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 0.0009291/0.0009291, allocations: 93.06 kB / 19.65 MB, free: 280 kB / 13.93 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 0.001062/0.001062, allocations: 169 kB / 23.03 MB, free: 1.547 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 0.9571/0.9571, allocations: 177.1 MB / 203.4 MB, free: 5.637 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 1.614/1.614, allocations: 273.5 MB / 0.5209 GB, free: 14.8 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 / 0.6469 GB, free: 38.5 MB / 0.5262 GB Notification: Performance of FrontEnd - Absyn->SCode: time 1.742e-05/1.888e-05, allocations: 3.594 kB / 0.647 GB, free: 38.49 MB / 0.5262 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.PKTwoCompartmentModelOral): time 0.00332/0.003339, allocations: 2.39 MB / 0.6493 GB, free: 36.94 MB / 0.5262 GB Notification: Performance of NFInst.instExpressions: time 0.001138/0.004478, allocations: 0.62 MB / 0.6499 GB, free: 36.54 MB / 0.5262 GB Notification: Performance of NFInst.updateImplicitVariability: time 0.0001068/0.004585, allocations: 3.594 kB / 0.6499 GB, free: 36.54 MB / 0.5262 GB Notification: Performance of NFTyping.typeComponents: time 7.905e-05/0.004664, allocations: 27.94 kB / 0.6499 GB, free: 36.52 MB / 0.5262 GB Notification: Performance of NFTyping.typeBindings: time 0.0002702/0.004934, allocations: 76.3 kB / 0.65 GB, free: 36.49 MB / 0.5262 GB Notification: Performance of NFTyping.typeClassSections: time 0.0002345/0.005168, allocations: 67.06 kB / 0.6501 GB, free: 36.45 MB / 0.5262 GB Notification: Performance of NFFlatten.flatten: time 0.0003559/0.005524, allocations: 294.4 kB / 0.6503 GB, free: 36.33 MB / 0.5262 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001782/0.005702, allocations: 61.02 kB / 0.6504 GB, free: 36.29 MB / 0.5262 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0002641/0.005966, allocations: 153.9 kB / 0.6505 GB, free: 36.23 MB / 0.5262 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001748/0.006141, allocations: 86.97 kB / 0.6506 GB, free: 36.2 MB / 0.5262 GB Notification: Performance of NFPackage.collectConstants: time 5.33e-05/0.006195, allocations: 23.06 kB / 0.6506 GB, free: 36.2 MB / 0.5262 GB Notification: Performance of NFFlatten.collectFunctions: time 4.917e-05/0.006244, allocations: 26.91 kB / 0.6507 GB, free: 36.2 MB / 0.5262 GB Notification: Performance of NFScalarize.scalarize: time 5.264e-05/0.006296, allocations: 52.56 kB / 0.6507 GB, free: 36.16 MB / 0.5262 GB Notification: Performance of NFVerifyModel.verify: time 0.0001138/0.00641, allocations: 83.91 kB / 0.6508 GB, free: 36.13 MB / 0.5262 GB Notification: Performance of NFConvertDAE.convert: time 0.000292/0.006702, allocations: 171 kB / 0.651 GB, free: 36.05 MB / 0.5262 GB Notification: Performance of FrontEnd - DAE generated: time 3.427e-06/0.006706, allocations: 6.781 kB / 0.651 GB, free: 36.05 MB / 0.5262 GB Notification: Performance of FrontEnd: time 5.41e-07/0.006706, allocations: 0 / 0.651 GB, free: 36.05 MB / 0.5262 GB Notification: Performance of Transformations before backend: time 6.703e-06/0.006713, allocations: 0 / 0.651 GB, free: 36.05 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 0.000842/0.007555, allocations: 0.6241 MB / 0.6516 GB, free: 35.48 MB / 0.5262 GB Notification: Performance of prepare preOptimizeDAE: time 4.164e-05/0.007597, allocations: 7.781 kB / 0.6516 GB, free: 35.48 MB / 0.5262 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001019/0.007698, allocations: 39.45 kB / 0.6516 GB, free: 35.47 MB / 0.5262 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002265/0.007925, allocations: 172.7 kB / 0.6518 GB, free: 35.3 MB / 0.5262 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.62e-05/0.007961, allocations: 19.41 kB / 0.6518 GB, free: 35.3 MB / 0.5262 GB Notification: Performance of preOpt expandDerOperator (simulation): time 4.867e-05/0.00801, allocations: 25.45 kB / 0.6518 GB, free: 35.29 MB / 0.5262 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003691/0.008379, allocations: 219.7 kB / 0.652 GB, free: 35.15 MB / 0.5262 GB Notification: Performance of preOpt findStateOrder (simulation): time 2.204e-05/0.008401, allocations: 1.156 kB / 0.652 GB, free: 35.15 MB / 0.5262 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.305e-05/0.008424, allocations: 4 kB / 0.652 GB, free: 35.14 MB / 0.5262 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.415e-05/0.008438, allocations: 5.156 kB / 0.6521 GB, free: 35.14 MB / 0.5262 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002579/0.008696, allocations: 154.2 kB / 0.6522 GB, free: 35.07 MB / 0.5262 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0008396/0.009536, allocations: 0.4924 MB / 0.6527 GB, free: 34.7 MB / 0.5262 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0002478/0.009783, allocations: 172.4 kB / 0.6528 GB, free: 34.58 MB / 0.5262 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.0001132/0.009897, allocations: 103.4 kB / 0.6529 GB, free: 34.5 MB / 0.5262 GB Notification: Performance of preOpt evalFunc (simulation): time 1.565e-05/0.009912, allocations: 11.17 kB / 0.653 GB, free: 34.49 MB / 0.5262 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002827/0.01019, allocations: 318.7 kB / 0.6533 GB, free: 34.23 MB / 0.5262 GB Notification: Performance of pre-optimization done (n=30): time 2.525e-06/0.0102, allocations: 0 / 0.6533 GB, free: 34.23 MB / 0.5262 GB Notification: Performance of matching and sorting (n=32): time 0.001229/0.01143, allocations: 0.8945 MB / 0.6541 GB, free: 33.59 MB / 0.5262 GB Notification: Performance of inlineWhenForInitialization (initialization): time 5.836e-05/0.01148, allocations: 223.7 kB / 0.6543 GB, free: 33.34 MB / 0.5262 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001638/0.01165, allocations: 217 kB / 0.6546 GB, free: 33.16 MB / 0.5262 GB Notification: Performance of collectPreVariables (initialization): time 2.795e-05/0.01168, allocations: 33.55 kB / 0.6546 GB, free: 33.12 MB / 0.5262 GB Notification: Performance of collectInitialEqns (initialization): time 6.708e-05/0.01174, allocations: 179.1 kB / 0.6548 GB, free: 32.96 MB / 0.5262 GB Notification: Performance of collectInitialBindings (initialization): time 7.231e-05/0.01182, allocations: 102.5 kB / 0.6549 GB, free: 32.88 MB / 0.5262 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001142/0.01193, allocations: 69.11 kB / 0.6549 GB, free: 32.83 MB / 0.5262 GB Notification: Performance of setup shared object (initialization): time 8.242e-05/0.01201, allocations: 0.5063 MB / 0.6554 GB, free: 32.32 MB / 0.5262 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001466/0.01216, allocations: 150.8 kB / 0.6556 GB, free: 32.2 MB / 0.5262 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001743/0.01233, allocations: 259.5 kB / 0.6558 GB, free: 31.94 MB / 0.5262 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0004184/0.01275, allocations: 481.5 kB / 0.6563 GB, free: 31.51 MB / 0.5262 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.835e-06/0.01275, allocations: 0 / 0.6563 GB, free: 31.51 MB / 0.5262 GB Notification: Performance of matching and sorting (n=47) (initialization): time 0.0005872/0.01334, allocations: 446.8 kB / 0.6567 GB, free: 31.22 MB / 0.5262 GB Notification: Performance of prepare postOptimizeDAE: time 4.842e-05/0.01339, allocations: 89.17 kB / 0.6568 GB, free: 31.12 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.997e-06/0.0134, allocations: 6.094 kB / 0.6568 GB, free: 31.12 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.997e-05/0.01342, allocations: 3.938 kB / 0.6568 GB, free: 31.12 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003221/0.01374, allocations: 78.38 kB / 0.6569 GB, free: 31.11 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.45e-05/0.01376, allocations: 7.75 kB / 0.6569 GB, free: 31.11 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001456/0.0139, allocations: 17.09 kB / 0.6569 GB, free: 31.11 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 3.82e-05/0.01394, allocations: 15.19 kB / 0.6569 GB, free: 31.1 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 0.0002292/0.01417, allocations: 289.5 kB / 0.6572 GB, free: 30.84 MB / 0.5262 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 6.668e-05/0.01424, allocations: 28.41 kB / 0.6572 GB, free: 30.83 MB / 0.5262 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 4.61e-05/0.01428, allocations: 24.75 kB / 0.6572 GB, free: 30.81 MB / 0.5262 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 7.745e-06/0.01429, allocations: 6.188 kB / 0.6572 GB, free: 30.81 MB / 0.5262 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 5.09e-06/0.01429, allocations: 0.5312 kB / 0.6572 GB, free: 30.81 MB / 0.5262 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.34e-06/0.0143, allocations: 0.5 kB / 0.6572 GB, free: 30.81 MB / 0.5262 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005891/0.01489, allocations: 0.7226 MB / 0.6579 GB, free: 30.28 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.624e-06/0.01489, allocations: 1.438 kB / 0.6579 GB, free: 30.28 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001508/0.01504, allocations: 47.38 kB / 0.658 GB, free: 30.28 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (simulation): time 3.627e-06/0.01505, allocations: 5.281 kB / 0.658 GB, free: 30.28 MB / 0.5262 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.579e-05/0.01506, allocations: 8.25 kB / 0.658 GB, free: 30.27 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.735e-06/0.01506, allocations: 1.469 kB / 0.658 GB, free: 30.27 MB / 0.5262 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.222e-06/0.01506, allocations: 2.469 kB / 0.658 GB, free: 30.27 MB / 0.5262 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004126/0.01548, allocations: 0.6493 MB / 0.6586 GB, free: 29.82 MB / 0.5262 GB Notification: Performance of postOpt removeConstants (simulation): time 1.776e-05/0.0155, allocations: 17.66 kB / 0.6587 GB, free: 29.81 MB / 0.5262 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.791e-05/0.01552, allocations: 9.5 kB / 0.6587 GB, free: 29.8 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.88e-05/0.0156, allocations: 15.97 kB / 0.6587 GB, free: 29.8 MB / 0.5262 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 6.095e-05/0.01566, allocations: 24.34 kB / 0.6587 GB, free: 29.8 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.433e-05/0.01568, allocations: 14.94 kB / 0.6587 GB, free: 29.79 MB / 0.5262 GB Notification: Performance of sorting global known variables: time 4.907e-05/0.01573, allocations: 158.9 kB / 0.6589 GB, free: 29.66 MB / 0.5262 GB Notification: Performance of sort global known variables: time 7e-08/0.01573, allocations: 3.938 kB / 0.6589 GB, free: 29.66 MB / 0.5262 GB Notification: Performance of remove unused functions: time 0.0002006/0.01593, allocations: 70.12 kB / 0.6589 GB, free: 29.65 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 7.797e-05/0.016, allocations: 125 kB / 0.6591 GB, free: 29.55 MB / 0.5262 GB Notification: Performance of simCode: created initialization part: time 0.0002943/0.0163, allocations: 0.4914 MB / 0.6595 GB, free: 29.16 MB / 0.5262 GB Notification: Performance of simCode: created event and clocks part: time 1.302e-06/0.0163, allocations: 1.375 kB / 0.6595 GB, free: 29.16 MB / 0.5262 GB Notification: Performance of simCode: created simulation system equations: time 0.0001331/0.01643, allocations: 272.1 kB / 0.6598 GB, free: 28.94 MB / 0.5262 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002691/0.0167, allocations: 64.53 kB / 0.6599 GB, free: 28.93 MB / 0.5262 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001269/0.01797, allocations: 0.7426 MB / 0.6606 GB, free: 28.44 MB / 0.5262 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 4.038e-05/0.01801, allocations: 84.75 kB / 0.6607 GB, free: 28.37 MB / 0.5262 GB Notification: Performance of simCode: alias equations: time 6.962e-05/0.01808, allocations: 25.47 kB / 0.6607 GB, free: 28.36 MB / 0.5262 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 4.806e-05/0.01813, allocations: 22.5 kB / 0.6607 GB, free: 28.36 MB / 0.5262 GB Notification: Performance of SimCode: time 5.71e-07/0.01813, allocations: 0 / 0.6607 GB, free: 28.36 MB / 0.5262 GB Notification: Performance of Templates: time 0.004949/0.02308, allocations: 3.595 MB / 0.6642 GB, free: 28.04 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: 4.768707854207605]