Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries/ --ompython_omhome=/usr Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.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.HemoglobinCarboxylation,tolerance=1e-05,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation") translateModel(Chemical.Examples.Hemoglobin.HemoglobinCarboxylation,tolerance=1e-05,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation") Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.007229/0.007229, allocations: 101.3 kB / 15.88 MB, free: 6.305 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001593/0.001594, allocations: 196.6 kB / 16.79 MB, free: 6.234 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.438/1.438, allocations: 222.9 MB / 240.5 MB, free: 4.566 MB / 190.1 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.2631/0.2631, allocations: 15.3 MB / 305.9 MB, free: 15.33 MB / 254.1 MB Warning: Ignoring unknown experiment annotation option: __Dymola_Algorithm = "Dassl" Notification: Performance of FrontEnd - loaded program: time 0.00122/0.00122, allocations: 59.91 kB / 370.3 MB, free: 4.402 MB / 302.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.1099/0.1111, allocations: 53.61 MB / 423.9 MB, free: 14.74 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.HemoglobinCarboxylation): time 0.2855/0.3966, allocations: 44.24 MB / 468.2 MB, free: 36.02 MB / 366.1 MB Notification: Performance of NFInst.instExpressions: time 0.07395/0.4706, allocations: 72.57 MB / 0.5281 GB, free: 10.02 MB / 398.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.005916/0.4766, allocations: 103.2 kB / 0.5282 GB, free: 9.918 MB / 398.1 MB Notification: Performance of NFTyping.typeComponents: time 0.005779/0.4824, allocations: 1.457 MB / 0.5296 GB, free: 8.809 MB / 398.1 MB Notification: Performance of NFTyping.typeBindings: time 0.0215/0.5039, allocations: 5.166 MB / 0.5346 GB, free: 4.52 MB / 398.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.03416/0.5381, allocations: 9.008 MB / 0.5434 GB, free: 11.82 MB / 414.1 MB Notification: Performance of NFFlatten.flatten: time 0.03181/0.5699, allocations: 25.66 MB / 0.5685 GB, free: 2.07 MB / 430.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.02382/0.5938, allocations: 17.92 MB / 0.586 GB, free: 36 kB / 446.1 MB Notification: Performance of NFEvalConstants.evaluate: time 0.5488/1.143, allocations: 16.16 MB / 0.6018 GB, free: 17.58 MB / 462.1 MB Notification: Performance of NFSimplifyModel.simplify: time 0.0294/1.172, allocations: 14.88 MB / 0.6163 GB, free: 17.18 MB / 462.1 MB Notification: Performance of NFPackage.collectConstants: time 0.01316/1.185, allocations: 1.685 MB / 0.6179 GB, free: 17.18 MB / 462.1 MB Notification: Performance of NFFlatten.collectFunctions: time 0.05869/1.244, allocations: 9.275 MB / 0.627 GB, free: 17.18 MB / 462.1 MB Notification: Performance of NFScalarize.scalarize: time 0.02125/1.265, allocations: 5.398 MB / 0.6323 GB, free: 16.58 MB / 462.1 MB Notification: Performance of NFVerifyModel.verify: time 0.0415/1.307, allocations: 10.52 MB / 0.6425 GB, free: 14.2 MB / 462.1 MB Notification: Performance of NFConvertDAE.convert: time 0.04746/1.354, allocations: 33.2 MB / 0.675 GB, free: 6.961 MB / 462.1 MB Notification: Performance of FrontEnd - DAE generated: time 8.396e-06/1.355, allocations: 0 / 0.675 GB, free: 6.961 MB / 462.1 MB Notification: Performance of FrontEnd: time 2.164e-06/1.355, allocations: 0 / 0.675 GB, free: 6.961 MB / 462.1 MB Notification: Performance of Transformations before backend: time 0.001254/1.356, allocations: 0 / 0.675 GB, free: 6.961 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 0.1025/1.458, allocations: 24.75 MB / 0.6991 GB, free: 9.387 MB / 478.1 MB Notification: Performance of prepare preOptimizeDAE: time 5.197e-05/1.458, allocations: 9.094 kB / 0.6991 GB, free: 9.387 MB / 478.1 MB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.03009/1.488, allocations: 3.889 MB / 0.7029 GB, free: 5.641 MB / 478.1 MB Notification: Performance of preOpt evaluateParameters (simulation): time 0.03414/1.523, allocations: 11.77 MB / 0.7144 GB, free: 10.28 MB / 494.1 MB Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.002538/1.525, allocations: 2.138 MB / 0.7165 GB, free: 7.93 MB / 494.1 MB Notification: Performance of preOpt expandDerOperator (simulation): time 0.01213/1.537, allocations: 1.531 MB / 0.718 GB, free: 6.398 MB / 494.1 MB Notification: Performance of preOpt clockPartitioning (simulation): time 0.112/1.649, allocations: 34.79 MB / 0.752 GB, free: 3.395 MB / 0.5138 GB Notification: Performance of preOpt findStateOrder (simulation): time 0.0008613/1.65, allocations: 8.594 kB / 0.752 GB, free: 3.391 MB / 0.5138 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.01209/1.662, allocations: 0.5925 MB / 0.7526 GB, free: 2.801 MB / 0.5138 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0003468/1.663, allocations: 360 kB / 0.7529 GB, free: 2.449 MB / 0.5138 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.1113/1.774, allocations: 46.83 MB / 0.7986 GB, free: 3.625 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 0.5892/2.363, allocations: 128 MB / 0.9237 GB, free: 119.4 MB / 0.5607 GB Notification: Performance of preOpt comSubExp (simulation): time 0.8704/3.234, allocations: 276 MB / 1.193 GB, free: 91.4 MB / 0.5607 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.03608/3.27, allocations: 19.81 MB / 1.213 GB, free: 75.34 MB / 0.5607 GB Notification: Performance of preOpt evalFunc (simulation): time 0.41/3.68, allocations: 87.57 MB / 1.298 GB, free: 176.2 MB / 0.5607 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001349/3.68, allocations: 141.4 kB / 1.298 GB, free: 176.2 MB / 0.5607 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.02419/3.704, allocations: 4.428 MB / 1.303 GB, free: 176 MB / 0.5607 GB Notification: Performance of pre-optimization done (n=995): time 5.854e-05/3.704, allocations: 0 / 1.303 GB, free: 176 MB / 0.5607 GB Notification: Performance of matching and sorting (n=1129): time 0.7291/4.433, allocations: 135.9 MB / 1.435 GB, free: 99.32 MB / 0.5607 GB Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001256/4.434, allocations: 168.2 kB / 1.435 GB, free: 99.14 MB / 0.5607 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.02259/4.456, allocations: 10.16 MB / 1.445 GB, free: 89.05 MB / 0.5607 GB Notification: Performance of collectPreVariables (initialization): time 0.004979/4.461, allocations: 209.7 kB / 1.446 GB, free: 88.84 MB / 0.5607 GB Notification: Performance of collectInitialEqns (initialization): time 0.005135/4.466, allocations: 6.896 MB / 1.452 GB, free: 81.92 MB / 0.5607 GB Notification: Performance of collectInitialBindings (initialization): time 0.008238/4.475, allocations: 3.906 MB / 1.456 GB, free: 78.05 MB / 0.5607 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.01704/4.492, allocations: 3.256 MB / 1.459 GB, free: 74.78 MB / 0.5607 GB Notification: Performance of setup shared object (initialization): time 5.185e-05/4.492, allocations: 305.1 kB / 1.46 GB, free: 74.48 MB / 0.5607 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.02179/4.514, allocations: 11.82 MB / 1.471 GB, free: 62.64 MB / 0.5607 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.2972/4.811, allocations: 16.55 MB / 1.487 GB, free: 168.7 MB / 0.5607 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.05241/4.863, allocations: 29.74 MB / 1.516 GB, free: 156.2 MB / 0.5607 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.00031/4.864, allocations: 45.84 kB / 1.516 GB, free: 156.2 MB / 0.5607 GB Notification: Performance of matching and sorting (n=1889) (initialization): time 0.4431/5.307, allocations: 81.46 MB / 1.596 GB, free: 119.9 MB / 0.5607 GB Notification: Performance of prepare postOptimizeDAE: time 0.000315/5.307, allocations: 68 kB / 1.596 GB, free: 119.8 MB / 0.5607 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0003607/5.308, allocations: 153.1 kB / 1.596 GB, free: 119.7 MB / 0.5607 GB Notification: Performance of postOpt tearingSystem (initialization): time 0.05806/5.366, allocations: 22.37 MB / 1.618 GB, free: 97.54 MB / 0.5607 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01722/5.383, allocations: 3.725 MB / 1.622 GB, free: 93.81 MB / 0.5607 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.4507/5.834, allocations: 88.27 MB / 1.708 GB, free: 148.8 MB / 0.5607 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.02239/5.856, allocations: 1.152 MB / 1.709 GB, free: 148.6 MB / 0.5607 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.00681/5.863, allocations: 0.9285 MB / 1.71 GB, free: 148.5 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 0.02079/5.884, allocations: 5.381 MB / 1.715 GB, free: 146.4 MB / 0.5607 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.007727/5.892, allocations: 1.052 MB / 1.716 GB, free: 