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 0.0008098/0.0008098, allocations: 91.92 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 0.001061/0.001061, allocations: 184.2 kB / 16.92 MB, free: 6.926 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.367/1.367, allocations: 223.3 MB / 241 MB, free: 5.246 MB / 190.1 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.2127/0.2127, allocations: 15.28 MB / 307.4 MB, free: 15.71 MB / 254.1 MB Warning: Ignoring unknown experiment annotation option: __Dymola_Algorithm = "Dassl" Notification: Performance of FrontEnd - loaded program: time 0.0003082/0.0003077, allocations: 8 kB / 372.8 MB, free: 3.605 MB / 302.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.2966/0.2969, allocations: 54.62 MB / 427.4 MB, free: 40.36 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.HemoglobinCarboxylation): time 0.04762/0.3445, allocations: 43.49 MB / 470.9 MB, free: 19.51 MB / 350.1 MB Notification: Performance of NFInst.instExpressions: time 0.07954/0.4241, allocations: 71.77 MB / 0.5299 GB, free: 2.59 MB / 398.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.006726/0.4309, allocations: 99.25 kB / 0.53 GB, free: 2.492 MB / 398.1 MB Notification: Performance of NFTyping.typeComponents: time 0.00588/0.4368, allocations: 1.461 MB / 0.5314 GB, free: 1.051 MB / 398.1 MB Notification: Performance of NFTyping.typeBindings: time 0.02191/0.4588, allocations: 5.166 MB / 0.5365 GB, free: 11.85 MB / 414.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.03543/0.4942, allocations: 9.005 MB / 0.5453 GB, free: 2.801 MB / 414.1 MB Notification: Performance of NFFlatten.flatten: time 0.02758/0.5218, allocations: 25.66 MB / 0.5703 GB, free: 9.051 MB / 446.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.3259/0.8478, allocations: 17.22 MB / 0.5871 GB, free: 11.93 MB / 446.1 MB Notification: Performance of NFEvalConstants.evaluate: time 0.03319/0.881, allocations: 15.54 MB / 0.6023 GB, free: 11.48 MB / 446.1 MB Notification: Performance of NFSimplifyModel.simplify: time 0.03656/0.9176, allocations: 14.09 MB / 0.6161 GB, free: 9.711 MB / 446.1 MB Notification: Performance of NFPackage.collectConstants: time 0.01556/0.9332, allocations: 1.427 MB / 0.6175 GB, free: 9.711 MB / 446.1 MB Notification: Performance of NFFlatten.collectFunctions: time 0.04483/0.9781, allocations: 9.021 MB / 0.6263 GB, free: 8.996 MB / 446.1 MB Notification: Performance of NFScalarize.scalarize: time 0.01382/0.992, allocations: 4.978 MB / 0.6311 GB, free: 7.176 MB / 446.1 MB Notification: Performance of NFVerifyModel.verify: time 0.02904/1.021, allocations: 10.05 MB / 0.641 GB, free: 3.645 MB / 446.1 MB Notification: Performance of NFConvertDAE.convert: time 0.0454/1.066, allocations: 32.5 MB / 0.6727 GB, free: 1.324 MB / 462.1 MB Notification: Performance of FrontEnd - DAE generated: time 1.09e-05/1.067, allocations: 7.984 kB / 0.6727 GB, free: 1.316 MB / 462.1 MB Notification: Performance of FrontEnd: time 2.615e-06/1.067, allocations: 0 / 0.6727 GB, free: 1.316 MB / 462.1 MB Notification: Performance of Transformations before backend: time 0.00121/1.068, allocations: 2.656 kB / 0.6727 GB, free: 1.316 MB / 462.1 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 0.07609/1.144, allocations: 20.16 MB / 0.6924 GB, free: 13.29 MB / 494.1 MB Notification: Performance of prepare preOptimizeDAE: time 5.08e-05/1.144, allocations: 12.03 kB / 0.6924 GB, free: 13.28 MB / 494.1 MB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.02667/1.171, allocations: 3.892 MB / 0.6962 GB, free: 9.371 MB / 494.1 MB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0309/1.202, allocations: 11.46 MB / 0.7074 GB, free: 14.32 MB / 0.4981 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.002459/1.204, allocations: 2.127 MB / 0.7095 GB, free: 11.98 MB / 0.4981 GB Notification: Performance of preOpt expandDerOperator (simulation): time 0.01075/1.215, allocations: 1.537 MB / 0.711 GB, free: 10.44 MB / 0.4981 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.09576/1.311, allocations: 34.79 MB / 0.745 GB, free: 7.438 MB / 0.5294 GB Notification: