Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Lithium.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 0.0002858/0.0002858, 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 0.0002431/0.0002431, 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 0.1171/0.1171, allocations: 0 / 0, free: 0 / 0
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[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 0.6212/0.6212, allocations: 0 / 0, free: 0 / 0
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[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_1C_Lithium,startTime=0,stopTime=864000,tolerance=1e-06,numberOfIntervals=864000,outputFormat="empty",variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Lithium",simflags="-abortSlowSimulation -alarm=240   -lv LOG_STATS")
simulate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Lithium,startTime=0,stopTime=864000,tolerance=1e-06,numberOfIntervals=864000,outputFormat="empty",variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Lithium",simflags="-abortSlowSimulation -alarm=240   -lv LOG_STATS") [Timeout 900]
"Notification: Performance of FrontEnd - loaded program: time 2.033e-06/2.033e-06, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - Absyn->SCode: time 1.966e-05/2.169e-05, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Lithium): time 0.003411/0.003433, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.instExpressions: time 0.001688/0.005121, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001027/0.005223, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeComponents: time 0.0003422/0.005566, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeBindings: time 0.0002795/0.005845, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeClassSections: time 0.000384/0.006229, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.flatten: time 0.0002961/0.006525, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.resolveConnections: time 0.0001218/0.006647, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFEvalConstants.evaluate: time 0.0002515/0.006899, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFSimplifyModel.simplify: time 0.0001675/0.007066, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFPackage.collectConstants: time 3.561e-05/0.007102, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.collectFunctions: time 0.0002363/0.007338, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFScalarize.scalarize: time 8.362e-05/0.007422, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFVerifyModel.verify: time 0.0001166/0.007538, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFConvertDAE.convert: time 0.0004694/0.008008, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - DAE generated: time 4.673e-05/0.008054, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd: time 2.956e-06/0.008057, allocations: 0 / 0, free: 0 / 0
Notification: Performance of Transformations before backend: time 1.166e-05/0.008069, 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: 58
 * Number of variables: 58
Notification: Performance of Generate backend data structure: time 0.0007489/0.008818, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare preOptimizeDAE: time 6.248e-05/0.00888, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0002448/0.009125, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002298/0.009355, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.736e-05/0.009392, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt expandDerOperator (simulation): time 5.174e-05/0.009444, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003752/0.009819, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt findStateOrder (simulation): time 1.342e-05/0.009833, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.206e-05/0.009865, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt inlineArrayEqn (simulation): time 5.721e-06/0.00987, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001722/0.01004, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0006306/0.01067, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt comSubExp (simulation): time 0.0002328/0.01091, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt resolveLoops (simulation): time 9.053e-05/0.011, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evalFunc (simulation): time 1.9e-05/0.01102, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002412/0.01126, allocations: 0 / 0, free: 0 / 0
Notification: Performance of pre-optimization done (n=39): time 3.627e-06/0.01126, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=41): time 0.001178/0.01244, allocations: 0 / 0, free: 0 / 0
Notification: Performance of inlineWhenForInitialization (initialization): time 3.955e-05/0.01248, allocations: 0 / 0, free: 0 / 0
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001561/0.01263, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectPreVariables (initialization): time 4.725e-05/0.01268, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialEqns (initialization): time 6.075e-05/0.01274, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialBindings (initialization): time 9.063e-05/0.01283, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simplifyInitialFunctions (initialization): time 9.625e-05/0.01293, allocations: 0 / 0, free: 0 / 0
Notification: Performance of setup shared object (initialization): time 2.788e-05/0.01296, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preBalanceInitialSystem (initialization): time 9.683e-05/0.01305, allocations: 0 / 0, free: 0 / 0
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001214/0.01318, allocations: 0 / 0, free: 0 / 0
Notification: Performance of analyzeInitialSystem (initialization): time 0.0003172/0.01349, allocations: 0 / 0, free: 0 / 0
