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 0.0002155/0.0002155, 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 0.0001979/0.0001979, 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 0.1055/0.1055, 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 0.6484/0.6484, 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 9.52e-07/9.52e-07, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - Absyn->SCode: time 1.009e-05/1.104e-05, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PBPK_OralDoseGUTWholeBody): time 0.008342/0.008353, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.instExpressions: time 0.002847/0.0112, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFInst.updateImplicitVariability: time 0.0003461/0.01155, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeComponents: time 0.0004907/0.01204, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeBindings: time 0.001195/0.01323, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFTyping.typeClassSections: time 0.0007031/0.01394, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.flatten: time 0.00124/0.01517, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.resolveConnections: time 0.002496/0.01767, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFEvalConstants.evaluate: time 0.002185/0.01986, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFSimplifyModel.simplify: time 0.002391/0.02225, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFPackage.collectConstants: time 0.000301/0.02255, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFFlatten.collectFunctions: time 0.0002879/0.02284, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFScalarize.scalarize: time 0.0005678/0.0234, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFVerifyModel.verify: time 0.0008609/0.02426, allocations: 0 / 0, free: 0 / 0
Notification: Performance of NFConvertDAE.convert: time 0.001899/0.02616, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd - DAE generated: time 0.0003142/0.02648, allocations: 0 / 0, free: 0 / 0
Notification: Performance of FrontEnd: time 4.699e-06/0.02648, allocations: 0 / 0, free: 0 / 0
Notification: Performance of Transformations before backend: time 1.754e-05/0.0265, 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 0.003052/0.02955, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare preOptimizeDAE: time 0.0001023/0.02965, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0003822/0.03004, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0009693/0.03101, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.0001145/0.03112, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt expandDerOperator (simulation): time 0.000327/0.03145, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt clockPartitioning (simulation): time 0.002195/0.03364, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt findStateOrder (simulation): time 4.095e-05/0.03368, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0002112/0.03389, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.658e-05/0.03392, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.00119/0.03511, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.006771/0.04188, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt comSubExp (simulation): time 0.0008437/0.04272, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt resolveLoops (simulation): time 0.0005349/0.04326, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt evalFunc (simulation): time 5.421e-05/0.04331, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.001081/0.0444, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preOpt simplifyInStream (simulation): time 0.003527/0.04792, allocations: 0 / 0, free: 0 / 0
Notification: Performance of pre-optimization done (n=113): time 8.365e-06/0.04793, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=113): time 0.002148/0.05008, allocations: 0 / 0, free: 0 / 0
Notification: Performance of inlineWhenForInitialization (initialization): time 3.389e-05/0.05011, allocations: 0 / 0, free: 0 / 0
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002405/0.05035, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectPreVariables (initialization): time 0.0002039/0.05056, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialEqns (initialization): time 0.0002054/0.05076, allocations: 0 / 0, free: 0 / 0
Notification: Performance of collectInitialBindings (initialization): time 0.0003718/0.05113, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0005524/0.05169, allocations: 0 / 0, free: 0 / 0
Notification: Performance of setup shared object (initialization): time 4.094e-05/0.05173, allocations: 0 / 0, free: 0 / 0
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0005581/0.05229, allocations: 0 / 0, free: 0 / 0
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0006162/0.0529, allocations: 0 / 0, free: 0 / 0
Notification: Performance of analyzeInitialSystem (initialization): time 0.001664/0.05457, allocations: 0 / 0, free: 0 / 0
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.2e-05/0.05458, allocations: 0 / 0, free: 0 / 0
Notification: Performance of matching and sorting (n=166) (initialization): time 0.001878/0.05646, allocations: 0 / 0, free: 0 / 0
Notification: Performance of prepare postOptimizeDAE: time 3.406e-05/0.05649, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.351e-05/0.0565, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (initialization): time 2.356e-05/0.05653, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001645/0.05817, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 3.012e-05/0.0582, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0008197/0.05902, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0002638/0.05929, 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 0.0005273/0.05981, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0002451/0.06006, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.002249/0.06231, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.139e-05/0.06232, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt constantLinearSystem (simulation): time 7.384e-06/0.06233, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.039e-05/0.06234, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001985/0.06432, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 7.514e-06/0.06433, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.001115/0.06544, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt tearingSystem (simulation): time 1.004e-05/0.06545, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 0.000137/0.06559, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.354e-05/0.0656, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.495e-06/0.06561, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001874/0.06748, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt removeConstants (simulation): time 0.0001048/0.06759, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0003408/0.06793, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0006489/0.06858, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0002198/0.06879, allocations: 0 / 0, free: 0 / 0
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.0001667/0.06896, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sorting global known variables: time 0.0001434/0.06911, allocations: 0 / 0, free: 0 / 0
Notification: Performance of sort global known variables: time 1.343e-05/0.06912, allocations: 0 / 0, free: 0 / 0
Notification: Performance of remove unused functions: time 0.001147/0.07027, 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 0.0003303/0.0706, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created initialization part: time 0.001429/0.07202, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created event and clocks part: time 2.024e-06/0.07203, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created simulation system equations: time 0.0006158/0.07264, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001216/0.07386, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003086/0.07694, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0002047/0.07715, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: alias equations: time 0.0006928/0.07784, allocations: 0 / 0, free: 0 / 0
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.001498/0.07934, allocations: 0 / 0, free: 0 / 0
Notification: Performance of SimCode: time 4.61e-05/0.07939, allocations: 0 / 0, free: 0 / 0
Notification: Performance of Templates: time 0.00304/0.08243, allocations: 0 / 0, free: 0 / 0
"
[Timeout remaining time 900]
[Calling sys.exit(0), Time elapsed: 1.4547570766881108]