Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_2C_Ibuprofen.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"[<interactive>: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 0.0002297/0.0002297, 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 0.0001757/0.0001757, 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 0.1099/0.1099, 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 0.672/0.672, 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_PKPG_2C_Ibuprofen,startTime=0,stopTime=86400,tolerance=1e-06,numberOfIntervals=86400,outputFormat="empty",variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_2C_Ibuprofen",simflags="-abortSlowSimulation -alarm=240   -lv LOG_STATS")
simulate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_2C_Ibuprofen,startTime=0,stopTime=86400,tolerance=1e-06,numberOfIntervals=86400,outputFormat="empty",variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_2C_Ibuprofen",simflags="-abortSlowSimulation -alarm=240   -lv LOG_STATS") [Timeout 900]
"Notification: Performance of FrontEnd - loaded program: time 1.242e-06/1.242e-06, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - Absyn->SCode: time 1.892e-05/2.017e-05, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_2C_Ibuprofen): time 0.004803/0.004823, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.instExpressions: time 0.001732/0.006556, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001308/0.006686, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeComponents: time 0.0003957/0.007082, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeBindings: time 0.0004207/0.007503, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeClassSections: time 0.0004172/0.00792, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.flatten: time 0.0003965/0.008316, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.resolveConnections: time 0.0001663/0.008483, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFEvalConstants.evaluate: time 0.0003363/0.008819, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFSimplifyModel.simplify: time 0.0002499/0.009069, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFPackage.collectConstants: time 4.529e-05/0.009114, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.collectFunctions: time 0.0002447/0.009359, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFScalarize.scalarize: time 9.995e-05/0.009459, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFVerifyModel.verify: time 0.0001736/0.009632, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFConvertDAE.convert: time 0.0005437/0.01018, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - DAE generated: time 5.893e-05/0.01023, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd: time 2.885e-06/0.01024, allocations: 0 / 0, free: 0 / 0
Notification: Performance of Transformations before backend: time 6.713e-06/0.01024, 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: 81
 * Number of variables: 81
Notification: Performance of Generate backend data structure: time 0.0008774/0.01112, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare preOptimizeDAE: time 7.156e-05/0.01119, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0002456/0.01144, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evaluateParameters (simulation): time 0.000285/0.01172, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt simplifyIfEquations (simulation): time 4.076e-05/0.01176, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt expandDerOperator (simulation): time 5.881e-05/0.01182, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004586/0.01228, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt findStateOrder (simulation): time 1.685e-05/0.0123, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.909e-05/0.01234, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.665e-06/0.01235, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002382/0.01258, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.00103/0.01361, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt comSubExp (simulation): time 0.00026/0.01387, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001066/0.01398, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evalFunc (simulation): time 1.752e-05/0.014, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002771/0.01428, allocations: 0 / 0, free: 0 / 0
Notification: Performance of pre-optimization done (n=52): time 3.928e-06/0.01428, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=55): time 0.001511/0.01579, allocations: 0 / 0, free: 0 / 0
Notification: Performance of inlineWhenForInitialization (initialization): time 4.712e-05/0.01584, allocations: 0 / 0, free: 0 / 0
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001884/0.01603, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectPreVariables (initialization): time 5.682e-05/0.01608, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialEqns (initialization): time 7.242e-05/0.01615, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialBindings (initialization): time 0.0001196/0.01627, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001145/0.01639, allocations: 0 / 0, free: 0 / 0
Notification: Performance of setup shared object (initialization): time 3.076e-05/0.01642, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001235/0.01654, allocations: 0 / 0, free: 0 / 0
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001493/0.01669, allocations: 0 / 0, free: 0 / 0
Notification: Performance of analyzeInitialSystem (initialization): time 0.0004036/0.0171, allocations: 0 / 0, free: 0 / 0
Notification: Performance of solveInitialSystemEqSystem (initialization): time 6.122e-06/0.0171, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=79) (initialization): time 0.000488/0.01759, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare postOptimizeDAE: time 4.419e-05/0.01763, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.965e-06/0.01764, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (initialization): time 1.653e-05/0.01766, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002774/0.01794, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.588e-05/0.01795, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001898/0.01814, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 6.725e-05/0.01821, 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: 31 ($PRE.peripheral.Cmin,peripheral.Cmin,$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,$PRE.central.rising,CYP2C19.status,SLC22A2.status,peripheral.rising,periodicDose.pulse.count,periodicDose.pulse.T_start,periodicDose.absorptionLumen.rising,central.rising,$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 (73):
 * Single equations (assignments): 67
 * Array equations: 0
 * Algorithm blocks: 6
 * 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 0.0002408/0.01845, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001159/0.01857, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 7.386e-05/0.01864, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.999e-06/0.01864, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.21e-06/0.01865, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.31e-06/0.01866, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0008285/0.01948, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.178e-06/0.01949, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002116/0.0197, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (simulation): time 4.899e-06/0.0197, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.912e-05/0.01974, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 5.591e-06/0.01975, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.663e-06/0.01975, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0006223/0.02037, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeConstants (simulation): time 0.0001491/0.02052, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001619/0.02068, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001725/0.02086, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001142/0.02097, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 5.916e-05/0.02103, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sorting global known variables: time 0.0001064/0.02114, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sort global known variables: time 9.949e-06/0.02115, allocations: 0 / 0, free: 0 / 0
Notification: Performance of remove unused functions: time 0.0005947/0.02174, 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: 20 ($whenCondition7,$whenCondition1,$whenCondition2,$whenCondition3,$whenCondition4,$whenCondition5,$whenCondition6,central.Cmax,central.Cmin,central.rising,periodicDose.absorptionLumen.Cmax,periodicDose.absorptionLumen.Cmin,periodicDose.absorptionLumen.rising,periodicDose.pulse.T_start,periodicDose.pulse.count,peripheral.Cmax,peripheral.Cmin,peripheral.rising,SLC22A2.status,CYP2C19.status)
 * Number of discrete states: 18 (periodicDose.pulse.count,CYP2C19.status,SLC22A2.status,peripheral.Cmin,$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 (44):
 * Single equations (assignments): 37
 * Array equations: 0
 * Algorithm blocks: 5
 * 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 0.0002793/0.02202, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created initialization part: time 0.0004502/0.02247, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created event and clocks part: time 1.493e-06/0.02247, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created simulation system equations: time 0.0002238/0.0227, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0006586/0.02335, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001491/0.02485, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001058/0.02495, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: alias equations: time 0.0001182/0.02507, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003252/0.02539, allocations: 0 / 0, free: 0 / 0
Notification: Performance of SimCode: time 2.762e-05/0.02542, allocations: 0 / 0, free: 0 / 0
Notification: Performance of Templates: time 0.001821/0.02724, allocations: 0 / 0, free: 0 / 0
"
[Timeout remaining time 900]
[Calling sys.exit(0), Time elapsed: 1.7195631582289934]