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 0.0009845/0.0009845, allocations: 93.06 kB / 19.65 MB, free: 276 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 0.00125/0.00125, allocations: 169 kB / 23.02 MB, free: 1.543 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 0.8876/0.8876, 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 1.481/1.481, allocations: 273.5 MB / 0.5209 GB, free: 14.79 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 2.735e-06/2.735e-06, allocations: 0.8438 kB / 0.6469 GB, free: 38.63 MB / 0.5262 GB Notification: Performance of FrontEnd - Absyn->SCode: time 2.729e-05/3.003e-05, allocations: 6.141 kB / 0.647 GB, free: 38.63 MB / 0.5262 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKTwoCompartmentModel): time 0.005956/0.005987, allocations: 2.369 MB / 0.6493 GB, free: 37.1 MB / 0.5262 GB Notification: Performance of NFInst.instExpressions: time 0.001099/0.007086, allocations: 0.6109 MB / 0.6499 GB, free: 36.69 MB / 0.5262 GB Notification: Performance of NFInst.updateImplicitVariability: time 0.0001063/0.007192, allocations: 3.781 kB / 0.6499 GB, free: 36.69 MB / 0.5262 GB Notification: Performance of NFTyping.typeComponents: time 0.0001315/0.007324, allocations: 27.56 kB / 0.6499 GB, free: 36.68 MB / 0.5262 GB Notification: Performance of NFTyping.typeBindings: time 0.003243/0.01057, allocations: 77.78 kB / 0.65 GB, free: 36.64 MB / 0.5262 GB Notification: Performance of NFTyping.typeClassSections: time 0.0002346/0.0108, allocations: 59.34 kB / 0.65 GB, free: 36.61 MB / 0.5262 GB Notification: Performance of NFFlatten.flatten: time 0.0003009/0.0111, allocations: 286.5 kB / 0.6503 GB, free: 36.49 MB / 0.5262 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001466/0.01125, allocations: 55.27 kB / 0.6504 GB, free: 36.46 MB / 0.5262 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0002101/0.01146, allocations: 148.7 kB / 0.6505 GB, free: 36.4 MB / 0.5262 GB Notification: Performance of NFSimplifyModel.simplify: time 0.000148/0.01161, allocations: 89.02 kB / 0.6506 GB, free: 36.37 MB / 0.5262 GB Notification: Performance of NFPackage.collectConstants: time 3.896e-05/0.01165, allocations: 18.88 kB / 0.6506 GB, free: 36.37 MB / 0.5262 GB Notification: Performance of NFFlatten.collectFunctions: time 3.457e-05/0.01168, allocations: 22.09 kB / 0.6506 GB, free: 36.37 MB / 0.5262 GB Notification: Performance of NFScalarize.scalarize: time 4.021e-05/0.01172, allocations: 54.19 kB / 0.6507 GB, free: 36.33 MB / 0.5262 GB Notification: Performance of NFVerifyModel.verify: time 9.247e-05/0.01181, allocations: 80.14 kB / 0.6507 GB, free: 36.3 MB / 0.5262 GB Notification: Performance of NFConvertDAE.convert: time 0.0002586/0.01207, allocations: 180.6 kB / 0.6509 GB, free: 36.21 MB / 0.5262 GB Notification: Performance of FrontEnd - DAE generated: time 5.31e-06/0.01208, allocations: 0 / 0.6509 GB, free: 36.21 MB / 0.5262 GB Notification: Performance of FrontEnd: time 1.272e-06/0.01208, allocations: 2.188 kB / 0.6509 GB, free: 36.21 MB / 0.5262 GB Notification: Performance of Transformations before backend: time 5.981e-06/0.01208, allocations: 0 / 0.6509 GB, free: 36.21 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 0.0008457/0.01293, allocations: 0.6031 MB / 0.6515 GB, free: 35.66 MB / 0.5262 GB Notification: Performance of prepare preOptimizeDAE: time 6.657e-05/0.013, allocations: 9.344 kB / 0.6515 GB, free: 35.66 MB / 0.5262 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001082/0.0131, allocations: 38.61 kB / 0.6516 GB, free: 35.64 MB / 0.5262 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.003236/0.01634, allocations: 172.6 kB / 0.6517 GB, free: 35.48 MB / 0.5262 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.381e-05/0.01637, allocations: 14.64 kB / 0.6517 GB, free: 35.48 MB / 0.5262 GB Notification: Performance of preOpt expandDerOperator (simulation): time 4.461e-05/0.01642, allocations: 24.73 kB / 0.6518 GB, free: 35.47 MB / 0.5262 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003111/0.01673, allocations: 216.4 kB / 0.652 GB, free: 35.33 MB / 0.5262 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.655e-05/0.01675, allocations: 