Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral.conf.json loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo", uses=false) [Timeout 180] "Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo): time 0.001055/0.001055, allocations: 84.53 kB / 19.93 MB, free: 4.609 MB / 18.57 MB " [Timeout remaining time 180] loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo", uses=false) [Timeout 180] "Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo): time 0.0009879/0.0009879, allocations: 174.3 kB / 23.21 MB, free: 1.328 MB / 18.57 MB " [Timeout remaining time 180] loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo", uses=false) [Timeout 180] "Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo): time 0.9802/0.9802, allocations: 177.1 MB / 203.5 MB, free: 5.742 MB / 186.7 MB " [Timeout remaining time 179] loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Pharmacolibrary 25.9.0/package.mo", uses=false) [Timeout 180] "[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Pharmacolibrary 25.9.0/Examples/package.order:0:0-0:0:readonly] Warning: The package.order file does not list all .mo files and directories (containing package.mo) present in its directory. Missing names are: Paracetamol_Experiment Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Pharmacolibrary 25.9.0/package.mo): time 1.63/1.63, allocations: 273.5 MB / 0.5209 GB, free: 15 MB / 458.7 MB " [Timeout remaining time 178] Using package Pharmacolibrary with version 25.09 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Pharmacolibrary 25.9.0/package.mo) Using package Modelica with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo) Using package Complex with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo) Using package ModelicaServices with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo) Running command: translateModel(Pharmacolibrary.DevModels.PKTwoCompartmentModelOral,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral") translateModel(Pharmacolibrary.DevModels.PKTwoCompartmentModelOral,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral") [Timeout 660] "Notification: Performance of FrontEnd - loaded program: time 1.453e-06/1.453e-06, allocations: 0 / 0.7558 GB, free: 10.74 MB / 0.5887 GB Notification: Performance of FrontEnd - Absyn->SCode: time 1.634e-05/1.779e-05, allocations: 2.281 kB / 0.7558 GB, free: 10.73 MB / 0.5887 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.PKTwoCompartmentModelOral): time 0.002454/0.002472, allocations: 2.248 MB / 0.758 GB, free: 8.5 MB / 0.5887 GB Notification: Performance of NFInst.instExpressions: time 0.001048/0.00352, allocations: 0.5963 MB / 0.7585 GB, free: 7.906 MB / 0.5887 GB Notification: Performance of NFInst.updateImplicitVariability: time 0.0001064/0.003626, allocations: 0 / 0.7585 GB, free: 7.906 MB / 0.5887 GB Notification: Performance of NFTyping.typeComponents: time 6.528e-05/0.003692, allocations: 27.72 kB / 0.7586 GB, free: 7.879 MB / 0.5887 GB Notification: Performance of NFTyping.typeBindings: time 0.0002096/0.003901, allocations: 78.5 kB / 0.7586 GB, free: 7.828 MB / 0.5887 GB Notification: Performance of NFTyping.typeClassSections: time 0.0002045/0.004106, allocations: 63.86 kB / 0.7587 GB, free: 7.766 MB / 0.5887 GB Notification: Performance of NFFlatten.flatten: time 0.0002727/0.004378, allocations: 296.3 kB / 0.759 GB, free: 7.492 MB / 0.5887 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001443/0.004523, allocations: 52.73 kB / 0.759 GB, free: 7.441 MB / 0.5887 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0001853/0.004708, allocations: 155.7 kB / 0.7592 GB, free: 7.289 MB / 0.5887 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001217/0.00483, allocations: 87.69 kB / 0.7593 GB, free: 7.203 MB / 0.5887 GB Notification: Performance of NFPackage.collectConstants: time 3.553e-05/0.004865, allocations: 24 kB / 0.7593 GB, free: 7.18 MB / 0.5887 GB Notification: Performance of NFFlatten.collectFunctions: time 2.964e-05/0.004895, allocations: 27.94 kB / 0.7593 GB, free: 7.152 MB / 0.5887 GB Notification: Performance of NFScalarize.scalarize: time 4.295e-05/0.004938, allocations: 43.83 kB / 0.7594 GB, free: 7.109 MB / 0.5887 GB Notification: Performance of NFVerifyModel.verify: time 8.436e-05/0.005022, allocations: 87.83 kB / 0.7594 GB, free: 7.023 MB / 0.5887 GB Notification: Performance of NFConvertDAE.convert: