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 0.001102/0.001102, allocations: 92.22 kB / 19.65 MB, free: 276 kB / 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 0.001136/0.001136, allocations: 169 kB / 23.02 MB, free: 1.551 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 0.9854/0.9854, allocations: 177.1 MB / 203.4 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 1.587/1.587, allocations: 273.5 MB / 0.5209 GB, free: 14.84 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 1.473e-06/1.473e-06, allocations: 0 / 0.647 GB, free: 38.77 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 3.269e-05/3.416e-05, allocations: 3.156 kB / 0.647 GB, free: 38.76 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin): time 0.002776/0.00281, allocations: 2.546 MB / 0.6495 GB, free: 37.13 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.001225/0.004034, allocations: 0.9373 MB / 0.6504 GB, free: 36.54 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001042/0.004138, allocations: 3.406 kB / 0.6504 GB, free: 36.54 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0004011/0.00454, allocations: 116 kB / 0.6505 GB, free: 36.49 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001454/0.004685, allocations: 80.98 kB / 0.6506 GB, free: 36.46 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0003739/0.005059, allocations: 150.1 kB / 0.6507 GB, free: 36.39 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0003149/0.005374, allocations: 299.9 kB / 0.651 GB, free: 36.26 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001415/0.005515, allocations: 50.52 kB / 0.6511 GB, free: 36.23 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001824/0.005698, allocations: 149.6 kB / 0.6512 GB, free: 36.17 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.000157/0.005855, allocations: 93.03 kB / 0.6513 GB, free: 36.14 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 3.458e-05/0.005889, allocations: 24.91 kB / 0.6513 GB, free: 36.13 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.0002122/0.006102, allocations: 169.1 kB / 0.6515 GB, free: 36.08 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 7.993e-05/0.006181, allocations: 67 kB / 0.6515 GB, free: 36.04 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 9.501e-05/0.006276, allocations: 82.36 kB / 0.6516 GB, free: 36 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.00041/0.006687, allocations: 341.3 kB / 0.6519 GB, free: 35.86 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 4.418e-06/0.006691, allocations: 1.094 kB / 0.6519 GB, free: 35.86 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 1.804e-06/0.006693, allocations: 0 / 0.6519 GB, free: 35.86 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 6.412e-06/0.006699, allocations: 0 / 0.6519 GB, free: 35.86 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 0.0007312/0.00743, allocations: 0.7216 MB / 0.6527 GB, free: 35.21 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.636e-05/0.007467, allocations: 9.156 kB / 0.6527 GB, free: 35.21 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0002295/0.007696, allocations: 110.1 kB / 0.6528 GB, free: 35.17 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002114/0.007908, allocations: 227.3 kB / 0.653 GB, free: 34.97 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.777e-05/0.007925, allocations: 13.53 kB / 0.653 GB, free: 34.96 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.194e-05/0.007967, allocations: 18.25 kB / 0.653 GB, free: 34.96 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002806/0.008248, allocations: 258.5 kB / 0.6533 GB, free: 34.78 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.422e-05/0.008262, allocations: 0.5625 kB / 0.6533 GB, free: 34.78 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.901e-05/0.008281, allocations: 7.75 kB / 0.6533 GB, free: 34.78 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.381e-05/0.008295, allocations: 3.938 kB / 0.6533 GB, free: 34.78 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002086/0.008504, allocations: 178.1 kB / 0.6534 GB, free: 34.66 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0006508/0.009154, allocations: 0.5264 MB / 0.654 GB, free: 34.28 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002123/0.009367, allocations: 206.5 kB / 0.6542 GB, free: 34.13 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001036/0.00947, allocations: 153.6 kB / 0.6543 GB, free: 34.01 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.279e-05/0.009483, allocations: 4.094 kB / 0.6543 GB, free: 34.01 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002395/0.009722, allocations: 293.7 kB / 0.6546 GB, free: 33.77 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=26): time 2.084e-06/0.009725, allocations: 1.281 kB / 0.6546 GB, free: 33.77 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=27): time 0.00134/0.01106, allocations: 1.097 MB / 0.6557 GB, free: 32.94 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.699e-05/0.01111, allocations: 195.1 kB / 0.6558 GB, free: 32.71 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002013/0.01131, allocations: 330.5 kB / 0.6562 GB, free: 32.5 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.71e-05/0.01133, allocations: 33.95 kB / 0.6562 GB, free: 32.46 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 7.833e-05/0.01141, allocations: 217.5 kB / 0.6564 GB, free: 32.28 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 5.967e-05/0.01147, allocations: 88.39 kB / 0.6565 GB, free: 32.21 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 