Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.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 0.001026/0.001026, 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 0.0009916/0.0009916, allocations: 173 kB / 23.49 MB, free: 1.059 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 0.9507/0.9507, allocations: 177.1 MB / 203.8 MB, free: 5.641 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 1.516/1.516, allocations: 273.5 MB / 0.5213 GB, free: 14.82 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.Examples.PKTwoCompartmentModel,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel") translateModel(Pharmacolibrary.Examples.PKTwoCompartmentModel,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel") [Timeout 660] "Notification: Performance of FrontEnd - loaded program: time 1.303e-06/1.303e-06, allocations: 1.641 kB / 0.647 GB, free: 38.83 MB / 0.5262 GB Notification: Performance of FrontEnd - Absyn->SCode: time 1.203e-05/1.334e-05, allocations: 2.312 kB / 0.647 GB, free: 38.83 MB / 0.5262 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKTwoCompartmentModel): time 0.001898/0.001911, allocations: 2.362 MB / 0.6493 GB, free: 37.29 MB / 0.5262 GB Notification: Performance of NFInst.instExpressions: time 0.0006242/0.002536, allocations: 0.6183 MB / 0.6499 GB, free: 36.88 MB / 0.5262 GB Notification: Performance of NFInst.updateImplicitVariability: time 7.651e-05/0.002612, allocations: 1.656 kB / 0.6499 GB, free: 36.88 MB / 0.5262 GB Notification: Performance of NFTyping.typeComponents: time 0.000104/0.002716, allocations: 26.83 kB / 0.6499 GB, free: 36.86 MB / 0.5262 GB Notification: Performance of NFTyping.typeBindings: time 0.0001344/0.002851, allocations: 76.92 kB / 0.65 GB, free: 36.84 MB / 0.5262 GB Notification: Performance of NFTyping.typeClassSections: time 0.0001557/0.003006, allocations: 64.27 kB / 0.65 GB, free: 36.8 MB / 0.5262 GB Notification: Performance of NFFlatten.flatten: time 0.0002197/0.003226, allocations: 288.2 kB / 0.6503 GB, free: 36.68 MB / 0.5262 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001143/0.00334, allocations: 47.78 kB / 0.6504 GB, free: 36.65 MB / 0.5262 GB Notification: Performance of NFEvalConstants.evaluate: time 0.000123/0.003463, allocations: 150.9 kB / 0.6505 GB, free: 36.59 MB / 0.5262 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001085/0.003572, allocations: 82.66 kB / 0.6506 GB, free: 36.57 MB / 0.5262 GB Notification: Performance of NFPackage.collectConstants: time 3.007e-05/0.003602, allocations: 21.09 kB / 0.6506 GB, free: 36.57 MB / 0.5262 GB Notification: Performance of NFFlatten.collectFunctions: time 2.45e-05/0.003626, allocations: 21.75 kB / 0.6506 GB, free: 36.57 MB / 0.5262 GB Notification: Performance of NFScalarize.scalarize: time 3.432e-05/0.003661, allocations: 49.02 kB / 0.6507 GB, free: 36.54 MB / 0.5262 GB Notification: Performance of NFVerifyModel.verify: time 7.025e-05/0.003731, allocations: 80.8 kB / 0.6507 GB, free: 36.5 MB / 0.5262 GB Notification: Performance of NFConvertDAE.convert: time 0.0001685/0.003899, allocations: 177.7 kB / 0.6509 GB, free: 36.42 MB / 0.5262 GB Notification: Performance of FrontEnd - DAE generated: time 2.034e-06/0.003901, allocations: 1.156 kB / 0.6509 GB, free: 36.42 MB / 0.5262 GB Notification: Performance of FrontEnd: time 5.61e-07/0.003902, allocations: 0 / 0.6509 GB, free: 36.42 MB / 0.5262 GB Notification: Performance of Transformations before backend: time 4.078e-06/0.003906, allocations: 0 / 0.6509 GB, free: 36.42 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: 42 * Number of variables: 42 Notification: Performance of Generate backend data structure: time 0.0005498/0.004456, allocations: 0.6117 MB / 0.6515 GB, free: 