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 0.007079/0.007079, allocations: 96.88 kB / 15.73 MB, free: 6.055 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001356/0.001356, allocations: 198.8 kB / 16.68 MB, free: 5.977 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.447/1.447, allocations: 222.9 MB / 240.4 MB, free: 4.301 MB / 190.1 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.2334/0.2334, allocations: 15.32 MB / 305.9 MB, free: 15.33 MB / 254.1 MB Notification: Performance of FrontEnd - loaded program: time 0.002035/0.002035, allocations: 63.91 kB / 425.2 MB, free: 13.04 MB / 366.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.3609/0.3629, allocations: 53.6 MB / 478.8 MB, free: 25.95 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 0.0445/0.4075, allocations: 41.69 MB / 0.5083 GB, free: 8.891 MB / 382.1 MB Notification: Performance of NFInst.instExpressions: time 0.08444/0.4919, allocations: 72.71 MB / 0.5793 GB, free: 15.89 MB / 462.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.008827/0.5008, allocations: 59.62 kB / 0.5794 GB, free: 15.84 MB / 462.1 MB Notification: Performance of NFTyping.typeComponents: time 0.006428/0.5073, allocations: 1.625 MB / 0.581 GB, free: 14.2 MB / 462.1 MB Notification: Performance of NFTyping.typeBindings: time 0.02122/0.5285, allocations: 5.919 MB / 0.5868 GB, free: 8.242 MB / 462.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.03017/0.5587, allocations: 10.2 MB / 0.5967 GB, free: 13.98 MB / 478.1 MB Notification: Performance of NFFlatten.flatten: time 0.6641/1.223, allocations: 26.69 MB / 0.6228 GB, free: 18.86 MB / 478.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.03519/1.258, allocations: 21.97 MB / 0.6442 GB, free: 17.43 MB / 478.1 MB Notification: Performance of NFEvalConstants.evaluate: time 0.0342/1.292, allocations: 17.47 MB / 0.6613 GB, free: 14.84 MB / 478.1 MB Notification: Performance of NFSimplifyModel.simplify: time 0.03258/1.325, allocations: 16.19 MB / 0.6771 GB, free: 3.289 MB / 478.1 MB Notification: Performance of NFPackage.collectConstants: time 0.01265/1.338, allocations: 3.094 MB / 0.6801 GB, free: 200 kB / 478.1 MB Notification: Performance of NFFlatten.collectFunctions: time 0.05411/1.392, allocations: 10.7 MB / 0.6906 GB, free: 6.094 MB / 494.1 MB Notification: Performance of NFScalarize.scalarize: time 0.02049/1.412, allocations: 6.983 MB / 0.6974 GB, free: 15.34 MB / 0.4982 GB Notification: Performance of NFVerifyModel.verify: time 0.03413/1.446, allocations: 12.15 MB / 0.7093 GB, free: 3.402 MB / 0.4982 GB Notification: Performance of NFConvertDAE.convert: time 0.09038/1.537, allocations: 42.32 MB / 0.7506 GB, free: 11.95 MB / 0.545 GB Notification: Performance of FrontEnd - DAE generated: time 8.466e-06/1.537, allocations: 3.938 kB / 0.7506 GB, free: 11.94 MB / 0.545 GB Notification: Performance of FrontEnd: time 1.674e-06/1.537, allocations: 4 kB / 0.7506 GB, free: 11.94 MB / 0.545 GB Notification: Performance of Transformations before backend: time 0.00139/1.538, allocations: 0 / 0.7506 GB, free: 11.94 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 0.09797/1.636, allocations: 25.2 MB / 0.7752 GB, free: 2.66 MB / 0.5607 GB Notification: Performance of prepare preOptimizeDAE: time 4.803e-05/1.636, allocations: 8.031 kB / 0.7752 GB, free: 2.652 MB / 0.5607 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.02728/1.664, allocations: 3.98 MB / 0.7791 GB, free: 14.66 MB / 0.5763 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.03164/1.695, allocations: 12.06 MB / 0.7909 GB, free: 3.008 MB / 0.5763 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.003002/1.698, allocations: 2.135 MB / 0.793 GB, free: 0.6562 MB / 0.5763 GB Notification: Performance of preOpt expandDerOperator (simulation): time 0.014/1.712, allocations: 1.536 MB / 0.7945 GB, free: 15.12 MB / 0.5919 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.09881/1.811, allocations: 34.79 MB / 0.8284 GB, free: 12.1 MB / 0.6232 GB Notification: Performance of preOpt findStateOrder (simulation): time 0.0008035/1.812, allocations: 7.469 kB / 0.8285 GB, free: 