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 0.0009749/0.0009749, allocations: 81.17 kB / 19.87 MB, free: 4.621 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 0.0009998/0.0009998, allocations: 169 kB / 23.27 MB, free: 1.223 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 0.9369/0.9369, allocations: 177.2 MB / 203.7 MB, free: 5.52 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 1.61/1.61, allocations: 273.5 MB / 0.5212 GB, free: 14.77 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 1.843e-06/1.843e-06, allocations: 0 / 0.6474 GB, free: 38.55 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.261e-05/1.446e-05, allocations: 6.828 kB / 0.6474 GB, free: 38.54 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin): time 0.002408/0.002422, allocations: 2.519 MB / 0.6499 GB, free: 36.91 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.001056/0.003478, allocations: 0.9263 MB / 0.6508 GB, free: 36.32 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 8.841e-05/0.003567, allocations: 2.281 kB / 0.6508 GB, free: 36.32 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0003338/0.003901, allocations: 118.5 kB / 0.6509 GB, free: 36.27 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001121/0.004013, allocations: 85.67 kB / 0.651 GB, free: 36.24 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0003023/0.004315, allocations: 147 kB / 0.6511 GB, free: 36.17 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002618/0.004577, allocations: 300.4 kB / 0.6514 GB, free: 36.04 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001184/0.004695, allocations: 49.36 kB / 0.6515 GB, free: 36.01 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001458/0.004841, allocations: 147.2 kB / 0.6516 GB, free: 35.95 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001376/0.004979, allocations: 103.7 kB / 0.6517 GB, free: 35.91 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 3.72e-05/0.005016, allocations: 21.56 kB / 0.6517 GB, free: 35.91 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.000213/0.005229, allocations: 162.2 kB / 0.6519 GB, free: 35.86 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 7.352e-05/0.005302, allocations: 66.45 kB / 0.6519 GB, free: 35.82 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 0.0001037/0.005406, allocations: 91.48 kB / 0.652 GB, free: 35.78 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0003795/0.005785, allocations: 328.5 kB / 0.6523 GB, free: 35.64 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 2.325e-06/0.005788, allocations: 0 / 0.6523 GB, free: 35.64 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 1.042e-06/0.005789, allocations: 0 / 0.6523 GB, free: 35.64 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 5.26e-06/0.005794, allocations: 0 / 0.6523 GB, free: 35.64 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 0.0006989/0.006493, allocations: 0.7286 MB / 0.6531 GB, free: 34.99 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.959e-05/0.006533, allocations: 9.594 kB / 0.6531 GB, free: 34.99 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0002055/0.006738, allocations: 111.1 kB / 0.6532 GB, free: 34.95 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001617/0.0069, allocations: 212.5 kB / 0.6534 GB, free: 34.76 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.914e-05/0.006919, allocations: 11.22 kB / 0.6534 GB, free: 34.75 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 2.745e-05/0.006946, allocations: 19.28 kB / 0.6534 GB, free: 34.75 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002233/0.00717, allocations: 244.5 kB / 0.6536 GB, free: 34.57 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.438e-05/0.007184, allocations: 0 / 0.6536 GB, free: 34.57 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.314e-05/0.007197, allocations: 11.75 kB / 0.6536 GB, free: 34.57 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.376e-06/0.007206, allocations: 3.75 kB / 0.6537 GB, free: 34.57 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001288/0.007334, allocations: 150.4 kB / 0.6538 GB, free: 34.47 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0005696/0.007904, allocations: 480.3 kB / 0.6543 GB, free: 34.12 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001633/0.008067, allocations: 196.5 kB / 0.6544 GB, free: 33.97 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 6.94e-05/0.008137, allocations: 136.1 kB / 0.6546 GB, free: 33.86 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.009e-05/0.008147, allocations: 6.688 kB / 0.6546 GB, free: 33.86 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001935/0.00834, allocations: 273.3 kB / 0.6548 GB, free: 33.62 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=26): time 1.743e-06/0.008342, allocations: 2.5 kB / 0.6548 GB, free: 33.62 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=27): time 0.001198/0.00954, allocations: 0.9852 MB / 0.6558 GB, free: 32.85 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.808e-05/0.009608, allocations: 190.4 kB / 0.656 GB, free: 32.63 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002975/0.009905, allocations: 330 kB / 0.6563 GB, free: 32.41 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.851e-05/0.009924, allocations: 34.11 kB / 0.6563 GB, free: 32.38 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 0.0001098/0.01003, allocations: 215 kB / 0.6565 GB, free: 32.19 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 5.544e-05/0.01009, allocations: 87.72 kB / 0.6566 GB, free: 32.12 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 