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 0.00239/0.00239, 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 0.002874/0.002874, allocations: 169.9 kB / 22.45 MB, free: 2.109 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 1.573/1.573, 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 3.416/3.416, allocations: 274 MB / 0.5207 GB, free: 14.87 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.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: Performance of FrontEnd - loaded program: time 1.443e-06/1.443e-06, allocations: 0 / 0.7563 GB, free: 9.926 MB / 0.5887 GB Notification: Performance of FrontEnd - Absyn->SCode: time 3.105e-05/3.249e-05, allocations: 4.812 kB / 0.7563 GB, free: 9.922 MB / 0.5887 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKTwoCompartmentModel): time 0.003906/0.003939, allocations: 2.235 MB / 0.7584 GB, free: 7.699 MB / 0.5887 GB Notification: Performance of NFInst.instExpressions: time 0.001247/0.005185, allocations: 0.5845 MB / 0.759 GB, free: 7.117 MB / 0.5887 GB Notification: Performance of NFInst.updateImplicitVariability: time 0.0001123/0.005298, allocations: 7.938 kB / 0.759 GB, free: 7.109 MB / 0.5887 GB Notification: Performance of NFTyping.typeComponents: time 0.0001593/0.005457, allocations: 37.02 kB / 0.7591 GB, free: 7.074 MB / 0.5887 GB Notification: Performance of NFTyping.typeBindings: time 0.0002054/0.005662, allocations: 68.61 kB / 0.7591 GB, free: 7.031 MB / 0.5887 GB Notification: Performance of NFTyping.typeClassSections: time 0.0002216/0.005884, allocations: 63.84 kB / 0.7592 GB, free: 6.969 MB / 0.5887 GB Notification: Performance of NFFlatten.flatten: time 0.0004304/0.006314, allocations: 284.4 kB / 0.7595 GB, free: 6.699 MB / 0.5887 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001888/0.006503, allocations: 42.91 kB / 0.7595 GB, free: 6.66 MB / 0.5887 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0002378/0.006741, allocations: 151.7 kB / 0.7596 GB, free: 6.512 MB / 0.5887 GB Notification: Performance of NFSimplifyModel.simplify: time 0.000173/0.006914, allocations: 79.77 kB / 0.7597 GB, free: 6.434 MB / 0.5887 GB Notification: Performance of NFPackage.collectConstants: time 5.164e-05/0.006965, allocations: 28 kB / 0.7597 GB, free: 6.406 MB / 0.5887 GB Notification: Performance of NFFlatten.collectFunctions: time 4.959e-05/0.007015, allocations: 20 kB / 0.7598 GB, free: 6.387 MB / 0.5887 GB Notification: Performance of NFScalarize.scalarize: time 6.904e-05/0.007084, allocations: 47.83 kB / 0.7598 GB, free: 6.34 MB / 0.5887 GB Notification: Performance of NFVerifyModel.verify: time 0.0001415/0.007226, allocations: 83.83 kB / 0.7599 GB, free: 6.258 MB / 0.5887 GB Notification: Performance of NFConvertDAE.convert: time 0.0003778/0.007603, allocations: 235.3 kB / 0.7601 GB, free: 6.027 MB / 0.5887 GB Notification: Performance of FrontEnd - DAE generated: time 4.248e-06/0.007608, allocations: 0 / 0.7601 GB, free: 6.027 MB / 0.5887 GB Notification: Performance of FrontEnd: time 1.513e-06/0.007609, allocations: 0 / 0.7601 GB, free: 6.027 MB / 0.5887 GB Notification: Performance of Transformations before backend: time 6.452e-06/0.007616, allocations: 0 / 0.7601 GB, free: 6.027 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: 42 * Number of variables: 42 Notification: Performance of Generate backend data structure: time 0.001138/0.008753, allocations: 0.5228 MB / 0.7606 GB, free: 5.453 MB / 0.5887 GB Notification: Performance of prepare preOptimizeDAE: time 4.937e-05/0.008803, allocations: 12.03 kB / 0.7606 GB, free: 5.441 MB / 0.5887 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 8.484e-05/0.008888, allocations: 24.8 kB / 0.7607 GB, free: 5.418 MB / 0.5887 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002808/0.009168, allocations: 174.1 kB / 0.7608 GB, free: 5.223 MB / 0.5887 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.437e-05/0.009193, allocations: 12.7 kB / 0.7608 GB, free: 5.211 MB / 0.5887 GB Notification: Performance of preOpt expandDerOperator (simulation): time 5.95e-05/0.009252, allocations: 28.27 kB / 0.7609 GB, free: 5.184 MB / 0.5887 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0005095/0.009762, allocations: 246.8 kB / 0.7611 GB, free: 4.926 MB / 0.5887 GB