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 0.001292/0.001292, allocations: 115.3 kB / 15.34 MB, free: 0.5117 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001413/0.001413, allocations: 187.2 kB / 16.25 MB, free: 6.582 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.4/1.4, allocations: 222.9 MB / 239.9 MB, free: 4.516 MB / 190.1 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.3112/0.3112, allocations: 15.32 MB / 305.4 MB, free: 15.3 MB / 254.1 MB Warning: Ignoring unknown experiment annotation option: __Dymola_Algorithm = "Dassl" Notification: Performance of FrontEnd - loaded program: time 0.001313/0.001313, allocations: 59.91 kB / 369.8 MB, free: 4.32 MB / 302.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.147/0.1484, allocations: 53.62 MB / 423.4 MB, free: 14.65 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 0.3549/0.5033, allocations: 43.58 MB / 467 MB, free: 35.48 MB / 366.1 MB Notification: Performance of NFInst.instExpressions: time 0.08072/0.5841, allocations: 71.79 MB / 0.5262 GB, free: 11.07 MB / 398.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.009556/0.5937, allocations: 103.2 kB / 0.5263 GB, free: 10.97 MB / 398.1 MB Notification: Performance of NFTyping.typeComponents: time 0.008365/0.6022, allocations: 1.453 MB / 0.5277 GB, free: 9.863 MB / 398.1 MB Notification: Performance of NFTyping.typeBindings: time 0.02648/0.6287, allocations: 5.324 MB / 0.5329 GB, free: 5.422 MB / 398.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.03707/0.6658, allocations: 9.18 MB / 0.5419 GB, free: 12.7 MB / 414.1 MB Notification: Performance of NFFlatten.flatten: time 0.03124/0.6971, allocations: 26.7 MB / 0.568 GB, free: 1.902 MB / 430.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.03059/0.7277, allocations: 21.84 MB / 0.5893 GB, free: 11.95 MB / 462.1 MB Notification: Performance of NFEvalConstants.evaluate: time 0.6397/1.367, allocations: 18.77 MB / 0.6076 GB, free: 24.31 MB / 462.1 MB Notification: Performance of NFSimplifyModel.simplify: time 0.03596/1.403, allocations: 16.51 MB / 0.6237 GB, free: 23.9 MB / 462.1 MB Notification: Performance of NFPackage.collectConstants: time 0.01872/1.422, allocations: 3.091 MB / 0.6268 GB, free: 23.9 MB / 462.1 MB Notification: Performance of NFFlatten.collectFunctions: time 0.05242/1.475, allocations: 10.89 MB / 0.6374 GB, free: 23.9 MB / 462.1 MB Notification: Performance of NFScalarize.scalarize: time 0.0212/1.496, allocations: 7.074 MB / 0.6443 GB, free: 23.31 MB / 462.1 MB Notification: Performance of NFVerifyModel.verify: time 0.03785/1.534, allocations: 12.27 MB / 0.6563 GB, free: 17.12 MB / 462.1 MB Notification: Performance of NFConvertDAE.convert: time 0.08316/1.617, allocations: 41.27 MB / 0.6966 GB, free: 12.74 MB / 478.1 MB Notification: Performance of FrontEnd - DAE generated: time 1.017e-05/1.617, allocations: 3.984 kB / 0.6966 GB, free: 12.74 MB / 478.1 MB Notification: Performance of FrontEnd: time 3.156e-06/1.617, allocations: 0 / 0.6966 GB, free: 12.74 MB / 478.1 MB Notification: Performance of Transformations before backend: time 0.001531/1.619, allocations: 3.406 kB / 0.6966 GB, free: 12.74 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 0.09809/1.717, allocations: 24.74 MB / 0.7207 GB, free: 4.273 MB / 494.1 MB Notification: Performance of prepare preOptimizeDAE: time 5.135e-05/1.717, allocations: 14.69 kB / 0.7208 GB, free: 4.262 MB / 494.1 MB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.02883/1.746, allocations: 3.892 MB / 0.7246 GB, free: 368 kB / 494.1 MB Notification: Performance of preOpt evaluateParameters (simulation): time 0.03294/1.779, allocations: 11.77 MB / 0.7361 GB, free: 4.996 MB / 0.4982 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.002248/1.781, allocations: 2.131 MB / 0.7381 GB, free: 2.648 MB / 0.4982 GB Notification: Performance of preOpt expandDerOperator (simulation): time 0.01179/1.793, allocations: 1.529 MB / 0.7396 GB, free: 1.121 MB / 0.4982 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.1179/1.911, allocations: 34.79 MB / 0.7736 GB, free: 14.12 MB / 0.545 GB Notification: Performance of preOpt findStateOrder (simulation): time 0.0009765/1.912, allocations: 10.84 kB / 0.7736 GB, free: 14.11 MB / 0.545 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.01395/1.926, allocations: 0.5898 MB / 0.7742 GB, free: 