35.86 MB / 0.5262 GB Notification: Performance of prepare preOptimizeDAE: time 3.263e-05/0.004488, allocations: 9.594 kB / 0.6515 GB, free: 35.86 MB / 0.5262 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 6.264e-05/0.004551, allocations: 40.05 kB / 0.6516 GB, free: 35.84 MB / 0.5262 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001445/0.004696, allocations: 170.2 kB / 0.6517 GB, free: 35.68 MB / 0.5262 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.461e-05/0.00471, allocations: 15.83 kB / 0.6517 GB, free: 35.68 MB / 0.5262 GB Notification: Performance of preOpt expandDerOperator (simulation): time 3.378e-05/0.004744, allocations: 29.3 kB / 0.6518 GB, free: 35.66 MB / 0.5262 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002241/0.004968, allocations: 209.7 kB / 0.652 GB, free: 35.53 MB / 0.5262 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.378e-05/0.004982, allocations: 6.094 kB / 0.652 GB, free: 35.52 MB / 0.5262 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.483e-05/0.004997, allocations: 5.469 kB / 0.652 GB, free: 35.52 MB / 0.5262 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.476e-06/0.005005, allocations: 4.406 kB / 0.652 GB, free: 35.52 MB / 0.5262 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001446/0.00515, allocations: 149.8 kB / 0.6521 GB, free: 35.45 MB / 0.5262 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0004939/0.005644, allocations: 491.2 kB / 0.6526 GB, free: 35.08 MB / 0.5262 GB Notification: Performance of preOpt comSubExp (simulation): time 0.00017/0.005814, allocations: 173 kB / 0.6528 GB, free: 34.96 MB / 0.5262 GB Notification: Performance of preOpt resolveLoops (simulation): time 8.402e-05/0.005898, allocations: 109.3 kB / 0.6529 GB, free: 34.88 MB / 0.5262 GB Notification: Performance of preOpt evalFunc (simulation): time 9.408e-06/0.005907, allocations: 3.562 kB / 0.6529 GB, free: 34.88 MB / 0.5262 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001925/0.0061, allocations: 315 kB / 0.6532 GB, free: 34.62 MB / 0.5262 GB Notification: Performance of pre-optimization done (n=31): time 1.783e-06/0.006101, allocations: 8.375 kB / 0.6532 GB, free: 34.61 MB / 0.5262 GB Notification: Performance of matching and sorting (n=33): time 0.0008759/0.006977, allocations: 0.9101 MB / 0.6541 GB, free: 33.97 MB / 0.5262 GB Notification: Performance of inlineWhenForInitialization (initialization): time 4.33e-05/0.007021, allocations: 214.7 kB / 0.6543 GB, free: 33.72 MB / 0.5262 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 9.525e-05/0.007116, allocations: 220.8 kB / 0.6545 GB, free: 33.54 MB / 0.5262 GB Notification: Performance of collectPreVariables (initialization): time 1.584e-05/0.007132, allocations: 37.61 kB / 0.6545 GB, free: 33.5 MB / 0.5262 GB Notification: Performance of collectInitialEqns (initialization): time 4.725e-05/0.007179, allocations: 170.1 kB / 0.6547 GB, free: 33.34 MB / 0.5262 GB Notification: Performance of collectInitialBindings (initialization): time 4.535e-05/0.007224, allocations: 109.2 kB / 0.6548 GB, free: 33.26 MB / 0.5262 GB Notification: Performance of simplifyInitialFunctions (initialization): time 7.052e-05/0.007295, allocations: 66.64 kB / 0.6548 GB, free: 33.21 MB / 0.5262 GB Notification: Performance of setup shared object (initialization): time 5.542e-05/0.00735, allocations: 0.5048 MB / 0.6553 GB, free: 32.71 MB / 0.5262 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001251/0.007475, allocations: 154.3 kB / 0.6555 GB, free: 32.59 MB / 0.5262 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001466/0.007622, allocations: 282 kB / 0.6558 GB, free: 32.31 MB / 0.5262 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.00029/0.007912, allocations: 