Notification: Performance of preOpt findStateOrder (simulation): time 2.359e-05/0.009785, allocations: 3.938 kB / 0.7611 GB, free: 4.922 MB / 0.5887 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.454e-05/0.00981, allocations: 8 kB / 0.7611 GB, free: 4.914 MB / 0.5887 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.716e-06/0.009819, allocations: 8 kB / 0.7611 GB, free: 4.906 MB / 0.5887 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0004977/0.01032, allocations: 211.9 kB / 0.7613 GB, free: 4.688 MB / 0.5887 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0009756/0.01129, allocations: 456.9 kB / 0.7618 GB, free: 4.211 MB / 0.5887 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0005263/0.01182, allocations: 240.4 kB / 0.762 GB, free: 3.957 MB / 0.5887 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.000271/0.01209, allocations: 147.7 kB / 0.7621 GB, free: 3.801 MB / 0.5887 GB Notification: Performance of preOpt evalFunc (simulation): time 1.85e-05/0.01211, allocations: 4 kB / 0.7621 GB, free: 3.797 MB / 0.5887 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0005655/0.01267, allocations: 352.7 kB / 0.7625 GB, free: 3.406 MB / 0.5887 GB Notification: Performance of pre-optimization done (n=31): time 1.933e-06/0.01268, allocations: 0 / 0.7625 GB, free: 3.406 MB / 0.5887 GB Notification: Performance of matching and sorting (n=33): time 0.002747/0.01542, allocations: 1.05 MB / 0.7635 GB, free: 2.266 MB / 0.5887 GB Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001669/0.01559, allocations: 225.5 kB / 0.7637 GB, free: 1.996 MB / 0.5887 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002035/0.01579, allocations: 174.2 kB / 0.7639 GB, free: 1.816 MB / 0.5887 GB Notification: Performance of collectPreVariables (initialization): time 3.966e-05/0.01583, allocations: 33.7 kB / 0.7639 GB, free: 1.777 MB / 0.5887 GB Notification: Performance of collectInitialEqns (initialization): time 0.0001034/0.01594, allocations: 121 kB / 0.764 GB, free: 1.656 MB / 0.5887 GB Notification: Performance of collectInitialBindings (initialization): time 0.0001053/0.01604, allocations: 103.1 kB / 0.7641 GB, free: 1.555 MB / 0.5887 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001249/0.01617, allocations: 65.69 kB / 0.7642 GB, free: 1.484 MB / 0.5887 GB Notification: Performance of setup shared object (initialization): time 0.0001808/0.01635, allocations: 338.8 kB / 0.7645 GB, free: 1.145 MB / 0.5887 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003329/0.01668, allocations: 195 kB / 0.7647 GB, free: 0.9336 MB / 0.5887 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0004091/0.01709, allocations: 291.7 kB / 0.765 GB, free: 0.5938 MB / 0.5887 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.001413/0.0185, allocations: 0.745 MB / 0.7657 GB, free: 15.75 MB / 0.6043 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.846e-06/0.0185, allocations: 4 kB / 0.7657 GB, free: 15.75 MB / 0.6043 GB Notification: Performance of matching and sorting (n=49) (initialization): time 0.0009168/0.01942, allocations: 0.5278 MB / 0.7662 GB, free: 15.18 MB / 0.6043 GB Notification: Performance of prepare postOptimizeDAE: time 8.422e-05/0.01951, allocations: 93.05 kB / 0.7663 GB, free: 15.07 MB / 0.6043 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.695e-06/0.01951, allocations: 0 / 0.7663 GB, free: 15.07 MB / 0.6043 GB Notification: Performance of postOpt tearingSystem (initialization): time 2.347e-05/0.01954, allocations: 4.281 kB / 0.7663 GB, free: 15.07 MB / 0.6043 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003118/0.01985, allocations: 83.83 kB / 0.7664 GB, free: 14.98 MB / 0.6043 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.191e-05/0.01986, allocations: 4 kB / 0.7664 GB, free: 14.98 MB / 0.6043 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001977/0.02006, allocations: 19.98 kB / 0.7664 GB, free: 14.96 MB / 0.6043 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 3.302e-05/0.02009, allocations: 16 kB / 0.7664 GB, free: 14.95 MB / 0.6043 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 0.0003483/0.02044, allocations: 252.6 kB / 0.7667 GB, free: 14.68 MB / 0.6043 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 4.414e-05/0.02048, allocations: 