time 0.0002419/0.005264, allocations: 239.3 kB / 0.7597 GB, free: 6.789 MB / 0.5887 GB Notification: Performance of FrontEnd - DAE generated: time 4.007e-06/0.005268, allocations: 8 kB / 0.7597 GB, free: 6.781 MB / 0.5887 GB Notification: Performance of FrontEnd: time 1.072e-06/0.005269, allocations: 0 / 0.7597 GB, free: 6.781 MB / 0.5887 GB Notification: Performance of Transformations before backend: time 6.011e-06/0.005275, allocations: 0 / 0.7597 GB, free: 6.781 MB / 0.5887 GB Notification: Model statistics after passing the front-end and creating the data structures used by the back-end: * Number of equations: 45 * Number of variables: 45 Notification: Performance of Generate backend data structure: time 0.0008846/0.00616, allocations: 0.5257 MB / 0.7602 GB, free: 6.207 MB / 0.5887 GB Notification: Performance of prepare preOptimizeDAE: time 5.039e-05/0.00621, allocations: 8.031 kB / 0.7602 GB, free: 6.199 MB / 0.5887 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 7.109e-05/0.006281, allocations: 24.8 kB / 0.7602 GB, free: 6.176 MB / 0.5887 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001504/0.006431, allocations: 149.5 kB / 0.7604 GB, free: 6.004 MB / 0.5887 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.308e-05/0.006455, allocations: 12.38 kB / 0.7604 GB, free: 5.992 MB / 0.5887 GB Notification: Performance of preOpt expandDerOperator (simulation): time 5.195e-05/0.006506, allocations: 28.33 kB / 0.7604 GB, free: 5.965 MB / 0.5887 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003715/0.006878, allocations: 250.4 kB / 0.7606 GB, free: 5.699 MB / 0.5887 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.692e-05/0.006895, allocations: 4 kB / 0.7607 GB, free: 5.695 MB / 0.5887 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.036e-05/0.006915, allocations: 8 kB / 0.7607 GB, free: 5.688 MB / 0.5887 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.041e-05/0.006926, allocations: 4 kB / 0.7607 GB, free: 5.684 MB / 0.5887 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002893/0.007215, allocations: 227 kB / 0.7609 GB, free: 5.453 MB / 0.5887 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0006881/0.007903, allocations: 476.5 kB / 0.7613 GB, free: 4.957 MB / 0.5887 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0002793/0.008182, allocations: 221.9 kB / 0.7615 GB, free: 4.719 MB / 0.5887 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.000139/0.008321, allocations: 152.1 kB / 0.7617 GB, free: 4.555 MB / 0.5887 GB Notification: Performance of preOpt evalFunc (simulation): time 1.254e-05/0.008334, allocations: 3.938 kB / 0.7617 GB, free: 4.551 MB / 0.5887 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0003179/0.008652, allocations: 344.5 kB / 0.762 GB, free: 4.168 MB / 0.5887 GB Notification: Performance of pre-optimization done (n=30): time 2.004e-06/0.008654, allocations: 0 / 0.762 GB, free: 4.168 MB / 0.5887 GB Notification: Performance of matching and sorting (n=32): time 0.001292/0.009946, allocations: 1.028 MB / 0.763 GB, free: 3.047 MB / 0.5887 GB Notification: Performance of inlineWhenForInitialization (initialization): time 8.476e-05/0.01003, allocations: 217.6 kB / 0.7632 GB, free: 2.785 MB / 0.5887 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001276/0.01016, allocations: 170 kB / 0.7634 GB, free: 2.613 MB / 0.5887 GB Notification: Performance of collectPreVariables (initialization): time 2.389e-05/0.01018, allocations: 33.7 kB / 0.7634 GB, free: 2.574 MB / 0.5887 GB Notification: Performance of collectInitialEqns (initialization): time 6.872e-05/0.01025, allocations: 128.9 kB / 0.7636 GB, free: 2.445 MB / 0.5887 GB Notification: Performance of collectInitialBindings (initialization): time 6.112e-05/0.01031, allocations: 111.1 kB / 0.7637 GB, free: 2.336 MB / 0.5887 GB Notification: Performance of simplifyInitialFunctions (initialization): time 7.268e-05/0.01038, allocations: 65.98 kB / 0.7637 GB, free: 2.262 MB / 0.5887 GB Notification: Performance of setup shared object (initialization): time 9.223e-05/0.01048, allocations: 338.7 kB / 0.764 GB, free: 1.922 MB / 0.5887 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001796/0.01066, allocations: 191.3 kB / 0.7642 GB, free: 1.715 MB / 0.5887 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002052/0.01086, allocations: 282.1 kB / 0.7645 GB, free: 1.387 MB / 0.5887 