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 0.002517/0.002517, allocations: 101.5 kB / 18.95 MB, free: 1.18 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 0.001945/0.001945, allocations: 213.7 kB / 22.25 MB, free: 3.57 MB / 13.93 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 1.729/1.729, allocations: 230.6 MB / 256 MB, free: 9.613 MB / 202.7 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 3.861/3.861, allocations: 335.3 MB / 0.6325 GB, free: 7.293 MB / 442.7 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: Pharmacolibrary requested package Modelica of version 4.0.0. Modelica 4.1.0 is used instead which states that it is fully compatible without conversion script needed. Notification: Performance of FrontEnd - loaded program: time 0.003817/0.003817, allocations: 71.88 kB / 0.868 GB, free: 5.98 MB / 0.573 GB Notification: Performance of FrontEnd - Absyn->SCode: time 0.2695/0.2733, allocations: 112.8 MB / 0.9782 GB, free: 4.906 MB / 0.6824 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.PKTwoCompartmentModelOral): time 0.004092/0.2774, allocations: 2.25 MB / 0.9804 GB, free: 2.645 MB / 0.6824 GB Notification: Performance of NFInst.instExpressions: time 0.001188/0.2786, allocations: 0.5844 MB / 0.9809 GB, free: 2.059 MB / 0.6824 GB Notification: Performance of NFInst.updateImplicitVariability: time 9.083e-05/0.2787, allocations: 7.938 kB / 0.981 GB, free: 2.051 MB / 0.6824 GB Notification: Performance of NFTyping.typeComponents: time 7.863e-05/0.2787, allocations: 31.7 kB / 0.981 GB, free: 2.02 MB / 0.6824 GB Notification: Performance of NFTyping.typeBindings: time 0.000247/0.279, allocations: 75.41 kB / 0.9811 GB, free: 1.945 MB / 0.6824 GB Notification: Performance of NFTyping.typeClassSections: time 0.0002172/0.2792, allocations: 71.84 kB / 0.9811 GB, free: 1.875 MB / 0.6824 GB Notification: Performance of NFFlatten.flatten: time 0.0003513/0.2796, allocations: 274.8 kB / 0.9814 GB, free: 1.605 MB / 0.6824 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001611/0.2797, allocations: 48.73 kB / 0.9814 GB, free: 1.555 MB / 0.6824 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0001653/0.2799, allocations: 103.7 kB / 0.9815 GB, free: 1.453 MB / 0.6824 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001973/0.2801, allocations: 103.5 kB / 0.9816 GB, free: 1.352 MB / 0.6824 GB Notification: Performance of NFPackage.collectConstants: time 4.529e-05/0.2801, allocations: 20 kB / 0.9816 GB, free: 1.332 MB / 0.6824 GB Notification: Performance of NFFlatten.collectFunctions: time 5.006e-05/0.2802, allocations: 28 kB / 0.9817 GB, free: 1.305 MB / 0.6824 GB Notification: Performance of NFScalarize.scalarize: time 6.195e-05/0.2802, allocations: 47.84 kB / 0.9817 GB, free: 1.258 MB / 0.6824 GB Notification: Performance of NFVerifyModel.verify: time 0.0001358/0.2804, allocations: 99.58 kB / 0.9818 GB, free: 1.16 MB / 0.6824 GB Notification: Performance of NFConvertDAE.convert: time 0.0003276/0.2807, allocations: 239 kB / 0.982 GB, free: 0.9258 MB / 0.6824 GB Notification: Performance of FrontEnd - DAE generated: time 4.498e-06/0.2807, allocations: 0 / 0.982 GB, free: 0.9258 MB / 0.6824 GB Notification: Performance of FrontEnd: time 1.382e-06/0.2807, allocations: 4 kB / 0.982 GB, free: 0.9219 MB / 0.6824 GB Notification: Performance of Transformations before backend: time 6.042e-06/0.2807, allocations: 0 / 0.982 GB, free: 0.9219 MB / 0.6824 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 0.001045/0.2818, allocations: 0.5258 MB / 0.9826 GB, free: 356 kB / 0.6824 GB Notification: Performance of prepare preOptimizeDAE: time 3.988e-05/0.2818, allocations: 10.11 kB / 0.9826 GB, free: 348 kB / 0.6824 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 6.143e-05/0.2819, allocations: 24.8 kB / 0.9826 GB, free: 324 kB / 0.6824 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.000196/0.2821, allocations: 152.6 kB / 0.9827 GB, free: 148 kB / 0.6824 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.194e-05/0.2821, allocations: 12.38 kB / 0.9828 GB, free: 136 kB / 0.6824 GB Notification: Performance of preOpt expandDerOperator (simulation): time 6.099e-05/0.2821, allocations: 35.89 kB / 0.9828 GB, free: 100 kB / 0.6824 