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 0.001402/0.001402, 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 0.001517/0.001517, allocations: 173 kB / 23.02 MB, free: 1.547 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 0.896/0.896, allocations: 177.1 MB / 203.4 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 1.52/1.52, allocations: 273.5 MB / 0.5209 GB, free: 14.85 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 1.593e-06/1.593e-06, allocations: 0 / 0.647 GB, free: 38.66 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.354e-05/2.514e-05, allocations: 6.406 kB / 0.647 GB, free: 38.65 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin): time 0.002882/0.002907, allocations: 2.545 MB / 0.6495 GB, free: 37.02 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.001295/0.004202, allocations: 0.931 MB / 0.6504 GB, free: 36.43 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 9.689e-05/0.004299, allocations: 4.188 kB / 0.6504 GB, free: 36.43 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0003741/0.004673, allocations: 119 kB / 0.6505 GB, free: 36.39 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001429/0.004816, allocations: 81.3 kB / 0.6506 GB, free: 36.36 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0003656/0.005181, allocations: 147.4 kB / 0.6507 GB, free: 36.29 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.000288/0.005469, allocations: 298.1 kB / 0.651 GB, free: 36.16 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001395/0.005609, allocations: 48.12 kB / 0.6511 GB, free: 36.12 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001675/0.005776, allocations: 155.7 kB / 0.6512 GB, free: 36.06 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001307/0.005907, allocations: 97.98 kB / 0.6513 GB, free: 36.03 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 3.02e-05/0.005937, allocations: 21.16 kB / 0.6513 GB, free: 36.03 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001956/0.006133, allocations: 166 kB / 0.6515 GB, free: 35.97 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 6.844e-05/0.006201, allocations: 63.36 kB / 0.6515 GB, free: 35.94 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 8.72e-05/0.006289, allocations: 88.06 kB / 0.6516 GB, free: 35.9 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0003531/0.006642, allocations: 333 kB / 0.6519 GB, free: 35.75 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 3.857e-06/0.006645, allocations: 2.5 kB / 0.6519 GB, free: 35.75 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 1.172e-06/0.006647, allocations: 0 / 0.6519 GB, free: 35.75 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 5.981e-06/0.006653, allocations: 0 / 0.6519 GB, free: 35.75 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 0.0006848/0.007337, allocations: 0.7236 MB / 0.6526 GB, free: 35.1 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.479e-05/0.007372, allocations: 10.75 kB / 0.6527 GB, free: 35.1 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0002538/0.007626, allocations: 109.7 kB / 0.6528 GB, free: 35.06 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002055/0.007832, allocations: 224.8 kB / 0.653 GB, free: 34.87 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.203e-05/0.007854, allocations: 12.72 kB / 0.653 GB, free: 34.86 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.267e-05/0.007886, allocations: 18.88 kB / 0.653 GB, free: 34.86 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002728/0.008159, allocations: 259 kB / 0.6532 GB, free: 34.68 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.349e-05/0.008173, allocations: 2.281 kB / 0.6533 GB, free: 34.68 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.6e-05/0.008189, allocations: 9.406 kB / 0.6533 GB, free: 34.68 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.885e-06/0.008196, allocations: 2 kB / 0.6533 GB, free: 34.68 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001479/0.008344, allocations: 178.3 kB / 0.6534 GB, free: 34.56 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0006317/0.008976, allocations: 0.5208 MB / 0.6539 GB, free: 34.18 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002215/0.009197, allocations: 217.1 kB / 0.6541 GB, free: 34.02 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 8.883e-05/0.009286, allocations: 154.4 kB / 0.6543 GB, free: 33.9 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.056e-05/0.009297, allocations: 3.875 kB / 0.6543 GB, free: 33.9 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.000209/0.009506, allocations: 293.8 kB / 0.6546 GB, free: 33.66 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=26): time 2.575e-06/0.009508, allocations: 1.125 kB / 0.6546 GB, free: 33.66 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=27): time 0.001214/0.01072, allocations: 1.094 MB / 0.6556 GB, free: 32.84 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.795e-05/0.01078, allocations: 190.6 kB / 0.6558 GB, free: 32.61 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002733/0.01105, allocations: 333.4 kB / 0.6561 GB, free: 32.4 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.906e-05/0.01107, allocations: 33.55 kB / 0.6562 GB, free: 32.36 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 8.303e-05/0.01116, allocations: 214.9 kB / 0.6564 GB, free: 32.18 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 4.627e-05/0.0112, allocations: 86.39 kB / 0.6565 GB, free: 32.11 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 