12.09 MB / 0.6232 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.009723/1.822, allocations: 0.5898 MB / 0.829 GB, free: 11.5 MB / 0.6232 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.0003532/1.822, allocations: 360 kB / 0.8294 GB, free: 11.15 MB / 0.6232 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.758/2.58, allocations: 46.84 MB / 0.8751 GB, free: 212.7 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 0.2625/2.843, allocations: 127.9 MB / 1 GB, free: 99.39 MB / 0.6233 GB Notification: Performance of preOpt comSubExp (simulation): time 0.9224/3.765, allocations: 276 MB / 1.27 GB, free: 78.47 MB / 0.6233 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.03404/3.799, allocations: 19.81 MB / 1.289 GB, free: 58.62 MB / 0.6233 GB Notification: Performance of preOpt evalFunc (simulation): time 0.4758/4.275, allocations: 87.53 MB / 1.374 GB, free: 192.6 MB / 0.6233 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001919/4.275, allocations: 138.5 kB / 1.375 GB, free: 192.5 MB / 0.6233 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.02248/4.298, allocations: 4.543 MB / 1.379 GB, free: 191.6 MB / 0.6233 GB Notification: Performance of pre-optimization done (n=995): time 9.551e-05/4.298, allocations: 2.859 kB / 1.379 GB, free: 191.6 MB / 0.6233 GB Notification: Performance of matching and sorting (n=1129): time 0.7936/5.092, allocations: 136.2 MB / 1.512 GB, free: 93.21 MB / 0.6233 GB Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001218/5.092, allocations: 164.2 kB / 1.512 GB, free: 93.04 MB / 0.6233 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.01874/5.111, allocations: 10.16 MB / 1.522 GB, free: 83.04 MB / 0.6233 GB Notification: Performance of collectPreVariables (initialization): time 0.005277/5.116, allocations: 217.7 kB / 1.522 GB, free: 82.82 MB / 0.6233 GB Notification: Performance of collectInitialEqns (initialization): time 0.005562/5.122, allocations: 7.096 MB / 1.529 GB, free: 76.56 MB / 0.6233 GB Notification: Performance of collectInitialBindings (initialization): time 0.009824/5.131, allocations: 4.098 MB / 1.533 GB, free: 73.01 MB / 0.6233 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.0158/5.147, allocations: 3.273 MB / 1.536 GB, free: 69.72 MB / 0.6233 GB Notification: Performance of setup shared object (initialization): time 7.334e-05/5.147, allocations: 301.1 kB / 1.537 GB, free: 69.43 MB / 0.6233 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.02355/5.171, allocations: 11.82 MB / 1.548 GB, free: 57.59 MB / 0.6233 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.02805/5.199, allocations: 16.55 MB / 1.564 GB, free: 38.96 MB / 0.6233 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.4611/5.66, allocations: 29.74 MB / 1.593 GB, free: 177 MB / 0.6233 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0003787/5.661, allocations: 44 kB / 1.593 GB, free: 177 MB / 0.6233 GB Notification: Performance of matching and sorting (n=1889) (initialization): time 0.4474/6.108, allocations: 81.52 MB / 1.673 GB, free: 140.5 MB / 0.6233 GB Notification: Performance of prepare postOptimizeDAE: time 0.0002171/6.108, allocations: 72 kB / 1.673 GB, free: 140.4 MB / 0.6233 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0003452/6.109, allocations: 148.1 kB / 1.673 GB, free: 140.2 MB / 0.6233 GB Notification: Performance of postOpt tearingSystem (initialization): time 0.05805/6.167, allocations: 22.37 MB / 1.695 GB, free: 118 MB / 0.6233 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01763/6.184, allocations: 3.732 MB / 1.699 GB, free: 114.3 MB / 0.6233 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.6936/6.878, allocations: 93.95 MB / 1.791 GB, free: 176 MB / 0.6233 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.02236/6.9, allocations: 0.83 MB / 1.791 GB, free: 176 MB / 0.6233 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.007858/6.908, allocations: 0.9395 MB / 1.792 GB, free: 176 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 0.02579/6.934, allocations: 5.37 MB / 1.798 GB, free: 175.9 MB / 0.6233 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.01008/6.944, allocations: 