Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_2C_Ibuprofen.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 0.001034/0.001034, allocations: 91.55 kB / 20.19 MB, free: 4.352 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 0.001192/0.001192, allocations: 169.3 kB / 23.5 MB, free: 1.043 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 0.8998/0.8998, allocations: 177.1 MB / 203.8 MB, free: 5.637 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 1.635/1.635, allocations: 273.5 MB / 0.5213 GB, free: 14.82 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_2C_Ibuprofen,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_2C_Ibuprofen")
translateModel(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_2C_Ibuprofen,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_2C_Ibuprofen") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.253e-06/1.253e-06, allocations: 1.312 kB / 0.6475 GB, free: 38.33 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.667e-05/1.792e-05, allocations: 2.312 kB / 0.6475 GB, free: 38.33 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_2C_Ibuprofen): time 0.003436/0.003454, allocations: 4.329 MB / 0.6517 GB, free: 35.52 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.001498/0.004952, allocations: 1.188 MB / 0.6529 GB, free: 34.76 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001534/0.005105, allocations: 5.031 kB / 0.6529 GB, free: 34.76 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0003758/0.005481, allocations: 146.2 kB / 0.653 GB, free: 34.7 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0002146/0.005696, allocations: 182 kB / 0.6532 GB, free: 34.59 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0004005/0.006096, allocations: 208 kB / 0.6534 GB, free: 34.48 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0003745/0.006471, allocations: 0.5753 MB / 0.6539 GB, free: 34.17 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001513/0.006622, allocations: 101.3 kB / 0.654 GB, free: 34.11 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002262/0.006848, allocations: 303.1 kB / 0.6543 GB, free: 34 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002503/0.007099, allocations: 184.1 kB / 0.6545 GB, free: 33.94 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 6.381e-05/0.007162, allocations: 42.62 kB / 0.6545 GB, free: 33.94 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.0002012/0.007364, allocations: 182.7 kB / 0.6547 GB, free: 33.88 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 9.101e-05/0.007455, allocations: 111.9 kB / 0.6548 GB, free: 33.81 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 0.0001804/0.007635, allocations: 176.5 kB / 0.655 GB, free: 33.74 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.000419/0.008054, allocations: 0.5002 MB / 0.6555 GB, free: 33.51 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 2.215e-06/0.008056, allocations: 0 / 0.6555 GB, free: 33.51 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 9.01e-07/0.008057, allocations: 2.25 kB / 0.6555 GB, free: 33.51 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 7.804e-06/0.008065, allocations: 0 / 0.6555 GB, free: 33.51 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: 81
 * Number of variables: 81
Notification: Performance of Generate backend data structure: time 0.0008668/0.008932, allocations: 0.9795 MB / 0.6564 GB, free: 32.68 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 4.139e-05/0.008973, allocations: 13.19 kB / 0.6565 GB, free: 32.68 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0002937/0.009267, allocations: 150.9 kB / 0.6566 GB, free: 32.62 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002861/0.009553, allocations: 288 kB / 0.6569 GB, free: 32.39 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.73e-05/0.00958, allocations: 24.5 kB / 0.6569 GB, free: 32.38 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 5.868e-05/0.009639, allocations: 44.39 kB / 0.6569 GB, free: 32.36 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004474/0.01009, allocations: 457.2 kB / 0.6574 GB, free: 32.07 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.852e-05/0.0101, allocations: 5.391 kB / 0.6574 GB, free: 32.07 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.147e-05/0.01013, allocations: 13.25 kB / 0.6574 GB, free: 32.06 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.174e-05/0.01014, allocations: 8.469 kB / 0.6574 GB, free: 32.06 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002589/0.0104, allocations: 327.2 kB / 0.6577 GB, free: 31.86 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0009781/0.01138, allocations: 1.042 MB / 0.6587 GB, free: 31.15 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0003485/0.01172, allocations: 346.5 kB / 0.6591 GB, free: 30.91 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001432/0.01187, allocations: 249 kB / 0.6593 GB, free: 30.72 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 2.321e-05/0.01189, allocations: 13.42 kB / 0.6593 GB, free: 30.71 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.000299/0.01219, allocations: 0.5273 MB / 0.6598 GB, free: 30.27 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=52): time 1.864e-06/0.01219, allocations: 1.375 kB / 0.6598 GB, free: 30.27 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=55): time 0.001479/0.01367, allocations: 1.822 MB / 0.6616 GB, free: 28.98 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.839e-05/0.01373, allocations: 363.2 kB / 0.662 GB, free: 28.57 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002606/0.01399, allocations: 427.8 kB / 0.6624 GB, free: 28.32 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 2.532e-05/0.01401, allocations: 39.36 kB / 0.6624 GB, free: 28.28 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 9.734e-05/0.01411, allocations: 281 kB / 0.6627 GB, free: 28.04 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 7.595e-05/0.01419, allocations: 181 kB / 0.6628 GB, free: 27.9 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001053/0.01429, allocations: 108.5 kB / 0.6629 GB, free: 27.84 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 7.755e-05/0.01437, allocations: 