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0007464/0.01161, allocations: 0.7295 MB / 0.7652 GB, free: 0.5625 MB / 0.5887 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.715e-06/0.01161, allocations: 0 / 0.7652 GB, free: 0.5625 MB / 0.5887 GB Notification: Performance of matching and sorting (n=47) (initialization): time 0.0004935/0.0121, allocations: 0.5127 MB / 0.7657 GB, free: 8 kB / 0.5887 GB Notification: Performance of prepare postOptimizeDAE: time 6.179e-05/0.01217, allocations: 99.44 kB / 0.7658 GB, free: 15.89 MB / 0.6043 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.064e-06/0.01217, allocations: 3.938 kB / 0.7658 GB, free: 15.89 MB / 0.6043 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.645e-05/0.01219, allocations: 8.25 kB / 0.7658 GB, free: 15.88 MB / 0.6043 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001684/0.01236, allocations: 63.91 kB / 0.7659 GB, free: 15.82 MB / 0.6043 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.206e-06/0.01237, allocations: 4 kB / 0.7659 GB, free: 15.82 MB / 0.6043 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001028/0.01247, allocations: 19.98 kB / 0.7659 GB, free: 15.8 MB / 0.6043 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.977e-05/0.01249, allocations: 19.98 kB / 0.7659 GB, free: 15.78 MB / 0.6043 GB Warning: Assuming fixed start value for the following 10 variables: central.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real peripheral.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real periodicDose1.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true ) \"Total dose adminitrated by this source\" type: Real periodicDose1.variableDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true ) \"Total dose adminitrated by this source\" type: Real central.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real central.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real peripheral.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real peripheral.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real peripheral.rising:DISCRETE(fixed = true protected = true ) type: Boolean central.rising:DISCRETE(fixed = true protected = true ) type: Boolean Notification: Model statistics after passing the back-end for initialization: * Number of independent subsystems: 9 * Number of states: 0 () * Number of discrete variables: 21 ($PRE.central.Cmin,central.Cmin,$PRE.central.Cmax,central.Cmax,$PRE.peripheral.Cmin,peripheral.Cmin,$PRE.peripheral.Cmax,peripheral.Cmax,$PRE.periodicDose1.pulse.count,$PRE.periodicDose1.pulse.T_start,$PRE.peripheral.rising,$PRE.central.rising,periodicDose1.pulse.count,periodicDose1.pulse.T_start,peripheral.rising,central.rising,$whenCondition5,$whenCondition4,$whenCondition3,$whenCondition2,$whenCondition1) * Number of discrete states: 0 () * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for initialization (44): * Single equations (assignments): 41 * Array equations: 0 * Algorithm blocks: 3 * Record equations: 0 * When equations: 0 * If-equations: 0 * Equation systems (not torn): 0 * Torn equation systems: 0 * Mixed (continuous/discrete) equation systems: 0 Notification: Performance of prepare postOptimizeDAE: time 0.0002055/0.01269, allocations: 244.7 kB / 0.7662 GB, free: 15.52 MB / 0.6043 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 2.274e-05/0.01272, allocations: 15.91 kB / 0.7662 GB, free: 15.5 MB / 0.6043 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.797e-05/0.01275, allocations: 33.89 kB / 0.7662 GB, free: 15.47 MB / 0.6043 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.707e-06/0.01276, allocations: 4 kB / 0.7662 GB, free: 15.46 MB / 0.6043 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 6.262e-06/0.01276, allocations: 0 / 0.7662 GB, free: 15.46 MB / 0.6043 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.94e-06/0.01277, allocations: 4 kB / 0.7662 GB, free: 15.46 MB / 0.6043 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0006723/0.01344, allocations: 0.726 MB / 0.7669 GB, free: 14.68 MB / 0.6043 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.434e-06/0.01344, allocations: 0 / 0.7669 GB, free: 14.68 MB / 0.6043 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001515/0.0136, allocations: 51.91 kB / 0.767 GB, free: 14.62 MB / 0.6043 GB Notification: Performance of postOpt tearingSystem (simulation): time 