3.938 kB / 0.652 GB, free: 35.32 MB / 0.5262 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.861e-05/0.01677, allocations: 9 kB / 0.652 GB, free: 35.32 MB / 0.5262 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.136e-05/0.01678, allocations: 7 kB / 0.652 GB, free: 35.32 MB / 0.5262 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001725/0.01695, allocations: 147.5 kB / 0.6521 GB, free: 35.25 MB / 0.5262 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0006591/0.01761, allocations: 483.5 kB / 0.6526 GB, free: 34.89 MB / 0.5262 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0002127/0.01782, allocations: 176.7 kB / 0.6528 GB, free: 34.77 MB / 0.5262 GB Notification: Performance of preOpt resolveLoops (simulation): time 8.914e-05/0.01791, allocations: 107.6 kB / 0.6529 GB, free: 34.68 MB / 0.5262 GB Notification: Performance of preOpt evalFunc (simulation): time 1.22e-05/0.01792, allocations: 5.625 kB / 0.6529 GB, free: 34.68 MB / 0.5262 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002471/0.01817, allocations: 321.2 kB / 0.6532 GB, free: 34.42 MB / 0.5262 GB Notification: Performance of pre-optimization done (n=31): time 5.811e-06/0.01817, allocations: 0 / 0.6532 GB, free: 34.42 MB / 0.5262 GB Notification: Performance of matching and sorting (n=33): time 0.004182/0.02236, allocations: 0.9075 MB / 0.6541 GB, free: 33.77 MB / 0.5262 GB Notification: Performance of inlineWhenForInitialization (initialization): time 7.229e-05/0.02243, allocations: 222.1 kB / 0.6543 GB, free: 33.52 MB / 0.5262 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001421/0.02257, allocations: 222.1 kB / 0.6545 GB, free: 33.34 MB / 0.5262 GB Notification: Performance of collectPreVariables (initialization): time 2.309e-05/0.02259, allocations: 37.98 kB / 0.6545 GB, free: 33.3 MB / 0.5262 GB Notification: Performance of collectInitialEqns (initialization): time 5.912e-05/0.02265, allocations: 166.1 kB / 0.6547 GB, free: 33.14 MB / 0.5262 GB Notification: Performance of collectInitialBindings (initialization): time 6.251e-05/0.02272, allocations: 109.2 kB / 0.6548 GB, free: 33.06 MB / 0.5262 GB Notification: Performance of simplifyInitialFunctions (initialization): time 8.785e-05/0.0228, allocations: 72.48 kB / 0.6548 GB, free: 33.01 MB / 0.5262 GB Notification: Performance of setup shared object (initialization): time 5.882e-05/0.02286, allocations: 0.5031 MB / 0.6553 GB, free: 32.51 MB / 0.5262 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001274/0.02299, allocations: 153.8 kB / 0.6555 GB, free: 32.39 MB / 0.5262 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001599/0.02315, allocations: 277.8 kB / 0.6557 GB, free: 32.11 MB / 0.5262 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0003708/0.02352, allocations: 489.3 kB / 0.6562 GB, free: 31.68 MB / 0.5262 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.306e-06/0.02352, allocations: 1.094 kB / 0.6562 GB, free: 31.68 MB / 0.5262 GB Notification: Performance of matching and sorting (n=49) (initialization): time 0.0005657/0.02409, allocations: 461.5 kB / 0.6567 GB, free: 31.38 MB / 0.5262 GB Notification: Performance of prepare postOptimizeDAE: time 5.238e-05/0.02414, allocations: 93.45 kB / 0.6567 GB, free: 31.27 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.178e-05/0.02415, allocations: 10.39 kB / 0.6568 GB, free: 31.27 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.911e-05/0.02417, allocations: 7.594 kB / 0.6568 GB, free: 31.27 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002844/0.02446, allocations: 73.11 kB / 0.6568 GB, free: 31.27 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 9.507e-06/0.02447, allocations: 12.7 kB / 0.6568 GB, free: 31.26 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001374/0.0246, allocations: 17.09 kB / 0.6569 GB, free: 31.25 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 3.029e-05/0.02463, allocations: 16.28 kB / 0.6569 GB, free: 31.25 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 0.0002213/0.02486, allocations: 280.6 kB / 0.6571 GB, free: 31 MB / 0.5262 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 5.938e-05/0.02492, allocations: 