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 0.001125/0.001126, allocations: 111.3 kB / 15.23 MB, free: 0.6406 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001188/0.001188, allocations: 194.2 kB / 16.14 MB, free: 6.711 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.376/1.376, allocations: 222.9 MB / 239.8 MB, free: 4.605 MB / 190.1 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.233/0.233, allocations: 15.31 MB / 305.3 MB, free: 15.32 MB / 254.1 MB Warning: Ignoring unknown experiment annotation option: __Dymola_Algorithm = "Dassl" Notification: Performance of FrontEnd - loaded program: time 0.00122/0.00122, allocations: 59.89 kB / 369.6 MB, free: 4.457 MB / 302.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.1136/0.1148, allocations: 53.61 MB / 423.3 MB, free: 14.79 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 0.2834/0.3983, allocations: 43.58 MB / 466.8 MB, free: 36.17 MB / 366.1 MB Notification: Performance of NFInst.instExpressions: time 0.07495/0.4732, allocations: 72.58 MB / 0.5268 GB, free: 10.64 MB / 398.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.006288/0.4796, allocations: 103.2 kB / 0.5269 GB, free: 10.54 MB / 398.1 MB Notification: Performance of NFTyping.typeComponents: time 0.006387/0.486, allocations: 1.457 MB / 0.5283 GB, free: 9.43 MB / 398.1 MB Notification: Performance of NFTyping.typeBindings: time 0.02319/0.5092, allocations: 5.166 MB / 0.5333 GB, free: 5.141 MB / 398.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.03602/0.5453, allocations: 9.004 MB / 0.5421 GB, free: 12.54 MB / 414.1 MB Notification: Performance of NFFlatten.flatten: time 0.03043/0.5758, allocations: 25.66 MB / 0.5672 GB, free: 2.785 MB / 430.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.02537/0.6012, allocations: 17.94 MB / 0.5847 GB, free: 0.7344 MB / 446.1 MB Notification: Performance of NFEvalConstants.evaluate: time 0.02513/0.6264, allocations: 16.17 MB / 0.6005 GB, free: 0.5195 MB / 462.1 MB Notification: Performance of NFSimplifyModel.simplify: time 0.4738/1.1, allocations: 14.88 MB / 0.615 GB, free: 24.66 MB / 462.1 MB Notification: Performance of NFPackage.collectConstants: time 0.0124/1.113, allocations: 1.687 MB / 0.6167 GB, free: 24.66 MB / 462.1 MB Notification: Performance of NFFlatten.collectFunctions: time 0.05131/1.164, allocations: 9.287 MB / 0.6257 GB, free: 24.66 MB / 462.1 MB Notification: Performance of NFScalarize.scalarize: time 0.01761/1.182, allocations: 5.379 MB / 0.631 GB, free: 24.07 MB / 462.1 MB Notification: Performance of NFVerifyModel.verify: time 0.04045/1.222, allocations: 10.52 MB / 0.6413 GB, free: 21.7 MB / 462.1 MB Notification: Performance of NFConvertDAE.convert: time 0.07798/1.3, allocations: 39.79 MB / 0.6801 GB, free: 9.762 MB / 462.1 MB Notification: Performance of FrontEnd - DAE generated: time 6.623e-06/1.3, allocations: 3.969 kB / 0.6801 GB, free: 9.762 MB / 462.1 MB Notification: Performance of FrontEnd: time 1.383e-06/1.3, allocations: 0 / 0.6801 GB, free: 9.762 MB / 462.1 MB Notification: Performance of Transformations before backend: time 0.001346/1.302, allocations: 2.656 kB / 0.6801 GB, free: 9.762 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 0.09952/1.401, allocations: 24.75 MB / 0.7043 GB, free: 9.371 MB / 478.1 MB Notification: Performance of prepare preOptimizeDAE: time 7.513e-05/1.401, allocations: 8.031 kB / 0.7043 GB, free: 9.363 MB / 478.1 MB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.02869/1.43, allocations: 3.89 MB / 0.7081 GB, free: 5.465 MB / 478.1 MB Notification: Performance of preOpt evaluateParameters (simulation): time 0.03302/1.463, allocations: 11.77 MB / 0.7196 GB, free: 10.1 MB / 494.1 MB Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.002432/1.465, allocations: 2.127 MB / 0.7217 GB, free: 7.754 MB / 494.1 MB Notification: Performance of preOpt expandDerOperator (simulation): time 0.01122/1.477, allocations: 1.527 MB / 0.7232 GB, free: 6.227 MB / 494.1 MB Notification: Performance of preOpt clockPartitioning (simulation): time 0.1012/1.578, allocations: 34.79 MB / 0.7572 GB, free: 3.215 MB / 0.5138 GB Notification: Performance of preOpt findStateOrder (simulation): time 