Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PK_2C_Ibuprofen.conf.json loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo", uses=false) [Timeout 180] "[:1:22-1:33:writable] Warning: Modelica only supports 32-bit signed integers! Transforming: 13743895347 into a real Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo): time 0.0002756/0.0002756, allocations: 0 / 0, free: 0 / 0 " [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 0.0002177/0.0002177, allocations: 0 / 0, free: 0 / 0 " [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 0.09266/0.09266, allocations: 0 / 0, free: 0 / 0 " [Timeout remaining time 180] 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/Drugs/ATC/B/B02BD15.mo:9:22-9:32:writable] Warning: Modelica only supports 32-bit signed integers! Transforming: 6000000000 into a real [/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 0.6427/0.6427, allocations: 0 / 0, free: 0 / 0 " [Timeout remaining time 179] 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: simulate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PK_2C_Ibuprofen,startTime=0,stopTime=86400,tolerance=1e-06,numberOfIntervals=86400,outputFormat="empty",variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PK_2C_Ibuprofen",simflags="-abortSlowSimulation -alarm=240 -lv LOG_STATS") simulate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PK_2C_Ibuprofen,startTime=0,stopTime=86400,tolerance=1e-06,numberOfIntervals=86400,outputFormat="empty",variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PK_2C_Ibuprofen",simflags="-abortSlowSimulation -alarm=240 -lv LOG_STATS") [Timeout 900] "Notification: Performance of FrontEnd - loaded program: time 6.51e-07/6.51e-07, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd - Absyn->SCode: time 1.471e-05/1.536e-05, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PK_2C_Ibuprofen): time 0.004663/0.004678, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.instExpressions: time 0.001434/0.006112, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.updateImplicitVariability: time 0.0001207/0.006233, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeComponents: time 0.0001549/0.006387, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeBindings: time 0.0003996/0.006787, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeClassSections: time 0.0002821/0.007069, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.flatten: time 0.000352/0.007421, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.resolveConnections: time 0.0001422/0.007563, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFEvalConstants.evaluate: time 0.0003116/0.007875, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFSimplifyModel.simplify: time 0.0002306/0.008106, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFPackage.collectConstants: time 3.996e-05/0.008146, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.collectFunctions: time 4.294e-05/0.008188, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFScalarize.scalarize: time 7.174e-05/0.00826, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFVerifyModel.verify: time 0.0001501/0.00841, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFConvertDAE.convert: time 0.0003431/0.008753, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd - DAE generated: time 4.839e-05/0.008802, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd: time 1.223e-06/0.008803, allocations: 0 / 0, free: 0 / 0 Notification: Performance of Transformations before backend: time 5.761e-06/0.008809, allocations: 0 / 0, free: 0 / 0 Notification: Model statistics after passing the front-end and creating the data structures used by the back-end: * Number of equations: 67 * Number of variables: 67 Notification: Performance of Generate backend data structure: time 0.0007621/0.009571, allocations: 0 / 0, free: 0 / 0 Notification: Performance of prepare preOptimizeDAE: time 6.132e-05/0.009632, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001038/0.009736, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002486/0.009985, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt simplifyIfEquations (simulation): time 4.265e-05/0.01003, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt expandDerOperator (simulation): time 5.537e-05/0.01008, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003837/0.01047, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt findStateOrder (simulation): time 1.756e-05/0.01048, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.612e-05/0.01052, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.174e-06/0.01053, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002011/0.01073, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0009551/0.01168, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt comSubExp (simulation): time 0.0002339/0.01192, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt resolveLoops (simulation): time 8.611e-05/0.012, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt evalFunc (simulation): time 1.862e-05/0.01202, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002502/0.01227, allocations: 0 / 0, free: 0 / 0 Notification: Performance of pre-optimization done (n=46): time 4.619e-06/0.01228, allocations: 0 / 0, free: 0 / 0 Notification: Performance of matching and sorting (n=49): time 0.001327/0.0136, allocations: 0 / 0, free: 0 / 0 Notification: Performance of inlineWhenForInitialization (initialization): time 4.947e-05/0.01365, allocations: 0 / 0, free: 0 / 0 Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001475/0.0138, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectPreVariables (initialization): time 5.126e-05/0.01385, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectInitialEqns (initialization): time 6.467e-05/0.01392, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectInitialBindings (initialization): time 0.0001128/0.01403, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001039/0.01413, allocations: 0 / 0, free: 0 / 0 Notification: Performance of setup shared object (initialization): time 2.704e-05/0.01416, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preBalanceInitialSystem (initialization): time 9.347e-05/0.01425, allocations: 0 / 0, free: 0 / 0 Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001297/0.01438, allocations: 0 / 0, free: 0 / 0 Notification: Performance of analyzeInitialSystem (initialization): time 0.0003323/0.01472, allocations: 0 / 0, free: 0 / 0 Notification: Performance of solveInitialSystemEqSystem (initialization): time 6.062e-06/0.01472, allocations: 0 / 0, free: 0 / 0 Notification: Performance of matching and sorting (n=73) (initialization): time 0.0003888/0.01511, allocations: 0 / 0, free: 0 / 0 Notification: Performance of prepare postOptimizeDAE: time 3.763e-05/0.01515, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.897e-06/0.01516, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt tearingSystem (initialization): time 1.781e-05/0.01518, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003554/0.01553, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.45e-05/0.01555, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001837/0.01573, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt collapseArrayExpressions (initialization): time 3.592e-05/0.01577, allocations: 0 / 0, free: 0 / 0 Warning: Assuming fixed start value for the following 14 variables: central.