Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.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.HemoglobinCarboxylation,tolerance=1e-05,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation") translateModel(Chemical.Examples.Hemoglobin.HemoglobinCarboxylation,tolerance=1e-05,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation") Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.009493/0.009493, allocations: 101.5 kB / 15.73 MB, free: 6.031 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.002009/0.002009, allocations: 188.6 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 1.497/1.497, allocations: 222.9 MB / 240.4 MB, free: 4.332 MB / 190.1 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.3098/0.3098, allocations: 15.31 MB / 305.8 MB, free: 15.27 MB / 254.1 MB Notification: Performance of FrontEnd - loaded program: time 0.001437/0.001437, allocations: 67.89 kB / 425.2 MB, free: 13.08 MB / 366.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.3837/0.3852, allocations: 53.61 MB / 478.8 MB, free: 25.66 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.HemoglobinCarboxylation): time 0.04938/0.4346, allocations: 41.6 MB / 0.5082 GB, free: 9.02 MB / 382.1 MB Notification: Performance of NFInst.instExpressions: time 0.08773/0.5224, allocations: 72.72 MB / 0.5793 GB, free: 12 kB / 446.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.007358/0.5298, allocations: 59.73 kB / 0.5793 GB, free: 15.95 MB / 462.1 MB Notification: Performance of NFTyping.typeComponents: time 0.006393/0.5362, allocations: 1.613 MB / 0.5809 GB, free: 14.33 MB / 462.1 MB Notification: Performance of NFTyping.typeBindings: time 0.02775/0.564, allocations: 5.919 MB / 0.5867 GB, free: 8.367 MB / 462.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.03531/0.5993, allocations: 10.21 MB / 0.5966 GB, free: 14.1 MB / 478.1 MB Notification: Performance of NFFlatten.flatten: time 0.7535/1.353, allocations: 26.68 MB / 0.6227 GB, free: 18.86 MB / 478.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.03152/1.384, allocations: 21.97 MB / 0.6441 GB, free: 17.43 MB / 478.1 MB Notification: Performance of NFEvalConstants.evaluate: time 0.03146/1.416, allocations: 17.48 MB / 0.6612 GB, free: 14.95 MB / 478.1 MB Notification: Performance of NFSimplifyModel.simplify: time 0.03096/1.447, allocations: 16.19 MB / 0.677 GB, free: 3.395 MB / 478.1 MB Notification: Performance of NFPackage.collectConstants: time 0.01072/1.458, allocations: 3.094 MB / 0.6801 GB, free: 308 kB / 478.1 MB Notification: Performance of NFFlatten.collectFunctions: time 0.03999/1.498, allocations: 10.7 MB / 0.6905 GB, free: 6.199 MB / 494.1 MB Notification: Performance of NFScalarize.scalarize: time 0.0141/1.512, allocations: 6.983 MB / 0.6973 GB, free: 15.44 MB / 0.4982 GB Notification: Performance of NFVerifyModel.verify: time 0.02932/1.541, allocations: 12.15 MB / 0.7092 GB, free: 3.516 MB / 0.4982 GB Notification: Performance of NFConvertDAE.convert: time 0.0785/1.62, allocations: 42.22 MB / 0.7504 GB, free: 12.18 MB / 0.545 GB Notification: Performance of FrontEnd - DAE generated: time 8.666e-06/1.62, allocations: 0 / 0.7504 GB, free: 12.18 MB / 0.545 GB Notification: Performance of FrontEnd: time 2.034e-06/1.62, allocations: 7.938 kB / 0.7504 GB, free: 12.17 MB / 0.545 GB Notification: Performance of Transformations before backend: time 0.001251/1.621, allocations: 0 / 0.7504 GB, free: 12.17 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 0.1099/1.731, allocations: 24.71 MB / 0.7745 GB, free: 3.406 MB / 0.5607 GB Notification: Performance of prepare preOptimizeDAE: time 5.969e-05/1.731, allocations: 8.031 kB / 0.7746 GB, free: 3.398 MB / 0.5607 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.02918/1.76, allocations: 3.897 MB / 0.7784 GB, free: 15.48 MB / 0.5763 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.03257/1.793, allocations: 12 MB / 0.7901 GB, free: 3.883 MB / 0.5763 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.002576/1.795, allocations: 2.139 MB / 0.7922 GB, free: 1.527 MB / 0.5763 GB Notification: Performance of preOpt expandDerOperator (simulation): time 0.01341/1.809, allocations: 1.527 MB / 0.7937 GB, free: 0 / 0.5763 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.09977/1.909, allocations: 34.79 MB / 0.8276 GB, free: 12.98 MB / 0.6232 GB Notification: Performance of preOpt findStateOrder (simulation): time 