Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.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 0.001062/0.001062, allocations: 92.2 kB / 20.19 MB, free: 4.359 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 0.001007/0.001007, allocations: 173 kB / 23.49 MB, free: 1.055 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 1.027/1.027, allocations: 177.1 MB / 203.8 MB, free: 5.602 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 1.666/1.666, allocations: 273.5 MB / 0.5213 GB, free: 14.83 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.PKTwoCompartmentModel,tolerance=1e-06,outputFormat="empty",numberOfIntervals=500,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel") translateModel(Pharmacolibrary.DevModels.PKTwoCompartmentModel,tolerance=1e-06,outputFormat="empty",numberOfIntervals=500,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel") [Timeout 660] "Notification: Performance of FrontEnd - loaded program: time 1.513e-06/1.513e-06, allocations: 0 / 0.6469 GB, free: 38.63 MB / 0.5262 GB Notification: Performance of FrontEnd - Absyn->SCode: time 2.094e-05/2.245e-05, allocations: 5.547 kB / 0.647 GB, free: 38.63 MB / 0.5262 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.PKTwoCompartmentModel): time 0.002247/0.00227, allocations: 2.395 MB / 0.6493 GB, free: 37.07 MB / 0.5262 GB Notification: Performance of NFInst.instExpressions: time 0.0006604/0.00293, allocations: 0.6106 MB / 0.6499 GB, free: 36.67 MB / 0.5262 GB Notification: Performance of NFInst.updateImplicitVariability: time 7.007e-05/0.003, allocations: 2.719 kB / 0.6499 GB, free: 36.67 MB / 0.5262 GB Notification: Performance of NFTyping.typeComponents: time 5.096e-05/0.003051, allocations: 25.69 kB / 0.6499 GB, free: 36.65 MB / 0.5262 GB Notification: Performance of NFTyping.typeBindings: time 0.0001682/0.003219, allocations: 81.19 kB / 0.65 GB, free: 36.62 MB / 0.5262 GB Notification: Performance of NFTyping.typeClassSections: time 0.0001576/0.003377, allocations: 68.38 kB / 0.6501 GB, free: 36.58 MB / 0.5262 GB Notification: Performance of NFFlatten.flatten: time 0.0002096/0.003586, allocations: 295.3 kB / 0.6503 GB, free: 36.46 MB / 0.5262 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001252/0.003711, allocations: 61.48 kB / 0.6504 GB, free: 36.42 MB / 0.5262 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0001487/0.00386, allocations: 156 kB / 0.6505 GB, free: 36.36 MB / 0.5262 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001162/0.003976, allocations: 84.48 kB / 0.6506 GB, free: 36.34 MB / 0.5262 GB Notification: Performance of NFPackage.collectConstants: time 3.143e-05/0.004008, allocations: 21.31 kB / 0.6506 GB, free: 36.34 MB / 0.5262 GB Notification: Performance of NFFlatten.collectFunctions: time 2.53e-05/0.004033, allocations: 22.91 kB / 0.6507 GB, free: 36.34 MB / 0.5262 GB Notification: Performance of NFScalarize.scalarize: time 3.847e-05/0.004072, allocations: 53.81 kB / 0.6507 GB, free: 36.3 MB / 0.5262 GB Notification: Performance of NFVerifyModel.verify: time 7.841e-05/0.00415, allocations: 86.36 kB / 0.6508 GB, free: 36.27 MB / 0.5262 GB Notification: Performance of NFConvertDAE.convert: time 0.0001872/0.004337, allocations: 185 kB / 0.651 GB, free: 36.18 MB / 0.5262 GB Notification: Performance of FrontEnd - DAE generated: time 1.893e-06/0.004339, allocations: 3.938 kB / 0.651 GB, free: 36.17 MB / 0.5262 GB Notification: Performance of FrontEnd: time 1.112e-06/0.00434, allocations: 0 / 0.651 GB, free: 36.17 MB / 0.5262 GB Notification: Performance of Transformations before backend: time 4.589e-06/0.004345, allocations: 0 / 0.651 GB, free: 36.17 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 0.0005661/0.004911, allocations: 0.6153 MB / 0.6516 GB, free: 35.62 MB / 0.5262 GB Notification: Performance of prepare preOptimizeDAE: time 3.222e-05/0.004943, allocations: 10.34 kB / 0.6516 