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 0.0009713/0.0009713, allocations: 73.88 kB / 20.66 MB, free: 3.844 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 0.001645/0.001645, allocations: 169 kB / 24.06 MB, free: 452 kB / 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 0.9066/0.9066, allocations: 177.1 MB / 204.5 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 1.562/1.562, allocations: 273.5 MB / 0.522 GB, free: 14.64 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 1.733e-06/1.733e-06, allocations: 0 / 0.6482 GB, free: 38.54 MB / 0.5262 GB Notification: Performance of FrontEnd - Absyn->SCode: time 1.604e-05/1.777e-05, allocations: 8.438 kB / 0.6482 GB, free: 38.54 MB / 0.5262 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKTwoCompartmentModel): time 0.002898/0.002916, allocations: 2.352 MB / 0.6505 GB, free: 37 MB / 0.5262 GB Notification: Performance of NFInst.instExpressions: time 0.0007338/0.00365, allocations: 0.6058 MB / 0.6511 GB, free: 36.6 MB / 0.5262 GB Notification: Performance of NFInst.updateImplicitVariability: time 9.232e-05/0.003742, allocations: 3.625 kB / 0.6511 GB, free: 36.6 MB / 0.5262 GB Notification: Performance of NFTyping.typeComponents: time 0.0001173/0.003859, allocations: 26.11 kB / 0.6511 GB, free: 36.59 MB / 0.5262 GB Notification: Performance of NFTyping.typeBindings: time 0.0001384/0.003998, allocations: 79.03 kB / 0.6512 GB, free: 36.55 MB / 0.5262 GB Notification: Performance of NFTyping.typeClassSections: time 0.0001424/0.00414, allocations: 60.19 kB / 0.6512 GB, free: 36.52 MB / 0.5262 GB Notification: Performance of NFFlatten.flatten: time 0.0002213/0.004361, allocations: 293.6 kB / 0.6515 GB, free: 36.4 MB / 0.5262 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001129/0.004474, allocations: 50.7 kB / 0.6515 GB, free: 36.37 MB / 0.5262 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0001258/0.0046, allocations: 151.8 kB / 0.6517 GB, free: 36.31 MB / 0.5262 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001152/0.004715, allocations: 84.61 kB / 0.6518 GB, free: 36.29 MB / 0.5262 GB Notification: Performance of NFPackage.collectConstants: time 2.998e-05/0.004745, allocations: 21 kB / 0.6518 GB, free: 36.29 MB / 0.5262 GB Notification: Performance of NFFlatten.collectFunctions: time 2.683e-05/0.004772, allocations: 25.12 kB / 0.6518 GB, free: 36.28 MB / 0.5262 GB Notification: Performance of NFScalarize.scalarize: time 3.371e-05/0.004806, allocations: 40.5 kB / 0.6518 GB, free: 36.25 MB / 0.5262 GB Notification: Performance of NFVerifyModel.verify: time 6.548e-05/0.004871, allocations: 85.45 kB / 0.6519 GB, free: 36.22 MB / 0.5262 GB Notification: Performance of NFConvertDAE.convert: time 0.0001621/0.005033, allocations: 178.2 kB / 0.6521 GB, free: 36.13 MB / 0.5262 GB Notification: Performance of FrontEnd - DAE generated: time 2.034e-06/0.005035, allocations: 0 / 0.6521 GB, free: 36.13 MB / 0.5262 GB Notification: Performance of FrontEnd: time 6.31e-07/0.005036, allocations: 1.344 kB / 0.6521 GB, free: 36.13 MB / 0.5262 GB Notification: Performance of Transformations before backend: time 4.489e-06/0.00504, allocations: 0 / 0.6521 GB, free: 36.13 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 0.0005029/0.005543, allocations: 0.6092 MB / 0.6527 GB, free: 35.57 MB / 0.5262 GB Notification: Performance of prepare preOptimizeDAE: time 3.48e-05/0.005578, allocations: 9.125 kB / 0.6527 GB, free: 35.57 MB / 0.5262 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 5.405e-05/0.005632, allocations: 39.36 kB / 0.6527 GB, free: 35.56 MB / 0.5262 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001253/0.005757, allocations: 176.8 kB / 0.6529 GB, free: 35.39 MB / 0.5262 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.901e-05/0.005776, allocations: 15.52 kB / 0.6529 GB, free: 35.39 MB / 0.5262 GB Notification: Performance of preOpt expandDerOperator (simulation): time 2.878e-05/0.005805, allocations: 22.64 kB / 0.6529 GB, free: 35.38 MB / 0.5262 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0001727/0.005978, allocations: 196.1 kB / 0.6531 GB, free: 35.25 MB / 0.5262 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.298e-05/0.005991, allocations: 