4.819e-06/0.0136, allocations: 4 kB / 0.767 GB, free: 14.62 MB / 0.6043 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.768e-05/0.01362, allocations: 8 kB / 0.767 GB, free: 14.61 MB / 0.6043 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.714e-06/0.01362, allocations: 4 kB / 0.767 GB, free: 14.61 MB / 0.6043 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.533e-06/0.01362, allocations: 0 / 0.767 GB, free: 14.61 MB / 0.6043 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0006175/0.01424, allocations: 0.6932 MB / 0.7677 GB, free: 13.86 MB / 0.6043 GB Notification: Performance of postOpt removeConstants (simulation): time 2.086e-05/0.01426, allocations: 19.89 kB / 0.7677 GB, free: 13.84 MB / 0.6043 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.214e-05/0.01429, allocations: 16 kB / 0.7677 GB, free: 13.83 MB / 0.6043 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 9.014e-05/0.01438, allocations: 15.98 kB / 0.7677 GB, free: 13.81 MB / 0.6043 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 7.45e-05/0.01446, allocations: 27.95 kB / 0.7677 GB, free: 13.79 MB / 0.6043 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.442e-05/0.01447, allocations: 19.94 kB / 0.7678 GB, free: 13.77 MB / 0.6043 GB Notification: Performance of sorting global known variables: time 6.974e-05/0.01454, allocations: 126.2 kB / 0.7679 GB, free: 13.64 MB / 0.6043 GB Notification: Performance of sort global known variables: time 8e-08/0.01454, allocations: 0 / 0.7679 GB, free: 13.64 MB / 0.6043 GB Notification: Performance of remove unused functions: time 0.0002216/0.01476, allocations: 68 kB / 0.7679 GB, free: 13.58 MB / 0.6043 GB Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 1 * Number of states: 6 (central.C,central.AUC,peripheral.C,peripheral.AUC,periodicDose1.TotalCumulativeMass,periodicDose1.variableDose.TotalCumulativeMass) * Number of discrete variables: 13 ($whenCondition1,$whenCondition2,$whenCondition3,$whenCondition4,$whenCondition5,central.Cmax,central.Cmin,central.rising,peripheral.Cmax,peripheral.Cmin,peripheral.rising,periodicDose1.pulse.T_start,periodicDose1.pulse.count) * Number of discrete states: 11 (periodicDose1.pulse.count,peripheral.Cmin,$whenCondition3,peripheral.Cmax,$whenCondition2,peripheral.rising,central.Cmin,$whenCondition5,central.Cmax,$whenCondition4,central.rising) * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for simulation (26): * Single equations (assignments): 22 * Array equations: 0 * Algorithm blocks: 2 * Record equations: 0 * When equations: 2 * If-equations: 0 * Equation systems (not torn): 0 * Torn equation systems: 0 * Mixed (continuous/discrete) equation systems: 0 Notification: Performance of Backend phase and start with SimCode phase: time 0.0001031/0.01487, allocations: 117.7 kB / 0.768 GB, free: 13.46 MB / 0.6043 GB Notification: Performance of simCode: created initialization part: time 0.0004817/0.01535, allocations: 0.5495 MB / 0.7686 GB, free: 12.84 MB / 0.6043 GB Notification: Performance of simCode: created event and clocks part: time 2.825e-06/0.01535, allocations: 4 kB / 0.7686 GB, free: 12.84 MB / 0.6043 GB Notification: Performance of simCode: created simulation system equations: time 0.0002053/0.01556, allocations: 290.1 kB / 0.7689 GB, free: 12.52 MB / 0.6043 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002803/0.01584, allocations: 70.44 kB / 0.7689 GB, free: 12.45 MB / 0.6043 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0009266/0.01676, allocations: 0.7335 MB / 0.7696 GB, free: 11.68 MB / 0.6043 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 9.056e-05/0.01685, allocations: 134.8 kB / 0.7698 GB, free: 11.53 MB / 0.6043 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 5.689e-05/0.01691, allocations: 24.5 kB / 0.7698 GB, free: 11.51 MB / 0.6043 GB Notification: Performance of SimCode: time 5.91e-07/0.01691, allocations: 0 / 0.7698 GB, free: 11.51 MB / 0.6043 GB Notification: Performance of Templates: time 0.003755/0.02067, allocations: 3.139 MB / 0.7729 GB, free: 8.438 MB / 0.6043 GB " [Timeout remaining time 660] make -j1 -f Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral.makefile [Timeout 660] (rm -f Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral.sim & ./Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral > Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 6.434794506058097]