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0005075/0.2827, allocations: 242.2 kB / 0.983 GB, free: 15.84 MB / 0.698 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.97e-05/0.2827, allocations: 3.984 kB / 0.983 GB, free: 15.83 MB / 0.698 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.358e-05/0.2827, allocations: 8 kB / 0.983 GB, free: 15.82 MB / 0.698 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.059e-05/0.2827, allocations: 7.984 kB / 0.983 GB, free: 15.82 MB / 0.698 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0004814/0.2832, allocations: 231.5 kB / 0.9833 GB, free: 15.58 MB / 0.698 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001234/0.2844, allocations: 476.5 kB / 0.9837 GB, free: 15.09 MB / 0.698 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0006577/0.2851, allocations: 221.9 kB / 0.9839 GB, free: 14.85 MB / 0.698 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.0003402/0.2854, allocations: 143.4 kB / 0.9841 GB, free: 14.7 MB / 0.698 GB Notification: Performance of preOpt evalFunc (simulation): time 2.407e-05/0.2854, allocations: 4 kB / 0.9841 GB, free: 14.69 MB / 0.698 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0006887/0.2861, allocations: 353.5 kB / 0.9844 GB, free: 14.3 MB / 0.698 GB Notification: Performance of pre-optimization done (n=30): time 1.913e-06/0.2861, allocations: 0 / 0.9844 GB, free: 14.3 MB / 0.698 GB Notification: Performance of matching and sorting (n=32): time 0.002776/0.2889, allocations: 1.027 MB / 0.9854 GB, free: 13.18 MB / 0.698 GB Notification: Performance of inlineWhenForInitialization (initialization): time 0.000199/0.2891, allocations: 217.6 kB / 0.9856 GB, free: 12.92 MB / 0.698 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002428/0.2894, allocations: 162.2 kB / 0.9858 GB, free: 12.75 MB / 0.698 GB Notification: Performance of collectPreVariables (initialization): time 5.327e-05/0.2894, allocations: 37.69 kB / 0.9858 GB, free: 12.71 MB / 0.698 GB Notification: Performance of collectInitialEqns (initialization): time 0.0001254/0.2895, allocations: 120.9 kB / 0.9859 GB, free: 12.59 MB / 0.698 GB Notification: Performance of collectInitialBindings (initialization): time 0.0002765/0.2898, allocations: 119 kB / 0.986 GB, free: 12.47 MB / 0.698 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001469/0.29, allocations: 57.98 kB / 0.9861 GB, free: 12.4 MB / 0.698 GB Notification: Performance of setup shared object (initialization): time 0.0002323/0.2902, allocations: 338.8 kB / 0.9864 GB, free: 12.06 MB / 0.698 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0004331/0.2906, allocations: 195.3 kB / 0.9866 GB, free: 11.85 MB / 0.698 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0005383/0.2912, allocations: 282 kB / 0.9869 GB, free: 11.52 MB / 0.698 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.001803/0.293, allocations: 0.7262 MB / 0.9876 GB, free: 10.7 MB / 0.698 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.796e-06/0.293, allocations: 0 / 0.9876 GB, free: 10.7 MB / 0.698 GB Notification: Performance of matching and sorting (n=47) (initialization): time 0.001223/0.2942, allocations: 0.515 MB / 0.9881 GB, free: 10.14 MB / 0.698 GB Notification: Performance of prepare postOptimizeDAE: time 0.0001084/0.2943, allocations: 93.09 kB / 0.9882 GB, free: 10.03 MB / 0.698 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.394e-06/0.2943, allocations: 0 / 0.9882 GB, free: 10.03 MB / 0.698 GB Notification: Performance of postOpt tearingSystem (initialization): time 2.161e-05/0.2943, allocations: 4 kB / 0.9882 GB, free: 10.02 MB / 0.698 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0004169/0.2947, allocations: 64.16 kB / 0.9882 GB, free: 9.961 MB / 0.698 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.608e-05/0.2948, allocations: 8 kB / 0.9882 GB, free: 9.953 MB / 0.698 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0002688/0.295, allocations: 23.98 kB / 0.9883 GB, free: 9.93 MB / 0.698 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.335e-05/0.2951, allocations: 19.92 kB / 0.9883 GB, free: 9.91 MB / 0.698 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 0.0004161/0.2955, allocations: 253 kB / 0.9885 GB, free: 9.641 MB / 0.698 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 