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 0.0009276/0.0009276, allocations: 88.23 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 0.001163/0.001163, allocations: 169 kB / 22.73 MB, free: 1.82 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 1.019/1.019, allocations: 177.1 MB / 203.1 MB, free: 5.359 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 1.706/1.706, 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.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 9.82e-07/9.82e-07, allocations: 0 / 0.6462 GB, free: 38.64 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.531e-05/1.629e-05, allocations: 2.312 kB / 0.6462 GB, free: 38.64 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin): time 0.005859/0.005875, allocations: 2.543 MB / 0.6487 GB, free: 37.01 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.001131/0.007006, allocations: 0.9332 MB / 0.6496 GB, free: 36.42 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 7.928e-05/0.007086, allocations: 3.375 kB / 0.6496 GB, free: 36.42 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0003191/0.007405, allocations: 118.8 kB / 0.6498 GB, free: 36.37 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001322/0.007537, allocations: 85.34 kB / 0.6498 GB, free: 36.34 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.003346/0.01088, allocations: 145.1 kB / 0.65 GB, free: 36.27 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002598/0.01114, allocations: 298.3 kB / 0.6503 GB, free: 36.14 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001021/0.01124, allocations: 49.31 kB / 0.6503 GB, free: 36.11 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001402/0.01139, allocations: 155.5 kB / 0.6505 GB, free: 36.05 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001385/0.01152, allocations: 99 kB / 0.6506 GB, free: 36.01 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 3.194e-05/0.01156, allocations: 20.16 kB / 0.6506 GB, free: 36.01 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001852/0.01174, allocations: 165.1 kB / 0.6507 GB, free: 35.96 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 6.122e-05/0.0118, allocations: 66.39 kB / 0.6508 GB, free: 35.92 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 8.647e-05/0.01189, allocations: 86.58 kB / 0.6509 GB, free: 35.88 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0003432/0.01223, allocations: 334.8 kB / 0.6512 GB, free: 35.74 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 1.914e-06/0.01223, allocations: 0 / 0.6512 GB, free: 35.74 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 1.012e-06/0.01223, allocations: 0 / 0.6512 GB, free: 35.74 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 4.027e-06/0.01224, allocations: 0 / 0.6512 GB, free: 35.74 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 0.0006215/0.01286, allocations: 0.72 MB / 0.6519 GB, free: 35.09 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.153e-05/0.01289, allocations: 14.75 kB / 0.6519 GB, free: 35.09 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0002392/0.01313, allocations: 118.1 kB / 0.652 GB, free: 35.04 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.000193/0.01332, allocations: 211.1 kB / 0.6522 GB, free: 34.86 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.99e-05/0.01334, allocations: 16.78 kB / 0.6522 GB, free: 34.85 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.906e-05/0.01338, allocations: 20.22 kB / 0.6523 GB, free: 34.84 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.003309/0.01669, allocations: 261 kB / 0.6525 GB, free: 34.66 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.466e-05/0.01671, allocations: 0 / 0.6525 GB, free: 34.66 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.722e-05/0.01672, allocations: 8.781 kB / 0.6525 GB, free: 34.66 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.047e-06/0.01673, allocations: 2.375 kB / 0.6525 GB, free: 34.66 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001753/0.01691, allocations: 181.8 kB / 0.6527 GB, free: 34.55 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0005929/0.0175, allocations: 0.522 MB / 0.6532 GB, free: 34.16 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001866/0.01769, allocations: 224.5 kB / 0.6534 GB, free: 34.01 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 8.291e-05/0.01777, allocations: 147.7 kB / 0.6536 GB, free: 33.89 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 8.856e-06/0.01778, allocations: 3.688 kB / 0.6536 GB, free: 33.89 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001936/0.01797, allocations: 288.5 kB / 0.6538 GB, free: 33.65 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=26): time 1.623e-06/0.01797, allocations: 1.406 kB / 0.6538 GB, free: 33.65 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=27): time 0.0009449/0.01892, allocations: 1.101 MB / 0.6549 GB, free: 32.82 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.452e-05/0.01895, allocations: 190.9 kB / 0.6551 GB, free: 32.6 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001747/0.01913, allocations: 329.3 kB / 0.6554 GB, free: 32.38 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.578e-05/0.01914, allocations: 36.88 kB / 0.6554 GB, free: 32.35 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 7.243e-05/0.01922, allocations: 213.2 kB / 0.6556 GB, free: 32.16 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 4.368e-05/0.01926, allocations: 89.62 kB / 0.6557 GB, free: 32.09 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 