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 0.001059/0.001059, allocations: 88.22 kB / 20.18 MB, free: 4.352 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 0.001114/0.001114, allocations: 169 kB / 23.5 MB, free: 1.039 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 0.9494/0.9494, allocations: 177.1 MB / 203.8 MB, free: 5.598 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 1.5/1.5, allocations: 273.5 MB / 0.5213 GB, free: 14.77 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 1.002e-06/1.002e-06, allocations: 0 / 0.6462 GB, free: 39.1 MB / 0.5262 GB Notification: Performance of FrontEnd - Absyn->SCode: time 1.002e-05/1.102e-05, allocations: 2.312 kB / 0.6462 GB, free: 39.09 MB / 0.5262 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKTwoCompartmentModel): time 0.00187/0.001881, allocations: 2.358 MB / 0.6485 GB, free: 37.56 MB / 0.5262 GB Notification: Performance of NFInst.instExpressions: time 0.0006177/0.002499, allocations: 0.616 MB / 0.6491 GB, free: 37.15 MB / 0.5262 GB Notification: Performance of NFInst.updateImplicitVariability: time 7.066e-05/0.002569, allocations: 2.156 kB / 0.6491 GB, free: 37.15 MB / 0.5262 GB Notification: Performance of NFTyping.typeComponents: time 0.0001019/0.002671, allocations: 27.3 kB / 0.6491 GB, free: 37.14 MB / 0.5262 GB Notification: Performance of NFTyping.typeBindings: time 0.0001319/0.002803, allocations: 80.44 kB / 0.6492 GB, free: 37.11 MB / 0.5262 GB Notification: Performance of NFTyping.typeClassSections: time 0.0001454/0.002949, allocations: 57.58 kB / 0.6493 GB, free: 37.07 MB / 0.5262 GB Notification: Performance of NFFlatten.flatten: time 0.0002199/0.003168, allocations: 289.3 kB / 0.6495 GB, free: 36.95 MB / 0.5262 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001177/0.003286, allocations: 49.67 kB / 0.6496 GB, free: 36.92 MB / 0.5262 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0001295/0.003416, allocations: 152.8 kB / 0.6497 GB, free: 36.86 MB / 0.5262 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001077/0.003523, allocations: 86.98 kB / 0.6498 GB, free: 36.83 MB / 0.5262 GB Notification: Performance of NFPackage.collectConstants: time 3e-05/0.003553, allocations: 21.62 kB / 0.6498 GB, free: 36.83 MB / 0.5262 GB Notification: Performance of NFFlatten.collectFunctions: time 2.5e-05/0.003578, allocations: 21.31 kB / 0.6499 GB, free: 36.83 MB / 0.5262 GB Notification: Performance of NFScalarize.scalarize: time 3.103e-05/0.003609, allocations: 42.3 kB / 0.6499 GB, free: 36.8 MB / 0.5262 GB Notification: Performance of NFVerifyModel.verify: time 7.318e-05/0.003683, allocations: 85.12 kB / 0.65 GB, free: 36.77 MB / 0.5262 GB Notification: Performance of NFConvertDAE.convert: time 0.0001717/0.003854, allocations: 175.8 kB / 0.6501 GB, free: 36.68 MB / 0.5262 GB Notification: Performance of FrontEnd - DAE generated: time 1.513e-06/0.003856, allocations: 0 / 0.6501 GB, free: 36.68 MB / 0.5262 GB Notification: Performance of FrontEnd: time 6.02e-07/0.003856, allocations: 1.781 kB / 0.6501 GB, free: 36.68 MB / 0.5262 GB Notification: Performance of Transformations before backend: time 3.076e-06/0.003859, allocations: 2.344 kB / 0.6501 GB, free: 36.68 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 0.0005182/0.004378, allocations: 0.6114 MB / 0.6507 GB, free: 36.12 MB / 0.5262 GB Notification: Performance of prepare preOptimizeDAE: time 3.146e-05/0.004409, allocations: 8.188 kB / 0.6508 GB, free: 36.12 MB / 0.5262 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 6.017e-05/0.004469, allocations: 37.52 kB / 0.6508 GB, free: 36.11 MB / 0.5262 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001462/0.004615, allocations: 171 kB / 0.651 GB, free: 35.95 MB / 0.5262 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.226e-05/0.004628, allocations: 17.39 kB / 0.651 GB, free: 35.94 MB / 0.5262 GB Notification: Performance of preOpt expandDerOperator (simulation): time 3.081e-05/0.004659, allocations: 25.53 kB / 0.651 GB, free: 35.93 MB / 0.5262 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002156/0.004874, allocations: 213 kB / 0.6512 GB, free: 35.79 MB / 0.5262 