorting (n=1129): time 0.6663/3.972, allocations: 130.7 MB / 1.506 GB, free: 23.75 MB / 0.6544 GB Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001293/3.973, allocations: 164.2 kB / 1.507 GB, free: 23.58 MB / 0.6544 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.02187/3.994, allocations: 10.16 MB / 1.516 GB, free: 13.48 MB / 0.6544 GB Notification: Performance of collectPreVariables (initialization): time 0.00526/4, allocations: 216.2 kB / 1.517 GB, free: 13.27 MB / 0.6544 GB Notification: Performance of collectInitialEqns (initialization): time 0.00478/4.005, allocations: 6.885 MB / 1.523 GB, free: 6.367 MB / 0.6544 GB Notification: Performance of collectInitialBindings (initialization): time 0.007995/4.013, allocations: 3.909 MB / 1.527 GB, free: 2.488 MB / 0.6544 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.3978/4.41, allocations: 3.256 MB / 1.53 GB, free: 239.6 MB / 0.6544 GB Notification: Performance of setup shared object (initialization): time 6.129e-05/4.411, allocations: 306.1 kB / 1.531 GB, free: 239.3 MB / 0.6544 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.02887/4.439, allocations: 11.83 MB / 1.542 GB, free: 239 MB / 0.6544 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.02931/4.469, allocations: 16.56 MB / 1.558 GB, free: 228.8 MB / 0.6544 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.05149/4.52, allocations: 29.73 MB / 1.587 GB, free: 212.6 MB / 0.6544 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0003562/4.521, allocations: 41.72 kB / 1.587 GB, free: 212.6 MB / 0.6544 GB Notification: Performance of matching and sorting (n=1889) (initialization): time 0.4249/4.946, allocations: 81.47 MB / 1.667 GB, free: 148.1 MB / 0.6544 GB Notification: Performance of prepare postOptimizeDAE: time 0.0003654/4.946, allocations: 68 kB / 1.667 GB, free: 148 MB / 0.6544 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0003793/4.946, allocations: 152.2 kB / 1.667 GB, free: 147.9 MB / 0.6544 GB Notification: Performance of postOpt tearingSystem (initialization): time 0.05634/5.003, allocations: 22.39 MB / 1.689 GB, free: 125.6 MB / 0.6544 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01752/5.02, allocations: 3.731 MB / 1.693 GB, free: 121.9 MB / 0.6544 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.5302/5.551, allocations: 93.95 MB / 1.784 GB, free: 210.2 MB / 0.6544 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.01963/5.57, allocations: 0.8367 MB / 1.785 GB, free: 210.2 MB / 0.6544 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.006057/5.576, allocations: 0.9367 MB / 1.786 GB, free: 210.2 MB / 0.6544 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 0.01749/5.594, allocations: 5.37 MB / 1.791 GB, free: 210 MB / 0.6544 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.006578/5.6, allocations: 1.061 MB / 1.793 GB, free: 210 MB / 0.6544 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.2667/5.867, allocations: 48.59 MB / 1.84 GB, free: 198.3 MB / 0.6544 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.0001544/5.867, allocations: 122.4 kB / 1.84 GB, free: 198.3 MB / 0.6544 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 0.0001664/5.868, allocations: 25.58 kB / 1.84 GB, free: 198.3 MB / 0.6544 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0004299/5.868, allocations: 59.83 kB / 1.84 GB, free: 198.3 MB / 0.6544 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.3097/6.178, allocations: 73.05 MB / 1.911 GB, free: 142.1 MB / 0.6544 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 0.0001047/6.178, allocations: 4 kB / 1.911 GB, free: 142.1 MB / 0.6544 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.01381/6.192, allocations: 2.415 MB / 1.914 GB, free: 139.7 MB / 0.6544 GB Notification: Performance of postOpt tearingSystem (simulation): time 0.03028/6.222, allocations: 11.88 MB / 1.925 GB, free: 128 MB / 0.6544 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.003909/6.226, allocations: 471.5 kB / 1.926 GB, free: 127.5 MB / 0.6544 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.1062/6.332, allocations: 46.94 MB / 1.972 GB, free: 80.25 MB / 0.6544 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 5.229e-06/6.332, allocations: 8.062 kB / 1.972 GB, free: 80.25 MB / 0.6544 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.5467/6.879, allocations: 62.73 MB / 2.033 GB, free: 204.5 MB / 0.6544 GB Notification: Performance of postOpt removeConstants (simulation): time 0.01/6.889, allocations: 3.292 MB / 2.036 GB, free: 203.6 MB / 0.6544 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.005762/6.895, allocations: 297 kB / 2.037 GB, free: 203.4 MB / 0.6544 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.01471/6.91, allocations: 0.5271 MB / 2.037 GB, free: 203.2 MB / 0.6544 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.008911/6.918, allocations: 1.504 MB / 2.038 GB, free: 203 MB / 0.6544 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.003785/6.922, allocations: 471.2 kB / 2.039 GB, free: 202.9 MB / 0.6544 GB Notification: Performance of sorting global known variables: time 0.01303/6.935, allocations: 6.97 MB / 2.046 GB, free: 200.6 MB / 0.6544 GB Notification: Performance of sort global known variables: time 9.02e-07/6.935, allocations: 2.219 kB / 2.046 GB, free: 200.6 MB / 0.6544 GB Notification: Performance of remove unused functions: time 0.03045/6.966, allocations: 6.674 MB / 2.052 GB, free: 200 MB / 0.6544 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 0.01124/6.977, allocations: 3.535 MB / 2.056 GB, free: 199.4 MB / 0.6544 GB Notification: Performance of simCode: created initialization part: time 0.06799/7.045, allocations: 27.79 MB / 2.083 GB, free: 189.1 MB / 0.6544 GB Notification: Performance of simCode: created event and clocks part: time 1.076e-05/7.045, allocations: 0 / 2.083 GB, free: 189.1 MB / 0.6544 GB Notification: Performance of simCode: created simulation system equations: time 0.04186/7.087, allocations: 14.87 MB / 2.097 GB, free: 183.3 MB / 0.6544 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.02432/7.111, allocations: 2.509 MB / 2.1 GB, free: 182.5 MB / 0.6544 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.1026/7.214, allocations: 37.52 MB / 2.136 GB, free: 151.8 MB / 0.6544 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.02122/7.235, allocations: 9.637 MB / 2.146 GB, free: 144.7 MB / 0.6544 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.01059/7.246, allocations: 1.562 MB / 2.147 GB, free: 143.4 MB / 0.6544 GB Notification: Performance of SimCode: time 1.032e-06/7.246, allocations: 0 / 2.147 GB, free: 143.4 MB / 0.6544 GB Notification: Performance of Templates: time 1.121/8.367, allocations: 0.5133 GB / 2.661 GB, free: 93.01 MB / 0.6544 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)