Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.PK_2C_single.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 0.001007/0.001007, 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 0.001041/0.001041, allocations: 169 kB / 23.5 MB, free: 1.047 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 0.9444/0.9444, allocations: 177.1 MB / 203.8 MB, free: 5.633 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 1.541/1.541, allocations: 273.5 MB / 0.5213 GB, free: 14.83 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.PK_2C_single,tolerance=1e-12,outputFormat="empty",numberOfIntervals=86,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.PK_2C_single")
translateModel(Pharmacolibrary.Examples.Pharmacogenomics.PK_2C_single,tolerance=1e-12,outputFormat="empty",numberOfIntervals=86,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.PK_2C_single") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 2.124e-06/2.124e-06, allocations: 3.562 kB / 0.647 GB, free: 38.74 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.295e-05/1.508e-05, allocations: 2.312 kB / 0.647 GB, free: 38.74 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.Pharmacogenomics.PK_2C_single): time 0.003047/0.003062, allocations: 3.915 MB / 0.6508 GB, free: 36.18 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.001046/0.004108, allocations: 0.8444 MB / 0.6516 GB, free: 35.61 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001113/0.004219, allocations: 3.5 kB / 0.6516 GB, free: 35.61 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001456/0.004365, allocations: 49.48 kB / 0.6517 GB, free: 35.59 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0002041/0.004569, allocations: 156.4 kB / 0.6518 GB, free: 35.51 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0002696/0.004839, allocations: 141.8 kB / 0.652 GB, free: 35.41 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0003359/0.005175, allocations: 0.543 MB / 0.6525 GB, free: 35.11 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001781/0.005353, allocations: 73.34 kB / 0.6526 GB, free: 35.07 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002177/0.00557, allocations: 283.7 kB / 0.6528 GB, free: 34.94 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.00022/0.00579, allocations: 160.7 kB / 0.653 GB, free: 34.89 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 4.774e-05/0.005838, allocations: 46.94 kB / 0.653 GB, free: 34.89 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 4.411e-05/0.005882, allocations: 48.72 kB / 0.6531 GB, free: 34.89 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 4.278e-05/0.005925, allocations: 85.91 kB / 0.6532 GB, free: 34.82 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 0.000115/0.00604, allocations: 160.8 kB / 0.6533 GB, free: 34.75 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002617/0.006302, allocations: 329 kB / 0.6536 GB, free: 34.58 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 1.864e-06/0.006304, allocations: 0 / 0.6536 GB, free: 34.58 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 6.71e-07/0.006304, allocations: 0 / 0.6536 GB, free: 34.58 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 5.29e-06/0.00631, allocations: 0 / 0.6536 GB, free: 34.58 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: 67
 * Number of variables: 67
Notification: Performance of Generate backend data structure: time 0.0007064/0.007016, allocations: 0.8065 MB / 0.6544 GB, free: 33.89 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.804e-05/0.007054, allocations: 9.281 kB / 0.6544 GB, free: 33.89 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 8.369e-05/0.007138, allocations: 65.97 kB / 0.6545 GB, free: 33.86 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002114/0.007349, allocations: 248.2 kB / 0.6547 GB, free: 33.65 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.954e-05/0.007369, allocations: 20.88 kB / 0.6547 GB, free: 33.64 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 6.007e-05/0.007429, allocations: 36.56 kB / 0.6548 GB, free: 33.63 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003658/0.007794, allocations: 350.5 kB / 0.6551 GB, free: 33.41 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.513e-05/0.00781, allocations: 7.891 kB / 0.6551 GB, free: 33.4 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.012e-05/0.00783, allocations: 11.72 kB / 0.6551 GB, free: 33.39 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.478e-06/0.007839, allocations: 7.125 kB / 0.6551 GB, free: 33.39 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002131/0.008052, allocations: 236.3 kB / 0.6554 GB, free: 33.27 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0008602/0.008912, allocations: 0.9298 MB / 0.6563 GB, free: 32.59 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0003643/0.009277, allocations: 248.3 kB / 0.6565 GB, free: 32.43 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001467/0.009423, allocations: 156.1 kB / 0.6567 GB, free: 32.31 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 3.197e-05/0.009455, allocations: 6.344 kB / 0.6567 GB, free: 32.31 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0003869/0.009842, allocations: 452.1 kB / 0.6571 GB, free: 31.95 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=44): time 2.575e-06/0.009845, allocations: 0 / 0.6571 GB, free: 31.95 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=47): time 0.001303/0.01115, allocations: 1.29 MB / 0.6584 GB, free: 31.06 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.987e-05/0.0112, allocations: 301.5 kB / 0.6586 GB, free: 30.71 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002103/0.01141, allocations: 316.5 kB / 0.6589 GB, free: 30.51 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 2.362e-05/0.01143, allocations: 40.7 kB / 0.659 GB, free: 30.47 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 7.301e-05/0.0115, allocations: 223.7 kB / 0.6592 GB, free: 30.27 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 6.696e-05/0.01157, allocations: 162.9 kB / 0.6594 GB, free: 30.14 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 8.825e-05/0.01166, allocations: 95.5 kB / 0.6594 GB, free: 30.08 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 6.607e-05/0.01173, allocations: 