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 0.002342/0.002342, allocations: 80.44 kB / 19.17 MB, free: 0.7422 MB / 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 0.002766/0.002766, allocations: 169.9 kB / 22.45 MB, free: 2.102 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 1.663/1.663, allocations: 177.1 MB / 202.8 MB, free: 5.746 MB / 186.7 MB " [Timeout remaining time 178] 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 3.454/3.454, allocations: 274 MB / 0.5207 GB, free: 14.86 MB / 458.7 MB " [Timeout remaining time 176] 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 1.533e-06/1.533e-06, allocations: 0 / 0.7563 GB, free: 9.934 MB / 0.5887 GB Notification: Performance of FrontEnd - Absyn->SCode: time 2.582e-05/2.735e-05, allocations: 4.391 kB / 0.7563 GB, free: 9.93 MB / 0.5887 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.PKTwoCompartmentModelOral): time 0.003743/0.003771, allocations: 2.254 MB / 0.7585 GB, free: 7.688 MB / 0.5887 GB Notification: Performance of NFInst.instExpressions: time 0.001152/0.004922, allocations: 0.5937 MB / 0.759 GB, free: 7.098 MB / 0.5887 GB Notification: Performance of NFInst.updateImplicitVariability: time 8.727e-05/0.00501, allocations: 4 kB / 0.759 GB, free: 7.094 MB / 0.5887 GB Notification: Performance of NFTyping.typeComponents: time 7.581e-05/0.005085, allocations: 23.72 kB / 0.7591 GB, free: 7.07 MB / 0.5887 GB Notification: Performance of NFTyping.typeBindings: time 0.0002237/0.005309, allocations: 85.73 kB / 0.7592 GB, free: 7.012 MB / 0.5887 GB Notification: Performance of NFTyping.typeClassSections: time 0.0002177/0.005527, allocations: 67.83 kB / 0.7592 GB, free: 6.945 MB / 0.5887 GB Notification: Performance of NFFlatten.flatten: time 0.0003677/0.005895, allocations: 290.4 kB / 0.7595 GB, free: 6.664 MB / 0.5887 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001578/0.006052, allocations: 48.73 kB / 0.7595 GB, free: 6.617 MB / 0.5887 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0002312/0.006284, allocations: 159.7 kB / 0.7597 GB, free: 6.461 MB / 0.5887 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001796/0.006463, allocations: 83.77 kB / 0.7598 GB, free: 6.379 MB / 0.5887 GB Notification: Performance of NFPackage.collectConstants: time 4.899e-05/0.006512, allocations: 24 kB / 0.7598 GB, free: 6.355 MB / 0.5887 GB Notification: Performance of NFFlatten.collectFunctions: time 4.85e-05/0.006561, allocations: 20 kB / 0.7598 GB, free: 6.336 MB / 0.5887 GB Notification: Performance of NFScalarize.scalarize: time 6.391e-05/0.006625, allocations: 51.81 kB / 0.7599 GB, free: 6.285 MB / 0.5887 GB Notification: Performance of NFVerifyModel.verify: time 0.0001335/0.006758, allocations: 91.77 kB / 0.7599 GB, free: 6.195 MB / 0.5887 GB Notification: Performance of NFConvertDAE.convert: time 0.0003461/0.007104, allocations: 251.2 kB / 0.7602 GB, free: 5.949 MB / 0.5887 GB Notification: Performance of FrontEnd - DAE generated: time 3.035e-06/0.007107, allocations: 0 / 0.7602 GB, free: 5.949 MB / 0.5887 GB Notification: Performance of FrontEnd: time 9.42e-07/0.007108, allocations: 0 / 0.7602 GB, free: 5.949 MB / 0.5887 GB Notification: Performance of Transformations before backend: time 5.51e-06/0.007114, allocations: 0 / 0.7602 GB, free: 5.949 MB / 0.5887 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 0.001171/0.008285, allocations: 0.5219 MB / 0.7607 GB, free: 5.379 MB / 0.5887 GB Notification: Performance of prepare preOptimizeDAE: time 5.562e-05/0.00834, allocations: 16.02 kB / 0.7607 GB, free: 5.363 MB / 0.5887 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 6.909e-05/0.008409, allocations: 24.8 kB / 0.7607 GB, free: 5.34 MB / 0.5887 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001713/0.008581, allocations: 145.4 kB / 0.7609 GB, free: 5.172 MB / 0.5887 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.533e-05/0.008606, allocations: 16.38 kB / 0.7609 GB, free: 5.156 MB / 0.5887 GB Notification: Performance of preOpt expandDerOperator (simulation): time 6.045e-05/0.008667, allocations: 32.25 kB / 0.7609 GB, free: 5.125 MB / 0.5887 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004845/0.009151, allocations: 250.4 kB / 0.7612 GB, free: 