Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.DevModels.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 0.001332/0.001332, allocations: 100.4 kB / 19.7 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 0.001017/0.001017, allocations: 215.3 kB / 23 MB, free: 2.945 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 1.007/1.007, allocations: 230.6 MB / 256.8 MB, free: 9.625 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 1.826/1.826, allocations: 334.3 MB / 0.6323 GB, free: 7.934 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.PKTwoCompartmentModel,tolerance=1e-06,outputFormat="empty",numberOfIntervals=500,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel") translateModel(Pharmacolibrary.DevModels.PKTwoCompartmentModel,tolerance=1e-06,outputFormat="empty",numberOfIntervals=500,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.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 0.001895/0.001895, allocations: 67.89 kB / 0.867 GB, free: 8.129 MB / 0.573 GB Notification: Performance of FrontEnd - Absyn->SCode: time 0.2004/0.2023, allocations: 112.8 MB / 0.9772 GB, free: 7.051 MB / 0.6824 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.PKTwoCompartmentModel): time 0.003013/0.2053, allocations: 2.249 MB / 0.9794 GB, free: 4.789 MB / 0.6824 GB Notification: Performance of NFInst.instExpressions: time 0.0009199/0.2062, allocations: 0.5845 MB / 0.98 GB, free: 4.203 MB / 0.6824 GB Notification: Performance of NFInst.updateImplicitVariability: time 0.0001026/0.2063, allocations: 4 kB / 0.98 GB, free: 4.199 MB / 0.6824 GB Notification: Performance of NFTyping.typeComponents: time 7.395e-05/0.2064, allocations: 31.7 kB / 0.98 GB, free: 4.168 MB / 0.6824 GB Notification: Performance of NFTyping.typeBindings: time 0.0002271/0.2066, allocations: 75.33 kB / 0.9801 GB, free: 4.094 MB / 0.6824 GB Notification: Performance of NFTyping.typeClassSections: time 0.0002006/0.2068, allocations: 63.92 kB / 0.9801 GB, free: 4.031 MB / 0.6824 GB Notification: Performance of NFFlatten.flatten: time 0.0002756/0.2071, allocations: 290.8 kB / 0.9804 GB, free: 3.746 MB / 0.6824 GB Notification: Performance of NFFlatten.resolveConnections: time 0.000149/0.2073, allocations: 40.77 kB / 0.9804 GB, free: 3.703 MB / 0.6824 GB Notification: Performance of NFEvalConstants.evaluate: time 0.000146/0.2074, allocations: 111.6 kB / 0.9805 GB, free: 3.594 MB / 0.6824 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001455/0.2076, allocations: 91.61 kB / 0.9806 GB, free: 3.504 MB / 0.6824 GB Notification: Performance of NFPackage.collectConstants: time 3.691e-05/0.2076, allocations: 20 kB / 0.9807 GB, free: 3.484 MB / 0.6824 GB Notification: Performance of NFFlatten.collectFunctions: time 3.68e-05/0.2076, allocations: 24 kB / 0.9807 GB, free: 3.461 MB / 0.6824 GB Notification: Performance of NFScalarize.scalarize: time 5.489e-05/0.2077, allocations: 59.7 kB / 0.9807 GB, free: 3.402 MB / 0.6824 GB Notification: Performance of NFVerifyModel.verify: time 0.0001064/0.2078, allocations: 99.59 kB / 0.9808 GB, free: 3.305 MB / 0.6824 GB Notification: Performance of NFConvertDAE.convert: time 0.0002792/0.2081, allocations: 243.1 kB / 0.9811 GB, free: 3.066 MB / 0.6824 GB Notification: Performance of FrontEnd - DAE generated: time 5.851e-06/0.2081, allocations: 0 / 0.9811 GB, free: 3.066 MB / 0.6824 GB Notification: Performance of FrontEnd: time 2.775e-06/0.2081, allocations: 4 kB / 0.9811 GB, free: 3.062 MB / 0.6824 GB Notification: Performance of Transformations before backend: time 7.193e-06/0.2081, allocations: 0 / 0.9811 GB, free: 3.062 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 0.0009077/0.209, allocations: 0.5185 MB / 0.9816 GB, free: 2.496 MB / 0.6824 GB Notification: Performance of prepare preOptimizeDAE: time 4.717e-05/0.209, allocations: 10.11 kB / 0.9816 GB, free: 2.488 MB / 0.6824 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 6.479e-05/0.2091, allocations: 24.8 kB / 0.9816 GB, free: 2.465 MB / 0.6824 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001513/0.2093, allocations: 160.8 kB / 0.9818 GB, free: 2.285 MB / 0.6824 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.88e-05/0.2093, allocations: 12.38 kB / 0.9818 GB, free: 2.273 MB / 0.6824 GB Notification: Performance of preOpt expandDerOperator (simulation): time 5.298e-05/0.2093, allocations: 31.88 kB / 0.9818 GB, free: 2.242 MB / 0.6824 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003729/0.2097, allocations: 250 kB / 0.982 GB, free: 1.977 MB / 0.6824 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.742e-05/0.2097, allocations: 4 kB / 0.982 GB, free: 1.973 MB / 0.6824 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.087e-05/0.2097, allocations: 4 kB / 0.982 GB, free: 1.969 MB / 0.6824 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.994e-06/0.2098, allocations: 4 kB / 0.982 