7.479e-05/0.01154, allocations: 66.69 kB / 0.6565 GB, free: 32.16 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 6.828e-05/0.01161, allocations: 0.5154 MB / 0.657 GB, free: 31.66 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001134/0.01172, allocations: 193.5 kB / 0.6572 GB, free: 31.5 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.000125/0.01185, allocations: 274.4 kB / 0.6575 GB, free: 31.23 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002955/0.01214, allocations: 0.5625 MB / 0.658 GB, free: 30.72 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.064e-06/0.01215, allocations: 0 / 0.658 GB, free: 30.72 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=38) (initialization): time 0.0004137/0.01256, allocations: 0.5397 MB / 0.6586 GB, free: 30.35 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 3.988e-05/0.0126, allocations: 122.8 kB / 0.6587 GB, free: 30.22 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.051e-06/0.01261, allocations: 5.375 kB / 0.6587 GB, free: 30.21 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 2.288e-05/0.01263, allocations: 2.781 kB / 0.6587 GB, free: 30.21 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001714/0.0128, allocations: 56.78 kB / 0.6587 GB, free: 30.21 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.01e-05/0.01281, allocations: 2.781 kB / 0.6588 GB, free: 30.21 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.775e-05/0.01291, allocations: 17.2 kB / 0.6588 GB, free: 30.2 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 6.601e-05/0.01297, allocations: 51.69 kB / 0.6588 GB, free: 30.2 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 0.0001922/0.01317, allocations: 281.2 kB / 0.6591 GB, free: 29.93 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001122/0.01328, allocations: 86.84 kB / 0.6592 GB, free: 29.9 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 4.418e-05/0.01332, allocations: 39.55 kB / 0.6592 GB, free: 29.88 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.276e-06/0.01333, allocations: 1.406 kB / 0.6592 GB, free: 29.88 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.963e-06/0.01333, allocations: 1.438 kB / 0.6592 GB, free: 29.88 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.051e-06/0.01334, allocations: 3.656 kB / 0.6592 GB, free: 29.88 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0006514/0.01399, allocations: 0.7916 MB / 0.66 GB, free: 29.28 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.896e-06/0.01399, allocations: 10.59 kB / 0.66 GB, free: 29.27 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001297/0.01412, allocations: 33.34 kB / 0.66 GB, free: 29.27 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 3.436e-06/0.01413, allocations: 1.469 kB / 0.66 GB, free: 29.27 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.812e-05/0.01414, allocations: 11.55 kB / 0.66 GB, free: 29.27 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.014e-06/0.01415, allocations: 1.375 kB / 0.66 GB, free: 29.27 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.553e-06/0.01415, allocations: 1.469 kB / 0.66 GB, free: 29.27 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005242/0.01467, allocations: 0.7995 MB / 0.6608 GB, free: 28.68 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.66e-05/0.0147, allocations: 25.34 kB / 0.6608 GB, free: 28.66 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.275e-05/0.01473, allocations: 12.78 kB / 0.6609 GB, free: 28.66 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 8.451e-05/0.01482, allocations: 10.38 kB / 0.6609 GB, free: 28.66 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.058e-05/0.01488, allocations: 31.12 kB / 0.6609 GB, free: 28.65 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 4.428e-05/0.01492, allocations: 46.89 kB / 0.6609 GB, free: 28.65 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 0.0001048/0.01503, allocations: 218.3 kB / 0.6612 GB, free: 28.5 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 7e-08/0.01503, allocations: 3.969 kB / 0.6612 GB, free: 28.5 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0002671/0.01529, allocations: 75.16 kB / 0.6612 GB, free: 28.5 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 0.0002169/0.01551, allocations: 165.5 kB / 0.6614 GB, free: 28.39 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0003348/0.01585, allocations: 0.6045 MB / 0.662 GB, free: 27.86 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.603e-06/0.01585, allocations: 0 / 0.662 GB, free: 27.86 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001504/0.016, allocations: 351.9 kB / 0.6623 GB, free: 27.54 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003152/0.01631, allocations: 71.27 kB / 0.6624 GB, free: 27.52 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001523/0.01784, allocations: 0.8598 MB / 0.6632 GB, free: 26.96 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 5.242e-05/0.01789, allocations: 96.09 kB / 0.6633 GB, free: 26.89 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 7.707e-05/0.01797, allocations: 24.02 kB / 0.6633 GB, free: 26.88 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 5.707e-05/0.01802, allocations: 21.12 kB / 0.6634 GB, free: 26.87 MB / 0.5262 GB
Notification: Performance of SimCode: time 1.002e-06/0.01802, allocations: 0 / 0.6634 GB, free: 26.87 MB / 0.5262 GB
Notification: Performance of Templates: time 0.0069/0.02492, allocations: 4.679 MB / 0.6679 GB, free: 26.43 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: 5.087538233958185]