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/Chemical 1.4.0-master/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/ModelicaServices 4.0.0+maint.om/package.mo", uses=false) Using package ModelicaServices with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/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 Chemical with version 1.4.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/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/Chemical 1.4.0-master/package.mo): time 0.07998/0.07998, allocations: 15.28 MB / 31.08 MB, free: 3.109 MB / 24.77 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001118/0.001118, allocations: 198.1 kB / 36.14 MB, free: 2.141 MB / 24.77 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.337/1.337, allocations: 222.9 MB / 264 MB, free: 4.879 MB / 202.7 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.0009377/0.0009378, allocations: 107.6 kB / 318.4 MB, free: 3.441 MB / 250.7 MB Warning: Ignoring unknown experiment annotation option: __Dymola_Algorithm = "Dassl" Notification: Performance of FrontEnd - loaded program: time 0.001058/0.001058, allocations: 54.5 kB / 382.7 MB, free: 48.86 MB / 298.7 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.1067/0.1077, allocations: 53.61 MB / 436.3 MB, free: 1.059 MB / 298.7 MB [/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.0-master/package.mo:4721:7-4721:66: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 1.4.0-master/package.mo:4721:7-4721:66: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 0.04935/0.1571, allocations: 41.75 MB / 478.1 MB, free: 7.348 MB / 346.7 MB Notification: Performance of NFInst.instExpressions: time 0.3102/0.4674, allocations: 71.9 MB / 0.5371 GB, free: 15.73 MB / 378.7 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.004508/0.4719, allocations: 103.5 kB / 0.5372 GB, free: 15.73 MB / 378.7 MB Notification: Performance of NFTyping.typeComponents: time 0.003965/0.4759, allocations: 1.456 MB / 0.5386 GB, free: 15.7 MB / 378.7 MB Notification: Performance of NFTyping.typeBindings: time 0.01437/0.4903, allocations: 4.999 MB / 0.5435 GB, free: 14.21 MB / 378.7 MB Notification: Performance of NFTyping.typeClassSections: time 0.0248/0.5151, allocations: 9.007 MB / 0.5523 GB, free: 11.19 MB / 378.7 MB Notification: Performance of NFFlatten.flatten: time 0.02499/0.5402, allocations: 25.83 MB / 0.5775 GB, free: 11.6 MB / 394.7 MB Notification: Performance of NFFlatten.resolveConnections: time 0.02152/0.5617, allocations: 17.93 MB / 0.595 GB, free: 10.62 MB / 410.7 MB Notification: Performance of NFEvalConstants.evaluate: time 0.02297/0.5847, allocations: 16.21 MB / 0.6109 GB, free: 10.62 MB / 426.7 MB Notification: Performance of NFSimplifyModel.simplify: time 0.02743/0.6122, allocations: 14.87 MB / 0.6254 GB, free: 12.18 MB / 442.7 MB Notification: Performance of NFPackage.collectConstants: time 0.007774/0.62, allocations: 1.688 MB / 0.627 GB, free: 10.5 MB / 442.7 MB Notification: Performance of NFFlatten.collectFunctions: time 0.03414/0.6542, allocations: 9.044 MB / 0.6359 GB, free: 1.527 MB / 442.7 MB Notification: Performance of NFScalarize.scalarize: time 0.0101/0.6643, allocations: 5.397 MB / 0.6411 GB, free: 12.31 MB / 458.7 MB Notification: Performance of NFVerifyModel.verify: time 0.02225/0.6866, allocations: 10.51 MB / 0.6514 GB, free: 1.961 MB / 458.7 MB Notification: Performance of NFConvertDAE.convert: time 0.4894/1.176, allocations: 39.58 MB / 0.6901 GB, free: 63.25 MB / 490.8 MB Notification: Performance of FrontEnd - DAE generated: time 7.143e-06/1.176, allocations: 0 / 0.6901 GB, free: 63.25 MB / 490.8 MB Notification: Performance of FrontEnd: time 1.903e-06/1.176, allocations: 0 / 0.6901 GB, free: 63.25 MB / 490.8 MB Notification: Performance of Transformations before backend: time 0.001042/1.177, allocations: 0 / 0.6901 GB, free: 63.25 MB / 490.8 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 0.08588/1.263, allocations: 24.71 MB / 0.7142 GB, free: 57.12 MB / 490.8 MB Notification: Performance of prepare preOptimizeDAE: time 4.729e-05/1.263, allocations: 11.06 kB / 0.7142 GB, free: 57.12 MB / 490.8 MB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.02375/1.287, allocations: 3.888 MB / 0.718 GB, free: 56.18 MB / 490.8 MB Notification: Performance of preOpt evaluateParameters (simulation): time 0.02876/1.316, allocations: 11.77 MB / 0.7295 GB, free: 54.59 MB / 490.8 