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 0.001881/0.001881, allocations: 80.44 kB / 19.17 MB, free: 0.7422 MB / 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 0.002179/0.002179, allocations: 169.9 kB / 22.45 MB, free: 2.105 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 1.636/1.636, allocations: 177.1 MB / 202.8 MB, free: 5.742 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 3.514/3.514, allocations: 274 MB / 0.5207 GB, free: 14.93 MB / 458.7 MB
"
[Timeout remaining time 176]
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 1.944e-06/1.944e-06, allocations: 0 / 0.7563 GB, free: 9.918 MB / 0.5887 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 3.178e-05/3.372e-05, allocations: 2.281 kB / 0.7563 GB, free: 9.914 MB / 0.5887 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin): time 0.006031/0.006064, allocations: 2.403 MB / 0.7586 GB, free: 7.523 MB / 0.5887 GB
Notification: Performance of NFInst.instExpressions: time 0.002676/0.00874, allocations: 0.9134 MB / 0.7595 GB, free: 6.617 MB / 0.5887 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001286/0.008869, allocations: 5.141 kB / 0.7595 GB, free: 6.613 MB / 0.5887 GB
Notification: Performance of NFTyping.typeComponents: time 0.0006097/0.009478, allocations: 110.3 kB / 0.7597 GB, free: 6.508 MB / 0.5887 GB
Notification: Performance of NFTyping.typeBindings: time 0.0002914/0.00977, allocations: 92.69 kB / 0.7597 GB, free: 6.441 MB / 0.5887 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0006656/0.01044, allocations: 145 kB / 0.7599 GB, free: 6.301 MB / 0.5887 GB
Notification: Performance of NFFlatten.flatten: time 0.0005673/0.011, allocations: 293.3 kB / 0.7602 GB, free: 6.016 MB / 0.5887 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.000218/0.01122, allocations: 45.41 kB / 0.7602 GB, free: 5.969 MB / 0.5887 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0003002/0.01152, allocations: 151.6 kB / 0.7603 GB, free: 5.82 MB / 0.5887 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002707/0.01179, allocations: 99.69 kB / 0.7604 GB, free: 5.723 MB / 0.5887 GB
Notification: Performance of NFPackage.collectConstants: time 6.214e-05/0.01185, allocations: 20 kB / 0.7605 GB, free: 5.703 MB / 0.5887 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.000379/0.01223, allocations: 159.3 kB / 0.7606 GB, free: 5.547 MB / 0.5887 GB
Notification: Performance of NFScalarize.scalarize: time 0.0001378/0.01237, allocations: 67.69 kB / 0.7607 GB, free: 5.48 MB / 0.5887 GB
Notification: Performance of NFVerifyModel.verify: time 0.0001743/0.01254, allocations: 87.77 kB / 0.7608 GB, free: 5.395 MB / 0.5887 GB
Notification: Performance of NFConvertDAE.convert: time 0.0008289/0.01337, allocations: 426.5 kB / 0.7612 GB, free: 4.977 MB / 0.5887 GB
Notification: Performance of FrontEnd - DAE generated: time 4.429e-06/0.01338, allocations: 4 kB / 0.7612 GB, free: 4.973 MB / 0.5887 GB
Notification: Performance of FrontEnd: time 1.673e-06/0.01338, allocations: 3.938 kB / 0.7612 GB, free: 4.969 MB / 0.5887 GB
Notification: Performance of Transformations before backend: time 7.084e-06/0.01339, allocations: 0 / 0.7612 GB, free: 4.969 MB / 0.5887 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 0.001406/0.01479, allocations: 0.617 MB / 0.7618 GB, free: 4.297 MB / 0.5887 GB
Notification: Performance of prepare preOptimizeDAE: time 4.466e-05/0.01484, allocations: 12.03 kB / 0.7618 GB, free: 4.285 MB / 0.5887 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0003449/0.01518, allocations: 56.59 kB / 0.7618 GB, free: 4.23 MB / 0.5887 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0004159/0.0156, allocations: 212.7 kB / 0.762 GB, free: 4 MB / 0.5887 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.885e-05/0.01563, allocations: 12.38 kB / 0.7621 GB, free: 3.988 MB / 0.5887 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 6.578e-05/0.01569, allocations: 20.38 kB / 0.7621 GB, free: 3.969 MB / 0.5887 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.00084/0.01653, allocations: 375.7 kB / 0.7624 GB, free: 3.578 MB / 0.5887 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.934e-05/0.01655, allocations: 0 / 0.7624 GB, free: 3.578 MB / 0.5887 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.458e-05/0.01659, allocations: 12 kB / 0.7624 