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 0.0003079/0.0003079, 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 0.0002503/0.0002503, 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 0.1254/0.1254, 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 0.5941/0.5941, 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 1.002e-06/1.002e-06, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - Absyn->SCode: time 1.375e-05/1.475e-05, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Lithium): time 0.003659/0.003673, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.instExpressions: time 0.001893/0.005566, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001056/0.005671, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeComponents: time 0.000435/0.006107, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeBindings: time 0.0002804/0.006387, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeClassSections: time 0.0004286/0.006816, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.flatten: time 0.0003416/0.007157, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.resolveConnections: time 0.0001432/0.0073, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFEvalConstants.evaluate: time 0.0002726/0.007573, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFSimplifyModel.simplify: time 0.0001732/0.007746, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFPackage.collectConstants: time 4.733e-05/0.007793, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.collectFunctions: time 0.000254/0.008047, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFScalarize.scalarize: time 0.0001169/0.008164, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFVerifyModel.verify: time 0.0001226/0.008287, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFConvertDAE.convert: time 0.0004779/0.008765, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - DAE generated: time 4.278e-05/0.008808, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd: time 1.432e-06/0.008809, allocations: 0 / 0, free: 0 / 0
Notification: Performance of Transformations before backend: time 8.587e-06/0.008818, 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 0.0008922/0.00971, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare preOptimizeDAE: time 7.371e-05/0.009784, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0002872/0.01007, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0003081/0.01038, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt simplifyIfEquations (simulation): time 6.04e-05/0.01044, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt expandDerOperator (simulation): time 5.761e-05/0.0105, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004419/0.01094, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt findStateOrder (simulation): time 1.715e-05/0.01096, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt replaceEdgeChange (simulation): time 4.116e-05/0.011, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.682e-06/0.011, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001938/0.0112, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0007257/0.01192, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt comSubExp (simulation): time 0.0002874/0.01221, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt resolveLoops (simulation): time 9.606e-05/0.01231, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evalFunc (simulation): time 2.843e-05/0.01234, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002987/0.01263, allocations: 0 / 0, free: 0 / 0
Notification: Performance of pre-optimization done (n=39): time 4.579e-06/0.01264, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=41): time 0.001465/0.0141, allocations: 0 / 0, free: 0 / 0
Notification: Performance of inlineWhenForInitialization (initialization): time 5.712e-05/0.01416, allocations: 0 / 0, free: 0 / 0
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001461/0.01431, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectPreVariables (initialization): time 6.49e-05/0.01437, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialEqns (initialization): time 6.727e-05/0.01444, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialBindings (initialization): time 0.0001044/0.01454, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001141/0.01466, allocations: 0 / 0, free: 0 / 0
Notification: Performance of setup shared object (initialization): time 2.697e-05/0.01468, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preBalanceInitialSystem (initialization): time 9.924e-05/0.01478, allocations: 0 / 0, free: 0 / 0
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001305/0.01491, allocations: 0 / 0, free: 0 / 0
Notification: Performance of analyzeInitialSystem (initialization): time 0.0003265/0.01524, allocations: 0 / 0, free: 0 / 0
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.568e-06/0.01524, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=57) (initialization): time 0.0004036/0.01565, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare postOptimizeDAE: time 4.323e-05/0.01569, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.356e-06/0.0157, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (initialization): time 1.75e-05/0.01572, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002165/0.01593, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.359e-05/0.01595, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001443/0.01609, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 6.895e-05/0.01616, 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 0.0002271/0.01639, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.000109/0.0165, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 8.055e-05/0.01658, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.62e-06/0.01658, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.241e-06/0.01659, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.573e-06/0.0166, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0007098/0.01731, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 5.65e-06/0.01731, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001986/0.01751, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (simulation): time 5.771e-06/0.01752, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.813e-05/0.01755, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 7.444e-06/0.01756, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.435e-06/0.01756, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005416/0.01811, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeConstants (simulation): time 0.0001242/0.01823, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001309/0.01836, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001536/0.01851, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001245/0.01864, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 6.265e-05/0.0187, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sorting global known variables: time 8.069e-05/0.01878, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sort global known variables: time 7.004e-06/0.01879, allocations: 0 / 0, free: 0 / 0
Notification: Performance of remove unused functions: time 0.0005431/0.01933, 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 0.0004397/0.01977, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created initialization part: time 0.0004313/0.0202, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created event and clocks part: time 4.608e-06/0.02021, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created simulation system equations: time 0.0001901/0.0204, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0006046/0.021, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.00145/0.02245, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: some other stuff during SimCode phase: time 9.287e-05/0.02255, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: alias equations: time 9.244e-05/0.02264, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.000269/0.02291, allocations: 0 / 0, free: 0 / 0
Notification: Performance of SimCode: time 3.854e-05/0.02295, allocations: 0 / 0, free: 0 / 0
Notification: Performance of Templates: time 0.001919/0.02486, allocations: 0 / 0, free: 0 / 0
"
[Timeout remaining time 898]
[Calling sys.exit(0), Time elapsed: 3.672691573854536]