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 0.001503/0.001503, allocations: 115.2 kB / 16.37 MB, free: 6.434 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001854/0.001854, allocations: 197.1 kB / 17.31 MB, free: 5.777 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.358/1.358, allocations: 222.9 MB / 241 MB, free: 15.14 MB / 206.1 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.08768/0.08768, allocations: 15.31 MB / 306.5 MB, free: 15.43 MB / 254.1 MB Notification: Performance of FrontEnd - loaded program: time 0.00149/0.00149, allocations: 66.41 kB / 371.8 MB, free: 50.72 MB / 302.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.1056/0.1071, allocations: 53.61 MB / 425.4 MB, free: 13.32 MB / 302.1 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 0.04966/0.1568, allocations: 41.37 MB / 466.7 MB, free: 4 MB / 334.1 MB Notification: Performance of NFInst.instExpressions: time 0.3119/0.4687, allocations: 72.7 MB / 0.5268 GB, free: 15.05 MB / 382.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.004622/0.4734, allocations: 60.41 kB / 0.5269 GB, free: 15.05 MB / 382.1 MB Notification: Performance of NFTyping.typeComponents: time 0.005705/0.4791, allocations: 1.623 MB / 0.5284 GB, free: 15.04 MB / 382.1 MB Notification: Performance of NFTyping.typeBindings: time 0.02057/0.4997, allocations: 5.918 MB / 0.5342 GB, free: 14.69 MB / 382.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.02875/0.5285, allocations: 10.21 MB / 0.5442 GB, free: 11.01 MB / 382.1 MB Notification: Performance of NFFlatten.flatten: time 0.02665/0.5552, allocations: 26.7 MB / 0.5703 GB, free: 9.742 MB / 398.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.0296/0.5848, allocations: 21.97 MB / 0.5917 GB, free: 4.984 MB / 414.1 MB Notification: Performance of NFEvalConstants.evaluate: time 0.0289/0.6138, allocations: 17.46 MB / 0.6088 GB, free: 3.77 MB / 430.1 MB Notification: Performance of NFSimplifyModel.simplify: time 0.02989/0.6437, allocations: 16.19 MB / 0.6246 GB, free: 4.008 MB / 446.1 MB Notification: Performance of NFPackage.collectConstants: time 0.01075/0.6545, allocations: 3.09 MB / 0.6276 GB, free: 0.918 MB / 446.1 MB Notification: Performance of NFFlatten.collectFunctions: time 0.0396/0.6941, allocations: 10.7 MB / 0.6381 GB, free: 6.301 MB / 462.1 MB Notification: Performance of NFScalarize.scalarize: time 0.01403/0.7082, allocations: 6.982 MB / 0.6449 GB, free: 15.5 MB / 478.1 MB Notification: Performance of NFVerifyModel.verify: time 0.02742/0.7356, allocations: 12.15 MB / 0.6567 GB, free: 3.512 MB / 478.1 MB Notification: Performance of NFConvertDAE.convert: time 0.5073/1.243, allocations: 42 MB / 0.6978 GB, free: 83.7 MB / 0.4982 GB Notification: Performance of FrontEnd - DAE generated: time 6.843e-06/1.243, allocations: 0 / 0.6978 GB, free: 83.7 MB / 0.4982 GB Notification: Performance of FrontEnd: time 2.034e-06/1.243, allocations: 0 / 0.6978 GB, free: 83.7 MB / 0.4982 GB Notification: Performance of Transformations before backend: time 0.001144/1.244, allocations: 0 / 0.6978 GB, free: 83.7 MB / 0.4982 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 0.08935/1.334, allocations: 24.75 MB / 0.7219 GB, free: 77.52 MB / 0.4982 GB Notification: Performance of prepare preOptimizeDAE: time 5.512e-05/1.334, allocations: 7 kB / 0.7219 GB, free: 77.52 MB / 0.4982 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.02769/1.361, allocations: 3.896 MB / 0.7257 GB, free: 76.59 MB / 0.4982 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.03565/1.397, allocations: 12.02 MB / 0.7375 GB, free: 74.99 MB / 0.4982 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.002214/1.399, allocations: 2.132 MB / 0.7396 GB, free: 73.87 MB / 0.4982 GB Notification: Performance of preOpt expandDerOperator (simulation): time 0.012/1.411, allocations: 1.529 MB / 0.7411 GB, free: 73.83 MB / 0.4982 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.08543/1.497, allocations: 34.79 MB / 0.775 GB, free: 51.44 MB / 0.4982 GB Notification: Performance of preOpt findStateOrder (simulation): time 0.0006356/1.497, allocations: 13.38 kB / 0.775 GB, free: 51.44 MB / 0.4982 