1.114 MB / 1.799 GB, free: 175.9 MB / 0.6233 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.3268/7.271, allocations: 48.6 MB / 1.846 GB, free: 166.9 MB / 0.6233 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.0002653/7.271, allocations: 120.3 kB / 1.846 GB, free: 166.9 MB / 0.6233 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 0.0002439/7.272, allocations: 22.28 kB / 1.846 GB, free: 166.9 MB / 0.6233 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0007015/7.272, allocations: 58.92 kB / 1.846 GB, free: 166.9 MB / 0.6233 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.3377/7.61, allocations: 73.05 MB / 1.918 GB, free: 120.3 MB / 0.6233 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 0.0001944/7.61, allocations: 0 / 1.918 GB, free: 120.3 MB / 0.6233 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.015/7.625, allocations: 2.421 MB / 1.92 GB, free: 117.9 MB / 0.6233 GB Notification: Performance of postOpt tearingSystem (simulation): time 0.0315/7.657, allocations: 11.9 MB / 1.932 GB, free: 106.4 MB / 0.6233 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.005349/7.662, allocations: 471.5 kB / 1.932 GB, free: 105.9 MB / 0.6233 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.16/7.822, allocations: 46.95 MB / 1.978 GB, free: 58.68 MB / 0.6233 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 9.457e-06/7.822, allocations: 4 kB / 1.978 GB, free: 58.67 MB / 0.6233 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.7475/8.57, allocations: 62.77 MB / 2.039 GB, free: 163.1 MB / 0.6233 GB Notification: Performance of postOpt removeConstants (simulation): time 0.01218/8.582, allocations: 3.351 MB / 2.042 GB, free: 162.1 MB / 0.6233 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.007057/8.589, allocations: 293.6 kB / 2.043 GB, free: 162 MB / 0.6233 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.01722/8.606, allocations: 0.5311 MB / 2.043 GB, free: 161.8 MB / 0.6233 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.008301/8.615, allocations: 1.503 MB / 2.045 GB, free: 161.6 MB / 0.6233 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.003663/8.618, allocations: 476.3 kB / 2.045 GB, free: 161.5 MB / 0.6233 GB Notification: Performance of sorting global known variables: time 0.01339/8.632, allocations: 6.964 MB / 2.052 GB, free: 159.2 MB / 0.6233 GB Notification: Performance of sort global known variables: time 4.81e-07/8.632, allocations: 0 / 2.052 GB, free: 159.2 MB / 0.6233 GB Notification: Performance of remove unused functions: time 0.03127/8.663, allocations: 6.722 MB / 2.059 GB, free: 158.6 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 0.01353/8.677, allocations: 3.579 MB / 2.062 GB, free: 158.2 MB / 0.6233 GB Notification: Performance of simCode: created initialization part: time 0.07373/8.751, allocations: 27.81 MB / 2.089 GB, free: 147.9 MB / 0.6233 GB Notification: Performance of simCode: created event and clocks part: time 1.145e-05/8.751, allocations: 1.312 kB / 2.089 GB, free: 147.9 MB / 0.6233 GB Notification: Performance of simCode: created simulation system equations: time 0.04199/8.793, allocations: 14.88 MB / 2.104 GB, free: 142.1 MB / 0.6233 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.02727/8.82, allocations: 2.5 MB / 2.106 GB, free: 141.3 MB / 0.6233 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.1037/8.924, allocations: 38.28 MB / 2.144 GB, free: 115.3 MB / 0.6233 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.02293/8.947, allocations: 9.936 MB / 2.153 GB, free: 108.1 MB / 0.6233 GB Notification: Performance of simCode: alias equations: time 0.02048/8.967, allocations: 5.214 MB / 2.158 GB, free: 104.7 MB / 0.6233 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.01005/8.977, allocations: 1.445 MB / 2.16 GB, free: 103.3 MB / 0.6233 GB Notification: Performance of SimCode: time 1.703e-06/8.977, allocations: 0 / 2.16 GB, free: 103.3 MB / 0.6233 GB Notification: Performance of Templates: time 0.8251/9.802, allocations: 321.2 MB / 2.473 GB, free: 15.95 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)