0.0007873/1.579, allocations: 10.38 kB / 0.7572 GB, free: 3.211 MB / 0.5138 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.01049/1.589, allocations: 0.5898 MB / 0.7577 GB, free: 2.621 MB / 0.5138 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0003506/1.59, allocations: 360 kB / 0.7581 GB, free: 2.27 MB / 0.5138 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.1013/1.691, allocations: 46.83 MB / 0.8038 GB, free: 3.445 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 0.5776/2.269, allocations: 128 MB / 0.9288 GB, free: 71.45 MB / 0.5607 GB Notification: Performance of preOpt comSubExp (simulation): time 0.8418/3.11, allocations: 276 MB / 1.198 GB, free: 76.24 MB / 0.5763 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.03767/3.148, allocations: 19.81 MB / 1.218 GB, free: 56.39 MB / 0.5763 GB Notification: Performance of preOpt evalFunc (simulation): time 0.4372/3.585, allocations: 87.58 MB / 1.303 GB, free: 188.9 MB / 0.5763 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 8.876e-05/3.586, allocations: 134.3 kB / 1.303 GB, free: 188.8 MB / 0.5763 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.02245/3.608, allocations: 4.427 MB / 1.308 GB, free: 187.7 MB / 0.5763 GB Notification: Performance of pre-optimization done (n=995): time 5.551e-05/3.608, allocations: 1.406 kB / 1.308 GB, free: 187.7 MB / 0.5763 GB Notification: Performance of matching and sorting (n=1129): time 0.7373/4.345, allocations: 135.9 MB / 1.44 GB, free: 95.16 MB / 0.5763 GB Notification: Performance of inlineWhenForInitialization (initialization): time 0.000153/4.346, allocations: 168.2 kB / 1.441 GB, free: 94.98 MB / 0.5763 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.01887/4.365, allocations: 10.15 MB / 1.451 GB, free: 84.89 MB / 0.5763 GB Notification: Performance of collectPreVariables (initialization): time 0.004572/4.369, allocations: 210.3 kB / 1.451 GB, free: 84.68 MB / 0.5763 GB Notification: Performance of collectInitialEqns (initialization): time 0.004634/4.374, allocations: 6.887 MB / 1.457 GB, free: 77.78 MB / 0.5763 GB Notification: Performance of collectInitialBindings (initialization): time 0.24/4.614, allocations: 3.916 MB / 1.461 GB, free: 194.7 MB / 0.5763 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.0148/4.629, allocations: 3.26 MB / 1.464 GB, free: 194.6 MB / 0.5763 GB Notification: Performance of setup shared object (initialization): time 5.792e-05/4.629, allocations: 304.1 kB / 1.465 GB, free: 194.3 MB / 0.5763 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.02213/4.651, allocations: 11.82 MB / 1.476 GB, free: 194.3 MB / 0.5763 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.02701/4.678, allocations: 16.55 MB / 1.492 GB, free: 184.3 MB / 0.5763 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.05022/4.728, allocations: 29.74 MB / 1.522 GB, free: 168.5 MB / 0.5763 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0002498/4.728, allocations: 45.34 kB / 1.522 GB, free: 168.5 MB / 0.5763 GB Notification: Performance of matching and sorting (n=1889) (initialization): time 0.426/5.154, allocations: 81.46 MB / 1.601 GB, free: 117.7 MB / 0.5763 GB Notification: Performance of prepare postOptimizeDAE: time 0.0004499/5.155, allocations: 68 kB / 1.601 GB, free: 117.6 MB / 0.5763 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.00052/5.156, allocations: 148 kB / 1.601 GB, free: 117.5 MB / 0.5763 GB Notification: Performance of postOpt tearingSystem (initialization): time 0.05868/5.214, allocations: 22.38 MB / 1.623 GB, free: 95.34 MB / 0.5763 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01797/5.232, allocations: 3.729 MB / 1.627 GB, free: 91.61 MB / 0.5763 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.4747/5.707, allocations: 88.28 MB / 1.713 GB, free: 163.6 MB / 0.5763 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.01962/5.727, allocations: 1.142 MB / 1.714 GB, free: 163.4 MB / 0.5763 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.006227/5.733, allocations: 0.931 MB / 1.715 GB, free: 163.3 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 0.0184/5.751, allocations: 5.381 MB / 1.72 GB, free: 161.2 MB / 0.5763 