GB, free: 3.566 MB / 0.5887 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.328e-06/0.0166, allocations: 4 kB / 0.7624 GB, free: 3.562 MB / 0.5887 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0008211/0.01742, allocations: 337.1 kB / 0.7628 GB, free: 3.215 MB / 0.5887 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.00141/0.01883, allocations: 476.5 kB / 0.7632 GB, free: 2.719 MB / 0.5887 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0008946/0.01972, allocations: 367.5 kB / 0.7636 GB, free: 2.332 MB / 0.5887 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0005503/0.02027, allocations: 271.7 kB / 0.7638 GB, free: 2.047 MB / 0.5887 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.937e-05/0.02029, allocations: 4 kB / 0.7638 GB, free: 2.043 MB / 0.5887 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0008019/0.02109, allocations: 422.5 kB / 0.7642 GB, free: 1.59 MB / 0.5887 GB
Notification: Performance of pre-optimization done (n=26): time 1.783e-06/0.0211, allocations: 0 / 0.7642 GB, free: 1.59 MB / 0.5887 GB
Notification: Performance of matching and sorting (n=27): time 0.003837/0.02493, allocations: 1.655 MB / 0.7659 GB, free: 15.81 MB / 0.6043 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001988/0.02513, allocations: 187.9 kB / 0.766 GB, free: 15.59 MB / 0.6043 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0004901/0.02562, allocations: 285.8 kB / 0.7663 GB, free: 15.3 MB / 0.6043 GB
Notification: Performance of collectPreVariables (initialization): time 5.017e-05/0.02567, allocations: 33.7 kB / 0.7663 GB, free: 15.27 MB / 0.6043 GB
Notification: Performance of collectInitialEqns (initialization): time 0.0002032/0.02587, allocations: 168.5 kB / 0.7665 GB, free: 15.1 MB / 0.6043 GB
Notification: Performance of collectInitialBindings (initialization): time 0.000118/0.02599, allocations: 83.28 kB / 0.7666 GB, free: 15.02 MB / 0.6043 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001623/0.02615, allocations: 57.92 kB / 0.7666 GB, free: 14.95 MB / 0.6043 GB
Notification: Performance of setup shared object (initialization): time 0.0002459/0.0264, allocations: 338.8 kB / 0.767 GB, free: 14.61 MB / 0.6043 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0006372/0.02704, allocations: 328.2 kB / 0.7673 GB, free: 14.26 MB / 0.6043 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.000687/0.02772, allocations: 395 kB / 0.7677 GB, free: 13.82 MB / 0.6043 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.002523/0.03025, allocations: 1.254 MB / 0.7689 GB, free: 12.46 MB / 0.6043 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.304e-06/0.03025, allocations: 0 / 0.7689 GB, free: 12.46 MB / 0.6043 GB
Notification: Performance of matching and sorting (n=38) (initialization): time 0.001619/0.03187, allocations: 0.7604 MB / 0.7696 GB, free: 11.64 MB / 0.6043 GB
Notification: Performance of prepare postOptimizeDAE: time 0.0002202/0.03209, allocations: 118.8 kB / 0.7697 GB, free: 11.5 MB / 0.6043 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.403e-05/0.0321, allocations: 7.938 kB / 0.7697 GB, free: 11.49 MB / 0.6043 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.925e-05/0.03212, allocations: 0 / 0.7697 GB, free: 11.49 MB / 0.6043 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003329/0.03246, allocations: 55.91 kB / 0.7698 GB, free: 11.44 MB / 0.6043 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.254e-05/0.03247, allocations: 4 kB / 0.7698 GB, free: 11.43 MB / 0.6043 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0002676/0.03274, allocations: 20.17 kB / 0.7698 GB, free: 11.41 MB / 0.6043 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 0.0001199/0.03286, allocations: 47.94 kB / 0.7699 GB, free: 11.37 MB / 0.6043 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 0.0004401/0.0333, allocations: 287.8 kB / 0.7701 GB, free: 11.06 MB / 0.6043 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001422/0.03344, allocations: 31.84 kB / 0.7702 GB, free: 11.03 MB / 0.6043 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 9.75e-05/0.03353, allocations: 38.89 kB / 0.7702 GB, free: 10.99 MB / 0.6043 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.288e-06/0.03354, allocations: 0 / 0.7702 GB, free: 10.99 MB / 0.6043 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 9.197e-06/0.03355, allocations: 4 kB / 0.7702 GB, free: 10.98 MB / 0.6043 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.089e-06/0.03355, allocations: 0 / 0.7702 GB, free: 10.98 MB / 0.6043 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001971/0.03552, allocations: 0.9807 MB / 0.7712 GB, free: 9.93 MB / 0.6043 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.775e-06/0.03553, allocations: 0 / 0.7712 GB, free: 9.93 MB / 0.6043 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0003187/0.03585, allocations: 39.97 kB / 0.7712 GB, free: 9.891 MB / 0.6043 GB
