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 0.001268/0.001268, allocations: 93.16 kB / 19.65 MB, free: 288 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 0.0009638/0.0009638, allocations: 168.9 kB / 23.01 MB, free: 1.562 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 0.9477/0.9477, allocations: 177.1 MB / 203.4 MB, free: 5.102 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 1.622/1.622, allocations: 273.5 MB / 0.5209 GB, free: 14.85 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 1.362e-06/1.362e-06, allocations: 0 / 0.6469 GB, free: 38.69 MB / 0.5262 GB Notification: Performance of FrontEnd - Absyn->SCode: time 1.986e-05/2.122e-05, allocations: 4.422 kB / 0.6469 GB, free: 38.68 MB / 0.5262 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.PKTwoCompartmentModelOral): time 0.002603/0.002624, allocations: 2.394 MB / 0.6493 GB, free: 37.13 MB / 0.5262 GB Notification: Performance of NFInst.instExpressions: time 0.0008892/0.003514, allocations: 0.6203 MB / 0.6499 GB, free: 36.72 MB / 0.5262 GB Notification: Performance of NFInst.updateImplicitVariability: time 7.975e-05/0.003593, allocations: 3.875 kB / 0.6499 GB, free: 36.72 MB / 0.5262 GB Notification: Performance of NFTyping.typeComponents: time 6.606e-05/0.003659, allocations: 27.83 kB / 0.6499 GB, free: 36.71 MB / 0.5262 GB Notification: Performance of NFTyping.typeBindings: time 0.0002062/0.003865, allocations: 75.36 kB / 0.65 GB, free: 36.68 MB / 0.5262 GB Notification: Performance of NFTyping.typeClassSections: time 0.0001982/0.004064, allocations: 66.95 kB / 0.6501 GB, free: 36.64 MB / 0.5262 GB Notification: Performance of NFFlatten.flatten: time 0.0002474/0.004311, allocations: 296.1 kB / 0.6503 GB, free: 36.52 MB / 0.5262 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001502/0.004461, allocations: 57.86 kB / 0.6504 GB, free: 36.48 MB / 0.5262 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0002013/0.004663, allocations: 152.5 kB / 0.6505 GB, free: 36.43 MB / 0.5262 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001598/0.004822, allocations: 90.23 kB / 0.6506 GB, free: 36.39 MB / 0.5262 GB Notification: Performance of NFPackage.collectConstants: time 3.707e-05/0.004859, allocations: 23.94 kB / 0.6506 GB, free: 36.39 MB / 0.5262 GB Notification: Performance of NFFlatten.collectFunctions: time 3.071e-05/0.00489, allocations: 21.75 kB / 0.6507 GB, free: 36.39 MB / 0.5262 GB Notification: Performance of NFScalarize.scalarize: time 3.697e-05/0.004927, allocations: 46.53 kB / 0.6507 GB, free: 36.36 MB / 0.5262 GB Notification: Performance of NFVerifyModel.verify: time 8.562e-05/0.005013, allocations: 89.47 kB / 0.6508 GB, free: 36.33 MB / 0.5262 GB Notification: Performance of NFConvertDAE.convert: time 0.0002123/0.005225, allocations: 181.9 kB / 0.651 GB, free: 36.24 MB / 0.5262 GB Notification: Performance of FrontEnd - DAE generated: time 1.913e-06/0.005227, allocations: 0 / 0.651 GB, free: 36.24 MB / 0.5262 GB Notification: Performance of FrontEnd: time 8.11e-07/0.005228, allocations: 0 / 0.651 GB, free: 36.24 MB / 0.5262 GB Notification: Performance of Transformations before backend: time 5.3e-06/0.005233, allocations: 0 / 0.651 GB, free: 36.24 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 0.0006603/0.005893, allocations: 0.6159 MB / 0.6516 GB, free: 35.68 MB / 0.5262 GB Notification: Performance of prepare preOptimizeDAE: time 4.446e-05/0.005938, allocations: 13.38 kB / 0.6516 GB, free: 35.68 MB / 0.5262 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 7.853e-05/0.006016, allocations: 43.55 kB / 0.6516 GB, free: 35.66 MB / 0.5262 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001099/0.006126, allocations: 140.8 kB / 0.6518 GB, free: 35.51 MB / 0.5262 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.068e-05/0.006147, allocations: 16.12 kB / 0.6518 GB, free: 35.51 MB / 0.5262 GB Notification: Performance of preOpt expandDerOperator (simulation): time 4.104e-05/0.006188, allocations: 25.95 kB / 0.6518 GB, free: 35.5 MB / 0.5262 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002569/0.006445, allocations: 221.4 kB / 0.652 GB, free: 35.35 MB / 0.5262 