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 0.001122/0.001122, allocations: 108 kB / 15.6 MB, free: 132 kB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001103/0.001103, allocations: 198.3 kB / 16.54 MB, free: 6.672 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.161/1.161, allocations: 222.9 MB / 240.2 MB, free: 4.395 MB / 190.1 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.1566/0.1566, allocations: 15.31 MB / 305.7 MB, free: 15.29 MB / 254.1 MB Notification: Performance of FrontEnd - loaded program: time 0.001059/0.001059, allocations: 59.91 kB / 370.3 MB, free: 3.953 MB / 302.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.07938/0.08045, allocations: 53.6 MB / 423.9 MB, free: 14.3 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 0.1655/0.246, allocations: 41.59 MB / 465.5 MB, free: 36.74 MB / 366.1 MB Notification: Performance of NFInst.instExpressions: time 0.05582/0.3018, allocations: 72.72 MB / 0.5256 GB, free: 12.21 MB / 398.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.003014/0.3048, allocations: 67.56 kB / 0.5257 GB, free: 12.15 MB / 398.1 MB Notification: Performance of NFTyping.typeComponents: time 0.00356/0.3084, allocations: 1.628 MB / 0.5273 GB, free: 10.87 MB / 398.1 MB Notification: Performance of NFTyping.typeBindings: time 0.01402/0.3225, allocations: 5.923 MB / 0.5331 GB, free: 5.824 MB / 398.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.02226/0.3447, allocations: 10.2 MB / 0.543 GB, free: 11.56 MB / 414.1 MB Notification: Performance of NFFlatten.flatten: time 0.02134/0.3661, allocations: 26.58 MB / 0.569 GB, free: 0.8945 MB / 430.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.02056/0.3867, allocations: 21.97 MB / 0.5904 GB, free: 10.81 MB / 462.1 MB Notification: Performance of NFEvalConstants.evaluate: time 0.3294/0.7161, allocations: 17.43 MB / 0.6075 GB, free: 24.64 MB / 462.1 MB Notification: Performance of NFSimplifyModel.simplify: time 0.01987/0.736, allocations: 16.2 MB / 0.6233 GB, free: 24.21 MB / 462.1 MB Notification: Performance of NFPackage.collectConstants: time 0.009293/0.7453, allocations: 3.094 MB / 0.6263 GB, free: 24.21 MB / 462.1 MB Notification: Performance of NFFlatten.collectFunctions: time 0.03038/0.7757, allocations: 10.7 MB / 0.6367 GB, free: 24.21 MB / 462.1 MB Notification: Performance of NFScalarize.scalarize: time 0.01032/0.786, allocations: 6.979 MB / 0.6436 GB, free: 23.61 MB / 462.1 MB Notification: Performance of NFVerifyModel.verify: time 0.01863/0.8047, allocations: 12.17 MB / 0.6554 GB, free: 16.74 MB / 462.1 MB Notification: Performance of NFConvertDAE.convert: time 0.04573/0.8504, allocations: 41.83 MB / 0.6963 GB, free: 12.93 MB / 478.1 MB Notification: Performance of FrontEnd - DAE generated: time 5.761e-06/0.8505, allocations: 0 / 0.6963 GB, free: 12.93 MB / 478.1 MB Notification: Performance of FrontEnd: time 1.282e-06/0.8505, allocations: 2.656 kB / 0.6963 GB, free: 12.93 MB / 478.1 MB Notification: Performance of Transformations before backend: time 0.000813/0.8513, allocations: 0 / 0.6963 GB, free: 12.93 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 0.0712/0.9225, allocations: 24.76 MB / 0.7205 GB, free: 4.445 MB / 494.1 MB Notification: Performance of prepare preOptimizeDAE: time 3.851e-05/0.9226, allocations: 12.03 kB / 0.7205 GB, free: 4.434 MB / 494.1 MB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.02093/0.9435, allocations: 3.886 MB / 0.7243 GB, free: 0.5391 MB / 494.1 MB Notification: Performance of preOpt evaluateParameters (simulation): time 0.02325/0.9668, allocations: 11.77 MB / 0.7358 GB, free: 5.172 MB / 0.4982 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.001627/0.9684, allocations: 2.131 MB / 0.7379 GB, free: 2.824 MB / 0.4982 GB Notification: Performance of preOpt expandDerOperator (simulation): time 0.007244/0.9757, allocations: 1.527 MB / 0.7394 GB, free: 1.297 MB / 0.4982 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.06544/1.041, allocations: 34.8 MB / 0.7733 GB, free: 14.29 MB / 0.545 GB Notification: Performance of preOpt findStateOrder (simulation): time 0.0002951/1.041, allocations: 7.75 kB / 0.7733 