GB, free: 1.965 MB / 0.6824 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003266/0.2101, allocations: 223.6 kB / 0.9823 GB, free: 1.734 MB / 0.6824 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0007499/0.2108, allocations: 464.7 kB / 0.9827 GB, free: 1.25 MB / 0.6824 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0003759/0.2112, allocations: 249.8 kB / 0.9829 GB, free: 0.9844 MB / 0.6824 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.0001755/0.2114, allocations: 147.5 kB / 0.9831 GB, free: 0.8281 MB / 0.6824 GB Notification: Performance of preOpt evalFunc (simulation): time 1.818e-05/0.2114, allocations: 7.938 kB / 0.9831 GB, free: 0.8203 MB / 0.6824 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0003658/0.2118, allocations: 339.9 kB / 0.9834 GB, free: 452 kB / 0.6824 GB Notification: Performance of pre-optimization done (n=31): time 2.995e-06/0.2118, allocations: 3.938 kB / 0.9834 GB, free: 448 kB / 0.6824 GB Notification: Performance of matching and sorting (n=33): time 0.001528/0.2133, allocations: 1.048 MB / 0.9844 GB, free: 15.3 MB / 0.698 GB Notification: Performance of inlineWhenForInitialization (initialization): time 8.737e-05/0.2134, allocations: 221.6 kB / 0.9847 GB, free: 15.03 MB / 0.698 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001346/0.2135, allocations: 162.2 kB / 0.9848 GB, free: 14.86 MB / 0.698 GB Notification: Performance of collectPreVariables (initialization): time 2.779e-05/0.2135, allocations: 41.69 kB / 0.9848 GB, free: 14.82 MB / 0.698 GB Notification: Performance of collectInitialEqns (initialization): time 7.071e-05/0.2136, allocations: 128.9 kB / 0.985 GB, free: 14.69 MB / 0.698 GB Notification: Performance of collectInitialBindings (initialization): time 6.849e-05/0.2137, allocations: 107.1 kB / 0.9851 GB, free: 14.58 MB / 0.698 GB Notification: Performance of simplifyInitialFunctions (initialization): time 8.157e-05/0.2138, allocations: 65.69 kB / 0.9851 GB, free: 14.51 MB / 0.698 GB Notification: Performance of setup shared object (initialization): time 9.451e-05/0.2139, allocations: 338.8 kB / 0.9855 GB, free: 14.17 MB / 0.698 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002148/0.2141, allocations: 195 kB / 0.9856 GB, free: 13.96 MB / 0.698 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002603/0.2143, allocations: 286.5 kB / 0.9859 GB, free: 13.62 MB / 0.698 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0008919/0.2152, allocations: 0.7377 MB / 0.9866 GB, free: 12.79 MB / 0.698 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.134e-06/0.2152, allocations: 0 / 0.9866 GB, free: 12.79 MB / 0.698 GB Notification: Performance of matching and sorting (n=48) (initialization): time 0.0005903/0.2158, allocations: 0.5152 MB / 0.9871 GB, free: 12.23 MB / 0.698 GB Notification: Performance of prepare postOptimizeDAE: time 5.549e-05/0.2159, allocations: 95 kB / 0.9872 GB, free: 12.12 MB / 0.698 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.055e-06/0.2159, allocations: 4 kB / 0.9872 GB, free: 12.11 MB / 0.698 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.744e-05/0.2159, allocations: 7.938 kB / 0.9872 GB, free: 12.11 MB / 0.698 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002242/0.2161, allocations: 71.89 kB / 0.9873 GB, free: 12.04 MB / 0.698 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.012e-05/0.2161, allocations: 11.88 kB / 0.9873 GB, free: 12.02 MB / 0.698 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001277/0.2163, allocations: 19.98 kB / 0.9873 GB, free: 12 MB / 0.698 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.974e-05/0.2163, allocations: 12 kB / 0.9874 GB, free: 11.99 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 intestine.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real blood.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real intestine.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real intestine.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real blood.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real blood.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real blood.rising:DISCRETE(fixed = true protected = true ) type: Boolean intestine.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 ($PRE.intestine.Cmin,intestine.Cmin,$PRE.intestine.Cmax,intestine.Cmax,$PRE.blood.Cmin,blood.Cmin,$PRE.blood.Cmax,blood.Cmax,$PRE.blood.rising,$PRE.intestine.rising,$PRE.periodicDose.pulse.count,$PRE.periodicDose.pulse.T_start,blood.rising,intestine.