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.008843/1.506, allocations: 0.5859 MB / 0.7756 GB, free: 50.85 MB / 0.4982 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0002123/1.506, allocations: 364 kB / 0.776 GB, free: 50.5 MB / 0.4982 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0837/1.59, allocations: 46.83 MB / 0.8217 GB, free: 3.672 MB / 0.4982 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 0.5068/2.097, allocations: 127.8 MB / 0.9465 GB, free: 186.5 MB / 0.5763 GB Notification: Performance of preOpt comSubExp (simulation): time 0.8121/2.909, allocations: 276 MB / 1.216 GB, free: 162.5 MB / 0.5763 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.0365/2.946, allocations: 19.81 MB / 1.235 GB, free: 158.2 MB / 0.5763 GB Notification: Performance of preOpt evalFunc (simulation): time 0.1513/3.097, allocations: 87.47 MB / 1.321 GB, free: 98.34 MB / 0.5763 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 9.096e-05/3.097, allocations: 142.2 kB / 1.321 GB, free: 98.2 MB / 0.5763 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.01861/3.116, allocations: 4.508 MB / 1.325 GB, free: 93.79 MB / 0.5763 GB Notification: Performance of pre-optimization done (n=995): time 4.529e-05/3.116, allocations: 0 / 1.325 GB, free: 93.79 MB / 0.5763 GB Notification: Performance of matching and sorting (n=1129): time 0.8712/3.987, allocations: 135.9 MB / 1.458 GB, free: 202.8 MB / 0.5763 GB Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001237/3.987, allocations: 163.4 kB / 1.458 GB, free: 202.7 MB / 0.5763 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.01867/4.006, allocations: 10.15 MB / 1.468 GB, free: 197.7 MB / 0.5763 GB Notification: Performance of collectPreVariables (initialization): time 0.004708/4.011, allocations: 211.1 kB / 1.468 GB, free: 197.5 MB / 0.5763 GB Notification: Performance of collectInitialEqns (initialization): time 0.005706/4.016, allocations: 6.894 MB / 1.475 GB, free: 193.1 MB / 0.5763 GB Notification: Performance of collectInitialBindings (initialization): time 0.007798/4.024, allocations: 3.903 MB / 1.479 GB, free: 189.7 MB / 0.5763 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.01619/4.04, allocations: 3.263 MB / 1.482 GB, free: 187.9 MB / 0.5763 GB Notification: Performance of setup shared object (initialization): time 4.868e-05/4.041, allocations: 305.1 kB / 1.482 GB, free: 187.6 MB / 0.5763 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.02246/4.063, allocations: 11.82 MB / 1.494 GB, free: 181.1 MB / 0.5763 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.02474/4.088, allocations: 16.56 MB / 1.51 GB, free: 167.8 MB / 0.5763 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0463/4.134, allocations: 29.74 MB / 1.539 GB, free: 135.9 MB / 0.5763 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0001642/4.134, allocations: 48 kB / 1.539 GB, free: 135.8 MB / 0.5763 GB Notification: Performance of matching and sorting (n=1889) (initialization): time 0.6491/4.783, allocations: 81.45 MB / 1.619 GB, free: 190.9 MB / 0.5763 GB Notification: Performance of prepare postOptimizeDAE: time 0.0001048/4.784, allocations: 70.19 kB / 1.619 GB, free: 190.9 MB / 0.5763 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0001972/4.784, allocations: 149.3 kB / 1.619 GB, free: 190.9 MB / 0.5763 GB Notification: Performance of postOpt tearingSystem (initialization): time 0.05549/4.839, allocations: 22.37 MB / 1.641 GB, free: 188.8 MB / 0.5763 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01752/4.857, allocations: 3.727 MB / 1.644 GB, free: 188.6 MB / 0.5763 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.1989/5.056, allocations: 93.96 MB / 1.736 GB, free: 120.6 MB / 0.5763 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.01812/5.074, allocations: 0.8351 MB / 1.737 GB, free: 119.8 MB / 0.5763 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.005389/5.079, allocations: 0.9348 MB / 1.738 GB, free: 118.8 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 0.01458/5.094, allocations: 5.373 MB / 1.743 GB, free: 113.8 MB / 0.5763 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.00664/5.101, allocations: 1.057 MB / 1.744 GB, free: 