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 0.001287/0.001287, allocations: 104.3 kB / 19.71 MB, free: 440 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 0.001693/0.001693, allocations: 208.9 kB / 22.99 MB, free: 2.98 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 1.048/1.048, allocations: 230.6 MB / 256.8 MB, free: 9.613 MB / 202.7 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 1.784/1.784, allocations: 334.2 MB / 0.6323 GB, free: 7.906 MB / 442.7 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.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 0.001684/0.001684, allocations: 71.89 kB / 0.867 GB, free: 8.008 MB / 0.573 GB Notification: Performance of FrontEnd - Absyn->SCode: time 0.1703/0.172, allocations: 112.8 MB / 0.9772 GB, free: 6.93 MB / 0.6824 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.PKTwoCompartmentModelOral): time 0.002697/0.1747, allocations: 2.25 MB / 0.9794 GB, free: 4.668 MB / 0.6824 GB Notification: Performance of NFInst.instExpressions: time 0.0008966/0.1756, allocations: 0.5883 MB / 0.98 GB, free: 4.078 MB / 0.6824 GB Notification: Performance of NFInst.updateImplicitVariability: time 0.0001094/0.1757, allocations: 0 / 0.98 GB, free: 4.078 MB / 0.6824 GB Notification: Performance of NFTyping.typeComponents: time 6.363e-05/0.1758, allocations: 27.72 kB / 0.98 GB, free: 4.051 MB / 0.6824 GB Notification: Performance of NFTyping.typeBindings: time 0.000202/0.176, allocations: 75.33 kB / 0.9801 GB, free: 3.977 MB / 0.6824 GB Notification: Performance of NFTyping.typeClassSections: time 0.0002017/0.1762, allocations: 71.91 kB / 0.9801 GB, free: 3.906 MB / 0.6824 GB Notification: Performance of NFFlatten.flatten: time 0.0002454/0.1764, allocations: 278.8 kB / 0.9804 GB, free: 3.633 MB / 0.6824 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001371/0.1765, allocations: 52.73 kB / 0.9804 GB, free: 3.578 MB / 0.6824 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0001449/0.1767, allocations: 99.66 kB / 0.9805 GB, free: 3.48 MB / 0.6824 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001267/0.1768, allocations: 103.5 kB / 0.9806 GB, free: 3.379 MB / 0.6824 GB Notification: Performance of NFPackage.collectConstants: time 3.169e-05/0.1768, allocations: 24 kB / 0.9807 GB, free: 3.355 MB / 0.6824 GB Notification: Performance of NFFlatten.collectFunctions: time 2.649e-05/0.1769, allocations: 20 kB / 0.9807 GB, free: 3.336 MB / 0.6824 GB Notification: Performance of NFScalarize.scalarize: time 4.007e-05/0.1769, allocations: 51.78 kB / 0.9807 GB, free: 3.285 MB / 0.6824 GB Notification: Performance of NFVerifyModel.verify: time 8.552e-05/0.177, allocations: 99.64 kB / 0.9808 GB, free: 3.188 MB / 0.6824 GB Notification: Performance of NFConvertDAE.convert: time 0.000216/0.1772, allocations: 243 kB / 0.9811 GB, free: 2.949 MB / 0.6824 GB Notification: Performance of FrontEnd - DAE generated: time 3.997e-06/0.1772, allocations: 0 / 0.9811 GB, free: 2.949 MB / 0.6824 GB Notification: Performance of FrontEnd: time 1.753e-06/0.1772, allocations: 0 / 0.9811 GB, free: 2.949 MB / 0.6824 GB Notification: Performance of Transformations before backend: time 6.442e-06/0.1772, allocations: 0 / 0.9811 GB, free: 2.949 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 0.0007213/0.178, allocations: 0.5335 MB / 0.9816 GB, free: 2.367 MB / 0.6824 GB Notification: Performance of prepare preOptimizeDAE: time 3.755e-05/0.178, allocations: 10.11 kB / 0.9816 GB, free: 2.359 MB / 0.6824 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 5.318e-05/0.178, allocations: 24.8 kB / 0.9816 GB, free: 2.336 MB / 0.6824 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001207/0.1782, allocations: 154.2 kB / 0.9818 GB, free: 2.16 MB / 0.6824 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.73e-05/0.1782, allocations: 12.38 kB / 0.9818 GB, free: 2.148 MB / 0.6824 GB Notification: Performance of preOpt expandDerOperator (simulation): time 4.023e-05/0.1782, allocations: 31.89 kB / 0.9818 GB, free: 2.117 MB / 0.6824 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.000303/0.1785, allocations: 246 kB / 0.982 GB, free: 1.855 MB / 0.6824 