36.78 kB / 0.6572 GB, free: 30.98 MB / 0.5262 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 4.207e-05/0.02496, allocations: 28.2 kB / 0.6572 GB, free: 30.96 MB / 0.5262 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.382e-06/0.02496, allocations: 3.219 kB / 0.6572 GB, free: 30.96 MB / 0.5262 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 6.372e-06/0.02497, allocations: 0.9062 kB / 0.6572 GB, free: 30.96 MB / 0.5262 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.97e-06/0.02497, allocations: 4.5 kB / 0.6572 GB, free: 30.95 MB / 0.5262 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.003714/0.02869, allocations: 0.7196 MB / 0.6579 GB, free: 30.43 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.316e-06/0.02869, allocations: 1.438 kB / 0.6579 GB, free: 30.43 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002061/0.0289, allocations: 49.22 kB / 0.658 GB, free: 30.43 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (simulation): time 4.678e-06/0.0289, allocations: 0.7812 kB / 0.658 GB, free: 30.43 MB / 0.5262 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.143e-05/0.02892, allocations: 9.531 kB / 0.658 GB, free: 30.42 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.955e-06/0.02893, allocations: 2.875 kB / 0.658 GB, free: 30.42 MB / 0.5262 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.284e-06/0.02893, allocations: 3.141 kB / 0.658 GB, free: 30.42 MB / 0.5262 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005173/0.02945, allocations: 0.6591 MB / 0.6586 GB, free: 29.96 MB / 0.5262 GB Notification: Performance of postOpt removeConstants (simulation): time 2.606e-05/0.02947, allocations: 14.94 kB / 0.6586 GB, free: 29.95 MB / 0.5262 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.865e-05/0.02951, allocations: 9.625 kB / 0.6586 GB, free: 29.95 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001237/0.02964, allocations: 16.12 kB / 0.6587 GB, free: 29.95 MB / 0.5262 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 7.205e-05/0.02971, allocations: 33.92 kB / 0.6587 GB, free: 29.94 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.8e-05/0.02973, allocations: 11.72 kB / 0.6587 GB, free: 29.93 MB / 0.5262 GB Notification: Performance of sorting global known variables: time 6.205e-05/0.02979, allocations: 161.5 kB / 0.6589 GB, free: 29.81 MB / 0.5262 GB Notification: Performance of sort global known variables: time 7e-08/0.02979, allocations: 0 / 0.6589 GB, free: 29.81 MB / 0.5262 GB Notification: Performance of remove unused functions: time 0.0003416/0.03013, allocations: 74.33 kB / 0.6589 GB, free: 29.8 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 9.988e-05/0.03023, allocations: 110.7 kB / 0.659 GB, free: 29.71 MB / 0.5262 GB Notification: Performance of simCode: created initialization part: time 0.0003754/0.0306, allocations: 0.493 MB / 0.6595 GB, free: 29.31 MB / 0.5262 GB Notification: Performance of simCode: created event and clocks part: time 2.034e-06/0.03061, allocations: 0 / 0.6595 GB, free: 29.31 MB / 0.5262 GB Notification: Performance of simCode: created simulation system equations: time 0.0001638/0.03077, allocations: 279.8 kB / 0.6598 GB, free: 29.09 MB / 0.5262 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.003351/0.03412, allocations: 64.34 kB / 0.6598 GB, free: 29.07 MB / 0.5262 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001413/0.03553, allocations: 0.7776 MB / 0.6606 GB, free: 28.55 MB / 0.5262 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 6.217e-05/0.0356, allocations: 85.28 kB / 0.6607 GB, free: 28.48 MB / 0.5262 GB Notification: Performance of simCode: alias equations: time 8.285e-05/0.03568, allocations: 29.17 kB / 0.6607 GB, free: 28.46 MB / 0.5262 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 5.23e-05/0.03573, allocations: 27.64 kB / 0.6607 GB, free: 28.46 MB / 0.5262 GB Notification: Performance of SimCode: time 8.42e-07/0.03573, allocations: 0 / 0.6607 GB, free: 28.46 MB / 0.5262 GB Notification: Performance of Templates: time 0.005641/0.04137, allocations: 3.665 MB / 0.6643 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: 4.558274300768971]