146.4 MB / 0.5607 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.2904/6.182, allocations: 48.62 MB / 1.764 GB, free: 129.2 MB / 0.5607 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.0002209/6.182, allocations: 122.7 kB / 1.764 GB, free: 129.2 MB / 0.5607 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 0.0002851/6.183, allocations: 19.12 kB / 1.764 GB, free: 129.2 MB / 0.5607 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0005668/6.183, allocations: 62.53 kB / 1.764 GB, free: 129.2 MB / 0.5607 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.3246/6.508, allocations: 73.04 MB / 1.835 GB, free: 65.32 MB / 0.5607 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 0.0001799/6.508, allocations: 9.562 kB / 1.835 GB, free: 65.31 MB / 0.5607 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.01493/6.523, allocations: 2.415 MB / 1.838 GB, free: 63.01 MB / 0.5607 GB Notification: Performance of postOpt tearingSystem (simulation): time 0.03205/6.555, allocations: 11.89 MB / 1.849 GB, free: 51.33 MB / 0.5607 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.004826/6.56, allocations: 475.5 kB / 1.85 GB, free: 50.87 MB / 0.5607 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.3738/6.934, allocations: 42.18 MB / 1.891 GB, free: 155.8 MB / 0.5607 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 8.356e-06/6.934, allocations: 7.781 kB / 1.891 GB, free: 155.8 MB / 0.5607 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.3101/7.244, allocations: 62.73 MB / 1.952 GB, free: 136.3 MB / 0.5607 GB Notification: Performance of postOpt removeConstants (simulation): time 0.01483/7.259, allocations: 3.289 MB / 1.955 GB, free: 134.8 MB / 0.5607 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.007408/7.266, allocations: 295.2 kB / 1.956 GB, free: 134.6 MB / 0.5607 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.01801/7.284, allocations: 0.7963 MB / 1.956 GB, free: 134.2 MB / 0.5607 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.007719/7.292, allocations: 1.495 MB / 1.958 GB, free: 133.4 MB / 0.5607 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.003744/7.296, allocations: 465.5 kB / 1.958 GB, free: 133.2 MB / 0.5607 GB Notification: Performance of sorting global known variables: time 0.0139/7.31, allocations: 6.966 MB / 1.965 GB, free: 129.6 MB / 0.5607 GB Notification: Performance of sort global known variables: time 6.61e-07/7.31, allocations: 1.656 kB / 1.965 GB, free: 129.6 MB / 0.5607 GB Notification: Performance of remove unused functions: time 0.03687/7.347, allocations: 6.667 MB / 1.972 GB, free: 124.6 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 0.01128/7.358, allocations: 3.542 MB / 1.975 GB, free: 122 MB / 0.5607 GB Notification: Performance of simCode: created initialization part: time 0.07636/7.434, allocations: 27.71 MB / 2.002 GB, free: 94.55 MB / 0.5607 GB Notification: Performance of simCode: created event and clocks part: time 1.339e-05/7.434, allocations: 0 / 2.002 GB, free: 94.55 MB / 0.5607 GB Notification: Performance of simCode: created simulation system equations: time 0.04543/7.48, allocations: 14.86 MB / 2.017 GB, free: 79.66 MB / 0.5607 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.02601/7.506, allocations: 2.343 MB / 2.019 GB, free: 77.52 MB / 0.5607 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.3445/7.851, allocations: 44.16 MB / 2.062 GB, free: 152.4 MB / 0.5607 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.01955/7.87, allocations: 9.63 MB / 2.071 GB, free: 151.4 MB / 0.5607 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.01096/7.881, allocations: 1.545 MB / 2.073 GB, free: 151.4 MB / 0.5607 GB Notification: Performance of SimCode: time 1.112e-06/7.881, allocations: 0 / 2.073 GB, free: 151.4 MB / 0.5607 GB Notification: Performance of Templates: time 1.201/9.082, allocations: 0.5109 GB / 2.584 GB, free: 85.73 MB / 0.5607 GB make -j1 -f Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.makefile (rm -f Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.pipe ; mkfifo Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.pipe ; head -c 1048576 < Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.pipe >> ../files/Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.sim & ./Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation -abortSlowSimulation -alarm=480 -lv LOG_STATS > Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.pipe 2>&1)