Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.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 0.000955/0.000955, allocations: 89.08 kB / 19.42 MB, free: 492 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 0.001154/0.001154, allocations: 173 kB / 22.72 MB, free: 1.824 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 0.9583/0.9583, allocations: 177.1 MB / 203.1 MB, free: 5.473 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 1.691/1.691, allocations: 273.5 MB / 0.5205 GB, free: 14.89 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.PKPG_1C_Gentamicin,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin")
translateModel(Pharmacolibrary.Examples.PKPG_1C_Gentamicin,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 2.054e-06/2.054e-06, allocations: 0 / 0.6462 GB, free: 38.76 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.938e-05/3.143e-05, allocations: 5.266 kB / 0.6462 GB, free: 38.75 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKPG_1C_Gentamicin): time 0.003716/0.003748, allocations: 2.503 MB / 0.6487 GB, free: 37.14 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.001476/0.005224, allocations: 0.9332 MB / 0.6496 GB, free: 36.55 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001146/0.005339, allocations: 5.656 kB / 0.6496 GB, free: 36.55 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0004744/0.005813, allocations: 110.5 kB / 0.6497 GB, free: 36.51 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001842/0.005997, allocations: 87.48 kB / 0.6498 GB, free: 36.48 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0004399/0.006437, allocations: 138.7 kB / 0.6499 GB, free: 36.41 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002711/0.006708, allocations: 294.6 kB / 0.6502 GB, free: 36.29 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001295/0.006838, allocations: 44.59 kB / 0.6502 GB, free: 36.26 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001523/0.00699, allocations: 151 kB / 0.6504 GB, free: 36.2 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001389/0.007129, allocations: 84.41 kB / 0.6505 GB, free: 36.17 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 3.225e-05/0.007161, allocations: 18.97 kB / 0.6505 GB, free: 36.17 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.000182/0.007343, allocations: 172.2 kB / 0.6506 GB, free: 36.11 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 6.734e-05/0.007411, allocations: 58.31 kB / 0.6507 GB, free: 36.08 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 8.198e-05/0.007493, allocations: 81.38 kB / 0.6508 GB, free: 36.05 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0003289/0.007821, allocations: 329.5 kB / 0.6511 GB, free: 35.9 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 3.426e-06/0.007825, allocations: 1.594 kB / 0.6511 GB, free: 35.9 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 1.012e-06/0.007826, allocations: 3.625 kB / 0.6511 GB, free: 35.9 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 6.122e-06/0.007832, allocations: 0 / 0.6511 GB, free: 35.9 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 0.0006352/0.008467, allocations: 0.7025 MB / 0.6518 GB, free: 35.27 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.366e-05/0.008501, allocations: 12.03 kB / 0.6518 GB, free: 35.26 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0002082/0.008709, allocations: 112 kB / 0.6519 GB, free: 35.22 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001838/0.008893, allocations: 212.4 kB / 0.6521 GB, free: 35.03 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.984e-05/0.008913, allocations: 15.47 kB / 0.6521 GB, free: 35.02 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.571e-05/0.008948, allocations: 24.48 kB / 0.6521 GB, free: 35.02 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002473/0.009196, allocations: 254.4 kB / 0.6524 GB, free: 34.84 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.214e-05/0.009208, allocations: 0 / 0.6524 GB, free: 34.84 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.508e-05/0.009223, allocations: 5.719 kB / 0.6524 GB, free: 34.84 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.216e-06/0.009231, allocations: 4.156 kB / 0.6524 GB, free: 34.84 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.000149/0.00938, allocations: 175.1 kB / 0.6526 GB, free: 34.73 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0005381/0.009918, allocations: 0.5223 MB / 0.6531 GB, free: 34.34 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001895/0.01011, allocations: 206.7 kB / 0.6533 GB, free: 34.19 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 8.195e-05/0.01019, allocations: 143 kB / 0.6534 GB, free: 34.07 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 9.177e-06/0.0102, allocations: 6.438 kB / 0.6534 GB, free: 34.07 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002015/0.0104, allocations: 295.4 kB / 0.6537 GB, free: 33.83 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=26): time 1.753e-06/0.0104, allocations: 0 / 0.6537 GB, free: 33.83 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=27): time 0.001/0.0114, allocations: 1.092 MB / 0.6548 GB, free: 33.01 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.097e-05/0.01144, allocations: 193.1 kB / 0.6549 GB, free: 32.79 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001764/0.01162, allocations: 318 kB / 0.6552 GB, free: 32.57 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.532e-05/0.01163, allocations: 33.58 kB / 0.6553 GB, free: 32.54 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 7.489e-05/0.01171, allocations: 210.8 kB / 0.6555 GB, free: 32.36 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 4.019e-05/0.01175, allocations: 90.88 kB / 0.6556 GB, free: 32.28 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 7.541e-05/0.01183, allocations: 62.42 kB / 0.6556 GB, free: 32.24 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 7.799e-05/0.0119, allocations: 0.5228 MB / 0.6561 GB, free: 31.73 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.000134/0.01204, allocations: 188.7 kB / 0.6563 GB, free: 31.57 