GB, free: 35.62 MB / 0.5262 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 6.626e-05/0.005009, allocations: 42.14 kB / 0.6516 GB, free: 35.6 MB / 0.5262 GB Notification: Performance of preOpt evaluateParameters (simulation): time 9.254e-05/0.005102, allocations: 141.5 kB / 0.6518 GB, free: 35.45 MB / 0.5262 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.61e-05/0.005118, allocations: 12.47 kB / 0.6518 GB, free: 35.45 MB / 0.5262 GB Notification: Performance of preOpt expandDerOperator (simulation): time 3.528e-05/0.005153, allocations: 27.42 kB / 0.6518 GB, free: 35.43 MB / 0.5262 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002353/0.005388, allocations: 215.9 kB / 0.652 GB, free: 35.29 MB / 0.5262 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.366e-05/0.005402, allocations: 2 kB / 0.652 GB, free: 35.29 MB / 0.5262 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.669e-05/0.005419, allocations: 7.688 kB / 0.652 GB, free: 35.29 MB / 0.5262 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.568e-06/0.005428, allocations: 5.75 kB / 0.652 GB, free: 35.29 MB / 0.5262 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001505/0.005579, allocations: 157 kB / 0.6522 GB, free: 35.21 MB / 0.5262 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0005377/0.006117, allocations: 0.4964 MB / 0.6527 GB, free: 34.84 MB / 0.5262 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0001992/0.006316, allocations: 184.9 kB / 0.6528 GB, free: 34.71 MB / 0.5262 GB Notification: Performance of preOpt resolveLoops (simulation): time 8.074e-05/0.006397, allocations: 110.1 kB / 0.6529 GB, free: 34.63 MB / 0.5262 GB Notification: Performance of preOpt evalFunc (simulation): time 1.054e-05/0.006407, allocations: 5.75 kB / 0.653 GB, free: 34.63 MB / 0.5262 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002101/0.006617, allocations: 323.7 kB / 0.6533 GB, free: 34.37 MB / 0.5262 GB Notification: Performance of pre-optimization done (n=31): time 1.824e-06/0.006619, allocations: 0 / 0.6533 GB, free: 34.37 MB / 0.5262 GB Notification: Performance of matching and sorting (n=33): time 0.0009193/0.007538, allocations: 0.9121 MB / 0.6541 GB, free: 33.72 MB / 0.5262 GB Notification: Performance of inlineWhenForInitialization (initialization): time 4.912e-05/0.007587, allocations: 217.6 kB / 0.6544 GB, free: 33.46 MB / 0.5262 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.000102/0.007689, allocations: 220.2 kB / 0.6546 GB, free: 33.29 MB / 0.5262 GB Notification: Performance of collectPreVariables (initialization): time 1.529e-05/0.007705, allocations: 35.23 kB / 0.6546 GB, free: 33.25 MB / 0.5262 GB Notification: Performance of collectInitialEqns (initialization): time 4.792e-05/0.007753, allocations: 171.1 kB / 0.6548 GB, free: 33.09 MB / 0.5262 GB Notification: Performance of collectInitialBindings (initialization): time 4.663e-05/0.007799, allocations: 110.6 kB / 0.6549 GB, free: 33 MB / 0.5262 GB Notification: Performance of simplifyInitialFunctions (initialization): time 6.245e-05/0.007862, allocations: 67.73 kB / 0.6549 GB, free: 32.96 MB / 0.5262 GB Notification: Performance of setup shared object (initialization): time 5.072e-05/0.007912, allocations: 0.5057 MB / 0.6554 GB, free: 32.46 MB / 0.5262 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001067/0.008019, allocations: 149.3 kB / 0.6556 GB, free: 32.34 MB / 0.5262 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001271/0.008146, allocations: 263.3 kB / 0.6558 GB, free: 32.07 MB / 0.5262 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0002992/0.008445, allocations: 493.2 kB / 0.6563 GB, free: 31.64 MB / 0.5262 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.224e-06/0.008448, allocations: 0.5312 kB / 0.6563 GB, free: 31.64 MB / 0.5262 GB Notification: Performance of matching and sorting (n=48) (initialization): time 