Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PBPK_OralDoseGUTWholeBody.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 0.0001735/0.0001735, 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 0.000159/0.000159, 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 0.1124/0.1124, 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 0.6148/0.6148, 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.PBPK_OralDoseGUTWholeBody,startTime=0,stopTime=3600,tolerance=1e-06,numberOfIntervals=3600,outputFormat="empty",variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PBPK_OralDoseGUTWholeBody",simflags="-abortSlowSimulation -alarm=240   -lv LOG_STATS")
simulate(Pharmacolibrary.Examples.PBPK_OralDoseGUTWholeBody,startTime=0,stopTime=3600,tolerance=1e-06,numberOfIntervals=3600,outputFormat="empty",variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PBPK_OralDoseGUTWholeBody",simflags="-abortSlowSimulation -alarm=240   -lv LOG_STATS") [Timeout 900]
"Notification: Performance of FrontEnd - loaded program: time 4.81e-07/4.81e-07, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - Absyn->SCode: time 1.442e-05/1.49e-05, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PBPK_OralDoseGUTWholeBody): time 0.00907/0.009085, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.instExpressions: time 0.003111/0.0122, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003729/0.01257, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeComponents: time 0.000508/0.01308, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeBindings: time 0.001234/0.01431, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeClassSections: time 0.0007372/0.01505, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.flatten: time 0.001243/0.01629, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.resolveConnections: time 0.002644/0.01894, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFEvalConstants.evaluate: time 0.002379/0.02131, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFSimplifyModel.simplify: time 0.002697/0.02401, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFPackage.collectConstants: time 0.0003514/0.02436, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.collectFunctions: time 0.0003338/0.0247, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFScalarize.scalarize: time 0.0006455/0.02534, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFVerifyModel.verify: time 0.0009933/0.02634, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFConvertDAE.convert: time 0.002066/0.0284, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - DAE generated: time 0.0003435/0.02875, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd: time 1.794e-06/0.02875, allocations: 0 / 0, free: 0 / 0
Notification: Performance of Transformations before backend: time 1.34e-05/0.02876, 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: 307
 * Number of variables: 307
Notification: Performance of Generate backend data structure: time 0.00355/0.03231, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare preOptimizeDAE: time 0.0001133/0.03242, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0004573/0.03288, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evaluateParameters (simulation): time 0.001155/0.03404, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001393/0.03418, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0003779/0.03455, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002535/0.03709, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt findStateOrder (simulation): time 4.607e-05/0.03713, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0002291/0.03736, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt inlineArrayEqn (simulation): time 3.083e-05/0.03739, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001402/0.0388, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.007812/0.04661, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt comSubExp (simulation): time 0.0009659/0.04758, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt resolveLoops (simulation): time 0.0005862/0.04816, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evalFunc (simulation): time 5.495e-05/0.04822, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.001145/0.04936, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt simplifyInStream (simulation): time 0.003971/0.05333, allocations: 0 / 0, free: 0 / 0
Notification: Performance of pre-optimization done (n=113): time 9.157e-06/0.05334, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=113): time 0.002418/0.05576, allocations: 0 / 0, free: 0 / 0
Notification: Performance of inlineWhenForInitialization (initialization): time 4.493e-05/0.05581, allocations: 0 / 0, free: 0 / 0
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002901/0.0561, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectPreVariables (initialization): time 0.0002472/0.05634, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialEqns (initialization): time 0.0002366/0.05658, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialBindings (initialization): time 0.0004247/0.057, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0006395/0.05764, allocations: 0 / 0, free: 0 / 0
Notification: Performance of setup shared object (initialization): time 5.037e-05/0.05769, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0006316/0.05833, allocations: 0 / 0, free: 0 / 0
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0007196/0.05905, allocations: 0 / 0, free: 0 / 0
Notification: Performance of analyzeInitialSystem (initialization): time 0.001908/0.06095, allocations: 0 / 0, free: 0 / 0
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.391e-05/0.06097, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=166) (initialization): time 0.002115/0.06308, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare postOptimizeDAE: time 3.981e-05/0.06312, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.683e-05/0.06314, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (initialization): time 3.212e-05/0.06317, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001838/0.06501, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 3.511e-05/0.06504, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0009528/0.066, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0002981/0.06629, allocations: 0 / 0, free: 0 / 0
Warning: Assuming fixed start value for the following 17 variables:
         singleDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         singleDose.variableDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         venous.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         lungs.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         arterial.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         adipose.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         bone.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         brain.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         heart.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         muscle.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         skin.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         gut.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         spleen.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         liver.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         kidney.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         gonads.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         rest.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 34
 * Number of states: 0 ()
 * Number of discrete variables: 5 (singleDose.pulse.count,$PRE.singleDose.pulse.count,singleDose.pulse.T_start,$PRE.singleDose.pulse.T_start,$whenCondition1)
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (165):
 * Single equations (assignments): 164
 * Array equations: 0
 * Algorithm blocks: 1
 * 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 0.0006611/0.06696, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0002728/0.06723, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.002542/0.06977, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.294e-05/0.06978, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt constantLinearSystem (simulation): time 7.564e-06/0.06979, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.472e-05/0.06981, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.002303/0.07211, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 7.855e-06/0.07212, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001256/0.07337, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (simulation): time 1.154e-05/0.07338, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.0001611/0.07354, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.535e-05/0.07356, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.917e-06/0.07356, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.002009/0.07557, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeConstants (simulation): time 0.0001121/0.07569, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0003574/0.07604, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0006734/0.07672, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0002438/0.07696, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0001739/0.07713, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sorting global known variables: time 0.0001469/0.07728, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sort global known variables: time 1.369e-05/0.07729, allocations: 0 / 0, free: 0 / 0
Notification: Performance of remove unused functions: time 0.001186/0.07848, allocations: 0 / 0, free: 0 / 0
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 4
 * Number of states: 34 (singleDose.TotalCumulativeMass,singleDose.variableDose.TotalCumulativeMass,venous.M,venous.AUC,lungs.M,lungs.AUC,arterial.M,arterial.AUC,adipose.M,adipose.AUC,bone.M,bone.AUC,brain.M,brain.AUC,heart.M,heart.AUC,muscle.M,muscle.AUC,skin.M,skin.AUC,gut.M,gut.AUC,spleen.M,spleen.AUC,liver.M,liver.AUC,kidney.M,kidney.AUC,kidneyElim.MExc,liverElim.MExc,gonads.M,gonads.AUC,rest.M,rest.AUC)
 * Number of discrete variables: 3 ($whenCondition1,singleDose.pulse.T_start,singleDose.pulse.count)
 * Number of discrete states: 1 (singleDose.pulse.count)
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (114):
 * Single equations (assignments): 112
 * Array equations: 0
 * Algorithm blocks: 0
 * 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 0.0004575/0.07894, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created initialization part: time 0.001524/0.08046, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created event and clocks part: time 1.896e-05/0.08048, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created simulation system equations: time 0.0006512/0.08113, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001325/0.08246, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003208/0.08566, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0002151/0.08588, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: alias equations: time 0.0007367/0.08662, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.00161/0.08823, allocations: 0 / 0, free: 0 / 0
Notification: Performance of SimCode: time 4.625e-05/0.08827, allocations: 0 / 0, free: 0 / 0
Notification: Performance of Templates: time 0.003192/0.09147, allocations: 0 / 0, free: 0 / 0
"
[Timeout remaining time 900]
[Calling sys.exit(0), Time elapsed: 1.420064453035593]