Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo): time 0.07129/0.07129, allocations: 81.5 kB / 19.44 MB, free: 336 kB / 13.93 MB
"
[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 0.002603/0.002603, allocations: 177.2 kB / 22.76 MB, free: 1.652 MB / 18.57 MB
"
[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 1.701/1.701, allocations: 177.1 MB / 203.1 MB, free: 5.266 MB / 186.7 MB
"
[Timeout remaining time 178]
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/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 7.658/7.658, allocations: 274.5 MB / 0.5215 GB, free: 14.19 MB / 458.7 MB
"
[Timeout remaining time 172]
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: translateModel(Pharmacolibrary.Examples.PKPG_1C_Gentamicin,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin")
translateModel(Pharmacolibrary.Examples.PKPG_1C_Gentamicin,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.343e-06/1.343e-06, allocations: 0 / 0.6472 GB, free: 39.1 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.593e-05/2.727e-05, allocations: 3.406 kB / 0.6472 GB, free: 39.1 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKPG_1C_Gentamicin): time 0.003331/0.003358, allocations: 2.46 MB / 0.6496 GB, free: 37.5 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.001325/0.004683, allocations: 0.9221 MB / 0.6505 GB, free: 36.91 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 9.322e-05/0.004776, allocations: 1.688 kB / 0.6505 GB, free: 36.91 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.001302/0.006078, allocations: 125.4 kB / 0.6507 GB, free: 36.86 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001515/0.00623, allocations: 80.25 kB / 0.6507 GB, free: 36.83 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0006822/0.006912, allocations: 142.6 kB / 0.6509 GB, free: 36.76 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002886/0.007201, allocations: 289 kB / 0.6511 GB, free: 36.63 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001348/0.007335, allocations: 48.86 kB / 0.6512 GB, free: 36.6 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001754/0.007511, allocations: 146.1 kB / 0.6513 GB, free: 36.54 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001663/0.007677, allocations: 91.53 kB / 0.6514 GB, free: 36.51 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 4.525e-05/0.007722, allocations: 22.22 kB / 0.6514 GB, free: 36.51 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.0002352/0.007957, allocations: 163.4 kB / 0.6516 GB, free: 36.46 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 7.452e-05/0.008032, allocations: 67.31 kB / 0.6517 GB, free: 36.42 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 0.0001029/0.008135, allocations: 81.91 kB / 0.6517 GB, free: 36.38 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0004476/0.008582, allocations: 418.4 kB / 0.6521 GB, free: 36.21 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 4.829e-06/0.008587, allocations: 3.562 kB / 0.6521 GB, free: 36.21 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 1.142e-06/0.008588, allocations: 0 / 0.6521 GB, free: 36.21 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 6.302e-06/0.008595, allocations: 3.938 kB / 0.6521 GB, free: 36.21 MB / 0.5262 GB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 40
 * Number of variables: 40
Notification: Performance of Generate backend data structure: time 0.00359/0.01219, allocations: 0.7192 MB / 0.6528 GB, free: 35.57 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.867e-05/0.01222, allocations: 9.312 kB / 0.6529 GB, free: 35.57 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0006614/0.01289, allocations: 108.3 kB / 0.653 GB, free: 35.53 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0009738/0.01386, allocations: 222.6 kB / 0.6532 GB, free: 35.34 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.958e-05/0.01388, allocations: 21.06 kB / 0.6532 GB, free: 35.33 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0003823/0.01426, allocations: 21.11 kB / 0.6532 GB, free: 35.33 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0009021/0.01516, allocations: 267.7 kB / 0.6535 GB, free: 35.15 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0003044/0.01547, allocations: 3.469 kB / 0.6535 GB, free: 35.15 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.253e-05/0.01549, allocations: 5.281 kB / 0.6535 GB, free: 35.15 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.129e-05/0.0155, allocations: 3.812 kB / 0.6535 GB, free: 35.15 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0007363/0.01624, allocations: 222.6 kB / 0.6537 GB, free: 35.02 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001621/0.01786, allocations: 0.5662 MB / 0.6542 GB, free: 34.61 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0006691/0.01853, allocations: 261 kB / 0.6545 GB, free: 34.44 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002154/0.01874, allocations: 170.9 kB / 0.6547 GB, free: 34.31 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 2.219e-05/0.01877, allocations: 5.594 kB / 0.6547 GB, free: 34.31 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.000647/0.01941, allocations: 322.4 kB / 0.655 GB, free: 34.05 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=26): time 2.234e-06/0.01941, allocations: 0 / 0.655 GB, free: 34.05 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=27): time 0.002765/0.02218, allocations: 1.21 MB / 0.6561 GB, free: 33.18 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.341e-05/0.02224, allocations: 195 kB / 0.6563 GB, free: 32.95 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002717/0.02251, allocations: 350.1 kB / 0.6567 GB, free: 32.72 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 2.363e-05/0.02254, allocations: 33.83 kB / 0.6567 GB, free: 32.69 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 0.0001028/0.02264, allocations: 215.4 kB / 0.6569 GB, free: 32.5 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 5.795e-05/0.0227, allocations: 97.34 kB / 0.657 GB, free: 32.43 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 9.912e-05/0.0228, allocations: 70.88 kB / 0.6571 GB, free: 32.39 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 0.0001103/0.02291, allocations: 0.5333 MB / 0.6576 GB, free: 31.87 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.000227/0.02314, allocations: 230.2 kB / 0.6578 GB, free: 31.69 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002465/0.02338, allocations: 322.4 kB / 0.6581 GB, free: 31.4 