Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_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 0.0009283/0.0009283, allocations: 91.55 kB / 20.19 MB, free: 4.348 MB / 18.57 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 0.001007/0.001007, allocations: 169 kB / 23.5 MB, free: 1.043 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 1.006/1.006, allocations: 177.1 MB / 203.8 MB, free: 5.605 MB / 186.7 MB
"
[Timeout remaining time 179]
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 1.597/1.597, allocations: 273.5 MB / 0.5213 GB, free: 14.87 MB / 458.7 MB
"
[Timeout remaining time 178]
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.Pharmacogenomics.Patient_PKPG_1C_Gentamicin,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin")
translateModel(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.724e-06/1.724e-06, allocations: 0 / 0.647 GB, free: 38.7 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.204e-05/2.377e-05, allocations: 4.156 kB / 0.647 GB, free: 38.7 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin): time 0.006257/0.006281, allocations: 2.538 MB / 0.6495 GB, free: 37.07 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.001098/0.007379, allocations: 0.9393 MB / 0.6504 GB, free: 36.47 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 8.204e-05/0.007461, allocations: 4.906 kB / 0.6504 GB, free: 36.47 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0003236/0.007785, allocations: 111 kB / 0.6505 GB, free: 36.43 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001084/0.007893, allocations: 86 kB / 0.6506 GB, free: 36.4 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0002749/0.008168, allocations: 146.1 kB / 0.6507 GB, free: 36.32 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002414/0.00841, allocations: 303.6 kB / 0.651 GB, free: 36.2 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001199/0.00853, allocations: 45.59 kB / 0.6511 GB, free: 36.16 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001312/0.008661, allocations: 150.4 kB / 0.6512 GB, free: 36.11 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001346/0.008795, allocations: 101.1 kB / 0.6513 GB, free: 36.07 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 2.98e-05/0.008825, allocations: 22.06 kB / 0.6513 GB, free: 36.07 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001569/0.008982, allocations: 165.7 kB / 0.6515 GB, free: 36.02 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 6.149e-05/0.009044, allocations: 65.59 kB / 0.6515 GB, free: 35.98 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 8.301e-05/0.009127, allocations: 90.06 kB / 0.6516 GB, free: 35.94 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.000319/0.009446, allocations: 334.4 kB / 0.652 GB, free: 35.79 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 2.565e-06/0.009448, allocations: 0 / 0.652 GB, free: 35.79 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 1.122e-06/0.009449, allocations: 0 / 0.652 GB, free: 35.79 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 4.859e-06/0.009454, allocations: 0 / 0.652 GB, free: 35.79 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 0.0006736/0.01013, allocations: 0.7282 MB / 0.6527 GB, free: 35.14 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.909e-05/0.01017, allocations: 7.344 kB / 0.6527 GB, free: 35.14 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0002768/0.01044, allocations: 115.5 kB / 0.6528 GB, free: 35.1 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001823/0.01063, allocations: 216.1 kB / 0.653 GB, free: 34.91 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.412e-05/0.01064, allocations: 15.72 kB / 0.653 GB, free: 34.9 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.134e-05/0.01067, allocations: 17.78 kB / 0.653 GB, free: 34.9 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002511/0.01092, allocations: 259.9 kB / 0.6533 GB, free: 34.72 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.239e-05/0.01093, allocations: 1.469 kB / 0.6533 GB, free: 34.72 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.656e-05/0.01095, allocations: 5.969 kB / 0.6533 GB, free: 34.71 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.147e-06/0.01096, allocations: 3.906 kB / 0.6533 GB, free: 34.71 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001497/0.01111, allocations: 175.4 kB / 0.6534 GB, free: 34.61 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0005684/0.01168, allocations: 0.5212 MB / 0.654 GB, free: 34.22 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001911/0.01187, allocations: 215.1 kB / 0.6542 GB, free: 34.07 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 8.491e-05/0.01195, allocations: 148.4 kB / 0.6543 GB, free: 33.95 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.222e-05/0.01197, allocations: 5.469 kB / 0.6543 GB, free: 33.95 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.000204/0.01217, allocations: 290.5 kB / 0.6546 GB, free: 33.71 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=26): time 