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 0.001888/0.001888, allocations: 105.5 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 0.001937/0.001937, allocations: 219.6 kB / 22.25 MB, free: 3.578 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 1.641/1.641, allocations: 230.6 MB / 256 MB, free: 9.656 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 3.791/3.791, allocations: 335.2 MB / 0.6325 GB, free: 7.277 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.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: 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 0.003763/0.003763, allocations: 69.3 kB / 0.868 GB, free: 5.785 MB / 0.573 GB Notification: Performance of FrontEnd - Absyn->SCode: time 0.2604/0.2642, allocations: 112.8 MB / 0.9782 GB, free: 4.707 MB / 0.6824 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKTwoCompartmentModel): time 0.004166/0.2684, allocations: 2.23 MB / 0.9804 GB, free: 2.465 MB / 0.6824 GB Notification: Performance of NFInst.instExpressions: time 0.001579/0.2699, allocations: 0.5844 MB / 0.9809 GB, free: 1.879 MB / 0.6824 GB Notification: Performance of NFInst.updateImplicitVariability: time 9.336e-05/0.27, allocations: 4 kB / 0.9809 GB, free: 1.875 MB / 0.6824 GB Notification: Performance of NFTyping.typeComponents: time 0.00015/0.2702, allocations: 31.7 kB / 0.981 GB, free: 1.844 MB / 0.6824 GB Notification: Performance of NFTyping.typeBindings: time 0.0002003/0.2704, allocations: 67.41 kB / 0.981 GB, free: 1.777 MB / 0.6824 GB Notification: Performance of NFTyping.typeClassSections: time 0.0002181/0.2706, allocations: 71.84 kB / 0.9811 GB, free: 1.707 MB / 0.6824 GB Notification: Performance of NFFlatten.flatten: time 0.0003827/0.271, allocations: 270.8 kB / 0.9814 GB, free: 1.441 MB / 0.6824 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001591/0.2712, allocations: 40.56 kB / 0.9814 GB, free: 1.398 MB / 0.6824 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0001545/0.2713, allocations: 103.6 kB / 0.9815 GB, free: 1.297 MB / 0.6824 GB Notification: Performance of NFSimplifyModel.simplify: time 0.000187/0.2715, allocations: 95.53 kB / 0.9816 GB, free: 1.203 MB / 0.6824 GB Notification: Performance of NFPackage.collectConstants: time 4.565e-05/0.2715, allocations: 28 kB / 0.9816 GB, free: 1.176 MB / 0.6824 GB Notification: Performance of NFFlatten.collectFunctions: time 4.635e-05/0.2716, allocations: 20 kB / 0.9816 GB, free: 1.156 MB / 0.6824 GB Notification: Performance of NFScalarize.scalarize: time 5.944e-05/0.2716, allocations: 43.83 kB / 0.9817 GB, free: 1.113 MB / 0.6824 GB Notification: Performance of NFVerifyModel.verify: time 0.0001459/0.2718, allocations: 103.6 kB / 0.9818 GB, free: 1.012 MB / 0.6824 GB Notification: Performance of NFConvertDAE.convert: time 0.0003297/0.2721, allocations: 231 kB / 0.982 GB, free: 0.7852 MB / 0.6824 GB Notification: Performance of FrontEnd - DAE generated: time 5.079e-06/0.2721, allocations: 0 / 0.982 GB, free: 0.7852 MB / 0.6824 GB Notification: Performance of FrontEnd: time 1.503e-06/0.2721, allocations: 0 / 0.982 GB, free: 0.7852 MB / 0.6824 GB Notification: Performance of Transformations before backend: time 6.833e-06/0.2721, allocations: 4 kB / 0.982 GB, free: 0.7812 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: 42 * Number of variables: 42 Notification: Performance of Generate backend data structure: time 0.001063/0.2732, allocations: 0.5151 MB / 0.9825 GB, free: 220 kB / 0.6824 GB Notification: Performance of prepare preOptimizeDAE: time 4.718e-05/0.2732, allocations: 14.11 kB / 0.9825 GB, free: 208 kB / 0.6824 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 6.865e-05/0.2733, allocations: 24.8 kB / 0.9825 GB, free: 184 kB / 0.6824 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0003241/0.2736, allocations: 174.3 kB / 0.9827 GB, free: 15.98 MB / 0.698 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.053e-05/0.2737, allocations: 12.7 kB / 0.9827 GB, free: 15.97 MB / 0.698 GB Notification: Performance of preOpt expandDerOperator (simulation): time 6.185e-05/0.2737, allocations: 28.08 kB / 0.9827 GB, free: 15.94 MB / 0.698 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0005058/0.2742, allocations: 