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0006083/0.02399, allocations: 0.6536 MB / 0.6588 GB, free: 30.86 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.814e-06/0.02399, allocations: 0 / 0.6588 GB, free: 30.86 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=38) (initialization): time 0.0007209/0.02471, allocations: 0.6116 MB / 0.6593 GB, free: 30.45 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 5.391e-05/0.02477, allocations: 118.7 kB / 0.6595 GB, free: 30.32 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.424e-06/0.02477, allocations: 5.344 kB / 0.6595 GB, free: 30.32 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.0007432/0.02552, allocations: 2.812 kB / 0.6595 GB, free: 30.32 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002218/0.02574, allocations: 55.72 kB / 0.6595 GB, free: 30.31 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 9.147e-06/0.02575, allocations: 4.219 kB / 0.6595 GB, free: 30.31 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001619/0.02591, allocations: 15.83 kB / 0.6595 GB, free: 30.3 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 7.551e-05/0.02599, allocations: 48.09 kB / 0.6596 GB, free: 30.3 MB / 0.5262 GB
Warning: Assuming fixed start value for the following 6 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
         central.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" 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
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 7
 * Number of states: 0 ()
 * Number of discrete variables: 15 ($PRE.central.Cmin,central.Cmin,$PRE.central.Cmax,central.Cmax,$PRE.central.rising,$PRE.singleDose.pulse.count,$PRE.singleDose.pulse.T_start,CYP2C19.status,SLC22A2.status,central.rising,singleDose.pulse.count,singleDose.pulse.T_start,$whenCondition3,$whenCondition2,$whenCondition1)
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (34):
 * Single equations (assignments): 30
 * Array equations: 0
 * Algorithm blocks: 4
 * 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 0.000669/0.02665, allocations: 313 kB / 0.6599 GB, free: 30.01 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001455/0.0268, allocations: 85.25 kB / 0.66 GB, free: 29.98 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 6.395e-05/0.02686, allocations: 33.58 kB / 0.66 GB, free: 29.96 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.649e-06/0.02687, allocations: 2.781 kB / 0.66 GB, free: 29.96 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 7.254e-06/0.02688, allocations: 0 / 0.66 GB, free: 29.96 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.629e-06/0.02688, allocations: 1.438 kB / 0.66 GB, free: 29.96 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.000908/0.02779, allocations: 0.8674 MB / 0.6609 GB, free: 29.33 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.946e-06/0.02779, allocations: 1.438 kB / 0.6609 GB, free: 29.33 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001795/0.02797, allocations: 35.69 kB / 0.6609 GB, free: 29.32 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 3.036e-06/0.02797, allocations: 1.375 kB / 0.6609 GB, free: 29.32 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.726e-05/0.028, allocations: 12.77 kB / 0.6609 GB, free: 29.32 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.315e-06/0.028, allocations: 5.312 kB / 0.6609 GB, free: 29.32 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.142e-06/0.02801, allocations: 0 / 0.6609 GB, free: 29.32 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0009065/0.02891, allocations: 0.885 MB / 0.6618 GB, free: 28.7 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 3.737e-05/0.02895, allocations: 29.11 kB / 0.6618 GB, free: 28.68 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 4.511e-05/0.02899, allocations: 9.594 kB / 0.6618 GB, free: 28.68 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001466/0.02914, allocations: 11 kB / 0.6618 GB, free: 28.67 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0003641/0.0295, allocations: 31.06 kB / 0.6618 GB, free: 28.66 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 6.105e-05/0.02957, allocations: 51.28 kB / 0.6619 GB, free: 28.66 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 0.0001568/0.02972, allocations: 224.1 kB / 0.6621 GB, free: 28.51 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 7e-08/0.02972, allocations: 0 / 0.6621 GB, free: 28.51 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0003728/0.0301, allocations: 72.19 kB / 0.6622 GB, free: 28.5 MB / 0.5262 GB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 5 (singleDose.TotalCumulativeMass,singleDose.variableDose.TotalCumulativeMass,central.C,central.AUC,elim.MExc)
 * Number of discrete variables: 10 ($whenCondition1,$whenCondition2,$whenCondition3,singleDose.pulse.T_start,singleDose.pulse.count,central.Cmax,central.Cmin,central.rising,SLC22A2.status,CYP2C19.status)
 * Number of discrete states: 8 (singleDose.pulse.count,SLC22A2.status,CYP2C19.status,central.Cmin,$whenCondition3,central.Cmax,$whenCondition2,central.rising)
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (22):
 * Single equations (assignments): 17
 * Array equations: 0
 * Algorithm blocks: 3
 * 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 0.001072/0.03117, allocations: 160.3 kB / 0.6623 GB, free: 28.39 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.001171/0.03234, allocations: 0.6736 MB / 0.663 GB, free: 27.84 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 2.134e-06/0.03234, allocations: 0 / 0.663 GB, free: 27.84 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.0002839/0.03262, allocations: 394.2 kB / 0.6634 GB, free: 27.5 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004848/0.03311, allocations: 71.62 kB / 0.6634 GB, free: 27.48 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001239/0.03435, allocations: 0.8159 MB / 0.6642 GB, free: 26.94 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001339/0.03448, allocations: 165.9 kB / 0.6644 GB, free: 26.84 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 8.516e-05/0.03457, allocations: 16.36 kB / 0.6644 GB, free: 26.84 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 5.118e-05/0.03462, allocations: 23.81 kB / 0.6644 GB, free: 26.83 MB / 0.5262 GB
Notification: Performance of SimCode: time 8.22e-07/0.03462, allocations: 0 / 0.6644 GB, free: 26.83 MB / 0.5262 GB
Notification: Performance of Templates: time 0.01326/0.04788, allocations: 4.456 MB / 0.6688 GB, free: 26.45 MB / 0.5262 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 14.203745499020442]