MB Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.001883/1.318, allocations: 2.132 MB / 0.7316 GB, free: 53.46 MB / 490.8 MB Notification: Performance of preOpt expandDerOperator (simulation): time 0.009619/1.327, allocations: 1.526 MB / 0.7331 GB, free: 53.43 MB / 490.8 MB Notification: Performance of preOpt clockPartitioning (simulation): time 0.07782/1.405, allocations: 34.79 MB / 0.767 GB, free: 34.89 MB / 490.8 MB Notification: Performance of preOpt findStateOrder (simulation): time 0.000689/1.406, allocations: 10.09 kB / 0.767 GB, free: 34.89 MB / 490.8 MB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.01089/1.417, allocations: 0.5859 MB / 0.7676 GB, free: 34.3 MB / 490.8 MB Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0002148/1.417, allocations: 360 kB / 0.768 GB, free: 33.95 MB / 490.8 MB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.07785/1.495, allocations: 46.83 MB / 0.8137 GB, free: 3.125 MB / 0.4949 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 0.5173/2.012, allocations: 128 MB / 0.9387 GB, free: 182.8 MB / 0.573 GB Notification: Performance of preOpt comSubExp (simulation): time 0.7598/2.772, allocations: 276 MB / 1.208 GB, free: 156.2 MB / 0.573 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.03647/2.809, allocations: 19.81 MB / 1.228 GB, free: 152.9 MB / 0.573 GB Notification: Performance of preOpt evalFunc (simulation): time 0.1514/2.96, allocations: 87.58 MB / 1.313 GB, free: 93.35 MB / 0.573 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 7.346e-05/2.96, allocations: 136.5 kB / 1.313 GB, free: 93.21 MB / 0.573 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.02012/2.98, allocations: 4.427 MB / 1.318 GB, free: 88.88 MB / 0.573 GB Notification: Performance of pre-optimization done (n=995): time 4.249e-05/2.98, allocations: 0 / 1.318 GB, free: 88.88 MB / 0.573 GB Notification: Performance of matching and sorting (n=1129): time 0.8842/3.864, allocations: 135.9 MB / 1.45 GB, free: 196.4 MB / 0.573 GB Notification: Performance of inlineWhenForInitialization (initialization): time 8.495e-05/3.865, allocations: 169.4 kB / 1.451 GB, free: 196.4 MB / 0.573 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.01315/3.878, allocations: 10.15 MB / 1.46 GB, free: 191.4 MB / 0.573 GB Notification: Performance of collectPreVariables (initialization): time 0.00355/3.881, allocations: 211.2 kB / 1.461 GB, free: 191.2 MB / 0.573 GB Notification: Performance of collectInitialEqns (initialization): time 0.0042/3.886, allocations: 6.887 MB / 1.467 GB, free: 186.7 MB / 0.573 GB Notification: Performance of collectInitialBindings (initialization): time 0.006371/3.892, allocations: 3.911 MB / 1.471 GB, free: 183.4 MB / 0.573 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.01347/3.905, allocations: 3.258 MB / 1.474 GB, free: 181.6 MB / 0.573 GB Notification: Performance of setup shared object (initialization): time 4.173e-05/3.906, allocations: 308.5 kB / 1.475 GB, free: 181.3 MB / 0.573 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.01922/3.925, allocations: 11.82 MB / 1.486 GB, free: 174.8 MB / 0.573 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.02319/3.948, allocations: 16.56 MB / 1.502 GB, free: 160.6 MB / 0.573 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.04435/3.992, allocations: 29.73 MB / 1.531 GB, free: 128.7 MB / 0.573 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0001283/3.993, allocations: 44 kB / 1.531 GB, free: 128.6 MB / 0.573 GB Notification: Performance of matching and sorting (n=1889) (initialization): time 0.6503/4.643, allocations: 81.45 MB / 1.611 GB, free: 188.9 MB / 0.573 GB Notification: Performance of prepare postOptimizeDAE: time 8.82e-05/4.643, allocations: 70.38 kB / 1.611 GB, free: 188.9 MB / 0.573 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0001625/4.643, allocations: 147.7 kB / 1.611 GB, free: 188.9 MB / 0.573 GB Notification: Performance of postOpt tearingSystem (initialization): time 0.05568/4.699, allocations: 22.39 MB / 1.633 GB, free: 186.3 MB / 0.573 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01564/4.714, allocations: 3.727 MB / 1.637 GB, free: 186.2 MB / 0.573 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.1903/4.905, allocations: 88.26 MB / 1.723 GB, free: 118.3 MB / 0.573 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.01961/4.924, allocations: 1.147 MB / 1.724 GB, free: 117.2 MB / 