Performance of preOpt findStateOrder (simulation): time 0.0007971/1.312, allocations: 10.19 kB / 0.745 GB, free: 7.434 MB / 0.5294 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.008527/1.32, allocations: 0.5937 MB / 0.7455 GB, free: 6.84 MB / 0.5294 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0003467/1.32, allocations: 360 kB / 0.7459 GB, free: 6.488 MB / 0.5294 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.5903/1.911, allocations: 46.84 MB / 0.7916 GB, free: 190 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 0.2658/2.177, allocations: 127.7 MB / 0.9164 GB, free: 110.6 MB / 0.5607 GB Notification: Performance of preOpt comSubExp (simulation): time 0.9757/3.152, allocations: 276 MB / 1.186 GB, free: 74.89 MB / 0.5608 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.03135/3.184, allocations: 19.81 MB / 1.205 GB, free: 55.21 MB / 0.5608 GB Notification: Performance of preOpt evalFunc (simulation): time 0.3961/3.58, allocations: 87.13 MB / 1.29 GB, free: 174.4 MB / 0.5608 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001195/3.58, allocations: 133.9 kB / 1.291 GB, free: 174.3 MB / 0.5608 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.02452/3.605, allocations: 4.437 MB / 1.295 GB, free: 173.2 MB / 0.5608 GB Notification: Performance of pre-optimization done (n=995): time 7.613e-05/3.605, allocations: 4.328 kB / 1.295 GB, free: 173.2 MB / 0.5608 GB Notification: Performance of matching and sorting (n=1129): time 0.74/4.345, allocations: 136.3 MB / 1.428 GB, free: 73.55 MB / 0.5608 GB Notification: Performance of inlineWhenForInitialization (initialization): time 9.744e-05/4.345, allocations: 168.2 kB / 1.428 GB, free: 73.37 MB / 0.5608 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.01692/4.362, allocations: 10.15 MB / 1.438 GB, free: 63.29 MB / 0.5608 GB Notification: Performance of collectPreVariables (initialization): time 0.00449/4.366, allocations: 217.6 kB / 1.438 GB, free: 63.07 MB / 0.5608 GB Notification: Performance of collectInitialEqns (initialization): time 0.005209/4.372, allocations: 6.89 MB / 1.445 GB, free: 56.16 MB / 0.5608 GB Notification: Performance of collectInitialBindings (initialization): time 0.3001/4.672, allocations: 3.911 MB / 1.449 GB, free: 180.3 MB / 0.5608 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.006841/4.679, allocations: 1.154 MB / 1.45 GB, free: 180.2 MB / 0.5608 GB Notification: Performance of setup shared object (initialization): time 5.367e-05/4.679, allocations: 303.7 kB / 1.45 GB, free: 179.9 MB / 0.5608 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.02331/4.702, allocations: 11.82 MB / 1.462 GB, free: 179.9 MB / 0.5608 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.02837/4.73, allocations: 16.55 MB / 1.478 GB, free: 170 MB / 0.5608 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.05267/4.783, allocations: 29.75 MB / 1.507 GB, free: 153.8 MB / 0.5608 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0002669/4.784, allocations: 42.59 kB / 1.507 GB, free: 153.8 MB / 0.5608 GB Notification: Performance of matching and sorting (n=1889) (initialization): time 0.4792/5.263, allocations: 81.54 MB / 1.587 GB, free: 98.7 MB / 0.5608 GB Notification: Performance of prepare postOptimizeDAE: time 0.0001603/5.263, allocations: 68 kB / 1.587 GB, free: 98.63 MB / 0.5608 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0002207/5.263, allocations: 148 kB / 1.587 GB, free: 98.48 MB / 0.5608 GB Notification: Performance of postOpt tearingSystem (initialization): time 0.061/5.324, allocations: 22.53 MB / 1.609 GB, free: 76.14 MB / 0.5608 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01736/5.342, allocations: 3.724 MB / 1.613 GB, free: 72.41 MB / 0.5608 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.4437/5.785, allocations: 88.3 MB / 1.699 GB, free: 147.8 MB / 0.5608 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.02041/5.806, allocations: 1.144 MB / 1.7 GB, free: 147.6 MB / 0.5608 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.005625/5.811, allocations: 0.9322 MB / 1.701 GB, free: 147.5 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 