Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.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.HemoglobinMultipleAllostery,tolerance=1e-06,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery") translateModel(Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery,tolerance=1e-06,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery") Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001302/0.001302, allocations: 110.7 kB / 16.41 MB, free: 6.496 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001395/0.001395, allocations: 188.1 kB / 17.34 MB, free: 5.762 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.447/1.447, allocations: 222.9 MB / 241 MB, free: 15.2 MB / 206.1 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.08529/0.08529, allocations: 15.31 MB / 306.5 MB, free: 15.42 MB / 254.1 MB Notification: Performance of FrontEnd - loaded program: time 0.00125/0.00125, allocations: 64.11 kB / 425.9 MB, free: 11.45 MB / 302.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.1087/0.11, allocations: 53.61 MB / 479.5 MB, free: 5.789 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.HemoglobinMultipleAllostery): time 0.4728/0.5828, allocations: 41.6 MB / 0.5089 GB, free: 2.305 MB / 382.1 MB Notification: Performance of NFInst.instExpressions: time 0.07607/0.6589, allocations: 72.73 MB / 0.5799 GB, free: 5.129 MB / 430.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.005168/0.6641, allocations: 58.88 kB / 0.58 GB, free: 5.109 MB / 430.1 MB Notification: Performance of NFTyping.typeComponents: time 0.0057/0.6698, allocations: 1.618 MB / 0.5815 GB, free: 3.816 MB / 430.1 MB Notification: Performance of NFTyping.typeBindings: time 0.01994/0.6898, allocations: 5.926 MB / 0.5873 GB, free: 15.14 MB / 446.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.0288/0.7187, allocations: 10.21 MB / 0.5973 GB, free: 7.109 MB / 446.1 MB Notification: Performance of NFFlatten.flatten: time 0.02582/0.7445, allocations: 26.69 MB / 0.6234 GB, free: 15.57 MB / 478.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.02669/0.7713, allocations: 21.96 MB / 0.6448 GB, free: 9.496 MB / 494.1 MB Notification: Performance of NFEvalConstants.evaluate: time 0.02558/0.7969, allocations: 17.48 MB / 0.6619 GB, free: 7.988 MB / 0.4982 GB Notification: Performance of NFSimplifyModel.simplify: time 0.02845/0.8254, allocations: 16.2 MB / 0.6777 GB, free: 7.742 MB / 0.5138 GB Notification: Performance of NFPackage.collectConstants: time 0.01149/0.8369, allocations: 3.09 MB / 0.6807 GB, free: 4.652 MB / 0.5138 GB Notification: Performance of NFFlatten.collectFunctions: time 0.04187/0.8788, allocations: 10.7 MB / 0.6912 GB, free: 9.941 MB / 0.5294 GB Notification: Performance of NFScalarize.scalarize: time 0.01434/0.8932, allocations: 6.977 MB / 0.698 GB, free: 2.949 MB / 0.5294 GB Notification: Performance of NFVerifyModel.verify: time 0.02709/0.9203, allocations: 12.16 MB / 0.7098 GB, free: 6.746 MB / 0.545 GB Notification: Performance of NFConvertDAE.convert: time 0.3747/1.295, allocations: 42.21 MB / 0.7511 GB, free: 60.11 MB / 0.545 GB Notification: Performance of FrontEnd - DAE generated: time 7.985e-06/1.295, allocations: 0 / 0.7511 GB, free: 60.11 MB / 0.545 GB Notification: Performance of FrontEnd: time 2.695e-06/1.295, allocations: 0 / 0.7511 GB, free: 60.11 MB / 0.545 GB Notification: Performance of Transformations before backend: time 0.001248/1.296, allocations: 0 / 0.7511 GB, free: 60.11 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 0.09925/1.396, allocations: 24.73 MB / 0.7752 GB, free: 53.14 MB / 0.545 GB Notification: Performance of prepare preOptimizeDAE: time 4.276e-05/1.396, allocations: 10.62 kB / 0.7752 GB, free: 53.14 MB / 0.545 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.02812/1.424, allocations: 3.893 MB / 0.779 GB, free: 51.65 MB / 0.545 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.03047/1.454, allocations: 12.01 MB / 0.7908 GB, free: 48.23 MB / 0.545 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.002205/1.457, allocations: 2.128 MB / 0.7928 GB, free: 47.06 MB / 0.545 GB Notification: Performance of preOpt expandDerOperator (simulation): time 0.01324/1.47, allocations: 1.53 MB / 0.7943 GB, free: 47.01 MB / 0.545 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.09604/1.566, allocations: 34.79 MB / 0.8283 GB, free: 15.45 MB / 0.545 