0.5394 MB / 0.6635 GB, free: 27.32 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.000173/0.01454, allocations: 296.6 kB / 0.6638 GB, free: 27.09 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.000207/0.01475, allocations: 469.2 kB / 0.6642 GB, free: 26.64 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0005365/0.01529, allocations: 0.9509 MB / 0.6651 GB, free: 25.78 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.306e-06/0.01529, allocations: 1.125 kB / 0.6651 GB, free: 25.78 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=79) (initialization): time 0.0007521/0.01604, allocations: 0.8745 MB / 0.666 GB, free: 25.2 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 6.263e-05/0.0161, allocations: 178 kB / 0.6662 GB, free: 25.01 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 9.999e-06/0.01611, allocations: 6.469 kB / 0.6662 GB, free: 25.01 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 2.421e-05/0.01614, allocations: 7.031 kB / 0.6662 GB, free: 25.01 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002621/0.0164, allocations: 120.6 kB / 0.6663 GB, free: 25 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.347e-05/0.01641, allocations: 7.031 kB / 0.6663 GB, free: 25 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001457/0.01656, allocations: 23.06 kB / 0.6663 GB, free: 24.99 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 6.315e-05/0.01662, allocations: 62.73 kB / 0.6664 GB, free: 24.99 MB / 0.5262 GB
Warning: Assuming fixed start value for the following 14 variables:
         central.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         periodicDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         periodicDose.absorptionLumen.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         periodicDose.variableDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         peripheral.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         peripheral.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         peripheral.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         periodicDose.absorptionLumen.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         periodicDose.absorptionLumen.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  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
         peripheral.rising:DISCRETE(fixed = true protected = true )  type: Boolean
         periodicDose.absorptionLumen.rising:DISCRETE(fixed = true protected = true )  type: Boolean
         central.rising:DISCRETE(fixed = true protected = true )  type: Boolean
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 16
 * Number of states: 0 ()
 * Number of discrete variables: 31 ($PRE.peripheral.Cmin,peripheral.Cmin,$PRE.peripheral.Cmax,peripheral.Cmax,$PRE.periodicDose.absorptionLumen.Cmin,periodicDose.absorptionLumen.Cmin,$PRE.periodicDose.absorptionLumen.Cmax,periodicDose.absorptionLumen.Cmax,$PRE.central.Cmin,central.Cmin,$PRE.central.Cmax,central.Cmax,$PRE.peripheral.rising,$PRE.periodicDose.pulse.count,$PRE.periodicDose.pulse.T_start,$PRE.periodicDose.absorptionLumen.rising,$PRE.central.rising,CYP2C19.status,SLC22A2.status,peripheral.rising,periodicDose.pulse.count,periodicDose.pulse.T_start,periodicDose.absorptionLumen.rising,central.rising,$whenCondition6,$whenCondition5,$whenCondition4,$whenCondition3,$whenCondition2,$whenCondition1,$whenCondition7)
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (73):
 * Single equations (assignments): 67
 * Array equations: 0
 * Algorithm blocks: 6
 * 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 0.0002215/0.01684, allocations: 408.8 kB / 0.6668 GB, free: 24.62 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001208/0.01697, allocations: 125.2 kB / 0.6669 GB, free: 24.57 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 4.84e-05/0.01701, allocations: 53.77 kB / 0.6669 GB, free: 24.54 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.7e-06/0.01702, allocations: 5.891 kB / 0.6669 GB, free: 24.54 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.543e-06/0.01702, allocations: 0 / 0.6669 GB, free: 24.54 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 0.0001104/0.01713, allocations: 88.56 kB / 0.667 GB, free: 24.49 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.409e-05/0.01719, allocations: 18.59 kB / 0.667 GB, free: 24.48 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 9.758e-05/0.01728, allocations: 18.8 kB / 0.6671 GB, free: 24.48 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 8.362e-05/0.01737, allocations: 49.06 kB / 0.6671 GB, free: 24.46 MB / 0.5262 GB
Notification: Performance of postOpt createDAEmodeBDAE (simulation): time 0.000672/0.01804, allocations: 0.8533 MB / 0.6679 GB, free: 23.89 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobianDAE (simulation): time 0.0008355/0.01887, allocations: 1.342 MB / 0.6692 GB, free: 22.93 MB / 0.5262 GB
Notification: Performance of postOpt setEvaluationStage (simulation): time 0.0002066/0.01908, allocations: 301.2 kB / 0.6695 GB, free: 22.72 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 0.0001674/0.01925, allocations: 279.3 kB / 0.6698 GB, free: 22.56 MB / 0.5262 GB
Notification: Performance of Backend: time 2.51e-07/0.01925, allocations: 0 / 0.6698 GB, free: 22.56 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.000778/0.02003, allocations: 0.8786 MB / 0.6707 GB, free: 21.84 MB / 0.5262 GB
Notification: Performance of SimCode: time 0.001992/0.02202, allocations: 2.114 MB / 0.6727 GB, free: 20.09 MB / 0.5262 GB
Notification: Performance of Templates: time 0.01129/0.03331, allocations: 7.999 MB / 0.6805 GB, free: 18.75 MB / 0.5262 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_2C_Ibuprofen.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_2C_Ibuprofen.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_2C_Ibuprofen.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_2C_Ibuprofen.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_2C_Ibuprofen.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_2C_Ibuprofen -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_2C_Ibuprofen.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 4.971476529957727]