491.1 kB / 0.6562 GB, free: 31.87 MB / 0.5262 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.894e-06/0.007914, allocations: 1.531 kB / 0.6562 GB, free: 31.87 MB / 0.5262 GB Notification: Performance of matching and sorting (n=49) (initialization): time 0.0003624/0.008276, allocations: 457 kB / 0.6567 GB, free: 31.57 MB / 0.5262 GB Notification: Performance of prepare postOptimizeDAE: time 3.481e-05/0.008311, allocations: 98.66 kB / 0.6568 GB, free: 31.47 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.963e-06/0.008318, allocations: 2.75 kB / 0.6568 GB, free: 31.47 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.618e-05/0.008334, allocations: 3.844 kB / 0.6568 GB, free: 31.47 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002212/0.008555, allocations: 74.81 kB / 0.6568 GB, free: 31.46 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.024e-05/0.008566, allocations: 12.73 kB / 0.6568 GB, free: 31.46 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.639e-05/0.008662, allocations: 13.81 kB / 0.6569 GB, free: 31.46 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.428e-05/0.008686, allocations: 16.28 kB / 0.6569 GB, free: 31.45 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 peripheral.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real central.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" 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 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 central.rising:DISCRETE(fixed = true protected = true ) type: Boolean peripheral.rising:DISCRETE(fixed = true protected = true ) type: Boolean Notification: Model statistics after passing the back-end for initialization: * Number of independent subsystems: 10 * Number of states: 0 () * Number of discrete variables: 21 ($PRE.peripheral.Cmin,peripheral.Cmin,$PRE.peripheral.Cmax,peripheral.Cmax,$PRE.central.Cmin,central.Cmin,$PRE.central.Cmax,central.Cmax,$PRE.central.rising,$PRE.peripheral.rising,$PRE.periodicDose.pulse.count,$PRE.periodicDose.pulse.T_start,central.rising,peripheral.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 (46): * Single equations (assignments): 43 * 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 0.0001729/0.008859, allocations: 284.6 kB / 0.6571 GB, free: 31.2 MB / 0.5262 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 4.791e-05/0.008907, allocations: 37.22 kB / 0.6572 GB, free: 31.18 MB / 0.5262 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.503e-05/0.008942, allocations: 31.34 kB / 0.6572 GB, free: 31.16 MB / 0.5262 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.569e-06/0.008947, allocations: 3.344 kB / 0.6572 GB, free: 31.16 MB / 0.5262 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 3.326e-06/0.00895, allocations: 2.969 kB / 0.6572 GB, free: 31.16 MB / 0.5262 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.889e-06/0.008955, allocations: 0.5312 kB / 0.6572 GB, free: 31.16 MB / 0.5262 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.000589/0.009544, allocations: 0.7245 MB / 0.6579 GB, free: 30.63 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.243e-06/0.009545, allocations: 0 / 0.6579 GB, free: 30.63 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001501/0.009695, allocations: 51.84 kB / 0.658 GB, free: 30.62 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (simulation): time 2.665e-06/0.009698, allocations: 1.406 kB / 0.658 GB, free: 30.62 MB / 0.5262 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.664e-05/0.009714, allocations: 11.61 kB / 0.658 GB, free: 30.62 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.034e-06/0.009716, allocations: 2.875 kB / 0.658 GB, free: 30.62 MB / 0.5262 