0.001054/1.91, allocations: 10.94 kB / 0.8276 GB, free: 12.97 MB / 0.6232 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.01083/1.921, allocations: 0.5898 MB / 0.8282 GB, free: 12.38 MB / 0.6232 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0004166/1.921, allocations: 360 kB / 0.8286 GB, free: 12.03 MB / 0.6232 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.8011/2.722, allocations: 46.83 MB / 0.8743 GB, free: 213.1 MB / 0.6233 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 0.2761/2.998, allocations: 127.8 MB / 0.9991 GB, free: 100.6 MB / 0.6233 GB Notification: Performance of preOpt comSubExp (simulation): time 0.9176/3.916, allocations: 276 MB / 1.269 GB, free: 80.41 MB / 0.6233 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.03577/3.952, allocations: 19.8 MB / 1.288 GB, free: 60.56 MB / 0.6233 GB Notification: Performance of preOpt evalFunc (simulation): time 0.5791/4.531, allocations: 87.46 MB / 1.373 GB, free: 193.5 MB / 0.6233 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001272/4.531, allocations: 134.4 kB / 1.374 GB, free: 193.4 MB / 0.6233 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.02286/4.554, allocations: 4.516 MB / 1.378 GB, free: 192.4 MB / 0.6233 GB Notification: Performance of pre-optimization done (n=995): time 9.412e-05/4.554, allocations: 3.938 kB / 1.378 GB, free: 192.4 MB / 0.6233 GB Notification: Performance of matching and sorting (n=1129): time 0.7325/5.287, allocations: 136 MB / 1.511 GB, free: 95.48 MB / 0.6233 GB Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001258/5.287, allocations: 168.2 kB / 1.511 GB, free: 95.3 MB / 0.6233 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.01859/5.305, allocations: 10.15 MB / 1.521 GB, free: 85.22 MB / 0.6233 GB Notification: Performance of collectPreVariables (initialization): time 0.005474/5.311, allocations: 217.7 kB / 1.521 GB, free: 85 MB / 0.6233 GB Notification: Performance of collectInitialEqns (initialization): time 0.004981/5.316, allocations: 6.887 MB / 1.528 GB, free: 78.1 MB / 0.6233 GB Notification: Performance of collectInitialBindings (initialization): time 0.009016/5.325, allocations: 3.906 MB / 1.532 GB, free: 74.22 MB / 0.6233 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.01575/5.341, allocations: 3.256 MB / 1.535 GB, free: 70.95 MB / 0.6233 GB Notification: Performance of setup shared object (initialization): time 6.135e-05/5.341, allocations: 305.1 kB / 1.535 GB, free: 70.65 MB / 0.6233 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.02141/5.362, allocations: 11.82 MB / 1.547 GB, free: 58.82 MB / 0.6233 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0242/5.386, allocations: 16.56 MB / 1.563 GB, free: 40.18 MB / 0.6233 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.4729/5.859, allocations: 29.74 MB / 1.592 GB, free: 178.9 MB / 0.6233 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0002074/5.86, allocations: 41.81 kB / 1.592 GB, free: 178.9 MB / 0.6233 GB Notification: Performance of matching and sorting (n=1889) (initialization): time 0.4523/6.312, allocations: 81.46 MB / 1.671 GB, free: 143.9 MB / 0.6233 GB Notification: Performance of prepare postOptimizeDAE: time 0.0003383/6.312, allocations: 68 kB / 1.671 GB, free: 143.8 MB / 0.6233 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0005261/6.313, allocations: 149.8 kB / 1.672 GB, free: 143.7 MB / 0.6233 GB Notification: Performance of postOpt tearingSystem (initialization): time 0.06121/6.374, allocations: 22.38 MB / 1.693 GB, free: 121.5 MB / 0.6233 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01828/6.392, allocations: 3.728 MB / 1.697 GB, free: 117.8 MB / 0.6233 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.2252/6.618, allocations: 93.93 MB / 1.789 GB, free: 23.48 MB / 0.6233 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.02101/6.639, allocations: 0.8391 MB / 1.79 GB, free: 22.64 MB / 0.6233 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.4119/7.051, allocations: 0.9311 MB / 1.791 GB, free: 178.1 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 0.01997/7.071, allocations: 5.374 MB / 1.796 GB, free: 177.9 MB / 0.6233 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.007613/7.078, allocations: 1.054 MB / 1.797 GB, free: 177.9 MB / 0.6233 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.2768/7.355, allocations: 48.6 MB / 1.844 GB, free: 169.1 MB / 0.6233 