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real periodicDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true ) \"Total dose adminitrated by this source\" type: Real periodicDose.absorptionLumen.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" 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 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 periodicDose.absorptionLumen.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real periodicDose.absorptionLumen.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 peripheral.rising:DISCRETE(fixed = true protected = true ) type: Boolean periodicDose.absorptionLumen.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: 16 * Number of states: 0 () * Number of discrete variables: 29 ($PRE.peripheral.Cmin,peripheral.Cmin,$PRE.peripheral.Cmax,peripheral.Cmax,$PRE.periodicDose.absorptionLumen.Cmin,periodicDose.absorptionLumen.Cmin,$PRE.periodicDose.absorptionLumen.Cmax,periodicDose.absorptionLumen.Cmax,$PRE.central.Cmin,central.Cmin,$PRE.central.Cmax,central.Cmax,$PRE.peripheral.rising,$PRE.periodicDose.pulse.count,$PRE.periodicDose.pulse.T_start,$PRE.periodicDose.absorptionLumen.rising,$PRE.central.rising,peripheral.rising,periodicDose.pulse.count,periodicDose.pulse.T_start,periodicDose.absorptionLumen.rising,central.rising,$whenCondition6,$whenCondition5,$whenCondition4,$whenCondition3,$whenCondition2,$whenCondition1,$whenCondition7) * Number of discrete states: 0 () * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for initialization (69): * Single equations (assignments): 65 * Array equations: 0 * Algorithm blocks: 4 * 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 0.0002666/0.01603, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt lateInlineFunction (simulation): time 5.828e-05/0.01609, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt wrapFunctionCalls (simulation): time 6.489e-05/0.01615, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.33e-06/0.01616, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt constantLinearSystem (simulation): time 4.538e-06/0.01616, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.209e-06/0.01617, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0007061/0.01688, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.647e-06/0.01688, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002704/0.01715, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt tearingSystem (simulation): time 5.47e-06/0.01716, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.785e-05/0.01719, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 5.921e-06/0.0172, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.633e-06/0.0172, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004802/0.01768, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt removeConstants (simulation): time 0.0001247/0.01781, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001412/0.01795, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001649/0.01811, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001023/0.01821, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.171e-05/0.01825, allocations: 0 / 0, free: 0 / 0 Notification: Performance of sorting global known variables: time 7.24e-05/0.01832, allocations: 0 / 0, free: 0 / 0 Notification: Performance of sort global known variables: time 6.963e-06/0.01833, allocations: 0 / 0, free: 0 / 0 Notification: Performance of remove unused functions: time 0.0005883/0.01891, allocations: 0 / 0, free: 0 / 0 Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 1 * Number of states: 9 (central.C,central.AUC,elim.MExc,periodicDose.TotalCumulativeMass,periodicDose.absorptionLumen.C,periodicDose.absorptionLumen.AUC,periodicDose.variableDose.TotalCumulativeMass,peripheral.C,peripheral.AUC) * Number of discrete variables: 18 ($whenCondition7,$whenCondition1,$whenCondition2,$whenCondition3,$whenCondition4,$whenCondition5,$whenCondition6,central.Cmax,central.Cmin,central.rising,periodicDose.absorptionLumen.Cmax,periodicDose.absorptionLumen.Cmin,periodicDose.absorptionLumen.rising,periodicDose.pulse.T_start,periodicDose.pulse.count,peripheral.Cmax,peripheral.Cmin,peripheral.rising) * Number of discrete states: 16 (periodicDose.pulse.count,peripheral.Cmin,$whenCondition6,peripheral.Cmax,$whenCondition5,peripheral.rising,periodicDose.absorptionLumen.Cmin,$whenCondition4,periodicDose.absorptionLumen.Cmax,$whenCondition3,periodicDose.absorptionLumen.rising,central.Cmin,$whenCondition2,central.Cmax,$whenCondition1,central.rising) * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for simulation (40): * Single equations (assignments): 35 * Array equations: 0 * Algorithm blocks: 3 * 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 0.0001542/0.01907, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created initialization part: time 0.0003811/0.01945, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created event and clocks part: time 6.232e-06/0.01946, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created simulation system equations: time 0.0001926/0.01965, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0006555/0.0203, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001397/0.0217, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: some other stuff during SimCode phase: time 8.14e-05/0.02178, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: alias equations: time 0.0001217/0.0219, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0002916/0.02219, allocations: 0 / 0, free: 0 / 0 Notification: Performance of SimCode: time 2.763e-05/0.02222, allocations: 0 / 0, free: 0 / 0 Notification: Performance of Templates: time 0.001458/0.02368, allocations: 0 / 0, free: 0 / 0 " [Timeout remaining time 900] [Calling sys.exit(0), Time elapsed: 1.4440361969172955]