GB Notification: Performance of preOpt findStateOrder (simulation): time 0.0007473/1.567, allocations: 13 kB / 0.8283 GB, free: 15.45 MB / 0.545 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.01155/1.578, allocations: 0.5898 MB / 0.8289 GB, free: 14.86 MB / 0.545 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.000228/1.579, allocations: 362.7 kB / 0.8292 GB, free: 14.51 MB / 0.545 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.1008/1.679, allocations: 46.83 MB / 0.875 GB, free: 15.68 MB / 0.5919 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 0.6271/2.307, allocations: 127.9 MB / 0.9999 GB, free: 215.6 MB / 0.6544 GB Notification: Performance of preOpt comSubExp (simulation): time 0.8656/3.172, allocations: 276 MB / 1.269 GB, free: 221.2 MB / 0.6544 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.03977/3.212, allocations: 19.81 MB / 1.289 GB, free: 218 MB / 0.6544 GB Notification: Performance of preOpt evalFunc (simulation): time 0.1644/3.376, allocations: 87.47 MB / 1.374 GB, free: 158.2 MB / 0.6544 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 8.925e-05/3.377, allocations: 141.1 kB / 1.374 GB, free: 158.1 MB / 0.6544 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.02169/3.398, allocations: 4.513 MB / 1.379 GB, free: 153.7 MB / 0.6544 GB Notification: Performance of pre-optimization done (n=995): time 6.027e-05/3.398, allocations: 0 / 1.379 GB, free: 153.7 MB / 0.6544 GB Notification: Performance of matching and sorting (n=1129): time 0.6762/4.075, allocations: 130.7 MB / 1.506 GB, free: 23.74 MB / 0.6544 GB Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001121/4.075, allocations: 171 kB / 1.507 GB, free: 23.56 MB / 0.6544 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.01715/4.092, allocations: 10.16 MB / 1.516 GB, free: 13.46 MB / 0.6544 GB Notification: Performance of collectPreVariables (initialization): time 0.005332/4.097, allocations: 209.7 kB / 1.517 GB, free: 13.25 MB / 0.6544 GB Notification: Performance of collectInitialEqns (initialization): time 0.00535/4.103, allocations: 6.877 MB / 1.523 GB, free: 6.355 MB / 0.6544 GB Notification: Performance of collectInitialBindings (initialization): time 0.008565/4.111, allocations: 3.916 MB / 1.527 GB, free: 2.477 MB / 0.6544 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.3683/4.48, allocations: 3.257 MB / 1.53 GB, free: 239.8 MB / 0.6544 GB Notification: Performance of setup shared object (initialization): time 5.594e-05/4.48, allocations: 311.9 kB / 1.531 GB, free: 239.5 MB / 0.6544 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.02721/4.507, allocations: 11.82 MB / 1.542 GB, free: 239.1 MB / 0.6544 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.02854/4.536, allocations: 16.55 MB / 1.558 GB, free: 228.9 MB / 0.6544 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.05175/4.587, allocations: 29.74 MB / 1.587 GB, free: 212.7 MB / 0.6544 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0003358/4.588, allocations: 41.88 kB / 1.587 GB, free: 212.7 MB / 0.6544 GB Notification: Performance of matching and sorting (n=1889) (initialization): time 0.4452/5.033, allocations: 81.46 MB / 1.667 GB, free: 148.1 MB / 0.6544 GB Notification: Performance of prepare postOptimizeDAE: time 0.0001652/5.033, allocations: 72 kB / 1.667 GB, free: 148 MB / 0.6544 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0002894/5.033, allocations: 148 kB / 1.667 GB, free: 147.9 MB / 0.6544 GB Notification: Performance of postOpt tearingSystem (initialization): time 0.05845/5.092, allocations: 22.39 MB / 1.689 GB, free: 125.6 MB / 0.6544 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01858/5.111, allocations: 3.729 MB / 1.693 GB, free: 121.9 MB / 0.6544 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.5341/5.645, allocations: 93.95 MB / 1.784 GB, free: 210.1 MB / 0.6544 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.02122/5.666, allocations: 0.8369 MB / 1.785 GB, free: 210.1 MB / 0.6544 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.00678/5.673, allocations: 0.9364 MB / 1.786 GB, free: 210.1 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 0.01917/5.692, allocations: 5.379 MB / 1.791 GB, free: 209.8 MB / 0.6544 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.007787/5.7, allocations: 1.056 MB / 1.792 GB, free: 209.8 MB / 0.6544 