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 0.0009827/0.0009827, allocations: 92.2 kB / 20.19 MB, free: 4.359 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 0.001011/0.001011, allocations: 173 kB / 23.49 MB, free: 1.055 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 0.9136/0.9136, allocations: 177.1 MB / 203.8 MB, free: 5.648 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 1.54/1.54, allocations: 273.5 MB / 0.5213 GB, free: 14.87 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 1.402e-06/1.402e-06, allocations: 0 / 0.647 GB, free: 38.72 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.222e-05/2.362e-05, allocations: 2.312 kB / 0.647 GB, free: 38.71 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin): time 0.002534/0.002558, allocations: 2.541 MB / 0.6495 GB, free: 37.08 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.001095/0.003653, allocations: 0.9307 MB / 0.6504 GB, free: 36.49 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 9.656e-05/0.003749, allocations: 4.438 kB / 0.6504 GB, free: 36.49 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0003322/0.004081, allocations: 118.7 kB / 0.6505 GB, free: 36.45 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001173/0.004199, allocations: 80.83 kB / 0.6506 GB, free: 36.41 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0003087/0.004507, allocations: 144.6 kB / 0.6507 GB, free: 36.34 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002389/0.004746, allocations: 303.2 kB / 0.651 GB, free: 36.21 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001205/0.004867, allocations: 48.75 kB / 0.6511 GB, free: 36.18 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001288/0.004996, allocations: 148.7 kB / 0.6512 GB, free: 36.12 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001321/0.005128, allocations: 98.33 kB / 0.6513 GB, free: 36.09 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 3.265e-05/0.00516, allocations: 21.19 kB / 0.6513 GB, free: 36.09 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001681/0.005329, allocations: 164.9 kB / 0.6515 GB, free: 36.03 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 6.767e-05/0.005396, allocations: 67.97 kB / 0.6515 GB, free: 35.99 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 7.937e-05/0.005476, allocations: 89.66 kB / 0.6516 GB, free: 35.95 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0003263/0.005802, allocations: 336.9 kB / 0.6519 GB, free: 35.8 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 3.286e-06/0.005805, allocations: 3.75 kB / 0.6519 GB, free: 35.8 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 9.02e-07/0.005806, allocations: 1.969 kB / 0.652 GB, free: 35.8 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 5.68e-06/0.005812, allocations: 1.094 kB / 0.652 GB, free: 35.8 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 0.0006474/0.006459, allocations: 0.7189 MB / 0.6527 GB, free: 35.16 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.369e-05/0.006493, allocations: 9.281 kB / 0.6527 GB, free: 35.16 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.000231/0.006724, allocations: 110.3 kB / 0.6528 GB, free: 35.12 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001904/0.006914, allocations: 218.8 kB / 0.653 GB, free: 34.92 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.556e-05/0.00693, allocations: 11.94 kB / 0.653 GB, free: 34.92 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.194e-05/0.006962, allocations: 20.8 kB / 0.653 GB, free: 34.91 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002522/0.007214, allocations: 257.5 kB / 0.6533 GB, free: 34.74 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.248e-05/0.007226, allocations: 0 / 0.6533 GB, free: 34.74 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.686e-05/0.007243, allocations: 10.94 kB / 0.6533 GB, free: 34.73 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.757e-06/0.007252, allocations: 5.281 kB / 0.6533 GB, free: 34.73 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001431/0.007395, allocations: 175.4 kB / 0.6534 GB, free: 34.62 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0005526/0.007948, allocations: 0.5313 MB / 0.654 GB, free: 34.23 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001948/0.008142, allocations: 207.2 kB / 0.6542 GB, free: 34.08 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 8.355e-05/0.008226, allocations: 148.2 kB / 0.6543 GB, free: 33.96 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.101e-05/0.008237, allocations: 5.188 kB / 0.6543 GB, free: 33.96 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001991/0.008436, allocations: 298.7 kB / 0.6546 GB, free: 33.72 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=26): time 2.174e-06/0.008438, allocations: 0 / 0.6546 GB, free: 33.72 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=27): time 0.001016/0.009454, allocations: 1.097 MB / 0.6557 GB, free: 32.89 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.612e-05/0.0095, allocations: 192.8 kB / 0.6558 GB, free: 32.66 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002366/0.009737, allocations: 324.1 kB / 0.6561 GB, free: 32.45 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 2.392e-05/0.009761, allocations: 33.61 kB / 0.6562 GB, free: 32.42 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 0.0001193/0.00988, allocations: 220.7 kB / 0.6564 GB, free: 32.23 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 7.085e-05/0.009951, allocations: 88.39 kB / 0.6565 GB, free: 32.16 