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 0.001974/0.001974, allocations: 105.5 kB / 18.95 MB, free: 1.176 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 0.00218/0.00218, allocations: 214.8 kB / 22.25 MB, free: 3.566 MB / 13.93 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 1.763/1.763, allocations: 230.6 MB / 256 MB, free: 9.613 MB / 202.7 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 3.701/3.701, allocations: 335.3 MB / 0.6325 GB, free: 7.301 MB / 442.7 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: Pharmacolibrary requested package Modelica of version 4.0.0. Modelica 4.1.0 is used instead which states that it is fully compatible without conversion script needed.
Notification: Performance of FrontEnd - loaded program: time 0.004243/0.004243, allocations: 75.88 kB / 0.868 GB, free: 5.996 MB / 0.573 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.2966/0.3009, allocations: 112.8 MB / 0.9782 GB, free: 4.926 MB / 0.6824 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin): time 0.008422/0.3093, allocations: 2.394 MB / 0.9805 GB, free: 2.52 MB / 0.6824 GB
Notification: Performance of NFInst.instExpressions: time 0.003205/0.3125, allocations: 0.9071 MB / 0.9814 GB, free: 1.609 MB / 0.6824 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.000265/0.3127, allocations: 4 kB / 0.9814 GB, free: 1.605 MB / 0.6824 GB
Notification: Performance of NFTyping.typeComponents: time 0.0007956/0.3135, allocations: 115.3 kB / 0.9815 GB, free: 1.492 MB / 0.6824 GB
Notification: Performance of NFTyping.typeBindings: time 0.0004512/0.314, allocations: 75.39 kB / 0.9816 GB, free: 1.418 MB / 0.6824 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0007661/0.3148, allocations: 151.6 kB / 0.9818 GB, free: 1.27 MB / 0.6824 GB
Notification: Performance of NFFlatten.flatten: time 0.0007401/0.3155, allocations: 290.8 kB / 0.982 GB, free: 0.9844 MB / 0.6824 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.000251/0.3158, allocations: 41.44 kB / 0.9821 GB, free: 0.9375 MB / 0.6824 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0003198/0.3161, allocations: 107.6 kB / 0.9822 GB, free: 0.832 MB / 0.6824 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.000346/0.3164, allocations: 111.5 kB / 0.9823 GB, free: 0.7227 MB / 0.6824 GB
Notification: Performance of NFPackage.collectConstants: time 8.055e-05/0.3165, allocations: 23.94 kB / 0.9823 GB, free: 0.6992 MB / 0.6824 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.0004665/0.317, allocations: 171.3 kB / 0.9825 GB, free: 0.5312 MB / 0.6824 GB
Notification: Performance of NFScalarize.scalarize: time 0.0001596/0.3171, allocations: 59.77 kB / 0.9825 GB, free: 484 kB / 0.6824 GB
Notification: Performance of NFVerifyModel.verify: time 0.0002408/0.3174, allocations: 103.5 kB / 0.9826 GB, free: 380 kB / 0.6824 GB
Notification: Performance of NFConvertDAE.convert: time 0.0009159/0.3183, allocations: 422.2 kB / 0.983 GB, free: 15.96 MB / 0.698 GB
Notification: Performance of FrontEnd - DAE generated: time 5.63e-06/0.3183, allocations: 0 / 0.983 GB, free: 15.96 MB / 0.698 GB
Notification: Performance of FrontEnd: time 2.093e-06/0.3183, allocations: 4 kB / 0.983 GB, free: 15.95 MB / 0.698 GB
Notification: Performance of Transformations before backend: time 7.114e-06/0.3183, allocations: 0 / 0.983 GB, free: 15.95 MB / 0.698 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 0.001462/0.3198, allocations: 0.6054 MB / 0.9836 GB, free: 15.29 MB / 0.698 GB
Notification: Performance of prepare preOptimizeDAE: time 5.948e-05/0.3198, allocations: 14.11 kB / 0.9836 GB, free: 15.28 MB / 0.698 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0003278/0.3201, allocations: 60.67 kB / 0.9837 GB, free: 15.22 MB / 0.698 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0004414/0.3206, allocations: 221.4 kB / 0.9839 GB, free: 14.98 MB / 0.698 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.471e-05/0.3206, allocations: 16.38 kB / 0.9839 GB, free: 14.97 MB / 0.698 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 7.1e-05/0.3207, allocations: 23.94 kB / 0.9839 GB, free: 14.95 MB / 0.698 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0007725/0.3215, allocations: 