Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries/ --ompython_omhome=/usr Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.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.HemoglobinMultipleAllostery,tolerance=1e-06,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery") translateModel(Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery,tolerance=1e-06,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery") Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.0007858/0.0007859, allocations: 98.03 kB / 15.36 MB, free: 0.7344 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.004752/0.004752, allocations: 168.9 kB / 16.26 MB, free: 6.648 MB / 14.72 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.35/1.35, allocations: 223.3 MB / 240.3 MB, free: 5.316 MB / 190.1 MB Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.2118/0.2118, allocations: 15.27 MB / 306.7 MB, free: 15.69 MB / 254.1 MB Notification: Performance of FrontEnd - loaded program: time 0.0003009/0.0003009, allocations: 8 kB / 372.1 MB, free: 3.594 MB / 302.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.3009/0.3012, allocations: 54.62 MB / 426.7 MB, free: 40.46 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.HemoglobinMultipleAllostery): time 0.04298/0.3443, allocations: 42.86 MB / 469.6 MB, free: 19.83 MB / 350.1 MB Notification: Performance of NFInst.instExpressions: time 0.07522/0.4195, allocations: 71.78 MB / 0.5287 GB, free: 3.215 MB / 398.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.006603/0.4262, allocations: 95.25 kB / 0.5288 GB, free: 3.121 MB / 398.1 MB Notification: Performance of NFTyping.typeComponents: time 0.005793/0.432, allocations: 1.459 MB / 0.5302 GB, free: 1.652 MB / 398.1 MB Notification: Performance of NFTyping.typeBindings: time 0.02244/0.4545, allocations: 5.166 MB / 0.5352 GB, free: 12.45 MB / 414.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.0306/0.4851, allocations: 9.005 MB / 0.544 GB, free: 3.402 MB / 414.1 MB Notification: Performance of NFFlatten.flatten: time 0.02716/0.5123, allocations: 25.65 MB / 0.5691 GB, free: 9.66 MB / 446.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.261/0.7733, allocations: 17.22 MB / 0.5859 GB, free: 11.79 MB / 446.1 MB Notification: Performance of NFEvalConstants.evaluate: time 0.02539/0.7988, allocations: 15.54 MB / 0.6011 GB, free: 11.34 MB / 446.1 MB Notification: Performance of NFSimplifyModel.simplify: time 0.03494/0.8338, allocations: 14.1 MB / 0.6148 GB, free: 9.566 MB / 446.1 MB Notification: Performance of NFPackage.collectConstants: time 0.01185/0.8456, allocations: 1.433 MB / 0.6162 GB, free: 9.566 MB / 446.1 MB Notification: Performance of NFFlatten.collectFunctions: time 0.04609/0.8918, allocations: 9.018 MB / 0.625 GB, free: 9.184 MB / 446.1 MB Notification: Performance of NFScalarize.scalarize: time 0.01496/0.9068, allocations: 4.977 MB / 0.6299 GB, free: 7.367 MB / 446.1 MB Notification: Performance of NFVerifyModel.verify: time 0.0259/0.9327, allocations: 10.04 MB / 0.6397 GB, free: 3.836 MB / 446.1 MB Notification: Performance of NFConvertDAE.convert: time 0.07078/1.004, allocations: 38.9 MB / 0.6777 GB, free: 11.37 MB / 478.1 MB Notification: Performance of FrontEnd - DAE generated: time 7.755e-06/1.004, allocations: 0 / 0.6777 GB, free: 11.37 MB / 478.1 MB Notification: Performance of FrontEnd: time 2.765e-06/1.004, allocations: 0 / 0.6777 GB, free: 11.37 MB / 478.1 MB Notification: Performance of Transformations before backend: time 0.001188/1.005, allocations: 0 / 0.6777 GB, free: 11.37 MB / 478.1 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 0.07081/1.076, allocations: 20.18 MB / 0.6974 GB, free: 7.32 MB / 494.1 MB Notification: Performance of prepare preOptimizeDAE: time 5.99e-05/1.076, allocations: 10.75 kB / 0.6974 GB, free: 7.312 MB / 494.1 MB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0261/1.102, allocations: 3.896 MB / 0.7012 GB, free: 3.402 MB / 494.1 MB Notification: Performance of preOpt evaluateParameters (simulation): time 0.03322/1.135, allocations: 11.46 MB / 0.7124 GB, free: 8.348 MB / 0.4981 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.002669/1.138, allocations: 2.131 MB / 0.7145 GB, free: 6 MB / 0.4981 GB Notification: Performance of preOpt expandDerOperator (simulation): time 0.01151/1.149, allocations: 1.537 MB / 0.716 GB, free: 4.469 MB / 0.4981 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0896/1.239, allocations: 