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.442e-05/0.1785, allocations: 0 / 0.982 GB, free: 1.855 MB / 0.6824 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.921e-05/0.1786, allocations: 12 kB / 0.982 GB, free: 1.844 MB / 0.6824 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.021e-06/0.1786, allocations: 4 kB / 0.982 GB, free: 1.84 MB / 0.6824 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002535/0.1788, allocations: 219.6 kB / 0.9823 GB, free: 1.613 MB / 0.6824 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0006435/0.1795, allocations: 476.6 kB / 0.9827 GB, free: 1.117 MB / 0.6824 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0002836/0.1797, allocations: 221.8 kB / 0.9829 GB, free: 0.8789 MB / 0.6824 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.0001316/0.1799, allocations: 139.5 kB / 0.9831 GB, free: 0.7305 MB / 0.6824 GB Notification: Performance of preOpt evalFunc (simulation): time 1.423e-05/0.1799, allocations: 3.984 kB / 0.9831 GB, free: 0.7266 MB / 0.6824 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002935/0.1802, allocations: 357.5 kB / 0.9834 GB, free: 336 kB / 0.6824 GB Notification: Performance of pre-optimization done (n=30): time 1.633e-06/0.1802, allocations: 0 / 0.9834 GB, free: 336 kB / 0.6824 GB Notification: Performance of matching and sorting (n=32): time 0.001371/0.1816, allocations: 1.027 MB / 0.9844 GB, free: 15.21 MB / 0.698 GB Notification: Performance of inlineWhenForInitialization (initialization): time 7.902e-05/0.1816, allocations: 225.6 kB / 0.9846 GB, free: 14.94 MB / 0.698 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001147/0.1817, allocations: 162.2 kB / 0.9848 GB, free: 14.77 MB / 0.698 GB Notification: Performance of collectPreVariables (initialization): time 2.294e-05/0.1818, allocations: 37.69 kB / 0.9848 GB, free: 14.73 MB / 0.698 GB Notification: Performance of collectInitialEqns (initialization): time 6.083e-05/0.1818, allocations: 124.9 kB / 0.9849 GB, free: 14.61 MB / 0.698 GB Notification: Performance of collectInitialBindings (initialization): time 5.594e-05/0.1819, allocations: 107.1 kB / 0.985 GB, free: 14.5 MB / 0.698 GB Notification: Performance of simplifyInitialFunctions (initialization): time 6.721e-05/0.182, allocations: 61.97 kB / 0.9851 GB, free: 14.43 MB / 0.698 GB Notification: Performance of setup shared object (initialization): time 8.217e-05/0.182, allocations: 342.8 kB / 0.9854 GB, free: 14.09 MB / 0.698 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001742/0.1822, allocations: 195.2 kB / 0.9856 GB, free: 13.88 MB / 0.698 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002026/0.1824, allocations: 278 kB / 0.9859 GB, free: 13.54 MB / 0.698 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0007087/0.1831, allocations: 0.7302 MB / 0.9866 GB, free: 12.72 MB / 0.698 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.006e-06/0.1831, allocations: 0 / 0.9866 GB, free: 12.72 MB / 0.698 GB Notification: Performance of matching and sorting (n=47) (initialization): time 0.0004709/0.1836, allocations: 0.5112 MB / 0.9871 GB, free: 12.16 MB / 0.698 GB Notification: Performance of prepare postOptimizeDAE: time 4.594e-05/0.1836, allocations: 89.11 kB / 0.9872 GB, free: 12.06 MB / 0.698 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.614e-06/0.1837, allocations: 7.984 kB / 0.9872 GB, free: 12.05 MB / 0.698 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.645e-05/0.1837, allocations: 4 kB / 0.9872 GB, free: 12.05 MB / 0.698 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.000166/0.1838, allocations: 63.91 kB / 0.9872 GB, free: 11.98 MB / 0.698 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 6.923e-06/0.1838, allocations: 4 kB / 0.9872 GB, free: 11.98 MB / 0.698 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.811e-05/0.1839, allocations: 19.98 kB / 0.9873 GB, free: 11.96 MB / 0.698 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.67e-05/0.184, allocations: 20.03 kB / 0.9873 GB, free: 11.94 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 0.0001994/0.1842, allocations: 258.6 kB / 0.9875 GB, free: 11.67 MB / 0.698 