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 0.001618/0.001618, allocations: 107 kB / 16.36 MB, free: 6.336 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.002114/0.002114, allocations: 195.3 kB / 17.29 MB, free: 5.883 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.334/1.334, allocations: 222.9 MB / 241 MB, free: 15.17 MB / 206.1 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.08586/0.08586, allocations: 15.31 MB / 306.5 MB, free: 15.45 MB / 254.1 MB Notification: Performance of FrontEnd - loaded program: time 0.00119/0.00119, allocations: 60.2 kB / 371.7 MB, free: 50.77 MB / 302.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.09339/0.0946, allocations: 53.62 MB / 425.4 MB, free: 13.35 MB / 302.1 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 0.04611/0.1407, allocations: 41.38 MB / 466.7 MB, free: 4.02 MB / 334.1 MB Notification: Performance of NFInst.instExpressions: time 0.3112/0.4519, allocations: 72.7 MB / 0.5268 GB, free: 15.05 MB / 382.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.005165/0.4572, allocations: 61 kB / 0.5269 GB, free: 15.05 MB / 382.1 MB Notification: Performance of NFTyping.typeComponents: time 0.005583/0.4628, allocations: 1.624 MB / 0.5284 GB, free: 15.05 MB / 382.1 MB Notification: Performance of NFTyping.typeBindings: time 0.02024/0.483, allocations: 5.923 MB / 0.5342 GB, free: 14.7 MB / 382.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.02801/0.5111, allocations: 10.21 MB / 0.5442 GB, free: 11.02 MB / 382.1 MB Notification: Performance of NFFlatten.flatten: time 0.02814/0.5392, allocations: 26.71 MB / 0.5703 GB, free: 9.766 MB / 398.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.02595/0.5652, allocations: 21.96 MB / 0.5917 GB, free: 5.008 MB / 414.1 MB Notification: Performance of NFEvalConstants.evaluate: time 0.02678/0.5921, allocations: 17.47 MB / 0.6088 GB, free: 3.785 MB / 430.1 MB Notification: Performance of NFSimplifyModel.simplify: time 0.0314/0.6235, allocations: 16.19 MB / 0.6246 GB, free: 4.031 MB / 446.1 MB Notification: Performance of NFPackage.collectConstants: time 0.01068/0.6342, allocations: 3.098 MB / 0.6276 GB, free: 0.9336 MB / 446.1 MB Notification: Performance of NFFlatten.collectFunctions: time 0.03829/0.6725, allocations: 10.7 MB / 0.6381 GB, free: 6.309 MB / 462.1 MB Notification: Performance of NFScalarize.scalarize: time 0.01327/0.6858, allocations: 6.972 MB / 0.6449 GB, free: 15.52 MB / 478.1 MB Notification: Performance of NFVerifyModel.verify: time 0.02695/0.7128, allocations: 12.16 MB / 0.6568 GB, free: 3.523 MB / 478.1 MB Notification: Performance of NFConvertDAE.convert: time 0.5972/1.31, allocations: 42 MB / 0.6978 GB, free: 84.08 MB / 0.4982 GB Notification: Performance of FrontEnd - DAE generated: time 6.011e-06/1.31, allocations: 0 / 0.6978 GB, free: 84.08 MB / 0.4982 GB Notification: Performance of FrontEnd: time 3.807e-06/1.31, allocations: 2.594 kB / 0.6978 GB, free: 84.08 MB / 0.4982 GB Notification: Performance of Transformations before backend: time 0.001221/1.311, allocations: 1.969 kB / 0.6978 GB, free: 84.08 MB / 0.4982 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 0.09602/1.407, allocations: 24.76 MB / 0.722 GB, free: 77.91 MB / 0.4982 GB Notification: Performance of prepare preOptimizeDAE: time 6.9e-05/1.408, allocations: 8.438 kB / 0.722 GB, free: 77.91 MB / 0.4982 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.03054/1.438, allocations: 3.894 MB / 0.7258 GB, free: 76.98 MB / 0.4982 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.03425/1.472, allocations: 12.02 MB / 0.7375 GB, free: 75.38 MB / 0.4982 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.002269/1.475, allocations: 2.134 MB / 0.7396 GB, free: 74.26 MB / 0.4982 GB Notification: Performance of preOpt expandDerOperator (simulation): time 0.01435/1.489, allocations: 1.525 MB / 0.7411 GB, free: 74.22 MB / 0.4982 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.09781/1.587, allocations: 34.8 MB / 0.7751 GB, free: 51.68 MB / 0.4982 GB Notification: Performance of preOpt findStateOrder (simulation): time 0.0007875/1.588, allocations: 7.469 kB / 0.7751 GB, free: 51.68 MB / 0.4982 