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.568e-05/0.00646, allocations: 1.406 kB / 0.652 GB, free: 35.35 MB / 0.5262 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.704e-05/0.006478, allocations: 5.812 kB / 0.652 GB, free: 35.35 MB / 0.5262 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.728e-06/0.006487, allocations: 6.438 kB / 0.652 GB, free: 35.35 MB / 0.5262 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002026/0.00669, allocations: 153.5 kB / 0.6522 GB, free: 35.27 MB / 0.5262 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0006505/0.00734, allocations: 0.4934 MB / 0.6526 GB, free: 34.9 MB / 0.5262 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0001843/0.007525, allocations: 170.6 kB / 0.6528 GB, free: 34.78 MB / 0.5262 GB Notification: Performance of preOpt resolveLoops (simulation): time 7.851e-05/0.007603, allocations: 107.1 kB / 0.6529 GB, free: 34.7 MB / 0.5262 GB Notification: Performance of preOpt evalFunc (simulation): time 1.324e-05/0.007616, allocations: 8.875 kB / 0.6529 GB, free: 34.69 MB / 0.5262 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002229/0.007839, allocations: 318.4 kB / 0.6532 GB, free: 34.43 MB / 0.5262 GB Notification: Performance of pre-optimization done (n=30): time 1.583e-06/0.007841, allocations: 0 / 0.6532 GB, free: 34.43 MB / 0.5262 GB Notification: Performance of matching and sorting (n=32): time 0.001202/0.009043, allocations: 0.9055 MB / 0.6541 GB, free: 33.79 MB / 0.5262 GB Notification: Performance of inlineWhenForInitialization (initialization): time 7.565e-05/0.009119, allocations: 220.5 kB / 0.6543 GB, free: 33.54 MB / 0.5262 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001311/0.00925, allocations: 217.9 kB / 0.6545 GB, free: 33.36 MB / 0.5262 GB Notification: Performance of collectPreVariables (initialization): time 2.045e-05/0.00927, allocations: 37.08 kB / 0.6546 GB, free: 33.32 MB / 0.5262 GB Notification: Performance of collectInitialEqns (initialization): time 6.788e-05/0.009338, allocations: 172 kB / 0.6547 GB, free: 33.16 MB / 0.5262 GB Notification: Performance of collectInitialBindings (initialization): time 5.582e-05/0.009394, allocations: 103.1 kB / 0.6548 GB, free: 33.08 MB / 0.5262 GB Notification: Performance of simplifyInitialFunctions (initialization): time 8.037e-05/0.009474, allocations: 69.66 kB / 0.6549 GB, free: 33.03 MB / 0.5262 GB Notification: Performance of setup shared object (initialization): time 6.921e-05/0.009544, allocations: 0.5028 MB / 0.6554 GB, free: 32.53 MB / 0.5262 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001173/0.009661, allocations: 157.3 kB / 0.6555 GB, free: 32.4 MB / 0.5262 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.000142/0.009803, allocations: 260.8 kB / 0.6558 GB, free: 32.14 MB / 0.5262 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0004007/0.0102, allocations: 482.2 kB / 0.6562 GB, free: 31.71 MB / 0.5262 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.244e-06/0.01021, allocations: 0 / 0.6562 GB, free: 31.71 MB / 0.5262 GB Notification: Performance of matching and sorting (n=47) (initialization): time 0.0005018/0.01071, allocations: 443.1 kB / 0.6567 GB, free: 31.42 MB / 0.5262 GB Notification: Performance of prepare postOptimizeDAE: time 4.397e-05/0.01075, allocations: 89.52 kB / 0.6568 GB, free: 31.32 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 9.307e-06/0.01076, allocations: 2.25 kB / 0.6568 GB, free: 31.32 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (initialization): time 2.51e-05/0.01079, allocations: 8.609 kB / 0.6568 GB, free: 31.32 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002327/0.01102, allocations: 67.59 kB / 0.6568 GB, free: 31.32 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.433e-05/0.01103, allocations: 7.875 kB / 0.6568 GB, free: 31.31 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001006/0.01113, allocations: 22.17 kB / 0.6569 GB, free: 31.3 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.747e-05/0.01116, allocations: 11.47 kB / 0.6569 GB, free: 31.3 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 0.000207/0.01137, allocations: 287.7 kB / 0.6571 GB, free: 31.05 MB / 0.5262 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 