2.615e-06/0.01217, allocations: 0 / 0.6546 GB, free: 33.71 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=27): time 0.001036/0.01321, allocations: 1.1 MB / 0.6557 GB, free: 32.88 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.411e-05/0.01325, allocations: 194.9 kB / 0.6558 GB, free: 32.65 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002066/0.01346, allocations: 326.2 kB / 0.6562 GB, free: 32.44 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.835e-05/0.01348, allocations: 33.64 kB / 0.6562 GB, free: 32.4 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 9.097e-05/0.01357, allocations: 220.2 kB / 0.6564 GB, free: 32.21 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 4.721e-05/0.01362, allocations: 89.62 kB / 0.6565 GB, free: 32.14 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 8.097e-05/0.0137, allocations: 63.83 kB / 0.6565 GB, free: 32.1 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 0.0001042/0.0138, allocations: 0.5193 MB / 0.6571 GB, free: 31.59 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001798/0.01398, allocations: 186 kB / 0.6572 GB, free: 31.44 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001687/0.01415, allocations: 274.7 kB / 0.6575 GB, free: 31.17 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0004092/0.01456, allocations: 0.5683 MB / 0.658 GB, free: 30.66 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.354e-06/0.01456, allocations: 1.125 kB / 0.658 GB, free: 30.66 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=38) (initialization): time 0.0004262/0.01499, allocations: 0.5434 MB / 0.6586 GB, free: 30.28 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 4.292e-05/0.01503, allocations: 118.7 kB / 0.6587 GB, free: 30.15 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.543e-06/0.01504, allocations: 2.688 kB / 0.6587 GB, free: 30.15 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.592e-05/0.01505, allocations: 10.34 kB / 0.6587 GB, free: 30.15 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001607/0.01521, allocations: 53.72 kB / 0.6588 GB, free: 30.14 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 9.728e-06/0.01522, allocations: 4.156 kB / 0.6588 GB, free: 30.14 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.315e-05/0.01532, allocations: 17.41 kB / 0.6588 GB, free: 30.14 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 6.118e-05/0.01538, allocations: 51.91 kB / 0.6588 GB, free: 30.14 MB / 0.5262 GB
Warning: Assuming fixed start value for the following 6 variables:
         dose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" 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
         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.dose.pulse.count,$PRE.dose.pulse.T_start,CYP2C19.status,SLC22A2.status,central.rising,dose.pulse.count,dose.pulse.T_start,$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 0.0001586/0.01554, allocations: 285.5 kB / 0.6591 GB, free: 29.86 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 9.138e-05/0.01563, allocations: 89.42 kB / 0.6592 GB, free: 29.83 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.718e-05/0.01567, allocations: 29.78 kB / 0.6592 GB, free: 29.82 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.919e-06/0.01567, allocations: 3.938 kB / 0.6592 GB, free: 29.81 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.533e-06/0.01567, allocations: 0 / 0.6592 GB, free: 29.81 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.427e-05/0.0157, allocations: 30.19 kB / 0.6592 GB, free: 29.79 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.175e-05/0.01573, allocations: 13.22 kB / 0.6593 GB, free: 29.79 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 6.323e-05/0.01579, allocations: 12.2 kB / 0.6593 GB, free: 29.79 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.911e-05/0.01586, allocations: 25.34 kB / 0.6593 GB, free: 29.78 MB / 0.5262 GB
Notification: Performance of postOpt createDAEmodeBDAE (simulation): time 0.0004148/0.01627, allocations: 0.5498 MB / 0.6598 GB, free: 29.38 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobianDAE (simulation): time 0.0005224/0.0168, allocations: 0.9056 MB / 0.6607 GB, free: 28.68 MB / 0.5262 GB
Notification: Performance of postOpt setEvaluationStage (simulation): time 0.0001208/0.01692, allocations: 190.1 kB / 0.6609 GB, free: 28.55 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 0.0001019/0.01702, allocations: 220.4 kB / 0.6611 GB, free: 28.41 MB / 0.5262 GB
Notification: Performance of Backend: time 4.01e-07/0.01702, allocations: 0 / 0.6611 GB, free: 28.41 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.000597/0.01762, allocations: 0.5985 MB / 0.6617 GB, free: 27.9 MB / 0.5262 GB
Notification: Performance of SimCode: time 0.001468/0.01909, allocations: 1.537 MB / 0.6632 GB, free: 26.57 MB / 0.5262 GB
Notification: Performance of Templates: time 0.006775/0.02586, allocations: 4.832 MB / 0.6679 GB, free: 26.15 MB / 0.5262 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 4.855081993155181]