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.01293/1.601, allocations: 0.5885 MB / 0.7756 GB, free: 51.09 MB / 0.4982 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0004001/1.601, allocations: 360 kB / 0.776 GB, free: 50.74 MB / 0.4982 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.09457/1.696, allocations: 46.84 MB / 0.8217 GB, free: 3.91 MB / 0.4982 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 0.5963/2.292, allocations: 127.9 MB / 0.9466 GB, free: 186.6 MB / 0.5763 GB Notification: Performance of preOpt comSubExp (simulation): time 0.8664/3.159, allocations: 276 MB / 1.216 GB, free: 162.9 MB / 0.5763 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.03852/3.197, allocations: 19.81 MB / 1.236 GB, free: 158.6 MB / 0.5763 GB Notification: Performance of preOpt evalFunc (simulation): time 0.1632/3.36, allocations: 87.46 MB / 1.321 GB, free: 98.56 MB / 0.5763 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 9.154e-05/3.36, allocations: 143.7 kB / 1.321 GB, free: 98.41 MB / 0.5763 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.01995/3.38, allocations: 4.509 MB / 1.326 GB, free: 94 MB / 0.5763 GB Notification: Performance of pre-optimization done (n=995): time 6.919e-05/3.381, allocations: 2.156 kB / 1.326 GB, free: 94 MB / 0.5763 GB Notification: Performance of matching and sorting (n=1129): time 0.9125/4.293, allocations: 130.7 MB / 1.453 GB, free: 205.5 MB / 0.5763 GB Notification: Performance of inlineWhenForInitialization (initialization): time 9.35e-05/4.293, allocations: 168.3 kB / 1.453 GB, free: 205.4 MB / 0.5763 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0166/4.31, allocations: 10.17 MB / 1.463 GB, free: 200.4 MB / 0.5763 GB Notification: Performance of collectPreVariables (initialization): time 0.004843/4.315, allocations: 212 kB / 1.463 GB, free: 200.2 MB / 0.5763 GB Notification: Performance of collectInitialEqns (initialization): time 0.005105/4.32, allocations: 6.88 MB / 1.47 GB, free: 195.8 MB / 0.5763 GB Notification: Performance of collectInitialBindings (initialization): time 0.007853/4.328, allocations: 3.907 MB / 1.474 GB, free: 192.4 MB / 0.5763 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.01324/4.341, allocations: 3.261 MB / 1.477 GB, free: 190.6 MB / 0.5763 GB Notification: Performance of setup shared object (initialization): time 4.83e-05/4.341, allocations: 304.3 kB / 1.477 GB, free: 190.3 MB / 0.5763 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0211/4.362, allocations: 11.82 MB / 1.489 GB, free: 183.8 MB / 0.5763 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.02559/4.388, allocations: 16.55 MB / 1.505 GB, free: 171.1 MB / 0.5763 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0527/4.44, allocations: 29.74 MB / 1.534 GB, free: 141.4 MB / 0.5763 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.00017/4.441, allocations: 44 kB / 1.534 GB, free: 141.3 MB / 0.5763 GB Notification: Performance of matching and sorting (n=1889) (initialization): time 0.6508/5.092, allocations: 81.46 MB / 1.614 GB, free: 189.6 MB / 0.5763 GB Notification: Performance of prepare postOptimizeDAE: time 0.0001403/5.092, allocations: 72.59 kB / 1.614 GB, free: 189.6 MB / 0.5763 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0002622/5.092, allocations: 148.1 kB / 1.614 GB, free: 189.6 MB / 0.5763 GB Notification: Performance of postOpt tearingSystem (initialization): time 0.05797/5.15, allocations: 22.4 MB / 1.636 GB, free: 188.8 MB / 0.5763 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01692/5.167, allocations: 3.728 MB / 1.639 GB, free: 188.7 MB / 0.5763 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.189/5.356, allocations: 93.94 MB / 1.731 GB, free: 126.1 MB / 0.5763 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.01712/5.373, allocations: 0.8351 MB / 1.732 GB, free: 125.2 MB / 0.5763 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.004916/5.378, allocations: 0.9406 MB / 1.733 GB, free: 124.3 MB / 0.5763 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 0.01557/5.394, allocations: 5.365 MB / 1.738 GB, free: 119.2 MB / 0.5763 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.006472/5.4, allocations: 1.059 MB / 1.739 