0.0003655/0.008813, allocations: 453.7 kB / 0.6567 GB, free: 31.34 MB / 0.5262 GB Notification: Performance of prepare postOptimizeDAE: time 3.043e-05/0.008844, allocations: 88.8 kB / 0.6568 GB, free: 31.25 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.7e-06/0.008849, allocations: 2.719 kB / 0.6568 GB, free: 31.25 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.514e-05/0.008864, allocations: 4.312 kB / 0.6568 GB, free: 31.25 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001778/0.009042, allocations: 78.7 kB / 0.6569 GB, free: 31.23 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 7.694e-06/0.00905, allocations: 7.125 kB / 0.6569 GB, free: 31.23 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 8.872e-05/0.009139, allocations: 14.06 kB / 0.6569 GB, free: 31.23 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.556e-05/0.009154, allocations: 15.38 kB / 0.6569 GB, free: 31.23 MB / 0.5262 GB Warning: Assuming fixed start value for the following 10 variables: periodicDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true ) \"Total dose adminitrated by this source\" type: Real periodicDose.variableDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true ) \"Total dose adminitrated by this source\" type: Real intestine.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real blood.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real intestine.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real intestine.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real blood.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real blood.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real blood.rising:DISCRETE(fixed = true protected = true ) type: Boolean intestine.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 ($PRE.intestine.Cmin,intestine.Cmin,$PRE.intestine.Cmax,intestine.Cmax,$PRE.blood.Cmin,blood.Cmin,$PRE.blood.Cmax,blood.Cmax,$PRE.blood.rising,$PRE.intestine.rising,$PRE.periodicDose.pulse.count,$PRE.periodicDose.pulse.T_start,blood.rising,intestine.rising,periodicDose.pulse.count,periodicDose.pulse.T_start,$whenCondition5,$whenCondition4,$whenCondition3,$whenCondition2,$whenCondition1) * Number of discrete states: 0 () * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for initialization (45): * Single equations (assignments): 42 * 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 0.0001617/0.009316, allocations: 280.4 kB / 0.6572 GB, free: 30.97 MB / 0.5262 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 3.565e-05/0.009352, allocations: 40.58 kB / 0.6572 GB, free: 30.95 MB / 0.5262 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.402e-05/0.009386, allocations: 28.59 kB / 0.6573 GB, free: 30.93 MB / 0.5262 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.276e-06/0.009389, allocations: 3.406 kB / 0.6573 GB, free: 30.93 MB / 0.5262 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 3.357e-06/0.009392, allocations: 0 / 0.6573 GB, free: 30.93 MB / 0.5262 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.988e-06/0.009396, allocations: 0 / 0.6573 GB, free: 30.93 MB / 0.5262 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0006482/0.01004, allocations: 0.7227 MB / 0.658 GB, free: 30.41 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.515e-06/0.01005, allocations: 4.469 kB / 0.658 GB, free: 30.41 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001779/0.01022, allocations: 48.67 kB / 0.658 GB, free: 30.4 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (simulation): time 3.597e-06/0.01023, allocations: 1.125 kB / 0.658 GB, free: 30.4 MB / 0.5262 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.824e-05/0.01025, allocations: 8.969 kB / 0.658 GB, free: 30.4 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.955e-06/0.01025, allocations: 4.594 kB / 0.658 GB, free: 30.4 MB / 0.5262 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.363e-06/0.01025, allocations: 