113.3 MB / 0.5763 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.2531/5.354, allocations: 48.6 MB / 1.792 GB, free: 64.8 MB / 0.5763 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.0001399/5.354, allocations: 120 kB / 1.792 GB, free: 64.68 MB / 0.5763 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 0.000151/5.354, allocations: 16 kB / 1.792 GB, free: 64.67 MB / 0.5763 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0004511/5.355, allocations: 66.64 kB / 1.792 GB, free: 64.61 MB / 0.5763 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.5197/5.874, allocations: 73.03 MB / 1.863 GB, free: 176.7 MB / 0.5763 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 0.00018/5.874, allocations: 5.219 kB / 1.863 GB, free: 176.7 MB / 0.5763 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.01399/5.888, allocations: 2.415 MB / 1.866 GB, free: 176.5 MB / 0.5763 GB Notification: Performance of postOpt tearingSystem (simulation): time 0.03038/5.919, allocations: 11.89 MB / 1.877 GB, free: 174.3 MB / 0.5763 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.004493/5.923, allocations: 473.4 kB / 1.878 GB, free: 174 MB / 0.5763 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.11/6.033, allocations: 46.93 MB / 1.923 GB, free: 128.9 MB / 0.5763 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.375e-05/6.034, allocations: 11.38 kB / 1.923 GB, free: 128.9 MB / 0.5763 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.2753/6.309, allocations: 62.72 MB / 1.985 GB, free: 66.55 MB / 0.5763 GB Notification: Performance of postOpt removeConstants (simulation): time 0.01129/6.32, allocations: 3.292 MB / 1.988 GB, free: 63.84 MB / 0.5763 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.005414/6.326, allocations: 299.9 kB / 1.988 GB, free: 63.55 MB / 0.5763 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.01335/6.339, allocations: 0.5189 MB / 1.989 GB, free: 63.03 MB / 0.5763 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.006907/6.346, allocations: 1.507 MB / 1.99 GB, free: 61.52 MB / 0.5763 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.003311/6.349, allocations: 475.6 kB / 1.991 GB, free: 61.05 MB / 0.5763 GB Notification: Performance of sorting global known variables: time 0.2593/6.609, allocations: 6.959 MB / 1.997 GB, free: 192.5 MB / 0.5763 GB Notification: Performance of sort global known variables: time 5.41e-07/6.609, allocations: 3.5 kB / 1.997 GB, free: 192.5 MB / 0.5763 GB Notification: Performance of remove unused functions: time 0.02747/6.636, allocations: 6.675 MB / 2.004 GB, free: 192.5 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 0.01113/6.647, allocations: 3.537 MB / 2.007 GB, free: 191.9 MB / 0.5763 GB Notification: Performance of simCode: created initialization part: time 0.06358/6.711, allocations: 27.8 MB / 2.035 GB, free: 185.7 MB / 0.5763 GB Notification: Performance of simCode: created event and clocks part: time 9.327e-06/6.711, allocations: 3.938 kB / 2.035 GB, free: 185.7 MB / 0.5763 GB Notification: Performance of simCode: created simulation system equations: time 0.04267/6.754, allocations: 14.87 MB / 2.049 GB, free: 179.9 MB / 0.5763 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.02011/6.774, allocations: 2.506 MB / 2.052 GB, free: 179 MB / 0.5763 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.09632/6.87, allocations: 37.81 MB / 2.088 GB, free: 150.2 MB / 0.5763 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.01957/6.89, allocations: 9.94 MB / 2.098 GB, free: 143 MB / 0.5763 GB Notification: Performance of simCode: alias equations: time 0.01876/6.909, allocations: 5.211 MB / 2.103 GB, free: 139.7 MB / 0.5763 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.007891/6.916, allocations: 1.442 MB / 2.105 GB, free: 138.5 MB / 0.5763 GB Notification: Performance of SimCode: time 2.164e-06/6.916, allocations: 0 / 2.105 GB, free: 138.5 MB / 0.5763 GB Notification: Performance of Templates: time 0.8838/7.8, allocations: 316.5 MB / 2.414 GB, free: 161.8 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 -s gbode -lv LOG_STATS > Chemical_Chemical.Examples.Hemoglobin.HemoglobinCarboxylation.pipe 2>&1)