238.4 kB / 0.983 GB, free: 15.69 MB / 0.698 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.924e-05/0.2742, allocations: 0 / 0.983 GB, free: 15.69 MB / 0.698 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.058e-05/0.2743, allocations: 15.97 kB / 0.983 GB, free: 15.68 MB / 0.698 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.686e-06/0.2743, allocations: 8 kB / 0.983 GB, free: 15.67 MB / 0.698 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0004889/0.2748, allocations: 215.9 kB / 0.9832 GB, free: 15.45 MB / 0.698 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0009819/0.2758, allocations: 460.8 kB / 0.9836 GB, free: 14.97 MB / 0.698 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0005076/0.2763, allocations: 226 kB / 0.9838 GB, free: 14.73 MB / 0.698 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.000258/0.2765, allocations: 148.2 kB / 0.984 GB, free: 14.57 MB / 0.698 GB Notification: Performance of preOpt evalFunc (simulation): time 3.253e-05/0.2766, allocations: 7.938 kB / 0.984 GB, free: 14.56 MB / 0.698 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0005298/0.2771, allocations: 351.7 kB / 0.9843 GB, free: 14.17 MB / 0.698 GB Notification: Performance of pre-optimization done (n=31): time 1.503e-06/0.2771, allocations: 0 / 0.9843 GB, free: 14.17 MB / 0.698 GB Notification: Performance of matching and sorting (n=33): time 0.002205/0.2793, allocations: 1.047 MB / 0.9854 GB, free: 13.03 MB / 0.698 GB Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001753/0.2795, allocations: 221.6 kB / 0.9856 GB, free: 12.77 MB / 0.698 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002127/0.2797, allocations: 173.5 kB / 0.9857 GB, free: 12.59 MB / 0.698 GB Notification: Performance of collectPreVariables (initialization): time 4.253e-05/0.2797, allocations: 33.7 kB / 0.9858 GB, free: 12.55 MB / 0.698 GB Notification: Performance of collectInitialEqns (initialization): time 0.0001075/0.2798, allocations: 125 kB / 0.9859 GB, free: 12.43 MB / 0.698 GB Notification: Performance of collectInitialBindings (initialization): time 0.0001176/0.2799, allocations: 107.1 kB / 0.986 GB, free: 12.32 MB / 0.698 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001164/0.2801, allocations: 61.69 kB / 0.986 GB, free: 12.25 MB / 0.698 GB Notification: Performance of setup shared object (initialization): time 0.0002143/0.2803, allocations: 342.8 kB / 0.9864 GB, free: 11.91 MB / 0.698 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.000364/0.2806, allocations: 198.9 kB / 0.9866 GB, free: 11.7 MB / 0.698 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0004264/0.2811, allocations: 291.4 kB / 0.9868 GB, free: 11.35 MB / 0.698 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.001691/0.2828, allocations: 0.7541 MB / 0.9876 GB, free: 10.5 MB / 0.698 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.254e-06/0.2828, allocations: 0 / 0.9876 GB, free: 10.5 MB / 0.698 GB Notification: Performance of matching and sorting (n=49) (initialization): time 0.0009089/0.2837, allocations: 0.5266 MB / 0.9881 GB, free: 9.926 MB / 0.698 GB Notification: Performance of prepare postOptimizeDAE: time 8.708e-05/0.2838, allocations: 89.09 kB / 0.9882 GB, free: 9.82 MB / 0.698 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.743e-06/0.2838, allocations: 0 / 0.9882 GB, free: 9.82 MB / 0.698 GB Notification: Performance of postOpt tearingSystem (initialization): time 2.005e-05/0.2838, allocations: 8.219 kB / 0.9882 GB, free: 9.812 MB / 0.698 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003166/0.2841, allocations: 79.89 kB / 0.9883 GB, free: 9.734 MB / 0.698 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.453e-05/0.2841, allocations: 7.938 kB / 0.9883 GB, free: 9.727 MB / 0.698 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001967/0.2843, allocations: 19.98 kB / 0.9883 GB, free: 9.707 MB / 0.698 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.932e-05/0.2843, allocations: 12 kB / 0.9883 GB, free: 9.695 MB / 0.698 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 0.0003465/0.2847, allocations: 264.9 kB / 0.9886 GB, free: 9.414 MB / 0.698 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 3.907e-05/0.2847, allocations: 