Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries/ --ompython_omhome=/usr Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllosteryCO.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.HemoglobinMultipleAllosteryCO,tolerance=1e-06,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllosteryCO") translateModel(Chemical.Examples.Hemoglobin.HemoglobinMultipleAllosteryCO,tolerance=1e-06,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllosteryCO") Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.0009588/0.0009588, allocations: 92.7 kB / 16.02 MB, free: 80 kB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.0008933/0.0008934, allocations: 183.8 kB / 16.92 MB, free: 6.922 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.383/1.383, allocations: 223.3 MB / 241 MB, free: 5.32 MB / 190.1 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.195/0.195, allocations: 15.28 MB / 307.4 MB, free: 15.78 MB / 254.1 MB Notification: Performance of FrontEnd - loaded program: time 0.0003678/0.0003675, allocations: 8 kB / 372.8 MB, free: 3.602 MB / 302.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.3174/0.3178, allocations: 54.62 MB / 427.4 MB, free: 40.31 MB / 350.1 MB [/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo:3019:6-3019:65: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:3019:6-3019:65: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.HemoglobinMultipleAllosteryCO): time 0.05434/0.3722, allocations: 47.38 MB / 474.8 MB, free: 16.62 MB / 350.1 MB Notification: Performance of NFInst.instExpressions: time 0.1019/0.4741, allocations: 85.63 MB / 0.5473 GB, free: 0.8047 MB / 414.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.007552/0.4817, allocations: 115.1 kB / 0.5474 GB, free: 0.6914 MB / 414.1 MB Notification: Performance of NFTyping.typeComponents: time 0.006684/0.4884, allocations: 1.735 MB / 0.5491 GB, free: 14.95 MB / 430.1 MB Notification: Performance of NFTyping.typeBindings: time 0.02638/0.5148, allocations: 6.125 MB / 0.555 GB, free: 8.781 MB / 430.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.03896/0.5538, allocations: 10.74 MB / 0.5655 GB, free: 13.98 MB / 446.1 MB Notification: Performance of NFFlatten.flatten: time 0.2894/0.8432, allocations: 29.86 MB / 0.5947 GB, free: 10.46 MB / 446.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.02917/0.8725, allocations: 20.82 MB / 0.615 GB, free: 8.625 MB / 446.1 MB Notification: Performance of NFEvalConstants.evaluate: time 0.03016/0.9027, allocations: 17.99 MB / 0.6326 GB, free: 7.383 MB / 446.1 MB Notification: Performance of NFSimplifyModel.simplify: time 0.02871/0.9314, allocations: 16.46 MB / 0.6487 GB, free: 1.648 MB / 446.1 MB Notification: Performance of NFPackage.collectConstants: time 0.008958/0.9404, allocations: 1.663 MB / 0.6503 GB, free: 1.648 MB / 446.1 MB Notification: Performance of NFFlatten.collectFunctions: time 0.03751/0.9779, allocations: 10.75 MB / 0.6608 GB, free: 9.113 MB / 462.1 MB Notification: Performance of NFScalarize.scalarize: time 0.01343/0.9914, allocations: 5.812 MB / 0.6665 GB, free: 3.559 MB / 462.1 MB Notification: Performance of NFVerifyModel.verify: time 0.02743/1.019, allocations: 11.65 MB / 0.6778 GB, free: 8.152 MB / 478.1 MB Notification: Performance of NFConvertDAE.convert: time 0.04931/1.068, allocations: 37.91 MB / 0.7149 GB, free: 5.32 MB / 0.4981 GB Notification: Performance of FrontEnd - DAE generated: time 4.168e-06/1.068, allocations: 0 / 0.7149 GB, free: 5.32 MB / 0.4981 GB Notification: Performance of FrontEnd: time 2.274e-06/1.068, allocations: 0 / 0.7149 GB, free: 5.32 MB / 0.4981 GB Notification: Performance of Transformations before backend: time 0.001042/1.069, allocations: 0 / 0.7149 GB, free: 5.32 MB / 0.4981 GB Notification: Model statistics after passing the front-end and creating the data structures used by the back-end: * Number of equations: 4405 * Number of variables: 4405 Notification: Performance of Generate backend data structure: time 0.07325/1.143, allocations: 23.53 MB / 0.7378 GB, free: 13.73 MB / 0.5294 GB Notification: Performance of prepare preOptimizeDAE: time 3.602e-05/1.143, allocations: 14.66 kB / 0.7379 GB, free: 13.72 MB / 0.5294 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.02603/1.169, allocations: 4.53 MB / 0.7423 GB, free: 9.164 MB / 0.5294 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.02862/1.197, allocations: 13.33 MB / 0.7553 GB, free: 12.33 MB / 0.545 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.002543/1.2, allocations: 2.54 MB / 0.7578 GB, free: 9.523 MB / 0.545 GB Notification: Performance of preOpt expandDerOperator (simulation): time 0.01011/1.21, allocations: 1.765 MB / 0.7595 GB, free: 7.758 MB / 0.545 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.5128/1.723, allocations: 40.45 MB / 0.799 GB, free: 179.5 MB / 0.5607 GB Notification: Performance of preOpt findStateOrder (simulation): time 0.0007231/1.724, allocations: 10.56 kB / 0.799 GB, free: 179.5 MB / 0.5607 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.008802/1.732, allocations: 0.6822 MB / 0.7997 GB, free: 179 MB / 0.5607 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0003069/1.733, allocations: 419.4 kB / 0.8001 GB, free: 179 MB / 0.5607 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.1026/1.835, allocations: 54.48 MB / 0.8533 GB, free: 159.8 MB / 0.5607 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 0.2995/2.135, allocations: 148.7 MB / 0.9985 GB, free: 18.83 MB / 0.5607 GB Notification: Performance of preOpt comSubExp (simulation): time 1.624/3.759, allocations: 351.6 MB / 1.342 GB, free: 95.66 MB / 0.5608 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.04753/3.807, allocations: 23.07 MB / 1.364 GB, free: 90.28 MB / 0.5608 GB Notification: Performance of preOpt evalFunc (simulation): time 0.2002/4.007, allocations: 101.6 MB / 1.464 GB, free: 11.79 MB / 0.5608 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001117/4.008, allocations: 151.6 kB / 1.464 GB, free: 11.62 MB / 0.5608 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.02832/4.036, allocations: 5.165 MB / 1.469 GB, free: 6.566 MB / 0.5608 GB Notification: Performance of pre-optimization done (n=1160): time 7.355e-05/4.036, allocations: 0 / 1.469 GB, free: 6.566 MB / 0.5608 GB Notification: Performance of matching and sorting (n=1312): time 1.081/5.117, allocations: 150 MB / 1.615 GB, free: 98.34 MB / 0.5608 GB Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001223/5.117, allocations: 185.7 kB / 1.615 GB, free: 98.15 MB / 0.5608 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.02053/5.137, allocations: 11.97 MB / 1.627 GB, free: 86.24 MB / 0.5608 GB Notification: Performance of collectPreVariables (initialization): time 0.00473/5.142, allocations: 241.7 kB / 1.627 GB, free: 86 MB / 0.5608 GB Notification: Performance of collectInitialEqns (initialization): time 0.005655/5.148, allocations: 8.037 MB / 1.635 GB, free: 77.94 MB / 0.5608 GB Notification: Performance of collectInitialBindings (initialization): time 0.008567/5.156, allocations: 4.553 MB / 1.64 GB, free: 73.43 MB / 0.5608 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.007372/5.164, allocations: 1.341 MB / 1.641 GB, free: 72.07 MB / 0.5608 GB Notification: Performance of setup shared object (initialization): time 4.736e-05/5.164, allocations: 305.1 kB / 1.641 GB, free: 71.77 MB / 0.5608 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.02421/5.188, allocations: 13.86 MB / 1.655 GB, free: 57.9 MB / 0.5608 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.2899/5.478, allocations: 19.33 MB / 1.674 GB, free: 148.4 MB / 0.5608 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.05433/5.532, allocations: 34.7 MB / 1.708 GB, free: 133.9 MB / 0.5608 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0002985/5.533, allocations: 48.12 kB / 1.708 GB, free: 133.9 MB / 0.5608 GB Notification: Performance of matching and sorting (n=2196) (initialization): time 0.5249/6.058, allocations: 93.24 MB / 1.799 GB, free: 98.31 MB / 0.5608 GB Notification: Performance of prepare postOptimizeDAE: time 0.0002539/6.058, allocations: 80.22 kB / 1.799 GB, free: 98.23 MB / 0.5608 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0003353/6.058, allocations: 178.7 kB / 1.799 GB, free: 98.06 MB / 0.5608 GB Notification: Performance of postOpt tearingSystem (initialization): time 0.07031/6.129, allocations: 26.08 MB / 1.824 GB, free: 72.2 MB / 0.5608 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.02025/6.149, allocations: 4.333 MB / 1.829 GB, free: 67.86 MB / 0.5608 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.5093/6.658, allocations: 102.3 MB / 1.928 GB, free: 128 MB / 0.5608 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.02323/6.681, allocations: 1.338 MB / 1.93 GB, free: 127.7 MB / 0.5608 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.006082/6.688, allocations: 1.089 MB / 1.931 GB, free: 127.6 MB / 0.5608 GB Notification: Model statistics after passing the back-end for initialization: * Number of independent subsystems: 782 * 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 (2138): * Single equations (assignments): 2135 * 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%), (41,12,73.3%)} * Non-linear torn systems (#iteration vars, #inner vars): 1 system {(1,3)} Notification: Performance of prepare postOptimizeDAE: time 0.01799/6.706, allocations: 6.21 MB / 1.937 GB, free: 125.1 MB / 0.5608 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.006375/6.712, allocations: 1.226 MB / 1.938 GB, free: 125.1 MB / 0.5608 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.3344/7.046, allocations: 57.5 MB / 1.994 GB, free: 94.6 MB / 0.5608 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.000138/7.047, allocations: 140 kB / 1.994 