13.52 MB / 0.545 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0003613/1.926, allocations: 360 kB / 0.7745 GB, free: 13.17 MB / 0.545 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.5396/2.466, allocations: 46.83 MB / 0.8203 GB, free: 186.2 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 0.2832/2.749, allocations: 128 MB / 0.9453 GB, free: 101.8 MB / 0.5608 GB Notification: Performance of preOpt comSubExp (simulation): time 0.8564/3.605, allocations: 276 MB / 1.215 GB, free: 64.32 MB / 0.5608 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.02991/3.635, allocations: 19.81 MB / 1.234 GB, free: 45.63 MB / 0.5608 GB Notification: Performance of preOpt evalFunc (simulation): time 0.4321/4.067, allocations: 87.58 MB / 1.32 GB, free: 165.8 MB / 0.5608 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001334/4.068, allocations: 139 kB / 1.32 GB, free: 165.7 MB / 0.5608 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.02602/4.094, allocations: 4.505 MB / 1.324 GB, free: 164.7 MB / 0.5608 GB Notification: Performance of pre-optimization done (n=995): time 9.902e-05/4.094, allocations: 0 / 1.324 GB, free: 164.7 MB / 0.5608 GB Notification: Performance of matching and sorting (n=1129): time 0.6847/4.778, allocations: 136 MB / 1.457 GB, free: 64.66 MB / 0.5608 GB Notification: Performance of inlineWhenForInitialization (initialization): time 8.377e-05/4.779, allocations: 168.2 kB / 1.457 GB, free: 64.48 MB / 0.5608 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.01418/4.793, allocations: 10.15 MB / 1.467 GB, free: 54.4 MB / 0.5608 GB Notification: Performance of collectPreVariables (initialization): time 0.006393/4.799, allocations: 214.3 kB / 1.467 GB, free: 54.18 MB / 0.5608 GB Notification: Performance of collectInitialEqns (initialization): time 0.291/5.09, allocations: 6.884 MB / 1.474 GB, free: 178 MB / 0.5608 GB Notification: Performance of collectInitialBindings (initialization): time 0.00947/5.1, allocations: 3.909 MB / 1.478 GB, free: 175.5 MB / 0.5608 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.021/5.121, allocations: 3.263 MB / 1.481 GB, free: 174.3 MB / 0.5608 GB Notification: Performance of setup shared object (initialization): time 5.022e-05/5.121, allocations: 301.1 kB / 1.481 GB, free: 174 MB / 0.5608 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.02161/5.142, allocations: 11.83 MB / 1.493 GB, free: 169.6 MB / 0.5608 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0301/5.173, allocations: 16.55 MB / 1.509 GB, free: 159.5 MB / 0.5608 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.05582/5.229, allocations: 29.74 MB / 1.538 GB, free: 143.7 MB / 0.5608 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0004086/5.229, allocations: 42.97 kB / 1.538 GB, free: 143.7 MB / 0.5608 GB Notification: Performance of matching and sorting (n=1889) (initialization): time 0.4068/5.636, allocations: 81.46 MB / 1.618 GB, free: 88.92 MB / 0.5608 GB Notification: Performance of prepare postOptimizeDAE: time 0.000149/5.636, allocations: 68 kB / 1.618 GB, free: 88.86 MB / 0.5608 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0002752/5.636, allocations: 148 kB / 1.618 GB, free: 88.71 MB / 0.5608 GB Notification: Performance of postOpt tearingSystem (initialization): time 0.05284/5.689, allocations: 22.38 MB / 1.64 GB, free: 66.48 MB / 0.5608 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01613/5.705, allocations: 3.725 MB / 1.643 GB, free: 62.75 MB / 0.5608 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.4388/6.144, allocations: 93.97 MB / 1.735 GB, free: 139.5 MB / 0.5608 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.02229/6.166, allocations: 1.148 MB / 1.736 GB, free: 139.2 MB / 0.5608 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.007273/6.174, allocations: 0.9339 MB / 1.737 GB, free: 139 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 0.02131/6.195, allocations: 5.376 MB / 1.742 GB, free: 136 MB / 0.5608 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.008185/6.203, allocations: 1.054 MB / 1.743 GB, free: 136 MB / 0.5608 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.2536/6.457, allocations: 48.61 MB / 1.791 GB, free: 100.5 MB / 0.5608 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.0001055/6.457, allocations: 124 kB / 1.791 GB, free: 100.4 MB / 0.5608 