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 2.176e-05/0.1842, allocations: 15.91 kB / 0.9875 GB, free: 11.65 MB / 0.698 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.723e-05/0.1842, allocations: 25.97 kB / 0.9876 GB, free: 11.62 MB / 0.698 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.735e-06/0.1842, allocations: 4 kB / 0.9876 GB, free: 11.62 MB / 0.698 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 5.61e-06/0.1842, allocations: 0 / 0.9876 GB, free: 11.62 MB / 0.698 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.131e-06/0.1842, allocations: 7.969 kB / 0.9876 GB, free: 11.61 MB / 0.698 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0006636/0.1849, allocations: 0.7272 MB / 0.9883 GB, free: 10.83 MB / 0.698 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.964e-06/0.1849, allocations: 4 kB / 0.9883 GB, free: 10.82 MB / 0.698 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001421/0.185, allocations: 51.95 kB / 0.9883 GB, free: 10.77 MB / 0.698 GB Notification: Performance of postOpt tearingSystem (simulation): time 5.099e-06/0.185, allocations: 4 kB / 0.9883 GB, free: 10.77 MB / 0.698 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.617e-05/0.1851, allocations: 8 kB / 0.9884 GB, free: 10.76 MB / 0.698 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.096e-06/0.1851, allocations: 3.938 kB / 0.9884 GB, free: 10.76 MB / 0.698 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.152e-06/0.1851, allocations: 0 / 0.9884 GB, free: 10.76 MB / 0.698 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005939/0.1857, allocations: 0.6935 MB / 0.989 GB, free: 10.01 MB / 0.698 GB Notification: Performance of postOpt removeConstants (simulation): time 2.314e-05/0.1857, allocations: 19.97 kB / 0.9891 GB, free: 9.992 MB / 0.698 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.27e-05/0.1857, allocations: 15.98 kB / 0.9891 GB, free: 9.977 MB / 0.698 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 8.813e-05/0.1858, allocations: 19.92 kB / 0.9891 GB, free: 9.957 MB / 0.698 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 7.018e-05/0.1859, allocations: 27.95 kB / 0.9891 GB, free: 9.93 MB / 0.698 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.423e-05/0.1859, allocations: 12 kB / 0.9891 GB, free: 9.918 MB / 0.698 GB Notification: Performance of sorting global known variables: time 6.435e-05/0.1859, allocations: 122.3 kB / 0.9892 GB, free: 9.801 MB / 0.698 GB Notification: Performance of sort global known variables: time 6e-08/0.1859, allocations: 0 / 0.9892 GB, free: 9.801 MB / 0.698 GB Notification: Performance of remove unused functions: time 0.0002109/0.1862, allocations: 68 kB / 0.9893 GB, free: 9.734 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 9.491e-05/0.1863, allocations: 129 kB / 0.9894 GB, free: 9.602 MB / 0.698 GB Notification: Performance of simCode: created initialization part: time 0.0004657/0.1867, allocations: 0.5562 MB / 0.99 GB, free: 8.98 MB / 0.698 GB Notification: Performance of simCode: created event and clocks part: time 2.144e-06/0.1867, allocations: 0 / 0.99 GB, free: 8.98 MB / 0.698 GB Notification: Performance of simCode: created simulation system equations: time 0.0002019/0.1869, allocations: 290.1 kB / 0.9902 GB, free: 8.66 MB / 0.698 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002921/0.1872, allocations: 60.53 kB / 0.9903 GB, free: 8.602 MB / 0.698 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001152/0.1884, allocations: 0.8933 MB / 0.9912 GB, free: 7.668 MB / 0.698 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 8.563e-05/0.1885, allocations: 138.8 kB / 0.9913 GB, free: 7.512 MB / 0.698 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 5.149e-05/0.1885, allocations: 19.44 kB / 0.9913 GB, free: 7.492 MB / 0.698 GB Notification: Performance of SimCode: time 7.11e-07/0.1885, allocations: 4 kB / 0.9913 GB, free: 7.488 MB / 0.698 GB Notification: Performance of Templates: time 0.3468/0.5353, allocations: 3.112 MB / 0.9944 GB, free: 26.55 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 > Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 7.797224133042619]