23.84 kB / 0.7667 GB, free: 14.66 MB / 0.6043 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 6.681e-05/0.02055, allocations: 25.97 kB / 0.7667 GB, free: 14.63 MB / 0.6043 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.707e-06/0.02055, allocations: 4 kB / 0.7667 GB, free: 14.62 MB / 0.6043 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 6.032e-06/0.02056, allocations: 0 / 0.7667 GB, free: 14.62 MB / 0.6043 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.542e-06/0.02057, allocations: 7.984 kB / 0.7667 GB, free: 14.62 MB / 0.6043 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001237/0.0218, allocations: 0.7251 MB / 0.7674 GB, free: 13.83 MB / 0.6043 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.929e-06/0.02181, allocations: 4 kB / 0.7674 GB, free: 13.83 MB / 0.6043 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002958/0.0221, allocations: 51.91 kB / 0.7675 GB, free: 13.78 MB / 0.6043 GB Notification: Performance of postOpt tearingSystem (simulation): time 7.424e-06/0.02211, allocations: 4 kB / 0.7675 GB, free: 13.77 MB / 0.6043 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.118e-05/0.02214, allocations: 11.98 kB / 0.7675 GB, free: 13.76 MB / 0.6043 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.244e-06/0.02215, allocations: 4 kB / 0.7675 GB, free: 13.76 MB / 0.6043 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.332e-06/0.02215, allocations: 0 / 0.7675 GB, free: 13.76 MB / 0.6043 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001177/0.02332, allocations: 0.7115 MB / 0.7682 GB, free: 12.99 MB / 0.6043 GB Notification: Performance of postOpt removeConstants (simulation): time 3.099e-05/0.02336, allocations: 11.91 kB / 0.7682 GB, free: 12.98 MB / 0.6043 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 4.976e-05/0.0234, allocations: 12 kB / 0.7682 GB, free: 12.97 MB / 0.6043 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001807/0.02359, allocations: 15.98 kB / 0.7682 GB, free: 12.95 MB / 0.6043 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001046/0.02369, allocations: 31.89 kB / 0.7683 GB, free: 12.92 MB / 0.6043 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.306e-05/0.02371, allocations: 11.98 kB / 0.7683 GB, free: 12.91 MB / 0.6043 GB Notification: Performance of sorting global known variables: time 0.0001254/0.02384, allocations: 134.3 kB / 0.7684 GB, free: 12.78 MB / 0.6043 GB Notification: Performance of sort global known variables: time 8e-08/0.02384, allocations: 0 / 0.7684 GB, free: 12.78 MB / 0.6043 GB Notification: Performance of remove unused functions: time 0.0003687/0.02421, allocations: 68 kB / 0.7685 GB, free: 12.71 MB / 0.6043 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 0.0001483/0.02436, allocations: 111.2 kB / 0.7686 GB, free: 12.6 MB / 0.6043 GB Notification: Performance of simCode: created initialization part: time 0.0008831/0.02524, allocations: 0.5614 MB / 0.7691 GB, free: 11.97 MB / 0.6043 GB Notification: Performance of simCode: created event and clocks part: time 1.663e-06/0.02524, allocations: 0 / 0.7691 GB, free: 11.97 MB / 0.6043 GB Notification: Performance of simCode: created simulation system equations: time 0.0004234/0.02566, allocations: 298.1 kB / 0.7694 GB, free: 11.64 MB / 0.6043 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004744/0.02614, allocations: 72.38 kB / 0.7695 GB, free: 11.57 MB / 0.6043 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001582/0.02772, allocations: 0.7383 MB / 0.7702 GB, free: 10.81 MB / 0.6043 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001662/0.02789, allocations: 138.1 kB / 0.7703 GB, free: 10.66 MB / 0.6043 GB Notification: Performance of simCode: alias equations: time 0.0001119/0.028, allocations: 25.94 kB / 0.7704 GB, free: 10.63 MB / 0.6043 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 6.529e-05/0.02806, allocations: 20.5 kB / 0.7704 GB, free: 10.61 MB / 0.6043 GB Notification: Performance of SimCode: time 7.22e-07/0.02806, allocations: 0 / 0.7704 GB, free: 10.61 MB / 0.6043 GB Notification: Performance of Templates: time 0.008288/0.03635, allocations: 3.455 MB / 0.7738 GB, free: 7.348 MB / 0.6043 GB " [Timeout remaining time 660] 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: 9.00820055603981]