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.198e-05/0.004886, allocations: 3.938 kB / 0.6512 GB, free: 35.79 MB / 0.5262 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.444e-05/0.004901, allocations: 6.188 kB / 0.6512 GB, free: 35.79 MB / 0.5262 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.404e-06/0.004908, allocations: 6.062 kB / 0.6512 GB, free: 35.79 MB / 0.5262 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001397/0.005048, allocations: 151.7 kB / 0.6514 GB, free: 35.71 MB / 0.5262 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0004856/0.005533, allocations: 489 kB / 0.6518 GB, free: 35.35 MB / 0.5262 GB Notification: Performance of preOpt comSubExp (simulation): time 0.000165/0.005698, allocations: 174.9 kB / 0.652 GB, free: 35.23 MB / 0.5262 GB Notification: Performance of preOpt resolveLoops (simulation): time 7.8e-05/0.005776, allocations: 108.2 kB / 0.6521 GB, free: 35.14 MB / 0.5262 GB Notification: Performance of preOpt evalFunc (simulation): time 1.143e-05/0.005788, allocations: 5.219 kB / 0.6521 GB, free: 35.14 MB / 0.5262 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001922/0.00598, allocations: 317 kB / 0.6524 GB, free: 34.88 MB / 0.5262 GB Notification: Performance of pre-optimization done (n=31): time 1.352e-06/0.005981, allocations: 0 / 0.6524 GB, free: 34.88 MB / 0.5262 GB Notification: Performance of matching and sorting (n=33): time 0.0008646/0.006846, allocations: 0.9081 MB / 0.6533 GB, free: 34.24 MB / 0.5262 GB Notification: Performance of inlineWhenForInitialization (initialization): time 4.371e-05/0.00689, allocations: 222.3 kB / 0.6535 GB, free: 33.98 MB / 0.5262 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 9.599e-05/0.006986, allocations: 220.6 kB / 0.6537 GB, free: 33.8 MB / 0.5262 GB Notification: Performance of collectPreVariables (initialization): time 1.78e-05/0.007003, allocations: 37.36 kB / 0.6537 GB, free: 33.76 MB / 0.5262 GB Notification: Performance of collectInitialEqns (initialization): time 4.493e-05/0.007048, allocations: 167.1 kB / 0.6539 GB, free: 33.61 MB / 0.5262 GB Notification: Performance of collectInitialBindings (initialization): time 4.559e-05/0.007094, allocations: 113.1 kB / 0.654 GB, free: 33.52 MB / 0.5262 GB Notification: Performance of simplifyInitialFunctions (initialization): time 6.275e-05/0.007157, allocations: 68.64 kB / 0.6541 GB, free: 33.48 MB / 0.5262 GB Notification: Performance of setup shared object (initialization): time 4.774e-05/0.007204, allocations: 0.5061 MB / 0.6546 GB, free: 32.97 MB / 0.5262 GB Notification: Performance of preBalanceInitialSystem (initialization): time 9.994e-05/0.007304, allocations: 154.2 kB / 0.6547 GB, free: 32.85 MB / 0.5262 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001236/0.007428, allocations: 274.6 kB / 0.655 GB, free: 32.57 MB / 0.5262 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0002779/0.007706, allocations: 493.5 kB / 0.6555 GB, free: 32.14 MB / 0.5262 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.523e-06/0.007707, allocations: 0 / 0.6555 GB, free: 32.14 MB / 0.5262 GB Notification: Performance of matching and sorting (n=49) (initialization): time 0.0003258/0.008033, allocations: 462.8 kB / 0.6559 GB, free: 31.84 MB / 0.5262 GB Notification: Performance of prepare postOptimizeDAE: time 2.965e-05/0.008063, allocations: 99.42 kB / 0.656 GB, free: 31.73 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.4e-06/0.008068, allocations: 2.375 kB / 0.656 GB, free: 31.73 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.491e-05/0.008083, allocations: 10.62 kB / 0.656 GB, free: 31.73 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002055/0.008289, allocations: 71.55 kB / 0.6561 GB, free: 31.73 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.946e-06/0.008297, allocations: 4.594 kB / 0.6561 GB, free: 31.73 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.401e-05/0.008391, allocations: 18.72 kB / 0.6561 GB, free: 31.72 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.471e-05/0.008416, allocations: 19.23 kB / 0.6561 GB, free: 31.72 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 0.0001575/0.008574, allocations: 282.8 kB / 0.6564 GB, free: 31.46 