19.91 kB / 0.9886 GB, free: 9.395 MB / 0.698 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 7.87e-05/0.2848, allocations: 25.97 kB / 0.9886 GB, free: 9.367 MB / 0.698 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.785e-06/0.2848, allocations: 4 kB / 0.9886 GB, free: 9.363 MB / 0.698 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 7.024e-06/0.2848, allocations: 0 / 0.9886 GB, free: 9.363 MB / 0.698 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 9.618e-06/0.2848, allocations: 7.984 kB / 0.9886 GB, free: 9.355 MB / 0.698 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001246/0.2861, allocations: 0.7289 MB / 0.9893 GB, free: 8.566 MB / 0.698 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.034e-06/0.2861, allocations: 0 / 0.9893 GB, free: 8.566 MB / 0.698 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002949/0.2864, allocations: 51.91 kB / 0.9894 GB, free: 8.516 MB / 0.698 GB Notification: Performance of postOpt tearingSystem (simulation): time 5.46e-06/0.2864, allocations: 4 kB / 0.9894 GB, free: 8.512 MB / 0.698 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.891e-05/0.2864, allocations: 8 kB / 0.9894 GB, free: 8.504 MB / 0.698 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.468e-06/0.2864, allocations: 7.984 kB / 0.9894 GB, free: 8.496 MB / 0.698 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.082e-06/0.2864, allocations: 0 / 0.9894 GB, free: 8.496 MB / 0.698 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001179/0.2876, allocations: 0.7076 MB / 0.9901 GB, free: 7.738 MB / 0.698 GB Notification: Performance of postOpt removeConstants (simulation): time 3.368e-05/0.2876, allocations: 11.91 kB / 0.9901 GB, free: 7.727 MB / 0.698 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.498e-05/0.2877, allocations: 16 kB / 0.9901 GB, free: 7.711 MB / 0.698 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001834/0.2879, allocations: 15.98 kB / 0.9901 GB, free: 7.695 MB / 0.698 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.000104/0.288, allocations: 28.02 kB / 0.9901 GB, free: 7.668 MB / 0.698 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.817e-05/0.288, allocations: 19.98 kB / 0.9902 GB, free: 7.648 MB / 0.698 GB Notification: Performance of sorting global known variables: time 0.0001248/0.2881, allocations: 123.2 kB / 0.9903 GB, free: 7.527 MB / 0.698 GB Notification: Performance of sort global known variables: time 1.1e-07/0.2881, allocations: 4 kB / 0.9903 GB, free: 7.523 MB / 0.698 GB Notification: Performance of remove unused functions: time 0.0003657/0.2885, allocations: 68 kB / 0.9904 GB, free: 7.457 MB / 0.698 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 0.0001581/0.2886, allocations: 121.2 kB / 0.9905 GB, free: 7.328 MB / 0.698 GB Notification: Performance of simCode: created initialization part: time 0.4229/0.7115, allocations: 0.5504 MB / 0.991 GB, free: 26.09 MB / 0.698 GB Notification: Performance of simCode: created event and clocks part: time 2.755e-06/0.7115, allocations: 3.312 kB / 0.991 GB, free: 26.09 MB / 0.698 GB Notification: Performance of simCode: created simulation system equations: time 0.000301/0.7118, allocations: 298.2 kB / 0.9913 GB, free: 25.9 MB / 0.698 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005212/0.7123, allocations: 57.73 kB / 0.9913 GB, free: 25.9 MB / 0.698 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001364/0.7137, allocations: 0.9029 MB / 0.9922 GB, free: 25.39 MB / 0.698 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001024/0.7138, allocations: 133.8 kB / 0.9924 GB, free: 25.32 MB / 0.698 GB Notification: Performance of simCode: alias equations: time 0.0001072/0.7139, allocations: 26.89 kB / 0.9924 GB, free: 25.31 MB / 0.698 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 6.064e-05/0.7139, allocations: 23.31 kB / 0.9924 GB, free: 25.3 MB / 0.698 GB Notification: Performance of SimCode: time 9.02e-07/0.714, allocations: 0 / 0.9924 GB, free: 25.3 MB / 0.698 GB Notification: Performance of Templates: time 0.008028/0.722, allocations: 3.738 MB / 0.9961 GB, free: 24.98 MB / 0.698 GB " [Timeout remaining time 659] 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: 10.360859470907599]