0.519 MB / 0.66 GB, free: 29.57 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001457/0.01187, allocations: 212.3 kB / 0.6602 GB, free: 29.42 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002394/0.01211, allocations: 377.2 kB / 0.6605 GB, free: 29.04 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0004344/0.01255, allocations: 0.7085 MB / 0.6612 GB, free: 28.39 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.865e-06/0.01255, allocations: 1.438 kB / 0.6612 GB, free: 28.39 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=71) (initialization): time 0.0004946/0.01304, allocations: 0.6281 MB / 0.6618 GB, free: 27.99 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 4.053e-05/0.01308, allocations: 115.9 kB / 0.6619 GB, free: 27.86 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.673e-06/0.01309, allocations: 4.219 kB / 0.6619 GB, free: 27.86 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.754e-05/0.01311, allocations: 7 kB / 0.6619 GB, free: 27.86 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002523/0.01336, allocations: 119.4 kB / 0.6621 GB, free: 27.85 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.194e-05/0.01337, allocations: 9.594 kB / 0.6621 GB, free: 27.85 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001227/0.01349, allocations: 27.89 kB / 0.6621 GB, free: 27.84 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.513e-05/0.01352, allocations: 20.78 kB / 0.6621 GB, free: 27.83 MB / 0.5262 GB
Warning: Assuming fixed start value for the following 14 variables:
         patient.central.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         patient.periodicDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         patient.periodicDose.absorptionLumen.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         patient.periodicDose.variableDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         patient.peripheral.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         patient.peripheral.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         patient.peripheral.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         patient.periodicDose.absorptionLumen.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         patient.periodicDose.absorptionLumen.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         patient.central.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         patient.central.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         patient.peripheral.rising:DISCRETE(fixed = true protected = true )  type: Boolean
         patient.periodicDose.absorptionLumen.rising:DISCRETE(fixed = true protected = true )  type: Boolean
         patient.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: 29 ($PRE.patient.peripheral.Cmin,patient.peripheral.Cmin,$PRE.patient.peripheral.Cmax,patient.peripheral.Cmax,$PRE.patient.periodicDose.absorptionLumen.Cmin,patient.periodicDose.absorptionLumen.Cmin,$PRE.patient.periodicDose.absorptionLumen.Cmax,patient.periodicDose.absorptionLumen.Cmax,$PRE.patient.central.Cmin,patient.central.Cmin,$PRE.patient.central.Cmax,patient.central.Cmax,$PRE.patient.peripheral.rising,$PRE.patient.periodicDose.pulse.count,$PRE.patient.periodicDose.pulse.T_start,$PRE.patient.periodicDose.absorptionLumen.rising,$PRE.patient.central.rising,patient.peripheral.rising,patient.periodicDose.pulse.count,patient.periodicDose.pulse.T_start,patient.periodicDose.absorptionLumen.rising,patient.central.rising,$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 (67):
 * Single equations (assignments): 63
 * 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 0.0001933/0.01371, allocations: 358.5 kB / 0.6625 GB, free: 27.52 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 5.158e-05/0.01376, allocations: 61.33 kB / 0.6625 GB, free: 27.5 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 4.102e-05/0.01381, allocations: 42 kB / 0.6626 GB, free: 27.46 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.718e-06/0.01381, allocations: 0 / 0.6626 GB, free: 27.46 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.603e-06/0.01381, allocations: 1.375 kB / 0.6626 GB, free: 27.46 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 9.227e-05/0.0139, allocations: 75.36 kB / 0.6626 GB, free: 27.42 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 4.424e-05/0.01395, allocations: 21.78 kB / 0.6626 GB, free: 27.41 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 8.079e-05/0.01403, allocations: 17.34 kB / 0.6627 GB, free: 27.41 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 8.03e-05/0.01411, allocations: 37.45 kB / 0.6627 GB, free: 27.4 MB / 0.5262 GB
Notification: Performance of postOpt createDAEmodeBDAE (simulation): time 0.000573/0.01468, allocations: 0.6561 MB / 0.6633 GB, free: 26.98 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobianDAE (simulation): time 0.0006399/0.01532, allocations: 0.9968 MB / 0.6643 GB, free: 26.27 MB / 0.5262 GB
Notification: Performance of postOpt setEvaluationStage (simulation): time 0.0001562/0.01548, allocations: 208.4 kB / 0.6645 GB, free: 26.12 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 0.0001012/0.01558, allocations: 214 kB / 0.6647 GB, free: 25.98 MB / 0.5262 GB
Notification: Performance of Backend: time 2.21e-07/0.01558, allocations: 0 / 0.6647 GB, free: 25.98 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0005252/0.01611, allocations: 0.6098 MB / 0.6653 GB, free: 25.48 MB / 0.5262 GB
Notification: Performance of SimCode: time 0.001803/0.01791, allocations: 1.845 MB / 0.6671 GB, free: 23.97 MB / 0.5262 GB
Notification: Performance of Templates: time 0.008163/0.02607, allocations: 6.494 MB / 0.6735 GB, free: 23.45 MB / 0.5262 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.PK_2C_single.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.PK_2C_single.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.PK_2C_single.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.PK_2C_single.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.PK_2C_single.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.PK_2C_single -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.PK_2C_single.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 4.6867002008948475]