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 0.001003/0.001003, allocations: 81.17 kB / 19.87 MB, free: 4.621 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 0.0009974/0.0009974, allocations: 169 kB / 23.27 MB, free: 1.223 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 0.9345/0.9345, allocations: 177.2 MB / 203.7 MB, free: 5.52 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 1.626/1.626, allocations: 273.5 MB / 0.5212 GB, free: 14.73 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 1.724e-06/1.724e-06, allocations: 0 / 0.6474 GB, free: 38.71 MB / 0.5262 GB Notification: Performance of FrontEnd - Absyn->SCode: time 2.585e-05/2.757e-05, allocations: 3.469 kB / 0.6474 GB, free: 38.71 MB / 0.5262 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.PKTwoCompartmentModelOral): time 0.00361/0.003637, allocations: 2.38 MB / 0.6497 GB, free: 37.16 MB / 0.5262 GB Notification: Performance of NFInst.instExpressions: time 0.001172/0.004809, allocations: 0.6158 MB / 0.6503 GB, free: 36.75 MB / 0.5262 GB Notification: Performance of NFInst.updateImplicitVariability: time 0.0001354/0.004945, allocations: 3.656 kB / 0.6503 GB, free: 36.75 MB / 0.5262 GB Notification: Performance of NFTyping.typeComponents: time 7.15e-05/0.005016, allocations: 28.59 kB / 0.6503 GB, free: 36.73 MB / 0.5262 GB Notification: Performance of NFTyping.typeBindings: time 0.0002576/0.005274, allocations: 75.56 kB / 0.6504 GB, free: 36.7 MB / 0.5262 GB Notification: Performance of NFTyping.typeClassSections: time 0.0002301/0.005504, allocations: 65.58 kB / 0.6505 GB, free: 36.67 MB / 0.5262 GB Notification: Performance of NFFlatten.flatten: time 0.0003345/0.005838, allocations: 303.7 kB / 0.6508 GB, free: 36.54 MB / 0.5262 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001694/0.006008, allocations: 44.59 kB / 0.6508 GB, free: 36.52 MB / 0.5262 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0003298/0.006338, allocations: 160.6 kB / 0.651 GB, free: 36.45 MB / 0.5262 GB Notification: Performance of NFSimplifyModel.simplify: time 0.000185/0.006522, allocations: 84.17 kB / 0.651 GB, free: 36.43 MB / 0.5262 GB Notification: Performance of NFPackage.collectConstants: time 4.898e-05/0.006571, allocations: 20.84 kB / 0.6511 GB, free: 36.43 MB / 0.5262 GB Notification: Performance of NFFlatten.collectFunctions: time 4.832e-05/0.00662, allocations: 25.22 kB / 0.6511 GB, free: 36.43 MB / 0.5262 GB Notification: Performance of NFScalarize.scalarize: time 4.649e-05/0.006666, allocations: 48.02 kB / 0.6511 GB, free: 36.39 MB / 0.5262 GB Notification: Performance of NFVerifyModel.verify: time 0.0001002/0.006767, allocations: 94.61 kB / 0.6512 GB, free: 36.35 MB / 0.5262 GB Notification: Performance of NFConvertDAE.convert: time 0.0002477/0.007014, allocations: 178.6 kB / 0.6514 GB, free: 36.27 MB / 0.5262 GB Notification: Performance of FrontEnd - DAE generated: time 4.248e-06/0.007019, allocations: 0 / 0.6514 GB, free: 36.27 MB / 0.5262 GB Notification: Performance of FrontEnd: time 1.092e-06/0.00702, allocations: 0 / 0.6514 GB, free: 36.27 MB / 0.5262 GB Notification: Performance of Transformations before backend: time 5.019e-06/0.007025, allocations: 0 / 0.6514 GB, free: 36.27 MB / 0.5262 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 0.0007553/0.00778, allocations: 0.6235 MB / 0.652 GB, free: 35.7 MB / 0.5262 GB Notification: Performance of prepare preOptimizeDAE: time 4.643e-05/0.007826, allocations: 9.281 kB / 0.652 GB, free: 35.7 MB / 0.5262 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 8.153e-05/0.007908, allocations: 42.78 kB / 0.6521 GB, free: 35.69 MB / 0.5262 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002141/0.008122, allocations: 174.6 kB / 0.6522 GB, free: 35.52 MB / 0.5262 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.035e-05/0.008152, allocations: 12.72 kB / 0.6522 GB, free: 35.52 MB / 0.5262 GB Notification: Performance of preOpt expandDerOperator (simulation): time 4.602e-05/0.008198, allocations: 28.48 kB / 0.6523 GB, free: 35.5 MB / 0.5262 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002907/0.008489, allocations: 201.6 kB / 0.6525 GB, free: 35.37 MB / 0.5262 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.887e-05/0.008508, allocations: 