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 0.007198/0.007199, allocations: 100.3 kB / 15.73 MB, free: 6.035 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001494/0.001494, allocations: 190.3 kB / 16.67 MB, free: 5.969 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.402/1.402, allocations: 222.9 MB / 240.4 MB, free: 4.328 MB / 190.1 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.2749/0.2749, allocations: 15.33 MB / 305.9 MB, free: 15.3 MB / 254.1 MB Notification: Performance of FrontEnd - loaded program: time 0.001251/0.001251, allocations: 63.91 kB / 425.2 MB, free: 13.05 MB / 366.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.3587/0.3599, allocations: 53.61 MB / 478.8 MB, free: 26.11 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.HemoglobinMultipleAllostery): time 0.05504/0.415, allocations: 41.61 MB / 0.5083 GB, free: 8.984 MB / 382.1 MB Notification: Performance of NFInst.instExpressions: time 0.09012/0.5052, allocations: 72.71 MB / 0.5793 GB, free: 15.98 MB / 462.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.007961/0.5132, allocations: 59.69 kB / 0.5793 GB, free: 15.92 MB / 462.1 MB Notification: Performance of NFTyping.typeComponents: time 0.006678/0.5199, allocations: 1.613 MB / 0.5809 GB, free: 14.3 MB / 462.1 MB Notification: Performance of NFTyping.typeBindings: time 0.02369/0.5436, allocations: 5.931 MB / 0.5867 GB, free: 8.324 MB / 462.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.03476/0.5784, allocations: 10.21 MB / 0.5967 GB, free: 14.05 MB / 478.1 MB Notification: Performance of NFFlatten.flatten: time 0.4242/1.003, allocations: 26.68 MB / 0.6227 GB, free: 19.04 MB / 478.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.03429/1.037, allocations: 21.96 MB / 0.6442 GB, free: 17.62 MB / 478.1 MB Notification: Performance of NFEvalConstants.evaluate: time 0.03823/1.075, allocations: 17.48 MB / 0.6612 GB, free: 14.84 MB / 478.1 MB Notification: Performance of NFSimplifyModel.simplify: time 0.03504/1.11, allocations: 16.2 MB / 0.6771 GB, free: 3.16 MB / 478.1 MB Notification: Performance of NFPackage.collectConstants: time 0.01447/1.125, allocations: 3.094 MB / 0.6801 GB, free: 68 kB / 478.1 MB Notification: Performance of NFFlatten.collectFunctions: time 0.05509/1.18, allocations: 10.7 MB / 0.6905 GB, free: 5.965 MB / 494.1 MB Notification: Performance of NFScalarize.scalarize: time 0.01794/1.198, allocations: 6.978 MB / 0.6973 GB, free: 15.21 MB / 0.4981 GB Notification: Performance of NFVerifyModel.verify: time 0.03638/1.234, allocations: 12.16 MB / 0.7092 GB, free: 3.277 MB / 0.4981 GB Notification: Performance of NFConvertDAE.convert: time 0.1004/1.335, allocations: 42.21 MB / 0.7504 GB, free: 11.95 MB / 0.545 GB Notification: Performance of FrontEnd - DAE generated: time 9.027e-06/1.335, allocations: 10.19 kB / 0.7504 GB, free: 11.94 MB / 0.545 GB Notification: Performance of FrontEnd: time 2.375e-06/1.335, allocations: 0 / 0.7504 GB, free: 11.94 MB / 0.545 GB Notification: Performance of Transformations before backend: time 0.001404/1.336, allocations: 0 / 0.7504 GB, free: 11.94 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 0.1112/1.448, allocations: 24.73 MB / 0.7746 GB, free: 3.16 MB / 0.5606 GB Notification: Performance of prepare preOptimizeDAE: time 5.144e-05/1.448, allocations: 8.031 kB / 0.7746 GB, free: 3.152 MB / 0.5606 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.02904/1.477, allocations: 3.893 MB / 0.7784 GB, free: 15.24 MB / 0.5762 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.03668/1.513, allocations: 12.01 MB / 0.7901 GB, free: 3.637 MB / 0.5762 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.002976/1.516, allocations: 2.127 MB / 0.7922 GB, free: 1.293 MB / 0.5762 GB Notification: Performance of preOpt expandDerOperator (simulation): time 0.01315/1.53, allocations: 1.539 MB / 0.7937 GB, free: 15.75 MB / 0.5919 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.1097/1.639, allocations: 34.79 MB / 0.8277 GB, free: 12.73 MB / 0.6231 GB Notification: Performance of preOpt findStateOrder (simulation): time 0.0006607/1.64, allocations: 15.2 kB / 0.8277 GB, free: 