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 0.001106/0.001106, allocations: 108 kB / 15.6 MB, free: 132 kB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001096/0.001096, allocations: 194.1 kB / 16.53 MB, free: 6.391 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.184/1.184, allocations: 222.9 MB / 240.2 MB, free: 4.387 MB / 190.1 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.1667/0.1667, allocations: 15.32 MB / 305.7 MB, free: 15.23 MB / 254.1 MB Warning: Ignoring unknown experiment annotation option: __Dymola_Algorithm = "Dassl" Notification: Performance of FrontEnd - loaded program: time 0.001128/0.001128, allocations: 59.91 kB / 370.3 MB, free: 3.914 MB / 302.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.08234/0.08348, allocations: 53.6 MB / 423.9 MB, free: 14.26 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 0.1817/0.2652, allocations: 41.58 MB / 465.5 MB, free: 36.79 MB / 366.1 MB Notification: Performance of NFInst.instExpressions: time 0.05849/0.3237, allocations: 72.71 MB / 0.5256 GB, free: 12.24 MB / 398.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.003604/0.3273, allocations: 59.69 kB / 0.5257 GB, free: 12.18 MB / 398.1 MB Notification: Performance of NFTyping.typeComponents: time 0.003907/0.3312, allocations: 1.624 MB / 0.5273 GB, free: 10.9 MB / 398.1 MB Notification: Performance of NFTyping.typeBindings: time 0.01549/0.3467, allocations: 5.928 MB / 0.5331 GB, free: 5.844 MB / 398.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.02475/0.3715, allocations: 10.2 MB / 0.543 GB, free: 11.58 MB / 414.1 MB Notification: Performance of NFFlatten.flatten: time 0.02415/0.3957, allocations: 26.59 MB / 0.569 GB, free: 0.9062 MB / 430.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.02194/0.4177, allocations: 21.96 MB / 0.5904 GB, free: 10.84 MB / 462.1 MB Notification: Performance of NFEvalConstants.evaluate: time 0.3965/0.8142, allocations: 17.43 MB / 0.6074 GB, free: 24.66 MB / 462.1 MB Notification: Performance of NFSimplifyModel.simplify: time 0.02414/0.8384, allocations: 16.19 MB / 0.6233 GB, free: 24.24 MB / 462.1 MB Notification: Performance of NFPackage.collectConstants: time 0.01293/0.8514, allocations: 3.094 MB / 0.6263 GB, free: 24.24 MB / 462.1 MB Notification: Performance of NFFlatten.collectFunctions: time 0.04629/0.8977, allocations: 10.7 MB / 0.6367 GB, free: 24.24 MB / 462.1 MB Notification: Performance of NFScalarize.scalarize: time 0.01505/0.9128, allocations: 6.976 MB / 0.6435 GB, free: 23.65 MB / 462.1 MB Notification: Performance of NFVerifyModel.verify: time 0.02649/0.9393, allocations: 12.16 MB / 0.6554 GB, free: 16.81 MB / 462.1 MB Notification: Performance of NFConvertDAE.convert: time 0.06436/1.004, allocations: 41.84 MB / 0.6963 GB, free: 12.99 MB / 478.1 MB Notification: Performance of FrontEnd - DAE generated: time 7.885e-06/1.004, allocations: 0 / 0.6963 GB, free: 12.99 MB / 478.1 MB Notification: Performance of FrontEnd: time 2.004e-06/1.004, allocations: 0 / 0.6963 GB, free: 12.99 MB / 478.1 MB Notification: Performance of Transformations before backend: time 0.001268/1.005, allocations: 0 / 0.6963 GB, free: 12.99 MB / 478.1 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 0.08066/1.086, allocations: 24.75 MB / 0.7205 GB, free: 4.516 MB / 494.1 MB Notification: Performance of prepare preOptimizeDAE: time 4.099e-05/1.086, allocations: 8.031 kB / 0.7205 GB, free: 4.508 MB / 494.1 MB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.02323/1.109, allocations: 3.884 MB / 0.7243 GB, free: 0.6133 MB / 494.1 MB Notification: Performance of preOpt evaluateParameters (simulation): time 0.02634/1.135, allocations: 11.77 MB / 0.7357 GB, free: 5.254 MB / 0.4982 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.002045/1.137, allocations: 2.131 MB / 0.7378 GB, free: 2.906 MB / 0.4982 GB Notification: Performance of preOpt expandDerOperator (simulation): time 0.009357/1.147, allocations: 1.531 MB / 0.7393 GB, free: 1.379 MB / 0.4982 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.077/1.224, allocations: 34.79 MB / 0.7733 GB, free: 14.37 MB / 0.545 GB Notification: Performance of preOpt findStateOrder (simulation): time 0.0005659/1.224, allocations: 13.62 kB / 0.7733 GB, free: 14.37 MB / 0.545 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.006906/1.231, allocations: 0.5879 MB / 0.7739 GB, free: 13.78 MB / 0.545 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0002658/1.232, allocations: 360 kB / 0.7742 GB, free: 13.43 MB / 0.545 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.4142/1.646, allocations: 46.83 MB / 0.82 GB, free: 185.4 MB / 0.5608 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 0.2338/1.88, allocations: 128.2 MB / 0.9452 GB, free: 101.4 MB / 0.5608 GB Notification: Performance of preOpt comSubExp (simulation): time 0.6907/2.57, allocations: 276 MB / 1.215 GB, free: 63.61 MB / 0.5608 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.03161/2.602, allocations: 19.81 MB / 1.234 GB, free: 44.87 MB / 0.5608 GB Notification: Performance of preOpt evalFunc (simulation): time 0.3216/2.924, allocations: 87.55 MB / 1.32 GB, free: 165.5 MB / 0.5608 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 9.503e-05/2.924, allocations: 138.3 kB / 1.32 GB, free: 165.4 MB / 0.5608 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.01764/2.941, allocations: 4.506 MB / 1.324 GB, free: 164.4 MB / 0.5608 GB Notification: Performance of pre-optimization done (n=995): time 4.203e-05/2.942, allocations: 0 / 1.324 GB, free: 164.4 MB / 0.5608 GB Notification: Performance of matching and sorting (n=1129): time 0.6386/3.58, allocations: 136 MB / 1.457 GB, free: 63.59 MB / 0.5608 GB Notification: Performance of inlineWhenForInitialization (initialization): time 9.929e-05/3.58, allocations: 171.2 kB / 1.457 GB, free: 63.41 MB / 0.5608 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.1919/3.772, allocations: 10.14 MB / 1.467 GB, free: 175.3 MB / 0.5608 GB Notification: Performance of collectPreVariables (initialization): time 0.003695/3.776, allocations: 212.3 kB / 1.467 GB, free: 175.3 MB / 0.5608 GB Notification: Performance of collectInitialEqns (initialization): time 0.004275/3.78, allocations: 6.893 MB / 1.474 GB, free: 173.8 MB / 0.5608 GB Notification: Performance of collectInitialBindings (initialization): time 0.005522/3.786, allocations: 3.908 MB / 1.478 GB, free: 171.3 MB / 0.5608 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.005051/3.791, allocations: 3.262 MB / 1.481 GB, free: 170 MB / 0.5608 GB Notification: Performance of setup shared object (initialization): time 3.74e-05/3.791, allocations: 303.7 kB / 1.481 GB, free: 169.8 MB / 0.5608 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.01454/3.805, allocations: 11.82 MB / 1.493 GB, free: 165.4 MB / 0.5608 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.01914/3.825, allocations: 16.55 MB / 1.509 GB, free: 155.3 MB / 0.5608 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0409/3.865, allocations: 29.74 MB / 1.538 GB, free: 139.5 MB / 0.5608 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0002276/3.866, allocations: 43.25 kB / 1.538 GB, free: 139.5 MB / 0.5608 GB Notification: Performance of matching and sorting (n=1889) (initialization): time 0.4064/4.272, allocations: 81.46 MB / 1.618 GB, free: 87.09 MB / 0.5608 GB Notification: Performance of prepare postOptimizeDAE: time 0.0002244/4.272, allocations: 68 kB / 1.618 GB, free: 87.02 MB / 0.5608 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0002563/4.273, allocations: 148.5 kB / 1.618 GB, free: 86.88 MB / 0.5608 GB Notification: Performance of postOpt tearingSystem (initialization): time 0.05266/4.325, allocations: 22.38 MB / 1.64 GB, free: 64.64 MB / 0.5608 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01522/4.341, allocations: 3.722 MB / 1.643 GB, free: 60.92 MB / 0.5608 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.365/4.706, allocations: 93.97 MB / 1.735 GB, free: 139.8 MB / 0.5608 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.01748/4.723, allocations: 0.8391 MB / 1.736 GB, free: 139.5 MB / 0.5608 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.005051/4.728, allocations: 0.9353 MB / 1.737 GB, free: 139.2 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 0.01482/4.743, allocations: 5.375 MB / 1.742 GB, free: 136.1 MB / 0.5608 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.006418/4.749, allocations: 1.052 MB / 1.743 GB, free: 136.1 MB / 0.5608 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.2564/5.006, allocations: 48.61 MB / 1.79 GB, free: 100.2 MB / 0.5608 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.0001256/5.006, allocations: 120 kB / 1.791 GB, free: 100.1 MB / 0.5608 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 0.0001495/5.006, allocations: 16.62 kB / 1.791 GB, free: 100.1 MB / 0.5608 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0004727/5.007, allocations: 63.77 kB / 1.791 GB, free: 100 MB / 0.5608 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.4734/5.48, allocations: 73.05 MB / 1.862 GB, free: 145 MB / 0.5608 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 9.25e-05/5.48, allocations: 3.969 kB / 1.862 GB, free: 145 MB / 0.5608 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0129/5.493, allocations: 2.413 MB / 1.864 GB, free: 145 MB / 0.5608 GB Notification: Performance of postOpt tearingSystem (simulation): time 0.02928/5.522, allocations: 11.89 MB / 1.876 GB, free: 144.9 MB / 0.5608 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.003564/5.526, allocations: 473.6 kB / 1.876 GB, free: 144.9 MB / 0.5608 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.1/5.626, allocations: 46.96 MB / 1.922 GB, free: 131 MB / 0.5608 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.378e-06/5.626, allocations: 3.906 kB / 1.922 GB, free: 131 MB / 0.5608 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.2636/5.89, allocations: 62.73 MB / 1.984 GB, free: 102.2 MB / 0.5608 GB Notification: Performance of postOpt removeConstants (simulation): time 0.008588/5.898, allocations: 3.3 MB / 1.987 GB, free: 99.45 MB / 0.5608 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.004621/5.903, allocations: 296.5 kB / 1.987 GB, free: 99.16 MB / 0.5608 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.01113/5.914, allocations: 0.5189 MB / 1.988 GB, free: 98.64 MB / 0.5608 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.004623/5.919, allocations: 1.506 MB / 1.989 GB, free: 97.13 MB / 0.5608 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.001039/5.92, allocations: 475.6 kB / 1.989 GB, free: 96.66 MB / 0.5608 GB Notification: Performance of sorting global known variables: time 0.007508/5.927, allocations: 6.965 MB / 1.996 GB, free: 89.75 MB / 0.5608 GB Notification: Performance of sort global known variables: time 2.2e-07/5.927, allocations: 0 / 1.996 GB, free: 89.75 MB / 0.5608 GB Notification: Performance of remove unused functions: time 0.02072/5.948, allocations: 6.678 MB / 2.003 GB, free: 83.44 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 0.00668/5.955, allocations: 3.53 MB / 2.006 GB, free: 80.8 MB / 0.5608 GB Notification: Performance of simCode: created initialization part: time 0.4201/6.375, allocations: 108.8 MB / 2.112 GB, free: 159.1 MB / 0.5608 GB Notification: Performance of simCode: created event and clocks part: time 6.783e-06/6.375, allocations: 0 / 2.112 GB, free: 159.1 MB / 0.5608 GB Notification: Performance of simCode: created simulation system equations: time 0.03413/6.409, allocations: 14.87 MB / 2.127 GB, free: 146.6 MB / 0.5608 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.01339/6.422, allocations: 2.505 MB / 2.129 GB, free: 144.8 MB / 0.5608 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.07208/6.495, allocations: 38.16 MB / 2.167 GB, free: 111.9 MB / 0.5608 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.01153/6.506, allocations: 9.94 MB / 2.176 GB, free: 104.7 MB / 0.5608 GB Notification: Performance of simCode: alias equations: time 0.0152/6.521, allocations: 5.198 MB / 2.181 GB, free: 101.5 MB / 0.5608 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.005835/6.527, allocations: 1.446 MB / 2.183 GB, free: 100.3 MB / 0.5608 GB Notification: Performance of SimCode: time 7.42e-07/6.527, allocations: 0 / 2.183 GB, free: 100.3 MB / 0.5608 GB Notification: Performance of Templates: time 0.7598/7.287, allocations: 327.1 MB / 2.502 GB, free: 142.9 MB / 0.5608 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)