3.062 kB / 0.6525 GB, free: 35.37 MB / 0.5262 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.852e-05/0.008526, allocations: 5.688 kB / 0.6525 GB, free: 35.37 MB / 0.5262 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.017e-06/0.008535, allocations: 4.188 kB / 0.6525 GB, free: 35.37 MB / 0.5262 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.000175/0.00871, allocations: 147.6 kB / 0.6526 GB, free: 35.29 MB / 0.5262 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0006689/0.009379, allocations: 475.2 kB / 0.6531 GB, free: 34.95 MB / 0.5262 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0001898/0.009569, allocations: 163.2 kB / 0.6532 GB, free: 34.84 MB / 0.5262 GB Notification: Performance of preOpt resolveLoops (simulation): time 7.573e-05/0.009645, allocations: 100.6 kB / 0.6533 GB, free: 34.75 MB / 0.5262 GB Notification: Performance of preOpt evalFunc (simulation): time 1.258e-05/0.009657, allocations: 5.375 kB / 0.6533 GB, free: 34.75 MB / 0.5262 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002523/0.00991, allocations: 309 kB / 0.6536 GB, free: 34.49 MB / 0.5262 GB Notification: Performance of pre-optimization done (n=30): time 2.805e-06/0.009913, allocations: 1.375 kB / 0.6536 GB, free: 34.49 MB / 0.5262 GB Notification: Performance of matching and sorting (n=32): time 0.001117/0.01103, allocations: 0.8454 MB / 0.6544 GB, free: 33.89 MB / 0.5262 GB Notification: Performance of inlineWhenForInitialization (initialization): time 5.057e-05/0.01108, allocations: 221.2 kB / 0.6547 GB, free: 33.64 MB / 0.5262 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001136/0.01119, allocations: 212.9 kB / 0.6549 GB, free: 33.46 MB / 0.5262 GB Notification: Performance of collectPreVariables (initialization): time 2.457e-05/0.01122, allocations: 37.55 kB / 0.6549 GB, free: 33.42 MB / 0.5262 GB Notification: Performance of collectInitialEqns (initialization): time 6e-05/0.01128, allocations: 176.1 kB / 0.6551 GB, free: 33.26 MB / 0.5262 GB Notification: Performance of collectInitialBindings (initialization): time 6.712e-05/0.01134, allocations: 104 kB / 0.6552 GB, free: 33.18 MB / 0.5262 GB Notification: Performance of simplifyInitialFunctions (initialization): time 9.428e-05/0.01144, allocations: 67.05 kB / 0.6552 GB, free: 33.13 MB / 0.5262 GB Notification: Performance of setup shared object (initialization): time 6.95e-05/0.01151, allocations: 0.5049 MB / 0.6557 GB, free: 32.62 MB / 0.5262 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001495/0.01166, allocations: 142.1 kB / 0.6558 GB, free: 32.51 MB / 0.5262 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001987/0.01186, allocations: 255.1 kB / 0.6561 GB, free: 32.25 MB / 0.5262 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0004602/0.01232, allocations: 458.8 kB / 0.6565 GB, free: 31.83 MB / 0.5262 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.079e-06/0.01232, allocations: 4.5 kB / 0.6565 GB, free: 31.82 MB / 0.5262 GB Notification: Performance of matching and sorting (n=47) (initialization): time 0.0005465/0.01287, allocations: 419.7 kB / 0.6569 GB, free: 31.54 MB / 0.5262 GB Notification: Performance of prepare postOptimizeDAE: time 4.692e-05/0.01292, allocations: 94.61 kB / 0.657 GB, free: 31.45 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 9.378e-06/0.01292, allocations: 2.25 kB / 0.657 GB, free: 31.45 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (initialization): time 2.626e-05/0.01295, allocations: 3.938 kB / 0.657 GB, free: 31.45 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002745/0.01323, allocations: 73.95 kB / 0.6571 GB, free: 31.44 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 6.432e-06/0.01323, allocations: 6.297 kB / 0.6571 GB, free: 31.44 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001445/0.01338, allocations: 19.03 kB / 0.6571 GB, free: 31.43 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.436e-05/0.0134, allocations: 8.094 kB / 0.6571 GB, free: 31.43 MB / 0.5262 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 0.0002121/0.01361, allocations: 283.6 kB / 0.6574 GB, free: 31.17 MB / 0.5262 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 4.879e-05/0.01366, allocations: 37.08 kB / 0.6574 GB, free: 