GB, free: 118.7 MB / 0.5763 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.3389/5.739, allocations: 48.61 MB / 1.787 GB, free: 70.29 MB / 0.5763 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.000155/5.739, allocations: 123.9 kB / 1.787 GB, free: 70.16 MB / 0.5763 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 0.0001018/5.739, allocations: 24 kB / 1.787 GB, free: 70.14 MB / 0.5763 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0003647/5.74, allocations: 59.77 kB / 1.787 GB, free: 70.08 MB / 0.5763 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.6032/6.343, allocations: 73.04 MB / 1.858 GB, free: 179.1 MB / 0.5763 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 0.0001411/6.343, allocations: 3.875 kB / 1.858 GB, free: 179.1 MB / 0.5763 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.01398/6.357, allocations: 2.427 MB / 1.861 GB, free: 178.9 MB / 0.5763 GB Notification: Performance of postOpt tearingSystem (simulation): time 0.03109/6.388, allocations: 11.88 MB / 1.872 GB, free: 177.1 MB / 0.5763 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.005912/6.394, allocations: 476.8 kB / 1.873 GB, free: 176.8 MB / 0.5763 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.09926/6.494, allocations: 46.93 MB / 1.918 GB, free: 134.2 MB / 0.5763 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.99e-06/6.494, allocations: 7.359 kB / 1.918 GB, free: 134.2 MB / 0.5763 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.2566/6.75, allocations: 62.73 MB / 1.98 GB, free: 71.92 MB / 0.5763 GB Notification: Performance of postOpt removeConstants (simulation): time 0.01032/6.761, allocations: 3.3 MB / 1.983 GB, free: 69.2 MB / 0.5763 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.005972/6.767, allocations: 299.9 kB / 1.983 GB, free: 68.91 MB / 0.5763 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0146/6.781, allocations: 0.5228 MB / 1.984 GB, free: 68.38 MB / 0.5763 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.007677/6.789, allocations: 1.495 MB / 1.985 GB, free: 66.88 MB / 0.5763 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.002973/6.792, allocations: 475.6 kB / 1.986 GB, free: 66.42 MB / 0.5763 GB Notification: Performance of sorting global known variables: time 0.01226/6.804, allocations: 6.972 MB / 1.992 GB, free: 59.5 MB / 0.5763 GB Notification: Performance of sort global known variables: time 6.51e-07/6.804, allocations: 0 / 1.992 GB, free: 59.5 MB / 0.5763 GB Notification: Performance of remove unused functions: time 0.2885/7.093, allocations: 6.676 MB / 1.999 GB, free: 194 MB / 0.5763 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 0.01504/7.108, allocations: 3.544 MB / 2.002 GB, free: 193.7 MB / 0.5763 GB Notification: Performance of simCode: created initialization part: time 0.07075/7.179, allocations: 27.79 MB / 2.03 GB, free: 188.7 MB / 0.5763 GB Notification: Performance of simCode: created event and clocks part: time 1.086e-05/7.179, allocations: 3.625 kB / 2.03 GB, free: 188.7 MB / 0.5763 GB Notification: Performance of simCode: created simulation system equations: time 0.04271/7.221, allocations: 14.87 MB / 2.044 GB, free: 182.9 MB / 0.5763 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.02309/7.244, allocations: 2.493 MB / 2.047 GB, free: 182.1 MB / 0.5763 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.09053/7.335, allocations: 37.84 MB / 2.084 GB, free: 155.6 MB / 0.5763 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.01663/7.352, allocations: 9.942 MB / 2.093 GB, free: 148.3 MB / 0.5763 GB Notification: Performance of simCode: alias equations: time 0.01877/7.371, allocations: 5.229 MB / 2.098 GB, free: 145.1 MB / 0.5763 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.007874/7.379, allocations: 1.437 MB / 2.1 GB, free: 143.9 MB / 0.5763 GB Notification: Performance of SimCode: time 1.543e-06/7.379, allocations: 0 / 2.1 GB, free: 143.9 MB / 0.5763 GB Notification: Performance of Templates: time 1.197/8.575, allocations: 316.5 MB / 2.409 GB, free: 183.6 MB / 0.5763 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 -s cvode -lv LOG_STATS > Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.pipe 2>&1)