12.73 MB / 0.6231 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.01103/1.651, allocations: 0.5859 MB / 0.8283 GB, free: 12.14 MB / 0.6231 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0003991/1.651, allocations: 360 kB / 0.8286 GB, free: 11.79 MB / 0.6231 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.8194/2.471, allocations: 46.84 MB / 0.8744 GB, free: 213.3 MB / 0.6232 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 0.2645/2.735, allocations: 127.9 MB / 0.9993 GB, free: 100.1 MB / 0.6232 GB Notification: Performance of preOpt comSubExp (simulation): time 1.23/3.966, allocations: 276 MB / 1.269 GB, free: 79.75 MB / 0.6233 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.03664/4.002, allocations: 19.81 MB / 1.288 GB, free: 59.89 MB / 0.6233 GB Notification: Performance of preOpt evalFunc (simulation): time 0.5715/4.574, allocations: 87.46 MB / 1.374 GB, free: 193.9 MB / 0.6233 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001485/4.574, allocations: 138.1 kB / 1.374 GB, free: 193.7 MB / 0.6233 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.02207/4.596, allocations: 4.508 MB / 1.378 GB, free: 192.8 MB / 0.6233 GB Notification: Performance of pre-optimization done (n=995): time 7.575e-05/4.596, allocations: 3.938 kB / 1.378 GB, free: 192.8 MB / 0.6233 GB Notification: Performance of matching and sorting (n=1129): time 0.6699/5.266, allocations: 130.7 MB / 1.506 GB, free: 99.98 MB / 0.6233 GB Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001028/5.266, allocations: 164.2 kB / 1.506 GB, free: 99.8 MB / 0.6233 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.01558/5.282, allocations: 10.15 MB / 1.516 GB, free: 89.71 MB / 0.6233 GB Notification: Performance of collectPreVariables (initialization): time 0.005838/5.288, allocations: 215.6 kB / 1.516 GB, free: 89.5 MB / 0.6233 GB Notification: Performance of collectInitialEqns (initialization): time 0.004993/5.293, allocations: 6.879 MB / 1.523 GB, free: 82.6 MB / 0.6233 GB Notification: Performance of collectInitialBindings (initialization): time 0.01031/5.303, allocations: 3.906 MB / 1.527 GB, free: 78.73 MB / 0.6233 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.01659/5.32, allocations: 3.264 MB / 1.53 GB, free: 75.45 MB / 0.6233 GB Notification: Performance of setup shared object (initialization): time 6.732e-05/5.32, allocations: 305.1 kB / 1.53 GB, free: 75.15 MB / 0.6233 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.02305/5.343, allocations: 11.82 MB / 1.542 GB, free: 63.32 MB / 0.6233 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.03052/5.374, allocations: 16.55 MB / 1.558 GB, free: 44.69 MB / 0.6233 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.4464/5.82, allocations: 29.73 MB / 1.587 GB, free: 181.4 MB / 0.6233 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0001603/5.82, allocations: 43.03 kB / 1.587 GB, free: 181.4 MB / 0.6233 GB Notification: Performance of matching and sorting (n=1889) (initialization): time 0.4525/6.273, allocations: 81.47 MB / 1.666 GB, free: 149.1 MB / 0.6233 GB Notification: Performance of prepare postOptimizeDAE: time 0.0001212/6.273, allocations: 72 kB / 1.666 GB, free: 149.1 MB / 0.6233 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0002515/6.273, allocations: 152.1 kB / 1.667 GB, free: 148.9 MB / 0.6233 GB Notification: Performance of postOpt tearingSystem (initialization): time 0.05959/6.333, allocations: 22.39 MB / 1.688 GB, free: 126.7 MB / 0.6233 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01881/6.352, allocations: 3.727 MB / 1.692 GB, free: 123 MB / 0.6233 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.1854/6.537, allocations: 93.95 MB / 1.784 GB, free: 28.66 MB / 0.6233 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.02304/6.56, allocations: 0.8312 MB / 1.785 GB, free: 27.83 MB / 0.6233 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.006951/6.567, allocations: 0.9407 MB / 1.786 GB, free: 26.89 MB / 0.6233 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 0.429/6.996, allocations: 5.374 MB / 1.791 GB, free: 181.5 MB / 0.6233 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.007563/7.004, allocations: 