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 0.0002448/0.0002448, 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 0.0001752/0.0001752, 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 0.09661/0.09661, 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 0.5632/0.5632, 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 1.042e-06/1.042e-06, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd - Absyn->SCode: time 8.095e-06/9.137e-06, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PK_2C_Ibuprofen): time 0.005163/0.005173, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.instExpressions: time 0.001827/0.006999, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.updateImplicitVariability: time 0.0001504/0.00715, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeComponents: time 0.0002028/0.007353, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeBindings: time 0.0005962/0.007949, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeClassSections: time 0.0003701/0.008319, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.flatten: time 0.0004141/0.008733, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.resolveConnections: time 0.0001727/0.008906, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFEvalConstants.evaluate: time 0.0003652/0.009271, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFSimplifyModel.simplify: time 0.0002303/0.009501, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFPackage.collectConstants: time 5.663e-05/0.009558, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.collectFunctions: time 4.308e-05/0.009601, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFScalarize.scalarize: time 7.358e-05/0.009675, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFVerifyModel.verify: time 0.0001491/0.009824, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFConvertDAE.convert: time 0.0004451/0.01027, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd - DAE generated: time 5.346e-05/0.01032, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd: time 9.82e-07/0.01032, allocations: 0 / 0, free: 0 / 0 Notification: Performance of Transformations before backend: time 5.551e-06/0.01033, 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 0.0008305/0.01116, allocations: 0 / 0, free: 0 / 0 Notification: Performance of prepare preOptimizeDAE: time 6.928e-05/0.01123, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001133/0.01134, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002691/0.01161, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt simplifyIfEquations (simulation): time 4.693e-05/0.01166, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt expandDerOperator (simulation): time 7.43e-05/0.01173, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004746/0.01221, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt findStateOrder (simulation): time 2.111e-05/0.01223, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt replaceEdgeChange (simulation): time 4.901e-05/0.01228, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.025e-06/0.01228, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002304/0.01252, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001074/0.01359, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt comSubExp (simulation): time 0.0002785/0.01387, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt resolveLoops (simulation): time 0.0001057/0.01397, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt evalFunc (simulation): time 2.147e-05/0.014, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002882/0.01428, allocations: 0 / 0, free: 0 / 0 Notification: Performance of pre-optimization done (n=46): time 6.222e-06/0.01429, allocations: 0 / 0, free: 0 / 0 Notification: Performance of matching and sorting (n=49): time 0.001615/0.0159, allocations: 0 / 0, free: 0 / 0 Notification: Performance of inlineWhenForInitialization (initialization): time 5.212e-05/0.01596, allocations: 0 / 0, free: 0 / 0 Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001676/0.01612, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectPreVariables (initialization): time 6.724e-05/0.01619, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectInitialEqns (initialization): time 7.285e-05/0.01626, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectInitialBindings (initialization): time 0.0001279/0.01639, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001394/0.01653, allocations: 0 / 0, free: 0 / 0 Notification: Performance of setup shared object (initialization): time 3.794e-05/0.01657, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001164/0.01669, allocations: 0 / 0, free: 0 / 0 Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001635/0.01685, allocations: 0 / 0, free: 0 / 0 Notification: Performance of analyzeInitialSystem (initialization): time 0.0004551/0.0173, allocations: 0 / 0, free: 0 / 0 Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.122e-05/0.01732, allocations: 0 / 0, free: 0 / 0 Notification: Performance of matching and sorting (n=73) (initialization): time 0.0006475/0.01796, allocations: 0 / 0, free: 0 / 0 Notification: Performance of prepare postOptimizeDAE: time 4.033e-05/0.018, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.041e-05/0.01801, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt tearingSystem (initialization): time 1.713e-05/0.01803, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.000328/0.01836, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.805e-05/0.01838, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0002093/0.01859, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt collapseArrayExpressions (initialization): time 5.062e-05/0.01864, 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 0.0002504/0.01889, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt lateInlineFunction (simulation): time 7.174e-05/0.01896, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt wrapFunctionCalls (simulation): time 7.738e-05/0.01904, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.611e-06/0.01904, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt constantLinearSystem (simulation): time 4.469e-06/0.01905, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifysemiLinear (simulation): time 7.704e-06/0.01905, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001028/0.02008, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.669e-06/0.02009, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002437/0.02033, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt tearingSystem (simulation): time 5.28e-06/0.02034, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt inputDerivativesUsed (simulation): time 4.785e-05/0.02038, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 5.631e-06/0.02039, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.664e-06/0.02039, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt symbolicJacobian (simulation): time 0.00075/0.02114, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt removeConstants (simulation): time 0.0001499/0.02129, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001531/0.02144, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001845/0.02163, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001412/0.02177, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt collapseArrayExpressions (simulation): time 4.095e-05/0.02181, allocations: 0 / 0, free: 0 / 0 Notification: Performance of sorting global known variables: time 9.275e-05/0.0219, allocations: 0 / 0, free: 0 / 0 Notification: Performance of sort global known variables: time 8.646e-06/0.02191, allocations: 0 / 0, free: 0 / 0 Notification: Performance of remove unused functions: time 0.0006485/0.02256, 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 0.0001638/0.02272, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created initialization part: time 0.0004444/0.02317, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created event and clocks part: time 1.523e-06/0.02317, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created simulation system equations: time 0.0002147/0.02338, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0008999/0.02428, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001619/0.0259, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: some other stuff during SimCode phase: time 7.925e-05/0.02598, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: alias equations: time 0.000131/0.02611, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003352/0.02645, allocations: 0 / 0, free: 0 / 0 Notification: Performance of SimCode: time 2.755e-05/0.02648, allocations: 0 / 0, free: 0 / 0 Notification: Performance of Templates: time 0.001381/0.02786, allocations: 0 / 0, free: 0 / 0 " [Timeout remaining time 900] [Calling sys.exit(0), Time elapsed: 1.4104733178392053]