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 0.0009882/0.0009882, allocations: 92.22 kB / 19.65 MB, free: 276 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 0.001039/0.001039, allocations: 169 kB / 23.02 MB, free: 1.547 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 0.9777/0.9777, allocations: 177.1 MB / 203.4 MB, free: 5.629 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 1.626/1.626, allocations: 273.5 MB / 0.5209 GB, free: 14.84 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.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 1.603e-06/1.603e-06, allocations: 0 / 0.647 GB, free: 38.66 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 3.121e-05/3.281e-05, allocations: 2.312 kB / 0.647 GB, free: 38.66 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKPG_1C_Gentamicin): time 0.003005/0.003037, allocations: 2.497 MB / 0.6494 GB, free: 37.06 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.001431/0.004468, allocations: 0.9356 MB / 0.6503 GB, free: 36.46 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.000128/0.004596, allocations: 5.5 kB / 0.6503 GB, free: 36.46 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0004496/0.005046, allocations: 111.6 kB / 0.6504 GB, free: 36.42 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001535/0.0052, allocations: 78.59 kB / 0.6505 GB, free: 36.39 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.000432/0.005632, allocations: 146.3 kB / 0.6506 GB, free: 36.32 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.000372/0.006004, allocations: 291 kB / 0.6509 GB, free: 36.2 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001684/0.006172, allocations: 47.88 kB / 0.651 GB, free: 36.17 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002241/0.006396, allocations: 148.9 kB / 0.6511 GB, free: 36.11 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.000195/0.006591, allocations: 95.25 kB / 0.6512 GB, free: 36.07 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 3.987e-05/0.006631, allocations: 19.59 kB / 0.6512 GB, free: 36.07 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.0002725/0.006903, allocations: 164.5 kB / 0.6514 GB, free: 36.02 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 0.0001019/0.007005, allocations: 67.86 kB / 0.6514 GB, free: 35.98 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 0.0001084/0.007114, allocations: 81.22 kB / 0.6515 GB, free: 35.95 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0004638/0.007578, allocations: 329.1 kB / 0.6518 GB, free: 35.8 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 4.147e-06/0.007582, allocations: 1.688 kB / 0.6518 GB, free: 35.8 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 1.603e-06/0.007583, allocations: 1.281 kB / 0.6518 GB, free: 35.8 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 8.646e-06/0.007592, allocations: 0 / 0.6518 GB, free: 35.8 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 0.0008209/0.008413, allocations: 0.7057 MB / 0.6525 GB, free: 35.16 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 4.363e-05/0.008457, allocations: 9.188 kB / 0.6525 GB, free: 35.16 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.000258/0.008715, allocations: 109.2 kB / 0.6526 GB, free: 35.13 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002854/0.009, allocations: 233.1 kB / 0.6529 GB, free: 34.93 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.062e-05/0.009021, allocations: 12.06 kB / 0.6529 GB, free: 34.93 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.168e-05/0.009062, allocations: 17.56 kB / 0.6529 GB, free: 34.93 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002966/0.009359, allocations: 263.4 kB / 0.6531 GB, free: 34.74 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.516e-05/0.009374, allocations: 0 / 0.6531 GB, free: 34.74 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.801e-05/0.009392, allocations: 8.844 kB / 0.6531 GB, free: 34.74 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.096e-05/0.009403, allocations: 2.281 kB / 0.6532 GB, free: 34.74 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001641/0.009567, allocations: 174.5 kB / 0.6533 GB, free: 34.63 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0007037/0.01027, allocations: 0.5139 MB / 0.6538 GB, free: 34.25 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0003005/0.01057, allocations: 216.7 kB / 0.654 GB, free: 34.09 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001039/0.01068, allocations: 151.7 kB / 0.6542 GB, free: 33.97 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.467e-05/0.01069, allocations: 5.75 kB / 0.6542 GB, free: 33.97 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002592/0.01095, allocations: 287.9 kB / 0.6545 GB, free: 33.74 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=26): time 2.084e-06/0.01095, allocations: 0 / 0.6545 GB, free: 33.74 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=27): time 0.001431/0.01238, allocations: 1.1 MB / 0.6555 GB, free: 32.91 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.98e-05/0.01244, allocations: 201.5 kB / 0.6557 GB, free: 32.68 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002855/0.01273, allocations: 312.6 kB / 0.656 GB, free: 32.46 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 2.362e-05/0.01275, allocations: 36.42 kB / 0.656 GB, free: 32.43 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 0.0001087/0.01286, allocations: 203.9 kB / 0.6562 GB, free: 32.25 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 6.44e-05/0.01292, allocations: 97.56 kB / 0.6563 