367.5 kB / 0.9843 GB, free: 14.56 MB / 0.698 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.88e-05/0.3215, allocations: 0 / 0.9843 GB, free: 14.56 MB / 0.698 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.165e-05/0.3215, allocations: 11.94 kB / 0.9843 GB, free: 14.55 MB / 0.698 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.428e-06/0.3215, allocations: 4 kB / 0.9843 GB, free: 14.55 MB / 0.698 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0005972/0.3221, allocations: 341.1 kB / 0.9846 GB, free: 14.2 MB / 0.698 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001013/0.3231, allocations: 480.4 kB / 0.9851 GB, free: 13.7 MB / 0.698 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0006933/0.3238, allocations: 363.6 kB / 0.9854 GB, free: 13.31 MB / 0.698 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0004026/0.3242, allocations: 281.6 kB / 0.9857 GB, free: 13.02 MB / 0.698 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.973e-05/0.3242, allocations: 4 kB / 0.9857 GB, free: 13.01 MB / 0.698 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0006408/0.3249, allocations: 415.6 kB / 0.9861 GB, free: 12.56 MB / 0.698 GB
Notification: Performance of pre-optimization done (n=26): time 1.803e-06/0.3249, allocations: 0 / 0.9861 GB, free: 12.56 MB / 0.698 GB
Notification: Performance of matching and sorting (n=27): time 0.003148/0.328, allocations: 1.645 MB / 0.9877 GB, free: 10.8 MB / 0.698 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001698/0.3282, allocations: 191.9 kB / 0.9879 GB, free: 10.57 MB / 0.698 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003668/0.3286, allocations: 281.8 kB / 0.9882 GB, free: 10.29 MB / 0.698 GB
Notification: Performance of collectPreVariables (initialization): time 4.174e-05/0.3286, allocations: 37.7 kB / 0.9882 GB, free: 10.24 MB / 0.698 GB
Notification: Performance of collectInitialEqns (initialization): time 0.0001582/0.3288, allocations: 156.6 kB / 0.9884 GB, free: 10.09 MB / 0.698 GB
Notification: Performance of collectInitialBindings (initialization): time 0.0001014/0.3289, allocations: 91.2 kB / 0.9884 GB, free: 9.996 MB / 0.698 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001172/0.329, allocations: 65.92 kB / 0.9885 GB, free: 9.926 MB / 0.698 GB
Notification: Performance of setup shared object (initialization): time 0.0002139/0.3292, allocations: 338.8 kB / 0.9888 GB, free: 9.586 MB / 0.698 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0004844/0.3297, allocations: 328.1 kB / 0.9891 GB, free: 9.238 MB / 0.698 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0005189/0.3302, allocations: 391.3 kB / 0.9895 GB, free: 8.801 MB / 0.698 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.4958/0.826, allocations: 1.253 MB / 0.9907 GB, free: 26.15 MB / 0.698 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.318e-06/0.826, allocations: 1.062 kB / 0.9907 GB, free: 26.15 MB / 0.698 GB
Notification: Performance of matching and sorting (n=38) (initialization): time 0.0009508/0.8269, allocations: 0.7591 MB / 0.9915 GB, free: 25.87 MB / 0.698 GB
Notification: Performance of prepare postOptimizeDAE: time 5.557e-05/0.827, allocations: 124.5 kB / 0.9916 GB, free: 25.74 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.494e-06/0.827, allocations: 0 / 0.9916 GB, free: 25.74 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (initialization): time 2.697e-05/0.827, allocations: 6.047 kB / 0.9916 GB, free: 25.74 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002273/0.8273, allocations: 51.8 kB / 0.9917 GB, free: 25.74 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.681e-05/0.8273, allocations: 3.156 kB / 0.9917 GB, free: 25.74 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001825/0.8275, allocations: 22.31 kB / 0.9917 GB, free: 25.74 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 7.266e-05/0.8275, allocations: 49.91 kB / 0.9917 GB, free: 25.74 MB / 0.698 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 0.0002478/0.8278, allocations: 275.8 kB / 0.992 GB, free: 25.54 MB / 0.698 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 8.155e-05/0.8279, allocations: 