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.022e-06/0.009717, allocations: 0 / 0.658 GB, free: 30.62 MB / 0.5262 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004173/0.01013, allocations: 0.659 MB / 0.6586 GB, free: 30.16 MB / 0.5262 GB Notification: Performance of postOpt removeConstants (simulation): time 1.827e-05/0.01015, allocations: 17.33 kB / 0.6586 GB, free: 30.15 MB / 0.5262 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.025e-05/0.01018, allocations: 14.94 kB / 0.6587 GB, free: 30.14 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 8.22e-05/0.01027, allocations: 10.53 kB / 0.6587 GB, free: 30.14 MB / 0.5262 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 6.067e-05/0.01033, allocations: 27.33 kB / 0.6587 GB, free: 30.13 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.357e-05/0.01034, allocations: 15.97 kB / 0.6587 GB, free: 30.13 MB / 0.5262 GB Notification: Performance of sorting global known variables: time 4.842e-05/0.01039, allocations: 158.8 kB / 0.6589 GB, free: 30 MB / 0.5262 GB Notification: Performance of sort global known variables: time 7.1e-08/0.01039, allocations: 0 / 0.6589 GB, free: 30 MB / 0.5262 GB Notification: Performance of remove unused functions: time 0.000208/0.0106, allocations: 71.53 kB / 0.6589 GB, free: 30 MB / 0.5262 GB Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 1 * Number of states: 7 (periodicDose.TotalCumulativeMass,periodicDose.variableDose.TotalCumulativeMass,peripheral.C,peripheral.AUC,central.C,central.AUC,elim.MExc) * Number of discrete variables: 13 ($whenCondition1,$whenCondition2,$whenCondition3,$whenCondition4,$whenCondition5,periodicDose.pulse.T_start,periodicDose.pulse.count,peripheral.Cmax,peripheral.Cmin,peripheral.rising,central.Cmax,central.Cmin,central.rising) * Number of discrete states: 11 (periodicDose.pulse.count,peripheral.Cmin,$whenCondition5,peripheral.Cmax,$whenCondition4,peripheral.rising,central.Cmin,$whenCondition3,central.Cmax,$whenCondition2,central.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 7.084e-05/0.01067, allocations: 121.1 kB / 0.659 GB, free: 29.9 MB / 0.5262 GB Notification: Performance of simCode: created initialization part: time 0.0003172/0.01098, allocations: 0.4904 MB / 0.6595 GB, free: 29.51 MB / 0.5262 GB Notification: Performance of simCode: created event and clocks part: time 1.283e-06/0.01099, allocations: 1.438 kB / 0.6595 GB, free: 29.51 MB / 0.5262 GB Notification: Performance of simCode: created simulation system equations: time 0.0001404/0.01113, allocations: 274.9 kB / 0.6598 GB, free: 29.29 MB / 0.5262 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002863/0.01141, allocations: 72.55 kB / 0.6599 GB, free: 29.27 MB / 0.5262 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001354/0.01277, allocations: 0.7765 MB / 0.6606 GB, free: 28.76 MB / 0.5262 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 4.298e-05/0.01281, allocations: 89.91 kB / 0.6607 GB, free: 28.68 MB / 0.5262 GB Notification: Performance of simCode: alias equations: time 6.387e-05/0.01287, allocations: 21.98 kB / 0.6607 GB, free: 28.68 MB / 0.5262 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 4.696e-05/0.01292, allocations: 28 kB / 0.6608 GB, free: 28.66 MB / 0.5262 GB Notification: Performance of SimCode: time 9.31e-07/0.01292, allocations: 0 / 0.6608 GB, free: 28.66 MB / 0.5262 GB Notification: Performance of Templates: time 0.00453/0.01745, allocations: 3.47 MB / 0.6641 GB, free: 28.38 MB / 0.5262 GB " [Timeout remaining time 660] make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.makefile [Timeout 660] (rm -f Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel -abortSlowSimulation -alarm=240 -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 4.515686523867771]