34.8 MB / 0.75 GB, free: 1.461 MB / 0.5294 GB Notification: Performance of preOpt findStateOrder (simulation): time 0.000634/1.24, allocations: 10.09 kB / 0.75 GB, free: 1.457 MB / 0.5294 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.00811/1.248, allocations: 0.5859 MB / 0.7506 GB, free: 0.8711 MB / 0.5294 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.000323/1.248, allocations: 364 kB / 0.7509 GB, free: 0.5156 MB / 0.5294 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.505/1.753, allocations: 46.83 MB / 0.7966 GB, free: 192.3 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 0.2743/2.027, allocations: 127.9 MB / 0.9215 GB, free: 104.5 MB / 0.5607 GB Notification: Performance of preOpt comSubExp (simulation): time 1.114/3.141, allocations: 276.1 MB / 1.191 GB, free: 68.73 MB / 0.5608 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.03121/3.173, allocations: 19.81 MB / 1.21 GB, free: 48.88 MB / 0.5608 GB Notification: Performance of preOpt evalFunc (simulation): time 0.4124/3.585, allocations: 87.12 MB / 1.296 GB, free: 171.5 MB / 0.5608 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001533/3.585, allocations: 134 kB / 1.296 GB, free: 171.4 MB / 0.5608 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.02565/3.611, allocations: 4.434 MB / 1.3 GB, free: 170.3 MB / 0.5608 GB Notification: Performance of pre-optimization done (n=995): time 7.563e-05/3.611, allocations: 3.875 kB / 1.3 GB, free: 170.3 MB / 0.5608 GB Notification: Performance of matching and sorting (n=1129): time 0.6903/4.301, allocations: 131.1 MB / 1.428 GB, free: 72.55 MB / 0.5608 GB Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001403/4.301, allocations: 164.2 kB / 1.428 GB, free: 72.38 MB / 0.5608 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.01972/4.321, allocations: 10.16 MB / 1.438 GB, free: 62.28 MB / 0.5608 GB Notification: Performance of collectPreVariables (initialization): time 0.005264/4.326, allocations: 209.7 kB / 1.438 GB, free: 62.07 MB / 0.5608 GB Notification: Performance of collectInitialEqns (initialization): time 0.005361/4.332, allocations: 6.884 MB / 1.445 GB, free: 55.17 MB / 0.5608 GB Notification: Performance of collectInitialBindings (initialization): time 0.2797/4.612, allocations: 3.912 MB / 1.449 GB, free: 181.6 MB / 0.5608 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.005828/4.617, allocations: 1.156 MB / 1.45 GB, free: 181.5 MB / 0.5608 GB Notification: Performance of setup shared object (initialization): time 4.862e-05/4.618, allocations: 301.1 kB / 1.45 GB, free: 181.2 MB / 0.5608 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.02121/4.639, allocations: 11.83 MB / 1.462 GB, free: 180.9 MB / 0.5608 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.024/4.663, allocations: 16.56 MB / 1.478 GB, free: 170.7 MB / 0.5608 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.04934/4.712, allocations: 29.74 MB / 1.507 GB, free: 154.5 MB / 0.5608 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0002339/4.712, allocations: 45.16 kB / 1.507 GB, free: 154.5 MB / 0.5608 GB Notification: Performance of matching and sorting (n=1889) (initialization): time 0.448/5.16, allocations: 81.54 MB / 1.587 GB, free: 98.44 MB / 0.5608 GB Notification: Performance of prepare postOptimizeDAE: time 0.0002287/5.161, allocations: 68 kB / 1.587 GB, free: 98.38 MB / 0.5608 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0002721/5.161, allocations: 152.8 kB / 1.587 GB, free: 98.23 MB / 0.5608 GB Notification: Performance of postOpt tearingSystem (initialization): time 0.06062/5.222, allocations: 22.55 MB / 1.609 GB, free: 75.86 MB / 0.5608 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01788/5.24, allocations: 3.729 MB / 1.612 GB, free: 72.13 MB / 0.5608 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.4898/5.729, allocations: 88.3 MB / 1.699 GB, free: 148.4 MB / 0.5608 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.02166/5.751, allocations: 1.149 MB / 1.7 GB, free: 148.2 MB / 0.5608 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.006296/5.758, allocations: 0.9352 MB / 1.701 GB, free: 148.1 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 0.01642/5.774, allocations: 5.374 MB / 1.706 GB, free: 146.1 MB / 0.5608 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.005358/5.779, allocations: 1.052 MB / 1.707 GB, free: 146.1 MB / 0.5608 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.2696/6.049, allocations: 