39.36 kB / 0.992 GB, free: 25.54 MB / 0.698 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 6.672e-05/0.8279, allocations: 33.72 kB / 0.9921 GB, free: 25.53 MB / 0.698 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.687e-06/0.8279, allocations: 2.406 kB / 0.9921 GB, free: 25.53 MB / 0.698 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.831e-06/0.8279, allocations: 0.8438 kB / 0.9921 GB, free: 25.53 MB / 0.698 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.54e-06/0.8279, allocations: 3.375 kB / 0.9921 GB, free: 25.53 MB / 0.698 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001033/0.829, allocations: 0.9762 MB / 0.993 GB, free: 25.11 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.685e-06/0.829, allocations: 5.953 kB / 0.993 GB, free: 25.1 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.000196/0.8292, allocations: 39.64 kB / 0.9931 GB, free: 25.1 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (simulation): time 3.286e-06/0.8292, allocations: 2.781 kB / 0.9931 GB, free: 25.1 MB / 0.698 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.548e-05/0.8292, allocations: 6.094 kB / 0.9931 GB, free: 25.1 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.437e-06/0.8292, allocations: 7.328 kB / 0.9931 GB, free: 25.1 MB / 0.698 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.332e-06/0.8292, allocations: 0 / 0.9931 GB, free: 25.1 MB / 0.698 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001164/0.8304, allocations: 1.15 MB / 0.9942 GB, free: 24.67 MB / 0.698 GB
Notification: Performance of postOpt removeConstants (simulation): time 3.365e-05/0.8304, allocations: 23.3 kB / 0.9942 GB, free: 24.67 MB / 0.698 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 4.76e-05/0.8305, allocations: 6.375 kB / 0.9942 GB, free: 24.67 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001671/0.8306, allocations: 18.28 kB / 0.9942 GB, free: 24.67 MB / 0.698 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 8.701e-05/0.8307, allocations: 27.56 kB / 0.9943 GB, free: 24.67 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 5.847e-05/0.8308, allocations: 47.62 kB / 0.9943 GB, free: 24.67 MB / 0.698 GB
Notification: Performance of sorting global known variables: time 0.0001673/0.8309, allocations: 205.6 kB / 0.9945 GB, free: 24.59 MB / 0.698 GB
Notification: Performance of sort global known variables: time 8e-08/0.8309, allocations: 0.5 kB / 0.9945 GB, free: 24.59 MB / 0.698 GB
Notification: Performance of remove unused functions: time 0.0003697/0.8313, allocations: 75.03 kB / 0.9946 GB, free: 24.59 MB / 0.698 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 0.0002421/0.8316, allocations: 159.6 kB / 0.9947 GB, free: 24.51 MB / 0.698 GB
Notification: Performance of simCode: created initialization part: time 0.0008112/0.8324, allocations: 0.8483 MB / 0.9956 GB, free: 24.03 MB / 0.698 GB
Notification: Performance of simCode: created event and clocks part: time 1.724e-06/0.8324, allocations: 0 / 0.9956 GB, free: 24.03 MB / 0.698 GB
Notification: Performance of simCode: created simulation system equations: time 0.0003817/0.8328, allocations: 475 kB / 0.996 GB, free: 23.75 MB / 0.698 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004675/0.8332, allocations: 64.59 kB / 0.9961 GB, free: 23.75 MB / 0.698 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001458/0.8347, allocations: 1.064 MB / 0.9971 GB, free: 23.21 MB / 0.698 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001482/0.8348, allocations: 174.4 kB / 0.9973 GB, free: 23.12 MB / 0.698 GB
Notification: Performance of simCode: alias equations: time 8.794e-05/0.8349, allocations: 21.33 kB / 0.9973 GB, free: 23.12 MB / 0.698 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.514e-05/0.835, allocations: 19.38 kB / 0.9973 GB, free: 23.11 MB / 0.698 GB
Notification: Performance of SimCode: time 4.31e-07/0.835, allocations: 0 / 0.9973 GB, free: 23.11 MB / 0.698 GB
Notification: Performance of Templates: time 0.01061/0.8456, allocations: 5.009 MB / 1.002 GB, free: 22.67 MB / 0.698 GB
"
[Timeout remaining time 659]
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: 10.759455465944484]