5.699e-05/0.2955, allocations: 19.91 kB / 0.9885 GB, free: 9.621 MB / 0.698 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 9.67e-05/0.2956, allocations: 25.97 kB / 0.9886 GB, free: 9.594 MB / 0.698 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 7.384e-06/0.2956, allocations: 7.922 kB / 0.9886 GB, free: 9.586 MB / 0.698 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 6.642e-06/0.2957, allocations: 0 / 0.9886 GB, free: 9.586 MB / 0.698 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.153e-05/0.2957, allocations: 8 kB / 0.9886 GB, free: 9.578 MB / 0.698 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001619/0.2973, allocations: 0.7234 MB / 0.9893 GB, free: 8.797 MB / 0.698 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.836e-06/0.2973, allocations: 0 / 0.9893 GB, free: 8.797 MB / 0.698 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0003936/0.2977, allocations: 55.91 kB / 0.9893 GB, free: 8.742 MB / 0.698 GB Notification: Performance of postOpt tearingSystem (simulation): time 3.497e-06/0.2977, allocations: 0 / 0.9893 GB, free: 8.742 MB / 0.698 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.554e-05/0.2977, allocations: 8 kB / 0.9893 GB, free: 8.734 MB / 0.698 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 5.881e-06/0.2977, allocations: 3.938 kB / 0.9894 GB, free: 8.73 MB / 0.698 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.332e-06/0.2977, allocations: 4 kB / 0.9894 GB, free: 8.727 MB / 0.698 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001538/0.2993, allocations: 0.6936 MB / 0.99 GB, free: 7.98 MB / 0.698 GB Notification: Performance of postOpt removeConstants (simulation): time 4.137e-05/0.2993, allocations: 19.91 kB / 0.9901 GB, free: 7.961 MB / 0.698 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 7.163e-05/0.2994, allocations: 15.98 kB / 0.9901 GB, free: 7.945 MB / 0.698 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002716/0.2996, allocations: 19.92 kB / 0.9901 GB, free: 7.926 MB / 0.698 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001186/0.2998, allocations: 23.95 kB / 0.9901 GB, free: 7.902 MB / 0.698 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.312e-05/0.2998, allocations: 12 kB / 0.9901 GB, free: 7.891 MB / 0.698 GB Notification: Performance of sorting global known variables: time 0.0001551/0.3, allocations: 122.5 kB / 0.9902 GB, free: 7.773 MB / 0.698 GB Notification: Performance of sort global known variables: time 1.41e-07/0.3, allocations: 0 / 0.9902 GB, free: 7.773 MB / 0.698 GB Notification: Performance of remove unused functions: time 0.000544/0.3005, allocations: 76 kB / 0.9903 GB, free: 7.699 MB / 0.698 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 0.000191/0.3007, allocations: 121.1 kB / 0.9904 GB, free: 7.574 MB / 0.698 GB Notification: Performance of simCode: created initialization part: time 0.001155/0.3018, allocations: 0.5525 MB / 0.991 GB, free: 6.957 MB / 0.698 GB Notification: Performance of simCode: created event and clocks part: time 1.994e-06/0.3018, allocations: 0 / 0.991 GB, free: 6.957 MB / 0.698 GB Notification: Performance of simCode: created simulation system equations: time 0.4661/0.768, allocations: 295.4 kB / 0.9912 GB, free: 26.29 MB / 0.698 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005653/0.7686, allocations: 57 kB / 0.9913 GB, free: 26.29 MB / 0.698 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001511/0.7701, allocations: 0.8617 MB / 0.9921 GB, free: 25.83 MB / 0.698 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001214/0.7702, allocations: 134.4 kB / 0.9923 GB, free: 25.75 MB / 0.698 GB Notification: Performance of simCode: alias equations: time 0.0001351/0.7703, allocations: 22.44 kB / 0.9923 GB, free: 25.74 MB / 0.698 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 9.557e-05/0.7704, allocations: 21 kB / 0.9923 GB, free: 25.73 MB / 0.698 GB Notification: Performance of SimCode: time 1.002e-06/0.7704, allocations: 2.281 kB / 0.9923 GB, free: 25.73 MB / 0.698 GB Notification: Performance of Templates: time 0.008527/0.7789, allocations: 3.684 MB / 0.9959 GB, free: 25.42 MB / 0.698 GB " [Timeout remaining time 659] 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: 10.712642042897642]