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 0.0008523/0.0008523, allocations: 98.27 kB / 15.36 MB, free: 0.7344 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.00516/0.00516, allocations: 170.7 kB / 16.27 MB, free: 6.652 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.331/1.331, allocations: 223.3 MB / 240.3 MB, free: 5.344 MB / 190.1 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.2166/0.2166, allocations: 15.28 MB / 306.7 MB, free: 15.7 MB / 254.1 MB Warning: Ignoring unknown experiment annotation option: __Dymola_Algorithm = "Dassl" Notification: Performance of FrontEnd - loaded program: time 0.0003169/0.0003166, allocations: 8.281 kB / 372.1 MB, free: 3.609 MB / 302.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.3002/0.3005, allocations: 54.62 MB / 426.7 MB, free: 40.34 MB / 350.1 MB [/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo:3019:6-3019:65: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:3019:6-3019:65: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 0.04339/0.344, allocations: 42.84 MB / 469.6 MB, free: 19.69 MB / 350.1 MB Notification: Performance of NFInst.instExpressions: time 0.07683/0.4208, allocations: 71.78 MB / 0.5287 GB, free: 3.246 MB / 398.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.006144/0.427, allocations: 95.25 kB / 0.5287 GB, free: 3.152 MB / 398.1 MB Notification: Performance of NFTyping.typeComponents: time 0.00529/0.4324, allocations: 1.457 MB / 0.5302 GB, free: 1.707 MB / 398.1 MB Notification: Performance of NFTyping.typeBindings: time 0.01981/0.4522, allocations: 5.178 MB / 0.5352 GB, free: 12.49 MB / 414.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.03012/0.4823, allocations: 8.993 MB / 0.544 GB, free: 3.457 MB / 414.1 MB Notification: Performance of NFFlatten.flatten: time 0.02859/0.511, allocations: 25.66 MB / 0.5691 GB, free: 9.707 MB / 446.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.4888/0.9998, allocations: 17.22 MB / 0.5859 GB, free: 11.84 MB / 446.1 MB Notification: Performance of NFEvalConstants.evaluate: time 0.02786/1.028, allocations: 15.54 MB / 0.6011 GB, free: 11.4 MB / 446.1 MB Notification: Performance of NFSimplifyModel.simplify: time 0.0328/1.061, allocations: 14.09 MB / 0.6148 GB, free: 9.625 MB / 446.1 MB Notification: Performance of NFPackage.collectConstants: time 0.01262/1.073, allocations: 1.427 MB / 0.6162 GB, free: 9.625 MB / 446.1 MB Notification: Performance of NFFlatten.collectFunctions: time 0.03809/1.111, allocations: 9.023 MB / 0.625 GB, free: 9.301 MB / 446.1 MB Notification: Performance of NFScalarize.scalarize: time 0.0144/1.126, allocations: 4.975 MB / 0.6299 GB, free: 7.484 MB / 446.1 MB Notification: Performance of NFVerifyModel.verify: time 0.02426/1.15, allocations: 10.05 MB / 0.6397 GB, free: 3.949 MB / 446.1 MB Notification: Performance of NFConvertDAE.convert: time 0.06605/1.216, allocations: 38.9 MB / 0.6777 GB, free: 11.6 MB / 478.1 MB Notification: Performance of FrontEnd - DAE generated: time 6.592e-06/1.216, allocations: 0 / 0.6777 GB, free: 11.6 MB / 478.1 MB Notification: Performance of FrontEnd: time 2.615e-06/1.216, allocations: 0 / 0.6777 GB, free: 11.6 MB / 478.1 MB Notification: Performance of Transformations before backend: time 0.001206/1.217, allocations: 0 / 0.6777 GB, free: 11.6 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 0.0656/1.283, allocations: 20.17 MB / 0.6974 GB, free: 7.562 MB / 494.1 MB Notification: Performance of prepare preOptimizeDAE: time 4.579e-05/1.283, allocations: 8.031 kB / 0.6974 GB, free: 7.555 MB / 494.1 MB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.02392/1.307, allocations: 3.896 MB / 0.7012 GB, free: 3.645 MB / 494.1 MB Notification: Performance of preOpt evaluateParameters (simulation): time 0.02599/1.333, allocations: 11.45 MB / 0.7124 GB, free: 8.594 MB / 0.4982 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.002396/1.335, allocations: 2.138 MB / 0.7145 GB, free: 6.242 MB / 0.4982 GB Notification: Performance of preOpt expandDerOperator (simulation): time 0.01032/1.346, allocations: 1.527 MB / 0.716 GB, free: 4.715 MB / 0.4982 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.08474/1.431, allocations: 34.79 MB / 0.7499 GB, free: 1.711 MB / 0.5294 GB Notification: Performance of preOpt findStateOrder (simulation): time 0.0004733/1.431, allocations: 10.34 kB / 0.7499 GB, free: 1.707 MB / 0.5294 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.006546/1.438, allocations: 0.5859 MB / 0.7505 GB, free: 1.117 MB / 0.5294 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0003357/1.438, allocations: 360 kB / 0.7509 GB, free: 0.7656 MB / 0.5294 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.4954/1.933, allocations: 46.84 MB / 0.7966 GB, free: 192 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 0.2825/2.216, allocations: 127.8 MB / 0.9214 GB, free: 104.8 MB / 0.5608 GB Notification: Performance of preOpt comSubExp (simulation): time 0.7711/2.987, allocations: 276 MB / 1.191 GB, free: 69.14 MB / 0.5608 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.03241/3.02, allocations: 19.81 MB / 1.21 GB, free: 49.3 MB / 0.5608 GB Notification: Performance of preOpt evalFunc (simulation): time 0.4321/3.452, allocations: 87.13 MB / 1.295 GB, free: 171.7 MB / 0.5608 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001142/3.452, allocations: 137.4 kB / 1.295 GB, free: 171.6 MB / 0.5608 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.02476/3.477, allocations: 4.442 MB / 1.3 GB, free: 170.4 MB / 0.5608 GB Notification: Performance of pre-optimization done (n=995): time 6.94e-05/3.477, allocations: 2.953 kB / 1.3 GB, free: 170.4 MB / 0.5608 GB Notification: Performance of matching and sorting (n=1129): time 0.7419/4.219, allocations: 136.3 MB / 1.433 GB, free: 67.73 MB / 0.5608 GB Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001116/4.219, allocations: 178.6 kB / 1.433 GB, free: 67.54 MB / 0.5608 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.01477/4.234, allocations: 10.15 MB / 1.443 GB, free: 57.46 MB / 0.5608 GB Notification: Performance of collectPreVariables (initialization): time 0.004563/4.238, allocations: 213.7 kB / 1.443 GB, free: 57.24 MB / 0.5608 GB Notification: Performance of collectInitialEqns (initialization): time 0.2931/4.531, allocations: 6.888 MB / 1.45 GB, free: 182.1 MB / 0.5608 GB Notification: Performance of collectInitialBindings (initialization): time 0.008198/4.54, allocations: 3.907 MB / 1.454 GB, free: 179.6 MB / 0.5608 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.006582/4.546, allocations: 1.158 MB / 1.455 GB, free: 179.6 MB / 0.5608 GB Notification: Performance of setup shared object (initialization): time 6.273e-05/4.546, allocations: 301.1 kB / 1.455 GB, free: 179.3 MB / 0.5608 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.02223/4.568, allocations: 11.83 MB / 1.467 GB, free: 178.2 MB / 0.5608 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.02634/4.595, allocations: 16.55 MB / 1.483 GB, free: 168 MB / 0.5608 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.05519/4.65, allocations: 29.74 MB / 1.512 GB, free: 151.8 MB / 0.5608 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0003265/4.65, allocations: 39.75 kB / 1.512 GB, free: 151.8 MB / 0.5608 GB Notification: Performance of matching and sorting (n=1889) (initialization): time 0.4565/5.107, allocations: 81.54 MB / 1.592 GB, free: 93.79 MB / 0.5608 GB Notification: Performance of prepare postOptimizeDAE: time 0.0001291/5.107, allocations: 68 kB / 1.592 GB, free: 93.72 MB / 0.5608 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0002677/5.107, allocations: 152.2 kB / 1.592 GB, free: 93.57 MB / 0.5608 GB Notification: Performance of postOpt tearingSystem (initialization): time 0.05927/5.167, allocations: 22.53 MB / 1.614 GB, free: 71.22 MB / 0.5608 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01738/5.184, allocations: 3.725 MB / 1.617 GB, free: 67.5 MB / 0.5608 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.47/5.654, allocations: 88.3 MB / 1.704 GB, free: 147.9 MB / 0.5608 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.02067/5.675, allocations: 1.15 MB / 1.705 GB, free: 147.6 MB / 0.5608 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.006681/5.682, allocations: 0.9377 MB / 1.706 GB, free: 147.5 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 0.01885/5.7, allocations: 5.371 MB / 