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) [Timeout 180] "Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.001793/0.001793, allocations: 103.3 kB / 16.45 MB, free: 6.457 MB / 14.72 MB " [Timeout remaining time 180] loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo", uses=false) [Timeout 180] "Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001957/0.001957, allocations: 198.8 kB / 19.41 MB, free: 3.645 MB / 14.72 MB " [Timeout remaining time 180] loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo", uses=false) [Timeout 180] "Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 1.497/1.497, allocations: 225.6 MB / 247.8 MB, free: 13.92 MB / 206.1 MB " [Timeout remaining time 178] loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo", uses=false) [Timeout 180] "Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Chemical 1.4.1-master/package.mo): time 0.09138/0.09138, allocations: 15.53 MB / 318.2 MB, free: 10.21 MB / 254.1 MB " [Timeout remaining time 180] 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=2500,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery") translateModel(Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery,tolerance=1e-06,outputFormat="empty",numberOfIntervals=2500,variableFilter="",fileNamePrefix="Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery") [Timeout 660] "Notification: Performance of FrontEnd - loaded program: time 0.002021/0.002021, allocations: 75.86 kB / 445.4 MB, free: 13 MB / 318.1 MB Notification: Performance of FrontEnd - Absyn->SCode: time 0.1163/0.1183, allocations: 56.54 MB / 0.4902 GB, free: 4.355 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.HemoglobinMultipleAllostery): time 0.3064/0.4247, allocations: 42.61 MB / 0.5318 GB, free: 2.047 MB / 382.1 MB Notification: Performance of NFInst.instExpressions: time 0.09269/0.5174, allocations: 72.91 MB / 0.603 GB, free: 6.875 MB / 446.1 MB Notification: Performance of NFInst.updateImplicitVariability: time 0.005325/0.5227, allocations: 63.69 kB / 0.6031 GB, free: 6.812 MB / 446.1 MB Notification: Performance of NFTyping.typeComponents: time 0.006528/0.5292, allocations: 1.632 MB / 0.6047 GB, free: 5.168 MB / 446.1 MB Notification: Performance of NFTyping.typeBindings: time 0.02189/0.5511, allocations: 5.974 MB / 0.6105 GB, free: 15.15 MB / 462.1 MB Notification: Performance of NFTyping.typeClassSections: time 0.03688/0.588, allocations: 10.28 MB / 0.6206 GB, free: 4.809 MB / 462.1 MB Notification: Performance of NFFlatten.flatten: time 0.03418/0.6222, allocations: 26.69 MB / 0.6466 GB, free: 10.03 MB / 494.1 MB Notification: Performance of NFFlatten.resolveConnections: time 0.0299/0.6521, allocations: 19.11 MB / 0.6653 GB, free: 6.809 MB / 0.4981 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0348/0.6869, allocations: 17.59 MB / 0.6825 GB, free: 5.188 MB / 0.5137 GB Notification: Performance of NFSimplifyModel.simplify: time 0.03424/0.7211, allocations: 16.73 MB / 0.6988 GB, free: 4.41 MB / 0.5294 GB Notification: Performance of NFPackage.collectConstants: time 0.01393/0.735, allocations: 3.133 MB / 0.7019 GB, free: 1.277 MB / 0.5294 GB Notification: Performance of NFFlatten.collectFunctions: time 0.05142/0.7865, allocations: 10.83 MB / 0.7125 GB, free: 6.434 MB / 0.545 GB Notification: Performance of NFScalarize.scalarize: time 0.672/1.458, allocations: 7.063 MB / 0.7193 GB, free: 48.38 MB / 0.545 GB Notification: Performance of NFVerifyModel.verify: time 0.04214/1.501, allocations: 12.24 MB / 0.7313 GB, free: 47.79 MB / 0.545 GB Notification: Performance of NFConvertDAE.convert: time 0.1134/1.614, allocations: 42.58 MB / 0.7729 GB, free: 44.06 MB / 0.545 GB Notification: Performance of FrontEnd - DAE generated: time 5.601e-06/1.614, allocations: 0 / 0.7729 GB, free: 44.06 MB / 0.545 GB Notification: Performance of FrontEnd: time 1.182e-06/1.614, allocations: 3.188 kB / 0.7729 GB, free: 44.06 MB / 0.545 GB Notification: Performance of Transformations before backend: time 0.001454/1.615, allocations: 0.5938 kB / 0.7729 GB, free: 44.06 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 0.1076/1.723, allocations: 23.76 MB / 0.7961 GB, free: 32.57 MB / 0.545 GB Notification: Performance of prepare preOptimizeDAE: time 5.501e-05/1.723, allocations: 11.34 kB / 0.7961 GB, free: 32.57 MB / 0.545 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0314/1.755, allocations: 3.979 MB / 0.8 GB, free: 30.79 MB / 0.545 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.03425/1.789, allocations: 