1.055 MB / 1.792 GB, free: 181.5 MB / 0.6233 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.2828/7.287, allocations: 48.6 MB / 1.839 GB, free: 174.4 MB / 0.6233 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.0001974/7.287, allocations: 119.9 kB / 1.839 GB, free: 174.4 MB / 0.6233 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 0.0001576/7.287, allocations: 22.12 kB / 1.839 GB, free: 174.4 MB / 0.6233 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0005264/7.287, allocations: 63.7 kB / 1.84 GB, free: 174.4 MB / 0.6233 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.3168/7.604, allocations: 73.05 MB / 1.911 GB, free: 128.3 MB / 0.6233 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 0.0001882/7.605, allocations: 4 kB / 1.911 GB, free: 128.3 MB / 0.6233 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0157/7.62, allocations: 2.423 MB / 1.913 GB, free: 125.9 MB / 0.6233 GB Notification: Performance of postOpt tearingSystem (simulation): time 0.03231/7.653, allocations: 11.88 MB / 1.925 GB, free: 114.4 MB / 0.6233 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.004478/7.657, allocations: 479.5 kB / 1.925 GB, free: 113.9 MB / 0.6233 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.1034/7.761, allocations: 46.94 MB / 1.971 GB, free: 66.66 MB / 0.6233 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.679e-06/7.761, allocations: 4 kB / 1.971 GB, free: 66.66 MB / 0.6233 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.6415/8.402, allocations: 62.71 MB / 2.032 GB, free: 165.6 MB / 0.6233 GB Notification: Performance of postOpt removeConstants (simulation): time 0.01587/8.418, allocations: 3.294 MB / 2.036 GB, free: 164.6 MB / 0.6233 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.007001/8.425, allocations: 298.3 kB / 2.036 GB, free: 164.4 MB / 0.6233 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.01537/8.44, allocations: 0.5277 MB / 2.036 GB, free: 164.3 MB / 0.6233 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.007274/8.448, allocations: 1.5 MB / 2.038 GB, free: 164.1 MB / 0.6233 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.002918/8.451, allocations: 473.1 kB / 2.038 GB, free: 164 MB / 0.6233 GB Notification: Performance of sorting global known variables: time 0.01538/8.466, allocations: 6.972 MB / 2.045 GB, free: 161.6 MB / 0.6233 GB Notification: Performance of sort global known variables: time 1.222e-06/8.466, allocations: 0 / 2.045 GB, free: 161.6 MB / 0.6233 GB Notification: Performance of remove unused functions: time 0.03519/8.501, allocations: 6.683 MB / 2.052 GB, free: 161 MB / 0.6233 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 0.01329/8.515, allocations: 3.533 MB / 2.055 GB, free: 160.4 MB / 0.6233 GB Notification: Performance of simCode: created initialization part: time 0.0713/8.586, allocations: 27.79 MB / 2.082 GB, free: 150.2 MB / 0.6233 GB Notification: Performance of simCode: created event and clocks part: time 1.015e-05/8.586, allocations: 2.844 kB / 2.082 GB, free: 150.2 MB / 0.6233 GB Notification: Performance of simCode: created simulation system equations: time 0.04347/8.63, allocations: 14.88 MB / 2.097 GB, free: 144.4 MB / 0.6233 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.02488/8.654, allocations: 2.501 MB / 2.099 GB, free: 143.6 MB / 0.6233 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.09501/8.75, allocations: 37.84 MB / 2.136 GB, free: 119.1 MB / 0.6233 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.01536/8.765, allocations: 9.936 MB / 2.146 GB, free: 111.9 MB / 0.6233 GB Notification: Performance of simCode: alias equations: time 0.01775/8.783, allocations: 5.231 MB / 2.151 GB, free: 108.6 MB / 0.6233 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.006343/8.789, allocations: 1.438 MB / 2.152 GB, free: 107.4 MB / 0.6233 GB Notification: Performance of SimCode: time 6.61e-07/8.789, allocations: 0 / 2.152 GB, free: 107.4 MB / 0.6233 GB Notification: Performance of Templates: time 0.8457/9.635, allocations: 326.4 MB / 2.471 GB, free: 1.371 MB / 0.6233 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)