0.01658/5.828, allocations: 5.377 MB / 1.706 GB, free: 145.5 MB / 0.5608 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.005428/5.833, allocations: 1.055 MB / 1.707 GB, free: 145.5 MB / 0.5608 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.2849/6.118, allocations: 48.56 MB / 1.754 GB, free: 117.4 MB / 0.5608 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.0001452/6.119, allocations: 124 kB / 1.755 GB, free: 117.3 MB / 0.5608 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 0.0001116/6.119, allocations: 20 kB / 1.755 GB, free: 117.3 MB / 0.5608 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.00036/6.119, allocations: 63.7 kB / 1.755 GB, free: 117.2 MB / 0.5608 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.3212/6.44, allocations: 72.94 MB / 1.826 GB, free: 44.49 MB / 0.5608 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 0.0001123/6.44, allocations: 4 kB / 1.826 GB, free: 44.48 MB / 0.5608 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.01439/6.455, allocations: 2.415 MB / 1.828 GB, free: 42.07 MB / 0.5608 GB Notification: Performance of postOpt tearingSystem (simulation): time 0.2793/6.734, allocations: 11.75 MB / 1.84 GB, free: 160.5 MB / 0.5608 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.003971/6.738, allocations: 477.2 kB / 1.84 GB, free: 160.5 MB / 0.5608 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.1112/6.849, allocations: 42.19 MB / 1.881 GB, free: 150.3 MB / 0.5608 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 6.943e-06/6.849, allocations: 6.719 kB / 1.881 GB, free: 150.3 MB / 0.5608 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.2956/7.145, allocations: 62.67 MB / 1.943 GB, free: 123.3 MB / 0.5608 GB Notification: Performance of postOpt removeConstants (simulation): time 0.01032/7.155, allocations: 3.302 MB / 1.946 GB, free: 120.6 MB / 0.5608 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.006691/7.162, allocations: 295.9 kB / 1.946 GB, free: 120.3 MB / 0.5608 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.01575/7.178, allocations: 0.7903 MB / 1.947 GB, free: 119.5 MB / 0.5608 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.007847/7.186, allocations: 1.499 MB / 1.948 GB, free: 118 MB / 0.5608 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.003064/7.189, allocations: 471.6 kB / 1.949 GB, free: 117.6 MB / 0.5608 GB Notification: Performance of sorting global known variables: time 0.01124/7.2, allocations: 6.962 MB / 1.956 GB, free: 110.7 MB / 0.5608 GB Notification: Performance of sort global known variables: time 4.6e-07/7.2, allocations: 0 / 1.956 GB, free: 110.7 MB / 0.5608 GB Notification: Performance of remove unused functions: time 0.03107/7.231, allocations: 6.66 MB / 1.962 GB, free: 104.5 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 0.01011/7.241, allocations: 3.529 MB / 1.966 GB, free: 101.9 MB / 0.5608 GB Notification: Performance of simCode: created initialization part: time 0.06644/7.308, allocations: 27.72 MB / 1.993 GB, free: 74.13 MB / 0.5608 GB Notification: Performance of simCode: created event and clocks part: time 8.666e-06/7.308, allocations: 0 / 1.993 GB, free: 74.13 MB / 0.5608 GB Notification: Performance of simCode: created simulation system equations: time 0.03946/7.347, allocations: 14.85 MB / 2.007 GB, free: 59.25 MB / 0.5608 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.02341/7.371, allocations: 2.339 MB / 2.009 GB, free: 57 MB / 0.5608 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.3487/7.72, allocations: 44.39 MB / 2.053 GB, free: 156.2 MB / 0.5608 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.02151/7.741, allocations: 9.633 MB / 2.062 GB, free: 155.2 MB / 0.5608 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.01092/7.752, allocations: 1.542 MB / 2.064 GB, free: 155.2 MB / 0.5608 GB Notification: Performance of SimCode: time 1.453e-06/7.752, allocations: 0 / 2.064 GB, free: 155.2 MB / 0.5608 GB Notification: Performance of Templates: time 1.167/8.919, allocations: 0.5087 GB / 2.572 GB, free: 65.45 MB / 0.5608 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)