9.688 kB / 0.6531 GB, free: 35.25 MB / 0.5262 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.306e-05/0.006004, allocations: 5.938 kB / 0.6532 GB, free: 35.24 MB / 0.5262 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 5.811e-06/0.00601, allocations: 3.938 kB / 0.6532 GB, free: 35.24 MB / 0.5262 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001116/0.006121, allocations: 133.7 kB / 0.6533 GB, free: 35.18 MB / 0.5262 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0004578/0.006579, allocations: 467.8 kB / 0.6537 GB, free: 34.84 MB / 0.5262 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0001537/0.006733, allocations: 159 kB / 0.6539 GB, free: 34.73 MB / 0.5262 GB Notification: Performance of preOpt resolveLoops (simulation): time 5.996e-05/0.006793, allocations: 108 kB / 0.654 GB, free: 34.64 MB / 0.5262 GB Notification: Performance of preOpt evalFunc (simulation): time 1.182e-05/0.006805, allocations: 3.656 kB / 0.654 GB, free: 34.64 MB / 0.5262 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.000178/0.006983, allocations: 311.1 kB / 0.6543 GB, free: 34.38 MB / 0.5262 GB Notification: Performance of pre-optimization done (n=31): time 1.423e-06/0.006984, allocations: 2.75 kB / 0.6543 GB, free: 34.38 MB / 0.5262 GB Notification: Performance of matching and sorting (n=33): time 0.0008209/0.007805, allocations: 0.8449 MB / 0.6551 GB, free: 33.78 MB / 0.5262 GB Notification: Performance of inlineWhenForInitialization (initialization): time 5.15e-05/0.007856, allocations: 224.4 kB / 0.6553 GB, free: 33.52 MB / 0.5262 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001032/0.00796, allocations: 219.7 kB / 0.6555 GB, free: 33.34 MB / 0.5262 GB Notification: Performance of collectPreVariables (initialization): time 1.805e-05/0.007978, allocations: 35.08 kB / 0.6556 GB, free: 33.3 MB / 0.5262 GB Notification: Performance of collectInitialEqns (initialization): time 5.262e-05/0.00803, allocations: 174.4 kB / 0.6557 GB, free: 33.14 MB / 0.5262 GB Notification: Performance of collectInitialBindings (initialization): time 4.91e-05/0.008079, allocations: 108.2 kB / 0.6558 GB, free: 33.05 MB / 0.5262 GB Notification: Performance of simplifyInitialFunctions (initialization): time 6.455e-05/0.008144, allocations: 74.94 kB / 0.6559 GB, free: 33.01 MB / 0.5262 GB Notification: Performance of setup shared object (initialization): time 5.66e-05/0.008201, allocations: 0.5047 MB / 0.6564 GB, free: 32.5 MB / 0.5262 GB Notification: Performance of preBalanceInitialSystem (initialization): time 7.548e-05/0.008276, allocations: 139.8 kB / 0.6565 GB, free: 32.39 MB / 0.5262 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001027/0.008379, allocations: 271.5 kB / 0.6568 GB, free: 32.11 MB / 0.5262 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0002336/0.008612, allocations: 472.9 kB / 0.6572 GB, free: 31.68 MB / 0.5262 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.893e-06/0.008614, allocations: 0.5625 kB / 0.6572 GB, free: 31.68 MB / 0.5262 GB Notification: Performance of matching and sorting (n=49) (initialization): time 0.0004049/0.009019, allocations: 430.1 kB / 0.6577 GB, free: 31.4 MB / 0.5262 GB Notification: Performance of prepare postOptimizeDAE: time 4.136e-05/0.00906, allocations: 97.09 kB / 0.6577 GB, free: 31.3 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.145e-06/0.009069, allocations: 6.156 kB / 0.6578 GB, free: 31.29 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.468e-05/0.009083, allocations: 5.938 kB / 0.6578 GB, free: 31.29 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002121/0.009295, allocations: 73.45 kB / 0.6578 GB, free: 31.29 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.123e-05/0.009307, allocations: 3.906 kB / 0.6578 GB, free: 31.29 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001007/0.009407, allocations: 23.14 kB / 0.6579 GB, free: 31.28 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.482e-05/0.009432, allocations: 12.81 kB / 0.6579 GB, free: 31.28 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 0.0001584/0.009591, allocations: 284 kB / 0.6581 GB, free: 31.02 MB / 0.5262 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 