7.281e-05/0.01127, allocations: 70.88 kB / 0.6565 GB, free: 32.06 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 7.165e-05/0.01135, allocations: 0.5185 MB / 0.657 GB, free: 31.55 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001129/0.01146, allocations: 193.3 kB / 0.6572 GB, free: 31.39 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001217/0.01158, allocations: 274.9 kB / 0.6575 GB, free: 31.12 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0003117/0.01189, allocations: 0.5616 MB / 0.658 GB, free: 30.62 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.645e-06/0.0119, allocations: 4.734 kB / 0.658 GB, free: 30.62 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=38) (initialization): time 0.0004472/0.01234, allocations: 0.5356 MB / 0.6586 GB, free: 30.24 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 4.352e-05/0.01239, allocations: 118.9 kB / 0.6587 GB, free: 30.11 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.622e-06/0.01239, allocations: 6.781 kB / 0.6587 GB, free: 30.11 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 2.142e-05/0.01241, allocations: 7.734 kB / 0.6587 GB, free: 30.11 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001552/0.01257, allocations: 57.2 kB / 0.6587 GB, free: 30.1 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 6.913e-06/0.01258, allocations: 2.781 kB / 0.6587 GB, free: 30.1 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 8.844e-05/0.01266, allocations: 13.88 kB / 0.6588 GB, free: 30.1 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 5.464e-05/0.01272, allocations: 52.02 kB / 0.6588 GB, free: 30.09 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 0.000162/0.01288, allocations: 294.9 kB / 0.6591 GB, free: 29.81 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 9.43e-05/0.01298, allocations: 87.14 kB / 0.6592 GB, free: 29.79 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.649e-05/0.01301, allocations: 40.11 kB / 0.6592 GB, free: 29.76 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.507e-06/0.01302, allocations: 2.781 kB / 0.6592 GB, free: 29.76 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 7.053e-06/0.01302, allocations: 0 / 0.6592 GB, free: 29.76 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.729e-06/0.01303, allocations: 1.438 kB / 0.6592 GB, free: 29.76 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005433/0.01357, allocations: 0.794 MB / 0.66 GB, free: 29.16 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.844e-06/0.01357, allocations: 0 / 0.66 GB, free: 29.16 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001231/0.0137, allocations: 33.78 kB / 0.66 GB, free: 29.16 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 3.386e-06/0.0137, allocations: 1.406 kB / 0.66 GB, free: 29.16 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.873e-05/0.01372, allocations: 9.656 kB / 0.66 GB, free: 29.16 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.535e-06/0.01372, allocations: 0 / 0.66 GB, free: 29.16 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.823e-06/0.01372, allocations: 1.375 kB / 0.66 GB, free: 29.16 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005119/0.01423, allocations: 0.7972 MB / 0.6608 GB, free: 28.57 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.618e-05/0.01426, allocations: 30.33 kB / 0.6608 GB, free: 28.55 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.947e-05/0.0143, allocations: 13.53 kB / 0.6609 GB, free: 28.55 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 8.652e-05/0.01439, allocations: 13.48 kB / 0.6609 GB, free: 28.55 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.901e-05/0.01445, allocations: 31.17 kB / 0.6609 GB, free: 28.54 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 4.683e-05/0.0145, allocations: 47.2 kB / 0.6609 GB, free: 28.54 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 0.000108/0.01461, allocations: 218 kB / 0.6612 GB, free: 28.39 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 7e-08/0.01461, allocations: 1.344 kB / 0.6612 GB, free: 28.39 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0002991/0.01491, allocations: 77.14 kB / 0.6612 GB, free: 28.38 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 0.0002285/0.01514, allocations: 158.1 kB / 0.6614 GB, free: 28.28 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0003453/0.01548, allocations: 0.6067 MB / 0.662 GB, free: 27.75 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.583e-06/0.01548, allocations: 0 / 0.662 GB, free: 27.75 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001496/0.01563, allocations: 354.1 kB / 0.6623 GB, free: 27.43 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.000315/0.01595, allocations: 71.55 kB / 0.6624 GB, free: 27.42 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001464/0.01741, allocations: 0.8588 MB / 0.6632 GB, free: 26.86 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 5.592e-05/0.01747, allocations: 98.14 kB / 0.6633 GB, free: 26.79 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 6.753e-05/0.01754, allocations: 26.25 kB / 0.6633 GB, free: 26.78 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.029e-05/0.01758, allocations: 21.09 kB / 0.6634 GB, free: 26.77 MB / 0.5262 GB
Notification: Performance of SimCode: time 1.052e-06/0.01758, allocations: 0 / 0.6634 GB, free: 26.77 MB / 0.5262 GB
Notification: Performance of Templates: time 0.007248/0.02483, allocations: 5.204 MB / 0.6684 GB, free: 26.27 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: 4.692582543939352]