3.57e-05/0.0114, allocations: 32.47 kB / 0.6572 GB, free: 31.04 MB / 0.5262 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.254e-05/0.01144, allocations: 25.86 kB / 0.6572 GB, free: 31.02 MB / 0.5262 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.966e-06/0.01144, allocations: 2.906 kB / 0.6572 GB, free: 31.02 MB / 0.5262 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 5.751e-06/0.01145, allocations: 0 / 0.6572 GB, free: 31.02 MB / 0.5262 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.719e-06/0.01145, allocations: 3.781 kB / 0.6572 GB, free: 31.02 MB / 0.5262 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005584/0.01201, allocations: 0.7186 MB / 0.6579 GB, free: 30.49 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.414e-06/0.01201, allocations: 1.469 kB / 0.6579 GB, free: 30.49 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001681/0.01218, allocations: 51.38 kB / 0.658 GB, free: 30.48 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (simulation): time 5.23e-06/0.01218, allocations: 1.5 kB / 0.658 GB, free: 30.48 MB / 0.5262 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.095e-05/0.01221, allocations: 14.28 kB / 0.658 GB, free: 30.48 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.855e-06/0.01221, allocations: 1.5 kB / 0.658 GB, free: 30.48 MB / 0.5262 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.192e-06/0.01221, allocations: 0 / 0.658 GB, free: 30.48 MB / 0.5262 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004969/0.01271, allocations: 0.65 MB / 0.6586 GB, free: 30.02 MB / 0.5262 GB Notification: Performance of postOpt removeConstants (simulation): time 2.272e-05/0.01273, allocations: 13.5 kB / 0.6586 GB, free: 30.01 MB / 0.5262 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.519e-05/0.01276, allocations: 9.562 kB / 0.6586 GB, free: 30.01 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 8.653e-05/0.01285, allocations: 20.84 kB / 0.6586 GB, free: 30 MB / 0.5262 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 8.319e-05/0.01293, allocations: 26.56 kB / 0.6587 GB, free: 30 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.636e-05/0.01295, allocations: 11 kB / 0.6587 GB, free: 30 MB / 0.5262 GB Notification: Performance of sorting global known variables: time 6.933e-05/0.01302, allocations: 158.6 kB / 0.6588 GB, free: 29.87 MB / 0.5262 GB Notification: Performance of sort global known variables: time 5e-08/0.01302, allocations: 5.312 kB / 0.6588 GB, free: 29.86 MB / 0.5262 GB Notification: Performance of remove unused functions: time 0.0002276/0.01325, allocations: 75.72 kB / 0.6589 GB, free: 29.86 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 0.0001018/0.01335, allocations: 107.9 kB / 0.659 GB, free: 29.77 MB / 0.5262 GB Notification: Performance of simCode: created initialization part: time 0.0003813/0.01373, allocations: 0.4905 MB / 0.6595 GB, free: 29.37 MB / 0.5262 GB Notification: Performance of simCode: created event and clocks part: time 2.815e-06/0.01373, allocations: 4 kB / 0.6595 GB, free: 29.36 MB / 0.5262 GB Notification: Performance of simCode: created simulation system equations: time 0.0001634/0.0139, allocations: 270.8 kB / 0.6598 GB, free: 29.15 MB / 0.5262 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003013/0.0142, allocations: 62.17 kB / 0.6598 GB, free: 29.14 MB / 0.5262 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001479/0.01568, allocations: 0.7543 MB / 0.6606 GB, free: 28.65 MB / 0.5262 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 4.951e-05/0.01573, allocations: 84.89 kB / 0.6606 GB, free: 28.58 MB / 0.5262 GB Notification: Performance of simCode: alias equations: time 7.751e-05/0.0158, allocations: 25.8 kB / 0.6607 GB, free: 28.57 MB / 0.5262 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 5.387e-05/0.01586, allocations: 26.5 kB / 0.6607 GB, free: 28.56 MB / 0.5262 GB Notification: Performance of SimCode: time 7.22e-07/0.01586, allocations: 0 / 0.6607 GB, free: 28.56 MB / 0.5262 GB Notification: Performance of Templates: time 0.005412/0.02127, allocations: 3.415 MB / 0.664 GB, free: 28.27 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: 4.974072969052941]