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001608/0.0122, allocations: 281.3 kB / 0.6566 GB, free: 31.3 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0003918/0.01259, allocations: 0.5549 MB / 0.6571 GB, free: 30.8 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.584e-06/0.01259, allocations: 0.5625 kB / 0.6571 GB, free: 30.8 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=38) (initialization): time 0.0005828/0.01318, allocations: 0.5457 MB / 0.6577 GB, free: 30.42 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 4.008e-05/0.01322, allocations: 118.5 kB / 0.6578 GB, free: 30.29 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.713e-06/0.01322, allocations: 8.062 kB / 0.6578 GB, free: 30.29 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.905e-05/0.01324, allocations: 2.75 kB / 0.6578 GB, free: 30.29 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001699/0.01341, allocations: 52.33 kB / 0.6578 GB, free: 30.28 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 6.943e-06/0.01342, allocations: 4.219 kB / 0.6578 GB, free: 30.28 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.692e-05/0.01351, allocations: 19.39 kB / 0.6578 GB, free: 30.28 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 5.627e-05/0.01357, allocations: 51 kB / 0.6579 GB, free: 30.27 MB / 0.5262 GB
Warning: Assuming fixed start value for the following 6 variables:
         singleDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         singleDose.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.singleDose.pulse.count,$PRE.singleDose.pulse.T_start,CYP2C19.status,SLC22A2.status,central.rising,singleDose.pulse.count,singleDose.pulse.T_start,$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 0.0001541/0.01373, allocations: 296.9 kB / 0.6582 GB, free: 30 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 9.151e-05/0.01382, allocations: 83.92 kB / 0.6583 GB, free: 29.97 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.898e-05/0.01386, allocations: 34.27 kB / 0.6583 GB, free: 29.95 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.015e-06/0.01386, allocations: 1.438 kB / 0.6583 GB, free: 29.95 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.439e-06/0.01386, allocations: 1.375 kB / 0.6583 GB, free: 29.95 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.538e-06/0.01387, allocations: 5.578 kB / 0.6583 GB, free: 29.95 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005987/0.01447, allocations: 0.7766 MB / 0.6591 GB, free: 29.36 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.414e-06/0.01447, allocations: 0 / 0.6591 GB, free: 29.36 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001653/0.01463, allocations: 36.3 kB / 0.6591 GB, free: 29.35 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 3.867e-06/0.01464, allocations: 1.406 kB / 0.6591 GB, free: 29.35 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.269e-05/0.01466, allocations: 14.48 kB / 0.6591 GB, free: 29.35 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.797e-06/0.01466, allocations: 4.438 kB / 0.6591 GB, free: 29.35 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.573e-06/0.01467, allocations: 0 / 0.6591 GB, free: 29.35 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0006524/0.01532, allocations: 0.7935 MB / 0.6599 GB, free: 28.77 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 3.195e-05/0.01535, allocations: 26.84 kB / 0.6599 GB, free: 28.75 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.852e-05/0.01539, allocations: 11.55 kB / 0.6599 GB, free: 28.75 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001219/0.01551, allocations: 8.188 kB / 0.6599 GB, free: 28.75 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 7.549e-05/0.01559, allocations: 27 kB / 0.66 GB, free: 28.74 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 6.742e-05/0.01565, allocations: 52.5 kB / 0.66 GB, free: 28.73 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 0.0001414/0.0158, allocations: 210 kB / 0.6602 GB, free: 28.59 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 8.1e-08/0.0158, allocations: 0 / 0.6602 GB, free: 28.59 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0002661/0.01606, allocations: 76.88 kB / 0.6603 GB, free: 28.58 MB / 0.5262 GB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 5 (singleDose.TotalCumulativeMass,singleDose.variableDose.TotalCumulativeMass,central.C,central.AUC,elim.MExc)
 * Number of discrete variables: 10 ($whenCondition1,$whenCondition2,$whenCondition3,singleDose.pulse.T_start,singleDose.pulse.count,central.Cmax,central.Cmin,central.rising,SLC22A2.status,CYP2C19.status)
 * Number of discrete states: 8 (singleDose.pulse.count,SLC22A2.status,CYP2C19.status,central.Cmin,$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 0.0002175/0.01628, allocations: 170.3 kB / 0.6604 GB, free: 28.47 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0003395/0.01662, allocations: 0.5939 MB / 0.661 GB, free: 27.95 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.403e-06/0.01662, allocations: 0 / 0.661 GB, free: 27.95 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001805/0.0168, allocations: 353.6 kB / 0.6614 GB, free: 27.63 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003137/0.01711, allocations: 76.33 kB / 0.6614 GB, free: 27.61 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001466/0.01858, allocations: 0.8352 MB / 0.6623 GB, free: 27.05 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 5.499e-05/0.01863, allocations: 100.2 kB / 0.6623 GB, free: 26.98 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 6.47e-05/0.0187, allocations: 18.72 kB / 0.6624 GB, free: 26.97 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.236e-05/0.01874, allocations: 20.56 kB / 0.6624 GB, free: 26.96 MB / 0.5262 GB
Notification: Performance of SimCode: time 8.92e-07/0.01874, allocations: 0 / 0.6624 GB, free: 26.96 MB / 0.5262 GB
Notification: Performance of Templates: time 0.006909/0.02565, allocations: 4.523 MB / 0.6668 GB, free: 26.55 MB / 0.5262 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PKPG_1C_Gentamicin.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 5.380434952210635]