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.0002778/7.356, allocations: 125.9 kB / 1.844 GB, free: 169.1 MB / 0.6233 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 0.0001258/7.356, allocations: 15.78 kB / 1.844 GB, free: 169.1 MB / 0.6233 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0005069/7.356, allocations: 60.56 kB / 1.844 GB, free: 169.1 MB / 0.6233 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.3093/7.665, allocations: 73.05 MB / 1.916 GB, free: 123.1 MB / 0.6233 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 0.0001567/7.666, allocations: 7.938 kB / 1.916 GB, free: 123.1 MB / 0.6233 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.01475/7.68, allocations: 2.417 MB / 1.918 GB, free: 120.6 MB / 0.6233 GB Notification: Performance of postOpt tearingSystem (simulation): time 0.03187/7.712, allocations: 11.88 MB / 1.93 GB, free: 109.2 MB / 0.6233 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.005324/7.718, allocations: 475.5 kB / 1.93 GB, free: 108.7 MB / 0.6233 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.1069/7.825, allocations: 46.93 MB / 1.976 GB, free: 61.45 MB / 0.6233 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 4.88e-06/7.825, allocations: 7.938 kB / 1.976 GB, free: 61.44 MB / 0.6233 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.716/8.541, allocations: 62.72 MB / 2.037 GB, free: 161.9 MB / 0.6233 GB Notification: Performance of postOpt removeConstants (simulation): time 0.01175/8.553, allocations: 3.29 MB / 2.041 GB, free: 160.9 MB / 0.6233 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.005998/8.559, allocations: 298.7 kB / 2.041 GB, free: 160.7 MB / 0.6233 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.01358/8.572, allocations: 0.5264 MB / 2.041 GB, free: 160.6 MB / 0.6233 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.009453/8.582, allocations: 1.503 MB / 2.043 GB, free: 160.4 MB / 0.6233 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.004868/8.587, allocations: 474.1 kB / 2.043 GB, free: 160.3 MB / 0.6233 GB Notification: Performance of sorting global known variables: time 0.01465/8.601, allocations: 6.968 MB / 2.05 GB, free: 157.9 MB / 0.6233 GB Notification: Performance of sort global known variables: time 3.71e-07/8.601, allocations: 2.953 kB / 2.05 GB, free: 157.9 MB / 0.6233 GB Notification: Performance of remove unused functions: time 0.03623/8.638, allocations: 6.677 MB / 2.057 GB, free: 157.3 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 0.00996/8.648, allocations: 3.528 MB / 2.06 GB, free: 156.7 MB / 0.6233 GB Notification: Performance of simCode: created initialization part: time 0.06834/8.716, allocations: 27.8 MB / 2.087 GB, free: 146.5 MB / 0.6233 GB Notification: Performance of simCode: created event and clocks part: time 9.528e-06/8.716, allocations: 0 / 2.087 GB, free: 146.5 MB / 0.6233 GB Notification: Performance of simCode: created simulation system equations: time 0.04249/8.758, allocations: 14.88 MB / 2.102 GB, free: 140.7 MB / 0.6233 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.02378/8.782, allocations: 2.503 MB / 2.104 GB, free: 139.8 MB / 0.6233 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.09863/8.881, allocations: 37.82 MB / 2.141 GB, free: 115.7 MB / 0.6233 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.01903/8.9, allocations: 9.939 MB / 2.151 GB, free: 108.5 MB / 0.6233 GB Notification: Performance of simCode: alias equations: time 0.02067/8.921, allocations: 5.215 MB / 2.156 GB, free: 105.2 MB / 0.6233 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.009379/8.93, allocations: 1.443 MB / 2.157 GB, free: 104 MB / 0.6233 GB Notification: Performance of SimCode: time 1.733e-06/8.93, allocations: 0 / 2.157 GB, free: 104 MB / 0.6233 GB Notification: Performance of Templates: time 1.323/10.25, allocations: 326.3 MB / 2.476 GB, free: 190.1 MB / 0.6389 GB make -j1 -f Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.makefile (rm -f Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.pipe ; mkfifo Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.pipe ; head -c 1048576 < Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.pipe >> ../files/Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.sim & ./Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation -abortSlowSimulation -alarm=480 -lv LOG_STATS > Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.pipe 2>&1)