7.131e-05/0.01933, allocations: 66.22 kB / 0.6558 GB, free: 32.05 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 7.886e-05/0.01941, allocations: 0.5239 MB / 0.6563 GB, free: 31.54 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001381/0.01955, allocations: 186.3 kB / 0.6565 GB, free: 31.38 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.000158/0.01971, allocations: 278.5 kB / 0.6568 GB, free: 31.11 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0003835/0.02009, allocations: 0.5667 MB / 0.6573 GB, free: 30.6 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.693e-06/0.02009, allocations: 0.5625 kB / 0.6573 GB, free: 30.6 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=38) (initialization): time 0.000436/0.02053, allocations: 0.5363 MB / 0.6578 GB, free: 30.23 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 3.284e-05/0.02056, allocations: 116 kB / 0.6579 GB, free: 30.1 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 4.398e-06/0.02057, allocations: 6.625 kB / 0.6579 GB, free: 30.1 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.22e-05/0.02058, allocations: 6.688 kB / 0.658 GB, free: 30.09 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001377/0.02072, allocations: 55.73 kB / 0.658 GB, free: 30.09 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 7.003e-06/0.02072, allocations: 9.312 kB / 0.658 GB, free: 30.09 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 8.292e-05/0.02081, allocations: 12.44 kB / 0.658 GB, free: 30.08 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 5.016e-05/0.02086, allocations: 53.58 kB / 0.6581 GB, free: 30.08 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 0.0001457/0.021, allocations: 296 kB / 0.6584 GB, free: 29.8 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 8.81e-05/0.02109, allocations: 85.38 kB / 0.6584 GB, free: 29.78 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.437e-05/0.02112, allocations: 32.08 kB / 0.6585 GB, free: 29.76 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.555e-06/0.02113, allocations: 2.844 kB / 0.6585 GB, free: 29.76 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.196e-06/0.02113, allocations: 1.375 kB / 0.6585 GB, free: 29.76 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.977e-06/0.02113, allocations: 0 / 0.6585 GB, free: 29.76 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005044/0.02164, allocations: 0.7966 MB / 0.6593 GB, free: 29.16 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.112e-06/0.02164, allocations: 0 / 0.6593 GB, free: 29.16 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001135/0.02175, allocations: 35.62 kB / 0.6593 GB, free: 29.15 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.905e-06/0.02176, allocations: 1.469 kB / 0.6593 GB, free: 29.15 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.557e-05/0.02177, allocations: 11.64 kB / 0.6593 GB, free: 29.15 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.313e-06/0.02177, allocations: 3.094 kB / 0.6593 GB, free: 29.15 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.272e-06/0.02177, allocations: 3.188 kB / 0.6593 GB, free: 29.15 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.000458/0.02223, allocations: 0.7948 MB / 0.6601 GB, free: 28.57 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.195e-05/0.02225, allocations: 24.22 kB / 0.6601 GB, free: 28.55 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.732e-05/0.02228, allocations: 8.812 kB / 0.6601 GB, free: 28.55 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 9.025e-05/0.02237, allocations: 17.39 kB / 0.6601 GB, free: 28.54 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.069e-05/0.02242, allocations: 26.89 kB / 0.6602 GB, free: 28.54 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.96e-05/0.02246, allocations: 51.55 kB / 0.6602 GB, free: 28.53 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 9.85e-05/0.02256, allocations: 217.7 kB / 0.6604 GB, free: 28.39 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 8e-08/0.02256, allocations: 0.875 kB / 0.6604 GB, free: 28.39 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0002299/0.02279, allocations: 73.78 kB / 0.6605 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 0.00017/0.02296, allocations: 171.7 kB / 0.6606 GB, free: 28.27 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0003362/0.0233, allocations: 0.594 MB / 0.6612 GB, free: 27.74 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.002e-06/0.0233, allocations: 1.25 kB / 0.6612 GB, free: 27.74 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001549/0.02345, allocations: 356.8 kB / 0.6616 GB, free: 27.42 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002826/0.02373, allocations: 73.84 kB / 0.6616 GB, free: 27.4 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001324/0.02506, allocations: 0.8583 MB / 0.6625 GB, free: 26.83 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 4.972e-05/0.02511, allocations: 99.33 kB / 0.6626 GB, free: 26.76 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 5.18e-05/0.02516, allocations: 17.08 kB / 0.6626 GB, free: 26.75 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 3.573e-05/0.0252, allocations: 25.12 kB / 0.6626 GB, free: 26.74 MB / 0.5262 GB
Notification: Performance of SimCode: time 5.51e-07/0.0252, allocations: 0 / 0.6626 GB, free: 26.74 MB / 0.5262 GB
Notification: Performance of Templates: time 0.005872/0.03107, allocations: 4.677 MB / 0.6672 GB, free: 26.31 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: 5.2533752312883735]