9.142e-05/0.01018, allocations: 66.12 kB / 0.6567 GB, free: 32.07 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 0.0001017/0.01028, allocations: 0.5232 MB / 0.6572 GB, free: 31.56 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001239/0.01041, allocations: 179.5 kB / 0.6574 GB, free: 31.41 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001198/0.01053, allocations: 257.6 kB / 0.6576 GB, free: 31.14 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002424/0.01077, allocations: 0.5113 MB / 0.6581 GB, free: 30.66 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.583e-06/0.01077, allocations: 0 / 0.6581 GB, free: 30.66 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=38) (initialization): time 0.0003726/0.01114, allocations: 0.5065 MB / 0.6586 GB, free: 30.3 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 4.269e-05/0.01119, allocations: 121.1 kB / 0.6587 GB, free: 30.17 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.651e-06/0.01119, allocations: 1.469 kB / 0.6587 GB, free: 30.17 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.571e-05/0.01121, allocations: 6.719 kB / 0.6587 GB, free: 30.17 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001401/0.01135, allocations: 57.69 kB / 0.6588 GB, free: 30.16 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 5.059e-06/0.01135, allocations: 4.281 kB / 0.6588 GB, free: 30.16 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 8.447e-05/0.01144, allocations: 17.06 kB / 0.6588 GB, free: 30.16 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 5.863e-05/0.01149, allocations: 49.92 kB / 0.6589 GB, free: 30.15 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 0.0001555/0.01165, allocations: 283.2 kB / 0.6591 GB, free: 29.88 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 9.305e-05/0.01174, allocations: 91.3 kB / 0.6592 GB, free: 29.85 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.865e-05/0.01178, allocations: 32.91 kB / 0.6592 GB, free: 29.83 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.056e-06/0.01179, allocations: 10.66 kB / 0.6592 GB, free: 29.82 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.515e-06/0.01179, allocations: 0 / 0.6592 GB, free: 29.82 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.88e-06/0.01179, allocations: 8.859 kB / 0.6593 GB, free: 29.82 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004774/0.01227, allocations: 0.7065 MB / 0.6599 GB, free: 29.28 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.784e-06/0.01227, allocations: 0 / 0.6599 GB, free: 29.28 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001151/0.01239, allocations: 30.11 kB / 0.66 GB, free: 29.28 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 3.647e-06/0.01239, allocations: 1.406 kB / 0.66 GB, free: 29.28 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.583e-05/0.01241, allocations: 13.48 kB / 0.66 GB, free: 29.27 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.243e-06/0.01241, allocations: 0 / 0.66 GB, free: 29.27 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.853e-06/0.01241, allocations: 5.344 kB / 0.66 GB, free: 29.27 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004804/0.01289, allocations: 0.7496 MB / 0.6607 GB, free: 28.7 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 3.016e-05/0.01292, allocations: 22.73 kB / 0.6607 GB, free: 28.69 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.45e-05/0.01295, allocations: 12.22 kB / 0.6608 GB, free: 28.69 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 8.442e-05/0.01304, allocations: 14.09 kB / 0.6608 GB, free: 28.68 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.419e-05/0.0131, allocations: 21.97 kB / 0.6608 GB, free: 28.68 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 5.647e-05/0.01316, allocations: 48.73 kB / 0.6608 GB, free: 28.68 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 0.0001088/0.01327, allocations: 208.7 kB / 0.661 GB, free: 28.54 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 7e-08/0.01327, allocations: 1.375 kB / 0.661 GB, free: 28.54 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0002617/0.01353, allocations: 77.17 kB / 0.6611 GB, free: 28.53 MB / 0.5262 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 0.0002292/0.01376, allocations: 169.1 kB / 0.6613 GB, free: 28.42 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0003337/0.01409, allocations: 0.5649 MB / 0.6618 GB, free: 27.91 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.123e-06/0.01409, allocations: 0 / 0.6618 GB, free: 27.91 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001539/0.01425, allocations: 338 kB / 0.6622 GB, free: 27.59 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002955/0.01454, allocations: 75.66 kB / 0.6622 GB, free: 27.57 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001409/0.01595, allocations: 0.842 MB / 0.663 GB, free: 27.02 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 6.4e-05/0.01602, allocations: 104.2 kB / 0.6631 GB, free: 26.94 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 6.411e-05/0.01608, allocations: 20.72 kB / 0.6632 GB, free: 26.93 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001702/0.01625, allocations: 144.8 kB / 0.6633 GB, free: 26.86 MB / 0.5262 GB
Notification: Performance of SimCode: time 6.91e-07/0.01625, allocations: 3.938 kB / 0.6633 GB, free: 26.86 MB / 0.5262 GB
Notification: Performance of Templates: time 0.00743/0.02368, allocations: 5.343 MB / 0.6685 GB, free: 26.31 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: 4.916334363166243]