12.15 MB / 0.8118 GB, free: 24.18 MB / 0.545 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.002322/1.791, allocations: 2.142 MB / 0.8139 GB, free: 22.51 MB / 0.545 GB Notification: Performance of preOpt expandDerOperator (simulation): time 0.01452/1.806, allocations: 1.533 MB / 0.8154 GB, free: 21.95 MB / 0.545 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.1129/1.919, allocations: 35.21 MB / 0.8498 GB, free: 12.08 MB / 0.5607 GB Notification: Performance of preOpt findStateOrder (simulation): time 0.0008038/1.919, allocations: 7.469 kB / 0.8498 GB, free: 12.08 MB / 0.5607 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.01429/1.934, allocations: 0.5898 MB / 0.8504 GB, free: 11.49 MB / 0.5607 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 0.000378/1.934, allocations: 362.7 kB / 0.8508 GB, free: 11.13 MB / 0.5607 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.1353/2.069, allocations: 47.7 MB / 0.8973 GB, free: 11.43 MB / 0.6075 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 0.725/2.794, allocations: 130.5 MB / 1.025 GB, free: 149.2 MB / 0.6544 GB Notification: Performance of preOpt comSubExp (simulation): time 1.069/3.864, allocations: 275 MB / 1.293 GB, free: 181.3 MB / 0.67 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.03835/3.902, allocations: 18.5 MB / 1.311 GB, free: 179.7 MB / 0.67 GB Notification: Performance of preOpt evalFunc (simulation): time 0.1851/4.087, allocations: 90 MB / 1.399 GB, free: 97.54 MB / 0.67 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001521/4.087, allocations: 140.7 kB / 1.399 GB, free: 97.39 MB / 0.67 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.0324/4.12, allocations: 6.339 MB / 1.406 GB, free: 91.61 MB / 0.67 GB Notification: Performance of pre-optimization done (n=995): time 6.865e-05/4.12, allocations: 0 / 1.406 GB, free: 91.61 MB / 0.67 GB Notification: Performance of matching and sorting (n=1129): time 1.169/5.289, allocations: 130.7 MB / 1.533 GB, free: 234.5 MB / 0.67 GB Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001137/5.289, allocations: 168.2 kB / 1.533 GB, free: 234.4 MB / 0.67 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.02355/5.312, allocations: 10.17 MB / 1.543 GB, free: 231.8 MB / 0.67 GB Notification: Performance of collectPreVariables (initialization): time 0.00797/5.32, allocations: 211.1 kB / 1.544 GB, free: 231.6 MB / 0.67 GB Notification: Performance of collectInitialEqns (initialization): time 0.007876/5.328, allocations: 7.092 MB / 1.55 GB, free: 227.2 MB / 0.67 GB Notification: Performance of collectInitialBindings (initialization): time 0.01089/5.339, allocations: 4.104 MB / 1.555 GB, free: 223.7 MB / 0.67 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.02496/5.364, allocations: 3.272 MB / 1.558 GB, free: 221.9 MB / 0.67 GB Notification: Performance of setup shared object (initialization): time 6.38e-05/5.364, allocations: 303.5 kB / 1.558 GB, free: 221.6 MB / 0.67 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.02722/5.391, allocations: 11.82 MB / 1.57 GB, free: 215.1 MB / 0.67 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.03395/5.425, allocations: 16.56 MB / 1.586 GB, free: 202.5 MB / 0.67 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.05953/5.485, allocations: 29.74 MB / 1.615 GB, free: 178 MB / 0.67 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 0.0002084/5.485, allocations: 40 kB / 1.615 GB, free: 178 MB / 0.67 GB Notification: Performance of matching and sorting (n=1889) (initialization): time 0.4566/5.942, allocations: 81.39 MB / 1.694 GB, free: 96.45 MB / 0.67 GB Notification: Performance of prepare postOptimizeDAE: time 0.0001016/5.942, allocations: 68 kB / 1.694 GB, free: 96.38 MB / 0.67 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 0.0001887/5.942, allocations: 148 kB / 1.694 GB, free: 96.24 MB / 0.67 GB Notification: Performance of postOpt tearingSystem (initialization): time 0.05896/6.001, allocations: 22.41 MB / 1.716 GB, free: 73.98 MB / 0.67 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.01816/6.019, allocations: 3.725 MB / 1.72 GB, free: 70.25 MB / 0.67 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 0.5227/6.542, allocations: 93.9 MB / 1.812 GB, free: 195.4 MB / 0.67 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.02451/6.566, allocations: 0.8299 MB / 1.813 GB, free: 194.9 MB / 0.67 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.008053/6.574, allocations: 0.933 MB / 