GB, free: 14.28 MB / 0.545 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.004315/1.046, allocations: 0.5859 MB / 0.7739 GB, free: 13.7 MB / 0.545 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0002289/1.046, allocations: 360 kB / 0.7743 GB, free: 13.34 MB / 0.545 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.3696/1.416, allocations: 46.83 MB / 0.82 GB, free: 185.5 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 0.2136/1.629, allocations: 128.3 MB / 0.9453 GB, free: 101.2 MB / 0.5608 GB Notification: Performance of preOpt comSubExp (simulation): time 0.6741/2.303, allocations: 276 MB / 1.215 GB, free: 63.34 MB / 0.5608 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.02419/2.328, allocations: 19.81 MB / 1.234 GB, free: 44.55 MB / 0.5608 GB Notification: Performance of preOpt evalFunc (simulation): time 0.3068/2.634, allocations: 87.54 MB / 1.32 GB, free: 165.4 MB / 0.5608 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 9.409e-05/2.635, allocations: 135.1 kB / 1.32 GB, free: 165.3 MB / 0.5608 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.01803/2.653, allocations: 4.513 MB / 1.324 GB, free: 164.4 MB / 0.5608 GB Notification: Performance of pre-optimization done (n=995): time 4.246e-05/2.653, allocations: 0 / 1.324 GB, free: 164.4 MB / 0.5608 GB Notification: Performance of matching and sorting (n=1129): time 0.5813/3.234, allocations: 130.7 MB / 1.452 GB, free: 68.52 MB / 0.5608 GB Notification: Performance of inlineWhenForInitialization (initialization): time 7.678e-05/3.234, allocations: 168.2 kB / 1.452 GB, free: 68.34 MB / 0.5608 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.01239/3.246, allocations: 10.16 MB / 1.462 GB, free: 58.24 MB / 0.5608 GB Notification: Performance of collectPreVariables (initialization): time 0.003423/3.25, allocations: 213.7 kB / 1.462 GB, free: 58.02 MB / 0.5608 GB Notification: Performance of collectInitialEqns (initialization): time 0.182/3.432, allocations: 6.875 MB / 1.469 GB, free: 177.1 MB / 0.5608 GB Notification: Performance of collectInitialBindings (initialization): time 0.005815/3.438, allocations: 3.903 MB / 1.473 GB, free: 174.9 MB / 0.5608 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.005278/3.443, allocations: 3.257 MB / 1.476 GB, free: 174.8 MB / 0.5608 GB Notification: Performance of setup shared object (initialization): time 3.545e-05/3.443, allocations: 311.3 kB / 1.476 GB, free: 174.5 MB / 0.5608 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.01447/3.458, allocations: 11.82 MB / 1.488 GB, free: 172.1 MB / 0.5608 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.01938/3.477, allocations: 16.55 MB / 1.504 GB, free: 162 MB / 0.5608 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.03991/3.517, allocations: 29.74 MB / 1.533 GB, free: 146.2 MB / 0.5608 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0002864/3.517, allocations: 41.03 kB / 1.533 GB, free: 146.2 MB / 0.5608 GB Notification: Performance of matching and sorting (n=1889) (initialization): time 0.3962/3.913, allocations: 81.46 MB / 1.613 GB, free: 92.55 MB / 0.5608 GB Notification: Performance of prepare postOptimizeDAE: time 0.0002285/3.914, allocations: 68 kB / 1.613 GB, free: 92.49 MB / 0.5608 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0002717/3.914, allocations: 152.9 kB / 1.613 GB, free: 92.34 MB / 0.5608 GB Notification: Performance of postOpt tearingSystem (initialization): time 0.05319/3.967, allocations: 22.41 MB / 1.635 GB, free: 70.09 MB / 0.5608 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01565/3.983, allocations: 3.725 MB / 1.638 GB, free: 66.36 MB / 0.5608 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.3646/4.348, allocations: 93.97 MB / 1.73 GB, free: 140.4 MB / 0.5608 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.01621/4.364, allocations: 0.8319 MB / 1.731 GB, free: 140.2 MB / 0.5608 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.00433/4.368, allocations: 0.9348 MB / 1.732 GB, free: 140.1 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 0.01191/4.38, allocations: 5.375 MB / 1.737 GB, free: 137.9 MB / 0.5608 