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 0.001826/0.001826, allocations: 101 kB / 16.4 MB, free: 6.508 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.002289/0.002289, allocations: 189.7 kB / 17.34 MB, free: 5.742 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.454/1.454, allocations: 222.9 MB / 241 MB, free: 15.15 MB / 206.1 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.08936/0.08936, allocations: 15.3 MB / 306.5 MB, free: 15.43 MB / 254.1 MB Notification: Performance of FrontEnd - loaded program: time 0.001202/0.001202, allocations: 63.91 kB / 425.9 MB, free: 11.44 MB / 302.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.1215/0.1227, allocations: 53.62 MB / 479.5 MB, free: 5.773 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.HemoglobinCarboxylation): time 0.5358/0.6586, allocations: 41.48 MB / 0.5088 GB, free: 2.402 MB / 382.1 MB Notification: Performance of NFInst.instExpressions: time 0.08866/0.7473, allocations: 72.7 MB / 0.5798 GB, free: 5.262 MB / 430.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.00535/0.7527, allocations: 63.19 kB / 0.5798 GB, free: 5.238 MB / 430.1 MB Notification: Performance of NFTyping.typeComponents: time 0.005978/0.7587, allocations: 1.616 MB / 0.5814 GB, free: 3.949 MB / 430.1 MB Notification: Performance of NFTyping.typeBindings: time 0.02575/0.7845, allocations: 5.933 MB / 0.5872 GB, free: 15.27 MB / 446.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.03626/0.8208, allocations: 10.2 MB / 0.5972 GB, free: 7.238 MB / 446.1 MB Notification: Performance of NFFlatten.flatten: time 0.03096/0.8517, allocations: 26.7 MB / 0.6232 GB, free: 15.7 MB / 478.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.02947/0.8813, allocations: 21.96 MB / 0.6447 GB, free: 9.625 MB / 494.1 MB Notification: Performance of NFEvalConstants.evaluate: time 0.03075/0.9121, allocations: 17.47 MB / 0.6617 GB, free: 8.125 MB / 0.4982 GB Notification: Performance of NFSimplifyModel.simplify: time 0.03177/0.9439, allocations: 16.19 MB / 0.6776 GB, free: 7.891 MB / 0.5138 GB Notification: Performance of NFPackage.collectConstants: time 0.01381/0.9578, allocations: 3.094 MB / 0.6806 GB, free: 4.797 MB / 0.5138 GB Notification: Performance of NFFlatten.collectFunctions: time 0.05315/1.011, allocations: 10.7 MB / 0.691 GB, free: 10.09 MB / 0.5294 GB Notification: Performance of NFScalarize.scalarize: time 0.01702/1.028, allocations: 6.981 MB / 0.6978 GB, free: 3.094 MB / 0.5294 GB Notification: Performance of NFVerifyModel.verify: time 0.03196/1.06, allocations: 12.15 MB / 0.7097 GB, free: 6.898 MB / 0.545 GB Notification: Performance of NFConvertDAE.convert: time 0.4626/1.523, allocations: 42 MB / 0.7507 GB, free: 60.29 MB / 0.545 GB Notification: Performance of FrontEnd - DAE generated: time 1.047e-05/1.523, allocations: 1.562 kB / 0.7507 GB, free: 60.29 MB / 0.545 GB Notification: Performance of FrontEnd: time 2.775e-06/1.523, allocations: 3.531 kB / 0.7507 GB, free: 60.29 MB / 0.545 GB Notification: Performance of Transformations before backend: time 0.001346/1.524, allocations: 0 / 0.7507 GB, free: 60.29 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 0.1185/1.643, allocations: 24.75 MB / 0.7749 GB, free: 53.39 MB / 0.545 GB Notification: Performance of prepare preOptimizeDAE: time 5.652e-05/1.643, allocations: 12.69 kB / 0.7749 GB, free: 53.39 MB / 0.545 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0329/1.676, allocations: 3.898 MB / 0.7787 GB, free: 51.91 MB / 0.545 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.03579/1.711, allocations: 12.02 MB / 0.7905 GB, free: 48.47 MB / 0.545 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.002667/1.714, allocations: 2.13 MB / 0.7925 GB, free: 47.3 MB / 0.545 GB Notification: Performance of preOpt expandDerOperator (simulation): time 0.01589/1.73, allocations: 1.528 MB / 0.794 GB, free: 47.26 MB / 0.545 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.1051/1.835, allocations: 34.79 MB / 0.828 GB, free: 15.8 MB / 0.545 GB Notification: Performance of preOpt findStateOrder (simulation): time 