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 5.909e-05/6.457, allocations: 20 kB / 1.791 GB, free: 100.3 MB / 0.5608 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0002973/6.457, allocations: 59.77 kB / 1.791 GB, free: 100.3 MB / 0.5608 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.4945/6.952, allocations: 73.03 MB / 1.862 GB, free: 146 MB / 0.5608 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 9.407e-05/6.952, allocations: 6.344 kB / 1.862 GB, free: 146 MB / 0.5608 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.01188/6.964, allocations: 2.415 MB / 1.865 GB, free: 146 MB / 0.5608 GB Notification: Performance of postOpt tearingSystem (simulation): time 0.0275/6.991, allocations: 11.89 MB / 1.876 GB, free: 145.9 MB / 0.5608 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.00371/6.995, allocations: 480.3 kB / 1.877 GB, free: 145.9 MB / 0.5608 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.1009/7.096, allocations: 46.95 MB / 1.923 GB, free: 131.7 MB / 0.5608 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.456e-06/7.096, allocations: 3.812 kB / 1.923 GB, free: 131.7 MB / 0.5608 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.2516/7.348, allocations: 62.73 MB / 1.984 GB, free: 102.3 MB / 0.5608 GB Notification: Performance of postOpt removeConstants (simulation): time 0.00876/7.357, allocations: 3.293 MB / 1.987 GB, free: 99.61 MB / 0.5608 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.004837/7.361, allocations: 299.8 kB / 1.987 GB, free: 99.31 MB / 0.5608 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.01248/7.374, allocations: 0.7915 MB / 1.988 GB, free: 98.55 MB / 0.5608 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.006179/7.38, allocations: 1.504 MB / 1.99 GB, free: 97.04 MB / 0.5608 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.002072/7.382, allocations: 468.4 kB / 1.99 GB, free: 96.59 MB / 0.5608 GB Notification: Performance of sorting global known variables: time 0.008537/7.391, allocations: 6.966 MB / 1.997 GB, free: 89.67 MB / 0.5608 GB Notification: Performance of sort global known variables: time 5.61e-07/7.391, allocations: 0 / 1.997 GB, free: 89.67 MB / 0.5608 GB Notification: Performance of remove unused functions: time 0.027/7.418, allocations: 6.663 MB / 2.003 GB, free: 83.36 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 0.008778/7.427, allocations: 3.541 MB / 2.007 GB, free: 80.72 MB / 0.5608 GB Notification: Performance of simCode: created initialization part: time 0.4641/7.891, allocations: 108.8 MB / 2.113 GB, free: 158.5 MB / 0.5608 GB Notification: Performance of simCode: created event and clocks part: time 8.677e-06/7.891, allocations: 2.25 kB / 2.113 GB, free: 158.5 MB / 0.5608 GB Notification: Performance of simCode: created simulation system equations: time 0.03676/7.927, allocations: 14.88 MB / 2.128 GB, free: 146 MB / 0.5608 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.01699/7.945, allocations: 2.513 MB / 2.13 GB, free: 144.2 MB / 0.5608 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.08391/8.028, allocations: 44.47 MB / 2.174 GB, free: 105 MB / 0.5608 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.01488/8.043, allocations: 9.941 MB / 2.183 GB, free: 97.81 MB / 0.5608 GB Notification: Performance of simCode: alias equations: time 0.01674/8.06, allocations: 5.315 MB / 2.188 GB, free: 94.51 MB / 0.5608 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.006876/8.067, allocations: 1.454 MB / 2.19 GB, free: 93.28 MB / 0.5608 GB Notification: Performance of SimCode: time 1.182e-06/8.067, allocations: 0 / 2.19 GB, free: 93.28 MB / 0.5608 GB Notification: Performance of Templates: time 0.7993/8.866, allocations: 325.8 MB / 2.508 GB, free: 129 MB / 0.5608 GB make -j1 -f Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.makefile Failed to read output from testmodel.py, exit status != 0: 8.868294761050493 8.881650035 7.262706485 Traceback (most recent call last): File "/var/lib/jenkins/ws/OpenModelicaLibraryTestingWork/OpenModelicaLibraryTesting/./testmodel.py", line 440, in resFile = "%s_res.%s" % (conf["fileName"], outputFormat if not shared.isFMPy(fmisimulator) else 'csv') File "/var/lib/jenkins/ws/OpenModelicaLibraryTestingWork/OpenModelicaLibraryTesting/shared.py", line 98, in isFMPy return 'fmpy' in fmisimulator TypeError: argument of type 'NoneType' is not iterable