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.2827/5.982, allocations: 48.59 MB / 1.84 GB, free: 198.1 MB / 0.6544 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.000152/5.983, allocations: 124.4 kB / 1.84 GB, free: 198.1 MB / 0.6544 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 0.0001256/5.983, allocations: 19.12 kB / 1.84 GB, free: 198.1 MB / 0.6544 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0004582/5.983, allocations: 62.48 kB / 1.84 GB, free: 198.1 MB / 0.6544 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.3219/6.305, allocations: 73.04 MB / 1.911 GB, free: 142.1 MB / 0.6544 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 0.0001209/6.305, allocations: 4 kB / 1.911 GB, free: 142.1 MB / 0.6544 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.01486/6.32, allocations: 2.419 MB / 1.914 GB, free: 139.6 MB / 0.6544 GB Notification: Performance of postOpt tearingSystem (simulation): time 0.03141/6.352, allocations: 11.88 MB / 1.925 GB, free: 127.9 MB / 0.6544 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.004679/6.356, allocations: 475.5 kB / 1.926 GB, free: 127.5 MB / 0.6544 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.103/6.459, allocations: 46.95 MB / 1.972 GB, free: 80.21 MB / 0.6544 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.987e-06/6.459, allocations: 4 kB / 1.972 GB, free: 80.21 MB / 0.6544 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.6151/7.075, allocations: 62.73 MB / 2.033 GB, free: 204.4 MB / 0.6544 GB Notification: Performance of postOpt removeConstants (simulation): time 0.01208/7.087, allocations: 3.295 MB / 2.036 GB, free: 203.4 MB / 0.6544 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.006897/7.094, allocations: 292.6 kB / 2.037 GB, free: 203.2 MB / 0.6544 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.01504/7.109, allocations: 0.5296 MB / 2.037 GB, free: 203.1 MB / 0.6544 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.007885/7.117, allocations: 1.499 MB / 2.038 GB, free: 202.9 MB / 0.6544 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.004127/7.121, allocations: 473.1 kB / 2.039 GB, free: 202.8 MB / 0.6544 GB Notification: Performance of sorting global known variables: time 0.01434/7.135, allocations: 6.966 MB / 2.046 GB, free: 200.4 MB / 0.6544 GB Notification: Performance of sort global known variables: time 1.102e-06/7.135, allocations: 0 / 2.046 GB, free: 200.4 MB / 0.6544 GB Notification: Performance of remove unused functions: time 0.03364/7.169, allocations: 6.686 MB / 2.052 GB, free: 199.9 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 0.01301/7.182, allocations: 3.541 MB / 2.056 GB, free: 199.2 MB / 0.6544 GB Notification: Performance of simCode: created initialization part: time 0.07363/7.256, allocations: 27.78 MB / 2.083 GB, free: 189 MB / 0.6544 GB Notification: Performance of simCode: created event and clocks part: time 1.187e-05/7.256, allocations: 2.438 kB / 2.083 GB, free: 189 MB / 0.6544 GB Notification: Performance of simCode: created simulation system equations: time 0.04281/7.298, allocations: 14.87 MB / 2.097 GB, free: 183.2 MB / 0.6544 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.02294/7.321, allocations: 2.501 MB / 2.1 GB, free: 182.3 MB / 0.6544 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0987/7.42, allocations: 37.53 MB / 2.136 GB, free: 151.8 MB / 0.6544 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.01644/7.437, allocations: 9.636 MB / 2.146 GB, free: 144.8 MB / 0.6544 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.00918/7.446, allocations: 1.564 MB / 2.147 GB, free: 143.4 MB / 0.6544 GB Notification: Performance of SimCode: time 1.202e-06/7.446, allocations: 0 / 2.147 GB, free: 143.4 MB / 0.6544 GB Notification: Performance of Templates: time 1.285/8.731, allocations: 0.5112 GB / 2.659 GB, free: 95.21 MB / 0.6544 GB make -j1 -f Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.makefile (rm -f Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.pipe ; mkfifo Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.pipe ; head -c 1048576 < Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.pipe >> ../files/Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.sim & ./Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery -abortSlowSimulation -alarm=480 -lv LOG_STATS > Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.pipe 2>&1)