0.573 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.005176/4.93, allocations: 0.9289 MB / 1.725 GB, free: 116.3 MB / 0.573 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 0.015/4.945, allocations: 5.38 MB / 1.73 GB, free: 111.2 MB / 0.573 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.00673/4.951, allocations: 1.05 MB / 1.731 GB, free: 110.7 MB / 0.573 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.2637/5.215, allocations: 48.61 MB / 1.779 GB, free: 62.16 MB / 0.573 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.0001553/5.215, allocations: 124 kB / 1.779 GB, free: 62.04 MB / 0.573 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 0.0001654/5.216, allocations: 16 kB / 1.779 GB, free: 62.02 MB / 0.573 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0004669/5.216, allocations: 63.7 kB / 1.779 GB, free: 61.96 MB / 0.573 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.5523/5.768, allocations: 73.03 MB / 1.85 GB, free: 174.2 MB / 0.573 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 0.0001239/5.769, allocations: 5.25 kB / 1.85 GB, free: 174.2 MB / 0.573 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0134/5.782, allocations: 2.418 MB / 1.853 GB, free: 174 MB / 0.573 GB Notification: Performance of postOpt tearingSystem (simulation): time 0.02961/5.812, allocations: 11.89 MB / 1.864 GB, free: 171.3 MB / 0.573 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.003388/5.815, allocations: 472.2 kB / 1.865 GB, free: 171 MB / 0.573 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.08901/5.904, allocations: 42.19 MB / 1.906 GB, free: 130.6 MB / 0.573 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.516e-06/5.904, allocations: 7.938 kB / 1.906 GB, free: 130.6 MB / 0.573 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.6932/6.597, allocations: 145.1 MB / 2.048 GB, free: 157.1 MB / 0.573 GB Notification: Performance of postOpt removeConstants (simulation): time 0.01048/6.608, allocations: 3.296 MB / 2.051 GB, free: 155.5 MB / 0.573 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.004303/6.612, allocations: 296.5 kB / 2.051 GB, free: 155.4 MB / 0.573 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.01273/6.625, allocations: 0.7959 MB / 2.052 GB, free: 155.2 MB / 0.573 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.00675/6.632, allocations: 1.492 MB / 2.053 GB, free: 155 MB / 0.573 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.002658/6.634, allocations: 472.8 kB / 2.054 GB, free: 154.9 MB / 0.573 GB Notification: Performance of sorting global known variables: time 0.009593/6.644, allocations: 6.967 MB / 2.061 GB, free: 152.6 MB / 0.573 GB Notification: Performance of sort global known variables: time 4.41e-07/6.644, allocations: 3.656 kB / 2.061 GB, free: 152.6 MB / 0.573 GB Notification: Performance of remove unused functions: time 0.04665/6.691, allocations: 8.26 MB / 2.069 GB, free: 148.9 MB / 0.573 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 0.008475/6.699, allocations: 3.451 MB / 2.072 GB, free: 146.5 MB / 0.573 GB Notification: Performance of simCode: created initialization part: time 0.06102/6.76, allocations: 27.72 MB / 2.099 GB, free: 123.3 MB / 0.573 GB Notification: Performance of simCode: created event and clocks part: time 8.235e-06/6.76, allocations: 0 / 2.099 GB, free: 123.3 MB / 0.573 GB Notification: Performance of simCode: created simulation system equations: time 0.0383/6.799, allocations: 14.87 MB / 2.114 GB, free: 110.8 MB / 0.573 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.01708/6.816, allocations: 2.338 MB / 2.116 GB, free: 109 MB / 0.573 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.09047/6.906, allocations: 52.55 MB / 2.167 GB, free: 58.63 MB / 0.573 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.2447/7.151, allocations: 10.24 MB / 2.177 GB, free: 163.8 MB / 0.573 GB Notification: Performance of simCode: alias equations: time 0.02044/7.172, allocations: 5.531 MB / 2.183 GB, free: 163.7 MB / 0.573 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.009241/7.181, allocations: 1.53 MB / 2.184 GB, free: 163.7 MB / 0.573 GB Notification: Performance of SimCode: time 8.52e-07/7.181, allocations: 0 / 2.184 GB, free: 163.7 MB / 0.573 GB Notification: Performance of Templates: time 0.6733/7.854, allocations: 355.8 MB / 2.531 GB, free: 58.25 MB / 0.573 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)