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.569e-06/0.0135, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=57) (initialization): time 0.0003846/0.01388, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare postOptimizeDAE: time 3.885e-05/0.01392, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.262e-06/0.01393, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (initialization): time 1.43e-05/0.01394, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001999/0.01414, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.232e-05/0.01415, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001378/0.01429, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 7.619e-05/0.01437, allocations: 0 / 0, free: 0 / 0
Warning: Assuming fixed start value for the following 10 variables:
         dose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         dose.absorptionLumen.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         dose.variableDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         central.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         dose.absorptionLumen.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         dose.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
         central.rising:DISCRETE(fixed = true protected = true )  type: Boolean
         dose.absorptionLumen.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: 23 ($PRE.dose.absorptionLumen.Cmin,dose.absorptionLumen.Cmin,$PRE.dose.absorptionLumen.Cmax,dose.absorptionLumen.Cmax,$PRE.central.Cmin,central.Cmin,$PRE.central.Cmax,central.Cmax,$PRE.central.rising,$PRE.dose.pulse.count,$PRE.dose.pulse.T_start,$PRE.dose.absorptionLumen.rising,CYP2C19.status,SLC22A2.status,central.rising,dose.pulse.count,dose.pulse.T_start,dose.absorptionLumen.rising,$whenCondition5,$whenCondition4,$whenCondition3,$whenCondition2,$whenCondition1)
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (52):
 * Single equations (assignments): 47
 * Array equations: 0
 * Algorithm blocks: 5
 * 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 0.0001982/0.01457, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt lateInlineFunction (simulation): time 9.746e-05/0.01466, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 6.062e-05/0.01472, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.258e-06/0.01473, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.607e-06/0.01473, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.639e-06/0.01474, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0006734/0.01541, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.477e-06/0.01541, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001622/0.01557, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (simulation): time 5.029e-06/0.01558, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.583e-05/0.01562, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.639e-06/0.01562, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.603e-06/0.01562, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.000508/0.01613, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeConstants (simulation): time 0.0001224/0.01625, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001185/0.01637, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001449/0.01652, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001036/0.01662, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 5.237e-05/0.01667, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sorting global known variables: time 7.909e-05/0.01675, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sort global known variables: time 7.063e-06/0.01676, allocations: 0 / 0, free: 0 / 0
Notification: Performance of remove unused functions: time 0.0005543/0.01731, allocations: 0 / 0, free: 0 / 0
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 7 (dose.TotalCumulativeMass,dose.absorptionLumen.C,dose.absorptionLumen.AUC,dose.variableDose.TotalCumulativeMass,central.C,central.AUC,elim.MExc)
 * Number of discrete variables: 15 ($whenCondition1,$whenCondition2,$whenCondition3,$whenCondition4,$whenCondition5,dose.absorptionLumen.Cmax,dose.absorptionLumen.Cmin,dose.absorptionLumen.rising,dose.pulse.T_start,dose.pulse.count,central.Cmax,central.Cmin,central.rising,SLC22A2.status,CYP2C19.status)
 * Number of discrete states: 13 (dose.pulse.count,SLC22A2.status,CYP2C19.status,dose.absorptionLumen.Cmin,$whenCondition5,dose.absorptionLumen.Cmax,$whenCondition4,dose.absorptionLumen.rising,central.Cmin,$whenCondition3,central.Cmax,$whenCondition2,central.rising)
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (33):
 * Single equations (assignments): 27
 * Array equations: 0
 * Algorithm blocks: 4
 * 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 0.0003082/0.01762, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created initialization part: time 0.0003888/0.01801, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created event and clocks part: time 1.734e-06/0.01801, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created simulation system equations: time 0.000173/0.01818, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005388/0.01872, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001287/0.02001, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: some other stuff during SimCode phase: time 8.893e-05/0.0201, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: alias equations: time 9.146e-05/0.02019, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0002419/0.02043, allocations: 0 / 0, free: 0 / 0
Notification: Performance of SimCode: time 2.725e-05/0.02046, allocations: 0 / 0, free: 0 / 0
Notification: Performance of Templates: time 0.00171/0.02217, allocations: 0 / 0, free: 0 / 0
"
[Timeout remaining time 897]
[Calling sys.exit(0), Time elapsed: 3.893852691166103]