0.5625 kB / 0.658 GB, free: 30.4 MB / 0.5262 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005041/0.01076, allocations: 0.6646 MB / 0.6587 GB, free: 29.93 MB / 0.5262 GB Notification: Performance of postOpt removeConstants (simulation): time 2.072e-05/0.01078, allocations: 13.53 kB / 0.6587 GB, free: 29.93 MB / 0.5262 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.084e-05/0.01081, allocations: 9.688 kB / 0.6587 GB, free: 29.92 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.963e-05/0.01089, allocations: 17.47 kB / 0.6587 GB, free: 29.92 MB / 0.5262 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 6.453e-05/0.01095, allocations: 28 kB / 0.6587 GB, free: 29.91 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.432e-05/0.01097, allocations: 11.06 kB / 0.6588 GB, free: 29.91 MB / 0.5262 GB Notification: Performance of sorting global known variables: time 5.109e-05/0.01102, allocations: 155.6 kB / 0.6589 GB, free: 29.79 MB / 0.5262 GB Notification: Performance of sort global known variables: time 7.1e-08/0.01102, allocations: 0 / 0.6589 GB, free: 29.79 MB / 0.5262 GB Notification: Performance of remove unused functions: time 0.0002107/0.01123, allocations: 75.34 kB / 0.659 GB, free: 29.77 MB / 0.5262 GB Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 1 * Number of states: 6 (periodicDose.TotalCumulativeMass,periodicDose.variableDose.TotalCumulativeMass,intestine.C,intestine.AUC,blood.C,blood.AUC) * Number of discrete variables: 13 ($whenCondition1,$whenCondition2,$whenCondition3,$whenCondition4,$whenCondition5,periodicDose.pulse.T_start,periodicDose.pulse.count,intestine.Cmax,intestine.Cmin,intestine.rising,blood.Cmax,blood.Cmin,blood.rising) * Number of discrete states: 11 (periodicDose.pulse.count,blood.Cmin,$whenCondition3,blood.Cmax,$whenCondition2,blood.rising,intestine.Cmin,$whenCondition5,intestine.Cmax,$whenCondition4,intestine.rising) * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for simulation (27): * Single equations (assignments): 23 * 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 7.896e-05/0.01131, allocations: 121.5 kB / 0.6591 GB, free: 29.68 MB / 0.5262 GB Notification: Performance of simCode: created initialization part: time 0.0003104/0.01162, allocations: 497 kB / 0.6596 GB, free: 29.29 MB / 0.5262 GB Notification: Performance of simCode: created event and clocks part: time 1.843e-06/0.01162, allocations: 1.375 kB / 0.6596 GB, free: 29.29 MB / 0.5262 GB Notification: Performance of simCode: created simulation system equations: time 0.0001344/0.01175, allocations: 274.2 kB / 0.6598 GB, free: 29.06 MB / 0.5262 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002769/0.01203, allocations: 72.8 kB / 0.6599 GB, free: 29.04 MB / 0.5262 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001326/0.01336, allocations: 0.749 MB / 0.6606 GB, free: 28.56 MB / 0.5262 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 4.542e-05/0.0134, allocations: 85.42 kB / 0.6607 GB, free: 28.49 MB / 0.5262 GB Notification: Performance of simCode: alias equations: time 5.967e-05/0.01346, allocations: 21.19 kB / 0.6607 GB, free: 28.48 MB / 0.5262 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 4.468e-05/0.01351, allocations: 25.5 kB / 0.6608 GB, free: 28.48 MB / 0.5262 GB Notification: Performance of SimCode: time 9.22e-07/0.01351, allocations: 0 / 0.6608 GB, free: 28.48 MB / 0.5262 GB Notification: Performance of Templates: time 0.004764/0.01827, allocations: 3.436 MB / 0.6641 GB, free: 28.18 MB / 0.5262 GB " [Timeout remaining time 660] make -j1 -f Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.makefile [Timeout 660] (rm -f Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.sim & ./Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel -abortSlowSimulation -alarm=240 -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 4.860173071036115]