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.004238/4.384, allocations: 1.058 MB / 1.738 GB, free: 137.9 MB / 0.5608 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.2448/4.629, allocations: 48.62 MB / 1.786 GB, free: 104.6 MB / 0.5608 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.0001078/4.629, allocations: 120 kB / 1.786 GB, free: 104.5 MB / 0.5608 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 0.0001015/4.629, allocations: 26.3 kB / 1.786 GB, free: 104.5 MB / 0.5608 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0003264/4.63, allocations: 59.77 kB / 1.786 GB, free: 104.5 MB / 0.5608 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.4579/5.088, allocations: 73.04 MB / 1.857 GB, free: 144.5 MB / 0.5608 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 0.0001035/5.088, allocations: 4.469 kB / 1.857 GB, free: 144.5 MB / 0.5608 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.01297/5.101, allocations: 2.42 MB / 1.859 GB, free: 144.5 MB / 0.5608 GB Notification: Performance of postOpt tearingSystem (simulation): time 0.0291/5.13, allocations: 11.89 MB / 1.871 GB, free: 144.4 MB / 0.5608 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.003388/5.133, allocations: 478.2 kB / 1.871 GB, free: 144.4 MB / 0.5608 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.1025/5.236, allocations: 46.95 MB / 1.917 GB, free: 130.2 MB / 0.5608 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.859e-06/5.236, allocations: 4.719 kB / 1.917 GB, free: 130.2 MB / 0.5608 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.2622/5.498, allocations: 62.74 MB / 1.979 GB, free: 106.5 MB / 0.5608 GB Notification: Performance of postOpt removeConstants (simulation): time 0.01063/5.509, allocations: 3.292 MB / 1.982 GB, free: 103.7 MB / 0.5608 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.005018/5.514, allocations: 291.9 kB / 1.982 GB, free: 103.5 MB / 0.5608 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.01216/5.526, allocations: 0.5306 MB / 1.983 GB, free: 102.9 MB / 0.5608 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.00599/5.532, allocations: 1.5 MB / 1.984 GB, free: 101.4 MB / 0.5608 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.002598/5.535, allocations: 471.6 kB / 1.985 GB, free: 101 MB / 0.5608 GB Notification: Performance of sorting global known variables: time 0.007888/5.543, allocations: 6.97 MB / 1.991 GB, free: 94.05 MB / 0.5608 GB Notification: Performance of sort global known variables: time 4.01e-07/5.543, allocations: 0 / 1.991 GB, free: 94.05 MB / 0.5608 GB Notification: Performance of remove unused functions: time 0.02241/5.565, allocations: 6.68 MB / 1.998 GB, free: 87.75 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 0.007543/5.573, allocations: 3.539 MB / 2.001 GB, free: 85.18 MB / 0.5608 GB Notification: Performance of simCode: created initialization part: time 0.4317/6.004, allocations: 108.8 MB / 2.108 GB, free: 164.7 MB / 0.5608 GB Notification: Performance of simCode: created event and clocks part: time 7.073e-06/6.004, allocations: 2.281 kB / 2.108 GB, free: 164.7 MB / 0.5608 GB Notification: Performance of simCode: created simulation system equations: time 0.03403/6.038, allocations: 14.87 MB / 2.122 GB, free: 152.3 MB / 0.5608 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.01309/6.051, allocations: 2.505 MB / 2.124 GB, free: 150.4 MB / 0.5608 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.06438/6.116, allocations: 38.19 MB / 2.162 GB, free: 117.6 MB / 0.5608 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.007541/6.123, allocations: 9.941 MB / 2.171 GB, free: 110.3 MB / 0.5608 GB Notification: Performance of simCode: alias equations: time 0.01275/6.136, allocations: 5.206 MB / 2.177 GB, free: 107.1 MB / 0.5608 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.003764/6.14, allocations: 1.438 MB / 2.178 GB, free: 105.9 MB / 0.5608 GB Notification: Performance of SimCode: time 1.323e-06/6.14, allocations: 0 / 2.178 GB, free: 105.9 MB / 0.5608 GB Notification: Performance of Templates: time 0.7227/6.863, allocations: 327.1 MB / 2.497 GB, free: 144.8 MB / 0.5608 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)