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 (45): * Single equations (assignments): 42 * 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 0.0002402/0.2165, allocations: 248.1 kB / 0.9876 GB, free: 11.73 MB / 0.698 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 2.816e-05/0.2166, allocations: 19.86 kB / 0.9876 GB, free: 11.71 MB / 0.698 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 4.315e-05/0.2166, allocations: 29.95 kB / 0.9876 GB, free: 11.68 MB / 0.698 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.627e-06/0.2166, allocations: 4 kB / 0.9876 GB, free: 11.68 MB / 0.698 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 5.34e-06/0.2166, allocations: 0 / 0.9876 GB, free: 11.68 MB / 0.698 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.238e-06/0.2166, allocations: 0 / 0.9876 GB, free: 11.68 MB / 0.698 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0008204/0.2174, allocations: 0.729 MB / 0.9884 GB, free: 10.89 MB / 0.698 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.344e-06/0.2174, allocations: 0 / 0.9884 GB, free: 10.89 MB / 0.698 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.000199/0.2176, allocations: 59.95 kB / 0.9884 GB, free: 10.83 MB / 0.698 GB Notification: Performance of postOpt tearingSystem (simulation): time 5.631e-06/0.2176, allocations: 4 kB / 0.9884 GB, free: 10.82 MB / 0.698 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.954e-05/0.2177, allocations: 8 kB / 0.9884 GB, free: 10.82 MB / 0.698 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.284e-06/0.2177, allocations: 3.938 kB / 0.9884 GB, free: 10.81 MB / 0.698 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.555e-06/0.2177, allocations: 3.938 kB / 0.9884 GB, free: 10.81 MB / 0.698 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.00077/0.2184, allocations: 0.7068 MB / 0.9891 GB, free: 10.05 MB / 0.698 GB Notification: Performance of postOpt removeConstants (simulation): time 2.485e-05/0.2185, allocations: 15.98 kB / 0.9891 GB, free: 10.04 MB / 0.698 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 4.074e-05/0.2185, allocations: 16.05 kB / 0.9891 GB, free: 10.02 MB / 0.698 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001218/0.2186, allocations: 23.98 kB / 0.9892 GB, free: 10 MB / 0.698 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 7.803e-05/0.2187, allocations: 31.89 kB / 0.9892 GB, free: 9.969 MB / 0.698 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.738e-05/0.2187, allocations: 8 kB / 0.9892 GB, free: 9.961 MB / 0.698 GB Notification: Performance of sorting global known variables: time 7.672e-05/0.2188, allocations: 127.2 kB / 0.9893 GB, free: 9.836 MB / 0.698 GB Notification: Performance of sort global known variables: time 9e-08/0.2188, allocations: 0 / 0.9893 GB, free: 9.836 MB / 0.698 GB Notification: Performance of remove unused functions: time 0.0003248/0.2191, allocations: 75.94 kB / 0.9894 GB, free: 9.762 MB / 0.698 GB Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 1 * Number of states: 6 (periodicDose.TotalCumulativeMass,periodicDose.variableDose.TotalCumulativeMass,intestine.C,intestine.AUC,blood.C,blood.AUC) * Number of discrete variables: 13 ($whenCondition1,$whenCondition2,$whenCondition3,$whenCondition4,$whenCondition5,periodicDose.pulse.T_start,periodicDose.pulse.count,intestine.Cmax,intestine.Cmin,intestine.rising,blood.Cmax,blood.Cmin,blood.rising) * Number of discrete states: 11 (periodicDose.pulse.count,blood.Cmin,$whenCondition3,blood.Cmax,$whenCondition2,blood.rising,intestine.Cmin,$whenCondition5,intestine.Cmax,$whenCondition4,intestine.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 0.0001114/0.2192, allocations: 123.2 kB / 0.9895 GB, free: 9.629 MB / 0.698 GB Notification: Performance of simCode: created initialization part: time 0.0005702/0.2198, allocations: 0.5492 MB / 0.9901 GB, free: 9.012 MB / 0.698 GB Notification: Performance of simCode: created event and clocks part: time 1.633e-06/0.2198, allocations: 0 / 0.9901 GB, free: 9.012 MB / 0.698 GB Notification: Performance of simCode: created simulation system equations: time 0.0002645/0.2201, allocations: 294 kB / 0.9903 GB, free: 8.688 MB / 0.698 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003908/0.2205, allocations: 68.44 kB / 0.9904 GB, free: 8.621 MB / 0.698 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001203/0.2217, allocations: 0.8785 MB / 0.9913 GB, free: 7.699 MB / 0.698 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001075/0.2218, allocations: 138.6 kB / 0.9914 GB, free: 7.543 MB / 0.698 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 6.415e-05/0.2218, allocations: 23.42 kB / 0.9914 GB, free: 7.52 MB / 0.698 GB Notification: Performance of SimCode: time 8.52e-07/0.2218, allocations: 0 / 0.9914 GB, free: 7.52 MB / 0.698 GB Notification: Performance of Templates: time 0.3903/0.6121, allocations: 3.148 MB / 0.9945 GB, free: 26.57 MB / 0.698 GB " [Timeout remaining time 659] make -j1 -f Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.makefile [Timeout 660] (rm -f Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.sim & ./Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel > Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 7.502671531168744]