0.0008071/1.836, allocations: 13.56 kB / 0.828 GB, free: 15.8 MB / 0.545 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.01383/1.85, allocations: 0.5859 MB / 0.8286 GB, free: 15.21 MB / 0.545 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0002626/1.85, allocations: 362.6 kB / 0.8289 GB, free: 14.86 MB / 0.545 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.1111/1.961, allocations: 46.83 MB / 0.8747 GB, free: 28 kB / 0.5763 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 0.714/2.675, allocations: 127.8 MB / 0.9995 GB, free: 216.2 MB / 0.6544 GB Notification: Performance of preOpt comSubExp (simulation): time 0.8802/3.556, allocations: 276 MB / 1.269 GB, free: 222.3 MB / 0.6544 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.04398/3.6, allocations: 19.81 MB / 1.288 GB, free: 218.9 MB / 0.6544 GB Notification: Performance of preOpt evalFunc (simulation): time 0.1757/3.775, allocations: 87.47 MB / 1.374 GB, free: 159.1 MB / 0.6544 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 9.179e-05/3.775, allocations: 138.3 kB / 1.374 GB, free: 159 MB / 0.6544 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.022/3.797, allocations: 4.511 MB / 1.378 GB, free: 154.5 MB / 0.6544 GB Notification: Performance of pre-optimization done (n=995): time 6.687e-05/3.798, allocations: 0 / 1.378 GB, free: 154.5 MB / 0.6544 GB Notification: Performance of matching and sorting (n=1129): time 0.684/4.482, allocations: 135.9 MB / 1.511 GB, free: 19.36 MB / 0.6544 GB Notification: Performance of inlineWhenForInitialization (initialization): time 8.558e-05/4.482, allocations: 168.2 kB / 1.511 GB, free: 19.18 MB / 0.6544 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.01558/4.497, allocations: 10.15 MB / 1.521 GB, free: 9.086 MB / 0.6544 GB Notification: Performance of collectPreVariables (initialization): time 0.004776/4.502, allocations: 217.7 kB / 1.521 GB, free: 8.867 MB / 0.6544 GB Notification: Performance of collectInitialEqns (initialization): time 0.005083/4.507, allocations: 6.884 MB / 1.528 GB, free: 1.961 MB / 0.6544 GB Notification: Performance of collectInitialBindings (initialization): time 0.3225/4.83, allocations: 3.904 MB / 1.532 GB, free: 242.9 MB / 0.6544 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.01865/4.848, allocations: 3.258 MB / 1.535 GB, free: 242.8 MB / 0.6544 GB Notification: Performance of setup shared object (initialization): time 5.168e-05/4.848, allocations: 307.8 kB / 1.535 GB, free: 242.5 MB / 0.6544 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.02543/4.874, allocations: 11.83 MB / 1.547 GB, free: 240.3 MB / 0.6544 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.02631/4.9, allocations: 16.55 MB / 1.563 GB, free: 230.2 MB / 0.6544 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.04912/4.949, allocations: 29.74 MB / 1.592 GB, free: 213.9 MB / 0.6544 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0002927/4.95, allocations: 41.62 kB / 1.592 GB, free: 213.9 MB / 0.6544 GB Notification: Performance of matching and sorting (n=1889) (initialization): time 0.4393/5.389, allocations: 81.46 MB / 1.672 GB, free: 145.3 MB / 0.6544 GB Notification: Performance of prepare postOptimizeDAE: time 0.0001181/5.389, allocations: 68 kB / 1.672 GB, free: 145.3 MB / 0.6544 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0002578/5.39, allocations: 148.6 kB / 1.672 GB, free: 145.1 MB / 0.6544 GB Notification: Performance of postOpt tearingSystem (initialization): time 0.05643/5.446, allocations: 22.37 MB / 1.694 GB, free: 122.9 MB / 0.6544 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01751/5.464, allocations: 3.737 MB / 1.697 GB, free: 119.2 MB / 0.6544 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.5084/5.972, allocations: 93.94 MB / 1.789 GB, free: 210.7 MB / 0.6544 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.02416/5.996, allocations: 0.8371 MB / 1.79 GB, free: 210.7 MB / 0.6544 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.006345/6.003, allocations: 0.9357 MB / 1.791 GB, free: 210.7 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 0.01871/6.021, allocations: 