MB / 0.5262 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 3.346e-05/0.008607, allocations: 35.56 kB / 0.6564 GB, free: 31.44 MB / 0.5262 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.016e-05/0.008637, allocations: 29.19 kB / 0.6564 GB, free: 31.42 MB / 0.5262 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.976e-06/0.00864, allocations: 5.281 kB / 0.6564 GB, free: 31.42 MB / 0.5262 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 6.312e-06/0.008647, allocations: 3.375 kB / 0.6564 GB, free: 31.42 MB / 0.5262 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.458e-06/0.008651, allocations: 3.562 kB / 0.6565 GB, free: 31.42 MB / 0.5262 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004913/0.009142, allocations: 0.7195 MB / 0.6572 GB, free: 30.89 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.573e-06/0.009144, allocations: 0 / 0.6572 GB, free: 30.89 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.000157/0.009301, allocations: 46.36 kB / 0.6572 GB, free: 30.89 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (simulation): time 2.485e-06/0.009303, allocations: 3.516 kB / 0.6572 GB, free: 30.89 MB / 0.5262 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.053e-05/0.009324, allocations: 13.28 kB / 0.6572 GB, free: 30.89 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.884e-06/0.009326, allocations: 1.094 kB / 0.6572 GB, free: 30.89 MB / 0.5262 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.393e-06/0.009327, allocations: 8.438 kB / 0.6572 GB, free: 30.88 MB / 0.5262 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005441/0.009871, allocations: 0.6576 MB / 0.6579 GB, free: 30.42 MB / 0.5262 GB Notification: Performance of postOpt removeConstants (simulation): time 2.18e-05/0.009893, allocations: 16.3 kB / 0.6579 GB, free: 30.41 MB / 0.5262 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.17e-05/0.009925, allocations: 10.41 kB / 0.6579 GB, free: 30.41 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 8.853e-05/0.01001, allocations: 15 kB / 0.6579 GB, free: 30.41 MB / 0.5262 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 6.472e-05/0.01008, allocations: 29.22 kB / 0.6579 GB, free: 30.4 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.773e-05/0.0101, allocations: 13.98 kB / 0.6579 GB, free: 30.39 MB / 0.5262 GB Notification: Performance of sorting global known variables: time 6.206e-05/0.01016, allocations: 159.1 kB / 0.6581 GB, free: 30.27 MB / 0.5262 GB Notification: Performance of sort global known variables: time 6e-08/0.01016, allocations: 0 / 0.6581 GB, free: 30.27 MB / 0.5262 GB Notification: Performance of remove unused functions: time 0.0002436/0.0104, allocations: 75.03 kB / 0.6582 GB, free: 30.26 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 7.165e-05/0.01047, allocations: 121.4 kB / 0.6583 GB, free: 30.16 MB / 0.5262 GB Notification: Performance of simCode: created initialization part: time 0.0003004/0.01077, allocations: 496.2 kB / 0.6588 GB, free: 29.77 MB / 0.5262 GB Notification: Performance of simCode: created event and clocks part: time 1.303e-06/0.01077, allocations: 0 / 0.6588 GB, free: 29.77 MB / 0.5262 GB Notification: Performance of simCode: created simulation system equations: time 0.0001287/0.0109, allocations: 280.3 kB / 0.659 GB, free: 29.55 MB / 0.5262 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002835/0.01119, allocations: 69.81 kB / 0.6591 GB, free: 29.53 MB / 0.5262 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001357/0.01254, allocations: 0.7978 MB / 0.6599 GB, free: 29 MB / 0.5262 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 7.945e-05/0.01262, allocations: 135.9 kB / 0.66 GB, free: 28.92 MB / 0.5262 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 5.898e-05/0.01268, allocations: 27.91 kB / 0.66 GB, free: 28.91 MB / 0.5262 GB Notification: Performance of SimCode: time 6.71e-07/0.01268, allocations: 0 / 0.66 GB, free: 28.91 MB / 0.5262 GB Notification: Performance of Templates: time 0.003292/0.01597, allocations: 3.147 MB / 0.6631 GB, free: 28.66 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 > Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 6.18382884003222]