48.56 MB / 1.754 GB, free: 116.3 MB / 0.5608 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.0001188/6.049, allocations: 120 kB / 1.755 GB, free: 116.2 MB / 0.5608 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 7.924e-05/6.049, allocations: 22.69 kB / 1.755 GB, free: 116.2 MB / 0.5608 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0003283/6.05, allocations: 59.77 kB / 1.755 GB, free: 116.1 MB / 0.5608 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.2976/6.347, allocations: 72.94 MB / 1.826 GB, free: 43.43 MB / 0.5608 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 0.0001081/6.347, allocations: 4 kB / 1.826 GB, free: 43.43 MB / 0.5608 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.01476/6.362, allocations: 2.425 MB / 1.828 GB, free: 41 MB / 0.5608 GB Notification: Performance of postOpt tearingSystem (simulation): time 0.3329/6.695, allocations: 11.75 MB / 1.84 GB, free: 161.4 MB / 0.5608 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.004131/6.699, allocations: 474.9 kB / 1.84 GB, free: 161.4 MB / 0.5608 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.1072/6.806, allocations: 42.2 MB / 1.881 GB, free: 150.3 MB / 0.5608 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 5.892e-06/6.806, allocations: 9.984 kB / 1.881 GB, free: 150.3 MB / 0.5608 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.2942/7.101, allocations: 62.67 MB / 1.943 GB, free: 122.3 MB / 0.5608 GB Notification: Performance of postOpt removeConstants (simulation): time 0.01023/7.111, allocations: 3.294 MB / 1.946 GB, free: 119.6 MB / 0.5608 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.005927/7.117, allocations: 299.8 kB / 1.946 GB, free: 119.3 MB / 0.5608 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.01489/7.132, allocations: 0.7926 MB / 1.947 GB, free: 118.6 MB / 0.5608 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.006423/7.138, allocations: 1.491 MB / 1.948 GB, free: 117.1 MB / 0.5608 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.002487/7.141, allocations: 473 kB / 1.949 GB, free: 116.7 MB / 0.5608 GB Notification: Performance of sorting global known variables: time 0.01101/7.152, allocations: 6.974 MB / 1.956 GB, free: 109.7 MB / 0.5608 GB Notification: Performance of sort global known variables: time 3.4e-07/7.152, allocations: 0 / 1.956 GB, free: 109.7 MB / 0.5608 GB Notification: Performance of remove unused functions: time 0.03246/7.184, allocations: 6.66 MB / 1.962 GB, free: 103.6 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 0.01146/7.196, allocations: 3.518 MB / 1.966 GB, free: 100.8 MB / 0.5608 GB Notification: Performance of simCode: created initialization part: time 0.06673/7.263, allocations: 27.73 MB / 1.993 GB, free: 73.09 MB / 0.5608 GB Notification: Performance of simCode: created event and clocks part: time 9.568e-06/7.263, allocations: 4 kB / 1.993 GB, free: 73.09 MB / 0.5608 GB Notification: Performance of simCode: created simulation system equations: time 0.0378/7.3, allocations: 14.86 MB / 2.007 GB, free: 58.2 MB / 0.5608 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.02206/7.323, allocations: 2.34 MB / 2.009 GB, free: 55.95 MB / 0.5608 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.3283/7.651, allocations: 44.71 MB / 2.053 GB, free: 156.7 MB / 0.5608 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.01868/7.67, allocations: 9.937 MB / 2.063 GB, free: 155.6 MB / 0.5608 GB Notification: Performance of simCode: alias equations: time 0.01966/7.689, allocations: 5.304 MB / 2.068 GB, free: 155.5 MB / 0.5608 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.01092/7.7, allocations: 1.425 MB / 2.069 GB, free: 155.5 MB / 0.5608 GB Notification: Performance of SimCode: time 1.022e-06/7.7, allocations: 2.75 kB / 2.069 GB, free: 155.5 MB / 0.5608 GB Notification: Performance of Templates: time 0.7343/8.435, allocations: 309.5 MB / 2.372 GB, free: 64.44 MB / 0.5608 GB make -j1 -f Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.makefile (rm -f Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.pipe ; mkfifo Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.pipe ; head -c 1048576 < Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.pipe >> ../files/Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.sim & ./Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery -abortSlowSimulation -alarm=480 -lv LOG_STATS > Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.pipe 2>&1)