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 0.001464/0.001464, allocations: 73.88 kB / 20.65 MB, free: 3.84 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 0.001608/0.001608, allocations: 169 kB / 24.05 MB, free: 452 kB / 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 0.9656/0.9656, allocations: 177.1 MB / 204.5 MB, free: 5.492 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 1.595/1.595, allocations: 273.5 MB / 0.522 GB, free: 14.62 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 1.272e-06/1.272e-06, allocations: 0 / 0.6482 GB, free: 38.45 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.482e-05/2.609e-05, allocations: 2.312 kB / 0.6482 GB, free: 38.44 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin): time 0.003502/0.003528, allocations: 2.523 MB / 0.6507 GB, free: 36.81 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.00101/0.004538, allocations: 0.9183 MB / 0.6516 GB, free: 36.22 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 8.537e-05/0.004623, allocations: 5.031 kB / 0.6516 GB, free: 36.22 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0003351/0.004958, allocations: 123.1 kB / 0.6517 GB, free: 36.17 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001142/0.005073, allocations: 78.42 kB / 0.6518 GB, free: 36.14 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0003138/0.005386, allocations: 147.4 kB / 0.6519 GB, free: 36.07 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002834/0.00567, allocations: 302.8 kB / 0.6522 GB, free: 35.95 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001163/0.005786, allocations: 49.2 kB / 0.6522 GB, free: 35.91 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001534/0.005939, allocations: 147.3 kB / 0.6524 GB, free: 35.86 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001377/0.006077, allocations: 106.5 kB / 0.6525 GB, free: 35.82 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 2.825e-05/0.006105, allocations: 19.59 kB / 0.6525 GB, free: 35.82 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001966/0.006302, allocations: 162.7 kB / 0.6526 GB, free: 35.77 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 6.794e-05/0.00637, allocations: 66.34 kB / 0.6527 GB, free: 35.73 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 7.657e-05/0.006447, allocations: 86.62 kB / 0.6528 GB, free: 35.69 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0003424/0.006789, allocations: 337.3 kB / 0.6531 GB, free: 35.54 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 4.589e-06/0.006794, allocations: 1.219 kB / 0.6531 GB, free: 35.54 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 7.82e-07/0.006794, allocations: 0 / 0.6531 GB, free: 35.54 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 4.769e-06/0.006799, allocations: 0 / 0.6531 GB, free: 35.54 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 0.0006399/0.007439, allocations: 0.7186 MB / 0.6538 GB, free: 34.89 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.156e-05/0.007471, allocations: 9.625 kB / 0.6538 GB, free: 34.89 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0002048/0.007675, allocations: 118.6 kB / 0.6539 GB, free: 34.85 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001699/0.007845, allocations: 208.6 kB / 0.6541 GB, free: 34.66 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.247e-05/0.007868, allocations: 15.31 kB / 0.6542 GB, free: 34.66 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.028e-05/0.007898, allocations: 19.75 kB / 0.6542 GB, free: 34.65 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002509/0.008149, allocations: 242.1 kB / 0.6544 GB, free: 34.48 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.283e-05/0.008162, allocations: 1.344 kB / 0.6544 GB, free: 34.48 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.669e-05/0.008179, allocations: 8.156 kB / 0.6544 GB, free: 34.47 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.212e-06/0.008185, allocations: 1.719 kB / 0.6544 GB, free: 34.47 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001251/0.00831, allocations: 154.1 kB / 0.6546 GB, free: 34.38 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0005155/0.008825, allocations: 479.5 kB / 0.655 GB, free: 34.03 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001641/0.008989, allocations: 202.3 kB / 0.6552 GB, free: 33.88 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 7.621e-05/0.009066, allocations: 127.6 kB / 0.6553 GB, free: 33.76 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.155e-05/0.009077, allocations: 6.969 kB / 0.6553 GB, free: 33.76 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001891/0.009266, allocations: 274.1 kB / 0.6556 GB, free: 33.53 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=26): time 2.014e-06/0.009268, allocations: 0 / 0.6556 GB, free: 33.53 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=27): time 0.0009829/0.01025, allocations: 0.9821 MB / 0.6566 GB, free: 32.76 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.029e-05/0.0103, allocations: 197.4 kB / 0.6567 GB, free: 32.54 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002804/0.01058, allocations: 328.2 kB / 0.6571 GB, free: 32.32 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 2.137e-05/0.0106, allocations: 34.42 kB / 0.6571 GB, free: 32.28 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 0.0001162/0.01072, allocations: 215.5 kB / 0.6573 GB, free: 32.09 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 5.454e-05/0.01077, allocations: 82.53 kB / 0.6574 GB, free: 32.03 