GB, free: 32.17 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 9.794e-05/0.01302, allocations: 63.16 kB / 0.6564 GB, free: 32.13 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 9.61e-05/0.01312, allocations: 0.5189 MB / 0.6569 GB, free: 31.62 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001418/0.01326, allocations: 188.2 kB / 0.6571 GB, free: 31.47 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.000135/0.01339, allocations: 274.5 kB / 0.6573 GB, free: 31.2 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0003356/0.01373, allocations: 0.5616 MB / 0.6579 GB, free: 30.7 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.315e-06/0.01373, allocations: 1.5 kB / 0.6579 GB, free: 30.7 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=38) (initialization): time 0.0004855/0.01422, allocations: 0.5368 MB / 0.6584 GB, free: 30.32 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 4.951e-05/0.01427, allocations: 119.1 kB / 0.6585 GB, free: 30.19 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.756e-06/0.01428, allocations: 8.891 kB / 0.6585 GB, free: 30.19 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 2.34e-05/0.0143, allocations: 3.781 kB / 0.6585 GB, free: 30.19 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001699/0.01447, allocations: 56.33 kB / 0.6586 GB, free: 30.18 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 7.955e-06/0.01448, allocations: 4.25 kB / 0.6586 GB, free: 30.18 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.689e-05/0.01457, allocations: 15 kB / 0.6586 GB, free: 30.18 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 7.018e-05/0.01464, allocations: 54.39 kB / 0.6587 GB, free: 30.17 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 0.0001932/0.01484, allocations: 288.4 kB / 0.6589 GB, free: 29.89 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001048/0.01494, allocations: 87 kB / 0.659 GB, free: 29.87 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 4.705e-05/0.01499, allocations: 32.03 kB / 0.6591 GB, free: 29.85 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.256e-06/0.01499, allocations: 2.781 kB / 0.6591 GB, free: 29.85 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 7.514e-06/0.015, allocations: 0 / 0.6591 GB, free: 29.85 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.591e-06/0.01501, allocations: 3.656 kB / 0.6591 GB, free: 29.85 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0006287/0.01563, allocations: 0.7885 MB / 0.6598 GB, free: 29.25 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.035e-06/0.01564, allocations: 1.375 kB / 0.6598 GB, free: 29.25 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001356/0.01577, allocations: 30.3 kB / 0.6599 GB, free: 29.25 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 3.136e-06/0.01578, allocations: 0 / 0.6599 GB, free: 29.25 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.911e-05/0.0158, allocations: 16.75 kB / 0.6599 GB, free: 29.25 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.166e-06/0.0158, allocations: 1.406 kB / 0.6599 GB, free: 29.25 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.794e-06/0.0158, allocations: 0 / 0.6599 GB, free: 29.25 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005776/0.01638, allocations: 0.7967 MB / 0.6607 GB, free: 28.66 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.999e-05/0.01641, allocations: 22.81 kB / 0.6607 GB, free: 28.64 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.497e-05/0.01644, allocations: 14.67 kB / 0.6607 GB, free: 28.64 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 8.868e-05/0.01653, allocations: 11 kB / 0.6607 GB, free: 28.64 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 7.031e-05/0.0166, allocations: 25.25 kB / 0.6607 GB, free: 28.63 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 5.309e-05/0.01666, allocations: 50.17 kB / 0.6608 GB, free: 28.62 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 0.0001152/0.01677, allocations: 207.7 kB / 0.661 GB, free: 28.48 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 7e-08/0.01677, allocations: 1 kB / 0.661 GB, free: 28.48 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0003166/0.01709, allocations: 76.28 kB / 0.661 GB, free: 28.47 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 0.0002637/0.01735, allocations: 158.1 kB / 0.6612 GB, free: 28.38 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0003944/0.01775, allocations: 0.603 MB / 0.6618 GB, free: 27.84 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 2.164e-06/0.01775, allocations: 0 / 0.6618 GB, free: 27.84 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001717/0.01792, allocations: 350.1 kB / 0.6621 GB, free: 27.53 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003466/0.01827, allocations: 67.27 kB / 0.6622 GB, free: 27.51 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001611/0.01988, allocations: 0.8506 MB / 0.663 GB, free: 26.95 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 6.669e-05/0.01994, allocations: 97.08 kB / 0.6631 GB, free: 26.87 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 7.859e-05/0.02002, allocations: 22.25 kB / 0.6631 GB, free: 26.86 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.503e-05/0.02007, allocations: 19.69 kB / 0.6632 GB, free: 26.86 MB / 0.5262 GB
Notification: Performance of SimCode: time 8.12e-07/0.02007, allocations: 1.438 kB / 0.6632 GB, free: 26.86 MB / 0.5262 GB
Notification: Performance of Templates: time 0.007537/0.0276, allocations: 4.532 MB / 0.6676 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: 5.211020262911916]