4.859 MB / 0.5887 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.691e-05/0.009168, allocations: 0 / 0.7612 GB, free: 4.859 MB / 0.5887 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.402e-05/0.009192, allocations: 8 kB / 0.7612 GB, free: 4.852 MB / 0.5887 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.373e-06/0.009199, allocations: 4 kB / 0.7612 GB, free: 4.848 MB / 0.5887 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0005047/0.009704, allocations: 223.6 kB / 0.7614 GB, free: 4.617 MB / 0.5887 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0009808/0.01068, allocations: 472.3 kB / 0.7618 GB, free: 4.129 MB / 0.5887 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0004995/0.01118, allocations: 229.9 kB / 0.7621 GB, free: 3.883 MB / 0.5887 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.0002744/0.01146, allocations: 136.2 kB / 0.7622 GB, free: 3.734 MB / 0.5887 GB Notification: Performance of preOpt evalFunc (simulation): time 1.749e-05/0.01148, allocations: 7.938 kB / 0.7622 GB, free: 3.727 MB / 0.5887 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.000527/0.012, allocations: 343.7 kB / 0.7625 GB, free: 3.344 MB / 0.5887 GB Notification: Performance of pre-optimization done (n=30): time 1.473e-06/0.012, allocations: 3.938 kB / 0.7625 GB, free: 3.34 MB / 0.5887 GB Notification: Performance of matching and sorting (n=32): time 0.002154/0.01416, allocations: 1.028 MB / 0.7635 GB, free: 2.219 MB / 0.5887 GB Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001746/0.01433, allocations: 221.5 kB / 0.7637 GB, free: 1.953 MB / 0.5887 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001868/0.01452, allocations: 166 kB / 0.7639 GB, free: 1.785 MB / 0.5887 GB Notification: Performance of collectPreVariables (initialization): time 4.041e-05/0.01456, allocations: 33.7 kB / 0.7639 GB, free: 1.746 MB / 0.5887 GB Notification: Performance of collectInitialEqns (initialization): time 0.0001036/0.01466, allocations: 128.9 kB / 0.7641 GB, free: 1.617 MB / 0.5887 GB Notification: Performance of collectInitialBindings (initialization): time 0.0001045/0.01477, allocations: 111.1 kB / 0.7642 GB, free: 1.508 MB / 0.5887 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001083/0.01488, allocations: 57.98 kB / 0.7642 GB, free: 1.441 MB / 0.5887 GB Notification: Performance of setup shared object (initialization): time 0.0001817/0.01506, allocations: 338.8 kB / 0.7645 GB, free: 1.102 MB / 0.5887 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003346/0.01539, allocations: 191.3 kB / 0.7647 GB, free: 0.8945 MB / 0.5887 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003885/0.01578, allocations: 282.1 kB / 0.765 GB, free: 0.5664 MB / 0.5887 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.001352/0.01713, allocations: 0.7294 MB / 0.7657 GB, free: 15.74 MB / 0.6043 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.254e-06/0.01714, allocations: 4 kB / 0.7657 GB, free: 15.74 MB / 0.6043 GB Notification: Performance of matching and sorting (n=47) (initialization): time 0.0008551/0.01799, allocations: 0.5088 MB / 0.7662 GB, free: 15.19 MB / 0.6043 GB Notification: Performance of prepare postOptimizeDAE: time 8.404e-05/0.01808, allocations: 93.09 kB / 0.7663 GB, free: 15.08 MB / 0.6043 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 9.367e-06/0.01809, allocations: 4.25 kB / 0.7663 GB, free: 15.07 MB / 0.6043 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.769e-05/0.0181, allocations: 8 kB / 0.7663 GB, free: 15.07 MB / 0.6043 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.000302/0.01841, allocations: 71.89 kB / 0.7664 GB, free: 15 MB / 0.6043 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 7.534e-06/0.01841, allocations: 0 / 0.7664 GB, free: 15 MB / 0.6043 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001779/0.01859, allocations: 23.92 kB / 0.7664 GB, free: 14.97 MB / 0.6043 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.91e-05/0.01862, allocations: 16 kB / 0.7664 GB, free: 14.96 MB / 0.6043 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 0.0002985/0.01892, allocations: 247.2 kB / 0.7666 GB, free: 14.7 MB / 0.6043 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 3.858e-05/0.01896, allocations: 