5.371 MB / 1.796 GB, free: 209.1 MB / 0.6544 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.007458/6.029, allocations: 1.059 MB / 1.797 GB, free: 209.1 MB / 0.6544 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.2859/6.315, allocations: 48.59 MB / 1.845 GB, free: 197.4 MB / 0.6544 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.0001317/6.315, allocations: 125.5 kB / 1.845 GB, free: 197.4 MB / 0.6544 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 9.483e-05/6.315, allocations: 15.53 kB / 1.845 GB, free: 197.4 MB / 0.6544 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0003777/6.315, allocations: 65.56 kB / 1.845 GB, free: 197.4 MB / 0.6544 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.3003/6.616, allocations: 73.05 MB / 1.916 GB, free: 138.3 MB / 0.6544 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 0.000128/6.616, allocations: 4 kB / 1.916 GB, free: 138.3 MB / 0.6544 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.01478/6.631, allocations: 2.411 MB / 1.919 GB, free: 135.9 MB / 0.6544 GB Notification: Performance of postOpt tearingSystem (simulation): time 0.03034/6.661, allocations: 11.89 MB / 1.93 GB, free: 124.2 MB / 0.6544 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.005129/6.666, allocations: 475.5 kB / 1.931 GB, free: 123.7 MB / 0.6544 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.102/6.768, allocations: 46.93 MB / 1.976 GB, free: 76.48 MB / 0.6544 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 5.661e-06/6.768, allocations: 4 kB / 1.976 GB, free: 76.48 MB / 0.6544 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.6301/7.398, allocations: 62.73 MB / 2.038 GB, free: 205.3 MB / 0.6544 GB Notification: Performance of postOpt removeConstants (simulation): time 0.01253/7.411, allocations: 3.292 MB / 2.041 GB, free: 204.4 MB / 0.6544 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.008051/7.419, allocations: 300.8 kB / 2.041 GB, free: 204.2 MB / 0.6544 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.01608/7.435, allocations: 0.52 MB / 2.042 GB, free: 204 MB / 0.6544 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.007444/7.443, allocations: 1.499 MB / 2.043 GB, free: 203.8 MB / 0.6544 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.004283/7.447, allocations: 482.9 kB / 2.044 GB, free: 203.7 MB / 0.6544 GB Notification: Performance of sorting global known variables: time 0.01492/7.462, allocations: 6.962 MB / 2.05 GB, free: 201.4 MB / 0.6544 GB Notification: Performance of sort global known variables: time 7.81e-07/7.462, allocations: 2.438 kB / 2.05 GB, free: 201.4 MB / 0.6544 GB Notification: Performance of remove unused functions: time 0.03688/7.499, allocations: 6.679 MB / 2.057 GB, free: 200.8 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 0.01349/7.512, allocations: 3.532 MB / 2.06 GB, free: 200.2 MB / 0.6544 GB Notification: Performance of simCode: created initialization part: time 0.07319/7.586, allocations: 27.79 MB / 2.088 GB, free: 189.9 MB / 0.6544 GB Notification: Performance of simCode: created event and clocks part: time 1.125e-05/7.586, allocations: 2.656 kB / 2.088 GB, free: 189.9 MB / 0.6544 GB Notification: Performance of simCode: created simulation system equations: time 0.04177/7.627, allocations: 14.87 MB / 2.102 GB, free: 184.1 MB / 0.6544 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.02272/7.65, allocations: 2.497 MB / 2.104 GB, free: 183.2 MB / 0.6544 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.102/7.752, allocations: 37.51 MB / 2.141 GB, free: 150.6 MB / 0.6544 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0175/7.77, allocations: 9.63 MB / 2.151 GB, free: 143.6 MB / 0.6544 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.01196/7.782, allocations: 1.568 MB / 2.152 GB, free: 142.2 MB / 0.6544 GB Notification: Performance of SimCode: time 1.443e-06/7.782, allocations: 0 / 2.152 GB, free: 142.2 MB / 0.6544 GB Notification: Performance of Templates: time 1.443/9.225, allocations: 0.5095 GB / 2.662 GB, free: 94.16 MB / 0.6544 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)