1.711 GB, free: 144.9 MB / 0.5608 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.005836/5.706, allocations: 1.053 MB / 1.712 GB, free: 144.9 MB / 0.5608 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.2827/5.989, allocations: 48.55 MB / 1.759 GB, free: 111.5 MB / 0.5608 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.0001405/5.989, allocations: 120 kB / 1.76 GB, free: 111.4 MB / 0.5608 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 9.548e-05/5.989, allocations: 20 kB / 1.76 GB, free: 111.3 MB / 0.5608 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0003934/5.99, allocations: 59.77 kB / 1.76 GB, free: 111.3 MB / 0.5608 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.3191/6.309, allocations: 72.95 MB / 1.831 GB, free: 38.58 MB / 0.5608 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 0.0001451/6.309, allocations: 4.438 kB / 1.831 GB, free: 38.58 MB / 0.5608 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.2789/6.588, allocations: 2.421 MB / 1.833 GB, free: 161.4 MB / 0.5608 GB Notification: Performance of postOpt tearingSystem (simulation): time 0.03203/6.62, allocations: 11.75 MB / 1.845 GB, free: 161.3 MB / 0.5608 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.003791/6.624, allocations: 474 kB / 1.845 GB, free: 161.3 MB / 0.5608 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.1108/6.734, allocations: 42.2 MB / 1.886 GB, free: 150.2 MB / 0.5608 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.88e-06/6.735, allocations: 7.906 kB / 1.886 GB, free: 150.2 MB / 0.5608 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.2893/7.024, allocations: 62.67 MB / 1.948 GB, free: 117.4 MB / 0.5608 GB Notification: Performance of postOpt removeConstants (simulation): time 0.0104/7.034, allocations: 3.299 MB / 1.951 GB, free: 114.7 MB / 0.5608 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.007393/7.042, allocations: 295.9 kB / 1.951 GB, free: 114.4 MB / 0.5608 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.01649/7.058, allocations: 0.7969 MB / 1.952 GB, free: 113.7 MB / 0.5608 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.008014/7.066, allocations: 1.499 MB / 1.953 GB, free: 112.2 MB / 0.5608 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.003663/7.07, allocations: 467.6 kB / 1.954 GB, free: 111.7 MB / 0.5608 GB Notification: Performance of sorting global known variables: time 0.01239/7.082, allocations: 6.962 MB / 1.961 GB, free: 104.8 MB / 0.5608 GB Notification: Performance of sort global known variables: time 6.81e-07/7.082, allocations: 4 kB / 1.961 GB, free: 104.8 MB / 0.5608 GB Notification: Performance of remove unused functions: time 0.03234/7.115, allocations: 6.656 MB / 1.967 GB, free: 98.61 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 0.01169/7.126, allocations: 3.53 MB / 1.971 GB, free: 95.87 MB / 0.5608 GB Notification: Performance of simCode: created initialization part: time 0.06729/7.194, allocations: 27.72 MB / 1.998 GB, free: 68.13 MB / 0.5608 GB Notification: Performance of simCode: created event and clocks part: time 1.417e-05/7.194, allocations: 1 kB / 1.998 GB, free: 68.13 MB / 0.5608 GB Notification: Performance of simCode: created simulation system equations: time 0.04118/7.235, allocations: 14.87 MB / 2.012 GB, free: 53.24 MB / 0.5608 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0221/7.257, allocations: 2.333 MB / 2.014 GB, free: 50.99 MB / 0.5608 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.3229/7.58, allocations: 44.69 MB / 2.058 GB, free: 155.4 MB / 0.5608 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.01982/7.6, allocations: 9.944 MB / 2.068 GB, free: 154.4 MB / 0.5608 GB Notification: Performance of simCode: alias equations: time 0.02157/7.622, allocations: 5.292 MB / 2.073 GB, free: 154.2 MB / 0.5608 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.007749/7.629, allocations: 1.419 MB / 2.074 GB, free: 154.2 MB / 0.5608 GB Notification: Performance of SimCode: time 2.194e-06/7.629, allocations: 3.312 kB / 2.074 GB, free: 154.2 MB / 0.5608 GB Notification: Performance of Templates: time 0.6495/8.279, allocations: 309.3 MB / 2.376 GB, free: 59.84 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)