19.91 kB / 0.7667 GB, free: 14.68 MB / 0.6043 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 6.277e-05/0.01902, allocations: 33.89 kB / 0.7667 GB, free: 14.64 MB / 0.6043 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.518e-06/0.01902, allocations: 4 kB / 0.7667 GB, free: 14.64 MB / 0.6043 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 4.409e-06/0.01903, allocations: 0 / 0.7667 GB, free: 14.64 MB / 0.6043 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.636e-06/0.01903, allocations: 0 / 0.7667 GB, free: 14.64 MB / 0.6043 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001311/0.02034, allocations: 0.7337 MB / 0.7674 GB, free: 13.85 MB / 0.6043 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.384e-06/0.02035, allocations: 4 kB / 0.7674 GB, free: 13.84 MB / 0.6043 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002666/0.02061, allocations: 43.97 kB / 0.7675 GB, free: 13.8 MB / 0.6043 GB Notification: Performance of postOpt tearingSystem (simulation): time 2.254e-06/0.02061, allocations: 0 / 0.7675 GB, free: 13.8 MB / 0.6043 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.195e-05/0.02065, allocations: 19.98 kB / 0.7675 GB, free: 13.78 MB / 0.6043 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.873e-06/0.02065, allocations: 0 / 0.7675 GB, free: 13.78 MB / 0.6043 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 7.91e-07/0.02065, allocations: 0 / 0.7675 GB, free: 13.78 MB / 0.6043 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001138/0.02179, allocations: 0.6931 MB / 0.7682 GB, free: 13.04 MB / 0.6043 GB Notification: Performance of postOpt removeConstants (simulation): time 3.533e-05/0.02182, allocations: 23.95 kB / 0.7682 GB, free: 13.01 MB / 0.6043 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 4.534e-05/0.02187, allocations: 8 kB / 0.7682 GB, free: 13 MB / 0.6043 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002013/0.02207, allocations: 15.98 kB / 0.7682 GB, free: 12.99 MB / 0.6043 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 9.894e-05/0.02217, allocations: 27.95 kB / 0.7682 GB, free: 12.96 MB / 0.6043 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.474e-05/0.02219, allocations: 16 kB / 0.7682 GB, free: 12.95 MB / 0.6043 GB Notification: Performance of sorting global known variables: time 0.0001255/0.02232, allocations: 126.2 kB / 0.7684 GB, free: 12.82 MB / 0.6043 GB Notification: Performance of sort global known variables: time 6e-08/0.02232, allocations: 0 / 0.7684 GB, free: 12.82 MB / 0.6043 GB Notification: Performance of remove unused functions: time 0.0003384/0.02266, allocations: 68 kB / 0.7684 GB, free: 12.76 MB / 0.6043 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 0.000157/0.02281, allocations: 125.1 kB / 0.7686 GB, free: 12.63 MB / 0.6043 GB Notification: Performance of simCode: created initialization part: time 0.0008504/0.02366, allocations: 0.5495 MB / 0.7691 GB, free: 12.01 MB / 0.6043 GB Notification: Performance of simCode: created event and clocks part: time 1.232e-06/0.02367, allocations: 0 / 0.7691 GB, free: 12.01 MB / 0.6043 GB Notification: Performance of simCode: created simulation system equations: time 0.00042/0.02409, allocations: 294.1 kB / 0.7694 GB, free: 11.69 MB / 0.6043 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.000456/0.02454, allocations: 65.08 kB / 0.7694 GB, free: 11.63 MB / 0.6043 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001453/0.02599, allocations: 0.7178 MB / 0.7701 GB, free: 10.89 MB / 0.6043 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.00015/0.02614, allocations: 134.8 kB / 0.7703 GB, free: 10.73 MB / 0.6043 GB Notification: Performance of simCode: alias equations: time 0.0001033/0.02625, allocations: 21.94 kB / 0.7703 GB, free: 10.71 MB / 0.6043 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 6.669e-05/0.02631, allocations: 24.5 kB / 0.7703 GB, free: 10.69 MB / 0.6043 GB Notification: Performance of SimCode: time 5.51e-07/0.02632, allocations: 0 / 0.7703 GB, free: 10.69 MB / 0.6043 GB Notification: Performance of Templates: time 0.008367/0.03468, allocations: 3.395 MB / 0.7736 GB, free: 7.484 MB / 0.6043 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: 9.198774857912213]