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001017/0.01005, allocations: 62.33 kB / 0.6565 GB, free: 32.12 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 8.22e-05/0.01013, allocations: 0.5226 MB / 0.657 GB, free: 31.61 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.000143/0.01028, allocations: 193.1 kB / 0.6572 GB, free: 31.45 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001606/0.01044, allocations: 273.4 kB / 0.6575 GB, free: 31.18 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0003695/0.01081, allocations: 0.5667 MB / 0.658 GB, free: 30.67 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.625e-06/0.01081, allocations: 0.5625 kB / 0.658 GB, free: 30.67 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=38) (initialization): time 0.0004341/0.01124, allocations: 0.5347 MB / 0.6586 GB, free: 30.3 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 4.382e-05/0.01129, allocations: 124.6 kB / 0.6587 GB, free: 30.17 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.392e-06/0.01129, allocations: 5.312 kB / 0.6587 GB, free: 30.16 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.709e-05/0.01131, allocations: 2.75 kB / 0.6587 GB, free: 30.16 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001601/0.01147, allocations: 57.12 kB / 0.6587 GB, free: 30.16 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.225e-06/0.01148, allocations: 2.75 kB / 0.6588 GB, free: 30.16 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.928e-05/0.01158, allocations: 18.73 kB / 0.6588 GB, free: 30.16 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 5.647e-05/0.01164, allocations: 54.91 kB / 0.6588 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 0.0001753/0.01181, allocations: 289.5 kB / 0.6591 GB, free: 29.87 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 9.182e-05/0.0119, allocations: 86.03 kB / 0.6592 GB, free: 29.84 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.582e-05/0.01194, allocations: 35.92 kB / 0.6592 GB, free: 29.82 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.785e-06/0.01194, allocations: 2.781 kB / 0.6592 GB, free: 29.82 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.196e-05/0.01195, allocations: 1.469 kB / 0.6592 GB, free: 29.82 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.679e-06/0.01196, allocations: 3.234 kB / 0.6592 GB, free: 29.82 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005589/0.01252, allocations: 0.7921 MB / 0.66 GB, free: 29.22 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.976e-06/0.01252, allocations: 4.531 kB / 0.66 GB, free: 29.22 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001299/0.01265, allocations: 37.75 kB / 0.66 GB, free: 29.21 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 3.907e-06/0.01265, allocations: 2.219 kB / 0.66 GB, free: 29.21 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.65e-05/0.01267, allocations: 11.81 kB / 0.66 GB, free: 29.21 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.206e-06/0.01267, allocations: 3.875 kB / 0.6601 GB, free: 29.21 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.543e-06/0.01268, allocations: 0 / 0.6601 GB, free: 29.21 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004905/0.01317, allocations: 0.7941 MB / 0.6608 GB, free: 28.63 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.716e-05/0.01319, allocations: 22.88 kB / 0.6608 GB, free: 28.61 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.062e-05/0.01322, allocations: 8.219 kB / 0.6609 GB, free: 28.61 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 8.771e-05/0.01331, allocations: 19.3 kB / 0.6609 GB, free: 28.61 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.489e-05/0.01338, allocations: 28.45 kB / 0.6609 GB, free: 28.6 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 4.956e-05/0.01343, allocations: 51.66 kB / 0.661 GB, free: 28.59 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 0.0001043/0.01353, allocations: 217.5 kB / 0.6612 GB, free: 28.45 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 6e-08/0.01353, allocations: 1.375 kB / 0.6612 GB, free: 28.45 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0002664/0.0138, allocations: 72.55 kB / 0.6612 GB, free: 28.45 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 0.0002228/0.01402, allocations: 165.4 kB / 0.6614 GB, free: 28.34 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0003323/0.01435, allocations: 0.595 MB / 0.662 GB, free: 27.81 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.733e-06/0.01435, allocations: 1.344 kB / 0.662 GB, free: 27.81 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001438/0.0145, allocations: 361.1 kB / 0.6623 GB, free: 27.49 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003083/0.01481, allocations: 71.56 kB / 0.6624 GB, free: 27.47 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001461/0.01627, allocations: 0.8613 MB / 0.6632 GB, free: 26.89 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 5.599e-05/0.01632, allocations: 101.8 kB / 0.6633 GB, free: 26.82 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 6.697e-05/0.01639, allocations: 16.23 kB / 0.6633 GB, free: 26.82 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.206e-05/0.01643, allocations: 23.16 kB / 0.6634 GB, free: 26.81 MB / 0.5262 GB
Notification: Performance of SimCode: time 1.182e-06/0.01643, allocations: 0 / 0.6634 GB, free: 26.81 MB / 0.5262 GB
Notification: Performance of Templates: time 0.006841/0.02327, allocations: 4.684 MB / 0.6679 GB, free: 26.38 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: 4.847102714935318]