Notification: Performance of postOpt tearingSystem (simulation): time 6.572e-06/0.03585, allocations: 8 kB / 0.7712 GB, free: 9.883 MB / 0.6043 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.56e-05/0.03589, allocations: 11.94 kB / 0.7712 GB, free: 9.871 MB / 0.6043 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.916e-06/0.03589, allocations: 0 / 0.7712 GB, free: 9.871 MB / 0.6043 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.423e-06/0.03589, allocations: 0 / 0.7712 GB, free: 9.871 MB / 0.6043 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.002271/0.03816, allocations: 1.138 MB / 0.7723 GB, free: 8.664 MB / 0.6043 GB
Notification: Performance of postOpt removeConstants (simulation): time 6.224e-05/0.03823, allocations: 23.81 kB / 0.7724 GB, free: 8.641 MB / 0.6043 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.742e-05/0.03829, allocations: 8.062 kB / 0.7724 GB, free: 8.633 MB / 0.6043 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002679/0.03856, allocations: 19.98 kB / 0.7724 GB, free: 8.613 MB / 0.6043 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.000129/0.03869, allocations: 31.89 kB / 0.7724 GB, free: 8.582 MB / 0.6043 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 0.000125/0.03882, allocations: 51.92 kB / 0.7725 GB, free: 8.531 MB / 0.6043 GB
Notification: Performance of sorting global known variables: time 0.0003251/0.03914, allocations: 201.2 kB / 0.7727 GB, free: 8.34 MB / 0.6043 GB
Notification: Performance of sort global known variables: time 1.3e-07/0.03914, allocations: 4 kB / 0.7727 GB, free: 8.336 MB / 0.6043 GB
Notification: Performance of remove unused functions: time 0.0006377/0.03978, allocations: 75.98 kB / 0.7727 GB, free: 8.262 MB / 0.6043 GB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 5 (dose.TotalCumulativeMass,dose.variableDose.TotalCumulativeMass,central.C,central.AUC,elim.MExc)
 * Number of discrete variables: 10 ($whenCondition1,$whenCondition2,$whenCondition3,dose.pulse.T_start,dose.pulse.count,central.Cmax,central.Cmin,central.rising,SLC22A2.status,CYP2C19.status)
 * Number of discrete states: 8 (dose.pulse.count,SLC22A2.status,CYP2C19.status,central.Cmin,$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 0.0003891/0.04017, allocations: 162.6 kB / 0.7729 GB, free: 8.102 MB / 0.6043 GB
Notification: Performance of simCode: created initialization part: time 0.001549/0.04172, allocations: 0.8486 MB / 0.7737 GB, free: 7.16 MB / 0.6043 GB
Notification: Performance of simCode: created event and clocks part: time 1.924e-06/0.04172, allocations: 0 / 0.7737 GB, free: 7.16 MB / 0.6043 GB
Notification: Performance of simCode: created simulation system equations: time 0.0007677/0.04249, allocations: 475 kB / 0.7742 GB, free: 6.641 MB / 0.6043 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.000708/0.04319, allocations: 64.7 kB / 0.7742 GB, free: 6.578 MB / 0.6043 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002256/0.04545, allocations: 0.9276 MB / 0.7751 GB, free: 5.617 MB / 0.6043 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0002725/0.04572, allocations: 170.2 kB / 0.7753 GB, free: 5.434 MB / 0.6043 GB
Notification: Performance of simCode: alias equations: time 0.0001257/0.04585, allocations: 21.95 kB / 0.7753 GB, free: 5.414 MB / 0.6043 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 7.576e-05/0.04592, allocations: 20.5 kB / 0.7753 GB, free: 5.395 MB / 0.6043 GB
Notification: Performance of SimCode: time 5.81e-07/0.04592, allocations: 0 / 0.7753 GB, free: 5.395 MB / 0.6043 GB
Notification: Performance of Templates: time 0.0117/0.05762, allocations: 4.584 MB / 0.7798 GB, free: 1.035 MB / 0.6043 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: 9.280046281404793]