GB, free: 94.46 MB / 0.5608 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 0.0001748/7.047, allocations: 24 kB / 1.994 GB, free: 94.44 MB / 0.5608 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0004408/7.047, allocations: 67.73 kB / 1.994 GB, free: 94.37 MB / 0.5608 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.6994/7.747, allocations: 86.1 MB / 2.079 GB, free: 131.6 MB / 0.5608 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 0.0001416/7.747, allocations: 3.125 kB / 2.079 GB, free: 131.6 MB / 0.5608 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.01827/7.765, allocations: 2.819 MB / 2.081 GB, free: 131.4 MB / 0.5608 GB Notification: Performance of postOpt tearingSystem (simulation): time 0.04259/7.808, allocations: 14.19 MB / 2.095 GB, free: 131.4 MB / 0.5608 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.006008/7.814, allocations: 0.5459 MB / 2.096 GB, free: 131.4 MB / 0.5608 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.132/7.946, allocations: 50.77 MB / 2.145 GB, free: 115.4 MB / 0.5608 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 6.071e-06/7.946, allocations: 7.406 kB / 2.145 GB, free: 115.4 MB / 0.5608 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.3484/8.294, allocations: 74.6 MB / 2.218 GB, free: 68.14 MB / 0.5608 GB Notification: Performance of postOpt removeConstants (simulation): time 0.0137/8.308, allocations: 3.884 MB / 2.222 GB, free: 64.94 MB / 0.5608 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.006797/8.315, allocations: 339.9 kB / 2.222 GB, free: 64.61 MB / 0.5608 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.01698/8.332, allocations: 0.9185 MB / 2.223 GB, free: 63.72 MB / 0.5608 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.00866/8.34, allocations: 1.798 MB / 2.225 GB, free: 61.92 MB / 0.5608 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.004285/8.345, allocations: 0.5449 MB / 2.225 GB, free: 61.38 MB / 0.5608 GB Notification: Performance of sorting global known variables: time 0.0141/8.359, allocations: 8.226 MB / 2.233 GB, free: 53.2 MB / 0.5608 GB Notification: Performance of sort global known variables: time 5.31e-07/8.359, allocations: 4 kB / 2.233 GB, free: 53.2 MB / 0.5608 GB Notification: Performance of remove unused functions: time 0.03562/8.395, allocations: 7.808 MB / 2.241 GB, free: 45.82 MB / 0.5608 GB Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 15 * Number of states: 69 (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,relaxed.COHm[1].logn,relaxed.COHm[2].logn,relaxed.COHm[3].logn,relaxed.COHm[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,tensed.COHm[1].logn,tensed.COHm[2].logn,tensed.COHm[3].logn,tensed.COHm[4].logn,CO2_free.logn,CO_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 (1436): * Single equations (assignments): 1433 * 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%), (41,12,73.3%)} * Non-linear torn systems (#iteration vars, #inner vars): 1 system {(1,3)} Notification: Performance of Backend phase and start with SimCode phase: time 0.01101/8.406, allocations: 4.193 MB / 2.245 GB, free: 42.55 MB / 0.5608 GB Notification: Performance of simCode: created initialization part: time 0.3075/8.713, allocations: 32.63 MB / 2.277 GB, free: 151.6 MB / 0.5608 GB Notification: Performance of simCode: created event and clocks part: time 9.147e-06/8.713, allocations: 0 / 2.277 GB, free: 151.6 MB / 0.5608 GB Notification: Performance of simCode: created simulation system equations: time 0.04802/8.761, allocations: 17.56 MB / 2.294 GB, free: 146.9 MB / 0.5608 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.02656/8.788, allocations: 2.678 MB / 2.297 GB, free: 146.1 MB / 0.5608 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.1075/8.895, allocations: 51.89 MB / 2.348 GB, free: 122.2 MB / 0.5608 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.01755/8.913, allocations: 11.05 MB / 2.358 GB, free: 119.4 MB / 0.5608 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.01055/8.923, allocations: 1.806 MB / 2.36 GB, free: 119.3 MB / 0.5608 GB Notification: Performance of SimCode: time 1.283e-06/8.924, allocations: 0 / 2.36 GB, free: 119.3 MB / 0.5608 GB Notification: Performance of Templates: time 1.488/10.41, allocations: 0.5939 GB / 2.954 GB, free: 157 MB / 0.592 GB make -j1 -f Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllosteryCO.makefile (rm -f Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllosteryCO.pipe ; mkfifo Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllosteryCO.pipe ; head -c 1048576 < Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllosteryCO.pipe >> ../files/Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllosteryCO.sim & ./Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllosteryCO -abortSlowSimulation -alarm=480 -lv LOG_STATS > Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllosteryCO.pipe 2>&1)