31.16 MB / 0.5262 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 4.415e-05/0.01371, allocations: 29.12 kB / 0.6575 GB, free: 31.13 MB / 0.5262 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.777e-06/0.01371, allocations: 2.844 kB / 0.6575 GB, free: 31.13 MB / 0.5262 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 4.438e-06/0.01371, allocations: 6.406 kB / 0.6575 GB, free: 31.13 MB / 0.5262 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.591e-06/0.01372, allocations: 1.438 kB / 0.6575 GB, free: 31.13 MB / 0.5262 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0006758/0.0144, allocations: 0.6643 MB / 0.6581 GB, free: 30.65 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.759e-06/0.0144, allocations: 1.344 kB / 0.6581 GB, free: 30.65 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002145/0.01461, allocations: 50.72 kB / 0.6582 GB, free: 30.64 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (simulation): time 4.358e-06/0.01462, allocations: 1.375 kB / 0.6582 GB, free: 30.64 MB / 0.5262 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.545e-05/0.01464, allocations: 17.92 kB / 0.6582 GB, free: 30.64 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.306e-06/0.01465, allocations: 1.344 kB / 0.6582 GB, free: 30.64 MB / 0.5262 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.723e-06/0.01465, allocations: 0 / 0.6582 GB, free: 30.64 MB / 0.5262 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005238/0.01517, allocations: 0.6238 MB / 0.6588 GB, free: 30.19 MB / 0.5262 GB Notification: Performance of postOpt removeConstants (simulation): time 2.569e-05/0.0152, allocations: 17.55 kB / 0.6588 GB, free: 30.18 MB / 0.5262 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.871e-05/0.01524, allocations: 9.656 kB / 0.6588 GB, free: 30.18 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001384/0.01538, allocations: 18.28 kB / 0.6588 GB, free: 30.17 MB / 0.5262 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 6.918e-05/0.01545, allocations: 26.53 kB / 0.6589 GB, free: 30.17 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.899e-05/0.01546, allocations: 9.688 kB / 0.6589 GB, free: 30.16 MB / 0.5262 GB Notification: Performance of sorting global known variables: time 5.534e-05/0.01552, allocations: 148.7 kB / 0.659 GB, free: 30.04 MB / 0.5262 GB Notification: Performance of sort global known variables: time 1.1e-07/0.01552, allocations: 0 / 0.659 GB, free: 30.04 MB / 0.5262 GB Notification: Performance of remove unused functions: time 0.0003661/0.01589, allocations: 80.91 kB / 0.6591 GB, free: 30.03 MB / 0.5262 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 0.0001081/0.01599, allocations: 114.9 kB / 0.6592 GB, free: 29.94 MB / 0.5262 GB Notification: Performance of simCode: created initialization part: time 0.0003418/0.01634, allocations: 487.2 kB / 0.6597 GB, free: 29.55 MB / 0.5262 GB Notification: Performance of simCode: created event and clocks part: time 2.554e-06/0.01634, allocations: 1.438 kB / 0.6597 GB, free: 29.55 MB / 0.5262 GB Notification: Performance of simCode: created simulation system equations: time 0.000158/0.0165, allocations: 259.1 kB / 0.6599 GB, free: 29.34 MB / 0.5262 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004757/0.01697, allocations: 65.56 kB / 0.66 GB, free: 29.32 MB / 0.5262 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001385/0.01836, allocations: 0.736 MB / 0.6607 GB, free: 28.86 MB / 0.5262 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 4.239e-05/0.0184, allocations: 86.16 kB / 0.6608 GB, free: 28.79 MB / 0.5262 GB Notification: Performance of simCode: alias equations: time 8.855e-05/0.01849, allocations: 24.17 kB / 0.6608 GB, free: 28.78 MB / 0.5262 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001504/0.01864, allocations: 149.4 kB / 0.661 GB, free: 28.71 MB / 0.5262 GB Notification: Performance of SimCode: time 8.52e-07/0.01864, allocations: 0 / 0.661 GB, free: 28.71 MB / 0.5262 GB Notification: Performance of Templates: time 0.004871/0.02351, allocations: 3.746 MB / 0.6646 GB, free: 28.34 MB / 0.5262 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 -abortSlowSimulation -alarm=240 -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 4.765022857114673]