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 8.865e-05/0.01086, allocations: 70.8 kB / 0.6574 GB, free: 31.98 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 7.306e-05/0.01094, allocations: 0.5225 MB / 0.658 GB, free: 31.47 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001089/0.01104, allocations: 177.9 kB / 0.6581 GB, free: 31.31 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001118/0.01116, allocations: 261.8 kB / 0.6584 GB, free: 31.05 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002718/0.01143, allocations: 0.5121 MB / 0.6589 GB, free: 30.57 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.783e-06/0.01143, allocations: 1.406 kB / 0.6589 GB, free: 30.57 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=38) (initialization): time 0.0003851/0.01182, allocations: 0.5046 MB / 0.6594 GB, free: 30.2 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 4.032e-05/0.01186, allocations: 114.4 kB / 0.6595 GB, free: 30.08 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.82e-06/0.01186, allocations: 1.469 kB / 0.6595 GB, free: 30.08 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.259e-05/0.01187, allocations: 8.094 kB / 0.6595 GB, free: 30.07 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001429/0.01202, allocations: 57.52 kB / 0.6595 GB, free: 30.07 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 4.217e-06/0.01202, allocations: 2.875 kB / 0.6595 GB, free: 30.07 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.048e-05/0.01211, allocations: 18.28 kB / 0.6596 GB, free: 30.06 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 6.306e-05/0.01217, allocations: 48.67 kB / 0.6596 GB, free: 30.06 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 0.0001657/0.01234, allocations: 289.9 kB / 0.6599 GB, free: 29.78 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 9.7e-05/0.01244, allocations: 91.66 kB / 0.66 GB, free: 29.75 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.547e-05/0.01247, allocations: 33.56 kB / 0.66 GB, free: 29.73 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.837e-06/0.01248, allocations: 5.438 kB / 0.66 GB, free: 29.73 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.24e-06/0.01248, allocations: 4.734 kB / 0.66 GB, free: 29.73 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.849e-06/0.01249, allocations: 3.422 kB / 0.66 GB, free: 29.73 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.000485/0.01297, allocations: 0.7043 MB / 0.6607 GB, free: 29.18 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.635e-06/0.01297, allocations: 0 / 0.6607 GB, free: 29.18 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001198/0.01309, allocations: 36.22 kB / 0.6607 GB, free: 29.18 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 3.136e-06/0.0131, allocations: 1.406 kB / 0.6607 GB, free: 29.18 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.229e-05/0.01312, allocations: 13.11 kB / 0.6608 GB, free: 29.18 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.174e-06/0.01312, allocations: 0 / 0.6608 GB, free: 29.18 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.002e-06/0.01312, allocations: 1.469 kB / 0.6608 GB, free: 29.18 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004463/0.01357, allocations: 0.7565 MB / 0.6615 GB, free: 28.61 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.363e-05/0.01359, allocations: 18.86 kB / 0.6615 GB, free: 28.59 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.127e-05/0.01362, allocations: 8.188 kB / 0.6615 GB, free: 28.59 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001/0.01372, allocations: 15.8 kB / 0.6615 GB, free: 28.59 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.357e-05/0.01378, allocations: 22.66 kB / 0.6616 GB, free: 28.58 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 4.451e-05/0.01382, allocations: 54.83 kB / 0.6616 GB, free: 28.57 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 8.901e-05/0.01391, allocations: 206.5 kB / 0.6618 GB, free: 28.44 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 6.1e-08/0.01391, allocations: 0 / 0.6618 GB, free: 28.44 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0002671/0.01418, allocations: 75.53 kB / 0.6619 GB, free: 28.43 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 0.0002246/0.0144, allocations: 166 kB / 0.662 GB, free: 28.32 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0003267/0.01473, allocations: 0.5655 MB / 0.6626 GB, free: 27.8 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.684e-06/0.01473, allocations: 0 / 0.6626 GB, free: 27.8 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001244/0.01486, allocations: 337.8 kB / 0.6629 GB, free: 27.5 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003169/0.01517, allocations: 78.3 kB / 0.663 GB, free: 27.48 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001393/0.01657, allocations: 0.8479 MB / 0.6638 GB, free: 26.91 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 5.378e-05/0.01662, allocations: 101.8 kB / 0.6639 GB, free: 26.83 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 7.045e-05/0.01669, allocations: 21.95 kB / 0.6639 GB, free: 26.82 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001497/0.01684, allocations: 144.9 kB / 0.6641 GB, free: 26.75 MB / 0.5262 GB
Notification: Performance of SimCode: time 5.21e-07/0.01684, allocations: 0 / 0.6641 GB, free: 26.75 MB / 0.5262 GB
Notification: Performance of Templates: time 0.007834/0.02467, allocations: 5.423 MB / 0.6694 GB, free: 26.2 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: 4.971636515110731]