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.008172/5.759, allocations: 1.057 MB / 1.721 GB, free: 161.2 MB / 0.5763 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.2788/6.038, allocations: 48.61 MB / 1.769 GB, free: 134.8 MB / 0.5763 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.0001803/6.039, allocations: 120 kB / 1.769 GB, free: 134.6 MB / 0.5763 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 0.0002402/6.039, allocations: 20 kB / 1.769 GB, free: 134.6 MB / 0.5763 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0006243/6.039, allocations: 59.77 kB / 1.769 GB, free: 134.6 MB / 0.5763 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.3346/6.374, allocations: 73.04 MB / 1.84 GB, free: 61.99 MB / 0.5763 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 0.0001364/6.374, allocations: 4 kB / 1.84 GB, free: 61.98 MB / 0.5763 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.01413/6.388, allocations: 2.411 MB / 1.843 GB, free: 59.68 MB / 0.5763 GB Notification: Performance of postOpt tearingSystem (simulation): time 0.3116/6.7, allocations: 11.89 MB / 1.854 GB, free: 176.2 MB / 0.5763 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.005705/6.706, allocations: 476.9 kB / 1.855 GB, free: 176.2 MB / 0.5763 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.1107/6.816, allocations: 42.19 MB / 1.896 GB, free: 165.1 MB / 0.5763 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 5.751e-06/6.816, allocations: 6.938 kB / 1.896 GB, free: 165.1 MB / 0.5763 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.2787/7.095, allocations: 62.72 MB / 1.957 GB, free: 140.2 MB / 0.5763 GB Notification: Performance of postOpt removeConstants (simulation): time 0.01121/7.106, allocations: 3.293 MB / 1.96 GB, free: 137.5 MB / 0.5763 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.006953/7.113, allocations: 295.9 kB / 1.961 GB, free: 137.3 MB / 0.5763 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.01365/7.127, allocations: 0.794 MB / 1.961 GB, free: 136.5 MB / 0.5763 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.006889/7.134, allocations: 1.493 MB / 1.963 GB, free: 135 MB / 0.5763 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.002937/7.137, allocations: 472.2 kB / 1.963 GB, free: 134.6 MB / 0.5763 GB Notification: Performance of sorting global known variables: time 0.0106/7.148, allocations: 6.969 MB / 1.97 GB, free: 127.6 MB / 0.5763 GB Notification: Performance of sort global known variables: time 3.91e-07/7.148, allocations: 3.938 kB / 1.97 GB, free: 127.6 MB / 0.5763 GB Notification: Performance of remove unused functions: time 0.03688/7.185, allocations: 6.662 MB / 1.977 GB, free: 121.4 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 0.01044/7.195, allocations: 3.532 MB / 1.98 GB, free: 118.7 MB / 0.5763 GB Notification: Performance of simCode: created initialization part: time 0.09078/7.286, allocations: 27.73 MB / 2.007 GB, free: 91.19 MB / 0.5763 GB Notification: Performance of simCode: created event and clocks part: time 1.122e-05/7.286, allocations: 2.062 kB / 2.007 GB, free: 91.19 MB / 0.5763 GB Notification: Performance of simCode: created simulation system equations: time 0.06186/7.348, allocations: 14.88 MB / 2.022 GB, free: 76.29 MB / 0.5763 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0292/7.377, allocations: 2.334 MB / 2.024 GB, free: 74.04 MB / 0.5763 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.3702/7.747, allocations: 44.45 MB / 2.067 GB, free: 169.6 MB / 0.5763 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.02597/7.773, allocations: 9.937 MB / 2.077 GB, free: 168.5 MB / 0.5763 GB Notification: Performance of simCode: alias equations: time 0.02629/7.8, allocations: 5.296 MB / 2.082 GB, free: 168.4 MB / 0.5763 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.01162/7.811, allocations: 1.424 MB / 2.084 GB, free: 168.4 MB / 0.5763 GB Notification: Performance of SimCode: time 1.624e-06/7.811, allocations: 5.719 kB / 2.084 GB, free: 168.4 MB / 0.5763 GB Notification: Performance of Templates: time 0.7149/8.526, allocations: 315.5 MB / 2.392 GB, free: 75.32 MB / 0.5763 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)