1.813 GB, free: 194.6 MB / 0.67 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 0.02348/6.598, allocations: 5.377 MB / 1.819 GB, free: 191.6 MB / 0.67 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.01171/6.61, allocations: 1.107 MB / 1.82 GB, free: 191.1 MB / 0.67 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.385/6.995, allocations: 48.48 MB / 1.867 GB, free: 143.5 MB / 0.67 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 0.0002073/6.995, allocations: 125.9 kB / 1.867 GB, free: 143.3 MB / 0.67 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 0.000259/6.995, allocations: 20 kB / 1.867 GB, free: 143.3 MB / 0.67 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 0.0006061/6.996, allocations: 59.77 kB / 1.867 GB, free: 143.3 MB / 0.67 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.3377/7.333, allocations: 72.92 MB / 1.939 GB, free: 70.75 MB / 0.67 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 0.0001425/7.333, allocations: 5.266 kB / 1.939 GB, free: 70.75 MB / 0.67 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.01493/7.348, allocations: 2.415 MB / 1.941 GB, free: 68.33 MB / 0.67 GB Notification: Performance of postOpt tearingSystem (simulation): time 0.3575/7.706, allocations: 11.87 MB / 1.952 GB, free: 217.6 MB / 0.67 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.006338/7.712, allocations: 480.4 kB / 1.953 GB, free: 217.6 MB / 0.67 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 0.1269/7.839, allocations: 46.9 MB / 1.999 GB, free: 208.7 MB / 0.67 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 7.675e-06/7.839, allocations: 7.469 kB / 1.999 GB, free: 208.7 MB / 0.67 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.3121/8.151, allocations: 62.67 MB / 2.06 GB, free: 180.2 MB / 0.67 GB Notification: Performance of postOpt removeConstants (simulation): time 0.01386/8.165, allocations: 3.351 MB / 2.063 GB, free: 177.5 MB / 0.67 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.01048/8.176, allocations: 298.7 kB / 2.063 GB, free: 177.2 MB / 0.67 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.02633/8.202, allocations: 0.5137 MB / 2.064 GB, free: 176.7 MB / 0.67 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0144/8.216, allocations: 1.502 MB / 2.065 GB, free: 175.2 MB / 0.67 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.006842/8.223, allocations: 471.6 kB / 2.066 GB, free: 174.7 MB / 0.67 GB Notification: Performance of sorting global known variables: time 0.0254/8.249, allocations: 6.966 MB / 2.073 GB, free: 167.8 MB / 0.67 GB Notification: Performance of sort global known variables: time 5.21e-07/8.249, allocations: 4 kB / 2.073 GB, free: 167.8 MB / 0.67 GB Notification: Performance of remove unused functions: time 0.05289/8.302, allocations: 6.724 MB / 2.079 GB, free: 161.3 MB / 0.67 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 0.01675/8.318, allocations: 3.585 MB / 2.083 GB, free: 158.3 MB / 0.67 GB Notification: Performance of simCode: created initialization part: time 0.07507/8.393, allocations: 26.38 MB / 2.109 GB, free: 132 MB / 0.67 GB Notification: Performance of simCode: created event and clocks part: time 1.085e-05/8.393, allocations: 0 / 2.109 GB, free: 132 MB / 0.67 GB Notification: Performance of simCode: created simulation system equations: time 0.04372/8.437, allocations: 13.61 MB / 2.122 GB, free: 118.4 MB / 0.67 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.02515/8.462, allocations: 2.504 MB / 2.124 GB, free: 116.2 MB / 0.67 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.1013/8.564, allocations: 38.3 MB / 2.162 GB, free: 77.88 MB / 0.67 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.01784/8.581, allocations: 9.942 MB / 2.171 GB, free: 67.98 MB / 0.67 GB Notification: Performance of simCode: alias equations: time 0.01853/8.6, allocations: 5.231 MB / 2.177 GB, free: 62.84 MB / 0.67 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.008971/8.609, allocations: 1.44 MB / 2.178 GB, free: 61.4 MB / 0.67 GB Notification: Performance of SimCode: time 1.813e-06/8.609, allocations: 0 / 2.178 GB, free: 61.4 MB / 0.67 GB Notification: Performance of Templates: time 1.226/9.835, allocations: 324.1 MB / 2.494 GB, free: 189.4 MB / 0.67 GB " [Timeout remaining time 650] make -j1 -f Chemical_Chemical.Examples.Hemoglobin.HemoglobinMultipleAllostery.makefile [Timeout 660] (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) [Timeout 480] [Calling os._exit(0), Time elapsed: 25.379534466192126]