5.102e-05/0.009642, allocations: 41.91 kB / 0.6582 GB, free: 31 MB / 0.5262 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.306e-05/0.009675, allocations: 25.25 kB / 0.6582 GB, free: 30.98 MB / 0.5262 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.649e-06/0.009679, allocations: 2.75 kB / 0.6582 GB, free: 30.98 MB / 0.5262 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 2.444e-06/0.009682, allocations: 1.062 kB / 0.6582 GB, free: 30.98 MB / 0.5262 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.598e-06/0.009686, allocations: 4.188 kB / 0.6582 GB, free: 30.98 MB / 0.5262 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004651/0.01015, allocations: 0.6692 MB / 0.6589 GB, free: 30.49 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.623e-06/0.01015, allocations: 0 / 0.6589 GB, free: 30.49 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001467/0.0103, allocations: 53.02 kB / 0.6589 GB, free: 30.49 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (simulation): time 4.007e-06/0.0103, allocations: 5.312 kB / 0.6589 GB, free: 30.48 MB / 0.5262 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.762e-05/0.01032, allocations: 15.42 kB / 0.6589 GB, free: 30.48 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.903e-06/0.01032, allocations: 1.531 kB / 0.6589 GB, free: 30.48 MB / 0.5262 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.393e-06/0.01032, allocations: 0 / 0.6589 GB, free: 30.48 MB / 0.5262 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003886/0.01071, allocations: 0.6304 MB / 0.6596 GB, free: 30.04 MB / 0.5262 GB Notification: Performance of postOpt removeConstants (simulation): time 1.661e-05/0.01073, allocations: 21.39 kB / 0.6596 GB, free: 30.02 MB / 0.5262 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.779e-05/0.01076, allocations: 13.62 kB / 0.6596 GB, free: 30.01 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.687e-05/0.01083, allocations: 11.88 kB / 0.6596 GB, free: 30.01 MB / 0.5262 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 5.244e-05/0.01089, allocations: 27.27 kB / 0.6596 GB, free: 30 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.194e-05/0.0109, allocations: 9.203 kB / 0.6596 GB, free: 30 MB / 0.5262 GB Notification: Performance of sorting global known variables: time 4.078e-05/0.01094, allocations: 153.8 kB / 0.6598 GB, free: 29.88 MB / 0.5262 GB Notification: Performance of sort global known variables: time 6e-08/0.01094, allocations: 2.156 kB / 0.6598 GB, free: 29.88 MB / 0.5262 GB Notification: Performance of remove unused functions: time 0.000206/0.01115, allocations: 74.78 kB / 0.6598 GB, free: 29.87 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 7.57e-05/0.01122, allocations: 113.9 kB / 0.66 GB, free: 29.77 MB / 0.5262 GB Notification: Performance of simCode: created initialization part: time 0.0002622/0.01148, allocations: 477.7 kB / 0.6604 GB, free: 29.39 MB / 0.5262 GB Notification: Performance of simCode: created event and clocks part: time 1.804e-06/0.01149, allocations: 5.312 kB / 0.6604 GB, free: 29.39 MB / 0.5262 GB Notification: Performance of simCode: created simulation system equations: time 0.0001231/0.01161, allocations: 269.9 kB / 0.6607 GB, free: 29.17 MB / 0.5262 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002712/0.01188, allocations: 65.66 kB / 0.6607 GB, free: 29.16 MB / 0.5262 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001186/0.01307, allocations: 0.7717 MB / 0.6615 GB, free: 28.66 MB / 0.5262 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 4.153e-05/0.01311, allocations: 85.72 kB / 0.6616 GB, free: 28.58 MB / 0.5262 GB Notification: Performance of simCode: alias equations: time 6.648e-05/0.01317, allocations: 24.84 kB / 0.6616 GB, free: 28.57 MB / 0.5262 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001519/0.01333, allocations: 151.1 kB / 0.6617 GB, free: 28.5 MB / 0.5262 GB Notification: Performance of SimCode: time 5.71e-07/0.01333, allocations: 0 / 0.6617 GB, free: 28.5 MB / 0.5262 GB Notification: Performance of Templates: time 0.005146/0.01847, allocations: 3.889 MB / 0.6655 GB, free: 28.14 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: 4.4525275295600295]