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 0.002429/0.002429, allocations: 85.48 kB / 19.44 MB, free: 348 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 0.003066/0.003066, allocations: 177.2 kB / 22.76 MB, free: 1.664 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 1.679/1.679, allocations: 177.1 MB / 203.1 MB, free: 5.594 MB / 186.7 MB
"
[Timeout remaining time 178]
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 5.85/5.85, allocations: 274.5 MB / 0.5215 GB, free: 14.15 MB / 458.7 MB
"
[Timeout remaining time 173]
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 1.232e-06/1.232e-06, allocations: 0 / 0.6472 GB, free: 39.21 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.666e-05/2.789e-05, allocations: 2.312 kB / 0.6472 GB, free: 39.21 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PKPG_1C_Gentamicin): time 0.003121/0.003149, allocations: 2.513 MB / 0.6497 GB, free: 37.57 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.001356/0.004506, allocations: 0.9298 MB / 0.6506 GB, free: 36.98 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 9.437e-05/0.0046, allocations: 1.688 kB / 0.6506 GB, free: 36.98 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0004086/0.005009, allocations: 120.9 kB / 0.6507 GB, free: 36.94 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001459/0.005154, allocations: 84.25 kB / 0.6508 GB, free: 36.91 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.000345/0.005499, allocations: 147.2 kB / 0.6509 GB, free: 36.83 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002801/0.00578, allocations: 295.4 kB / 0.6512 GB, free: 36.7 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001295/0.005909, allocations: 48.48 kB / 0.6513 GB, free: 36.67 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.000172/0.006081, allocations: 155.6 kB / 0.6514 GB, free: 36.61 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001632/0.006244, allocations: 92.67 kB / 0.6515 GB, free: 36.58 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 4.105e-05/0.006285, allocations: 24.69 kB / 0.6515 GB, free: 36.57 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.0002095/0.006495, allocations: 165.1 kB / 0.6517 GB, free: 36.52 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 7.158e-05/0.006566, allocations: 63.95 kB / 0.6518 GB, free: 36.48 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 0.0001105/0.006677, allocations: 85.84 kB / 0.6518 GB, free: 36.45 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0004392/0.007116, allocations: 431.9 kB / 0.6522 GB, free: 36.27 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 3.847e-06/0.00712, allocations: 0 / 0.6522 GB, free: 36.27 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 1.232e-06/0.007121, allocations: 0 / 0.6522 GB, free: 36.27 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 6.543e-06/0.007128, allocations: 0 / 0.6522 GB, free: 36.27 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 0.0008054/0.007933, allocations: 0.7325 MB / 0.653 GB, free: 35.62 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.532e-05/0.007968, allocations: 9.219 kB / 0.653 GB, free: 35.62 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0002778/0.008246, allocations: 110.8 kB / 0.6531 GB, free: 35.58 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002572/0.008503, allocations: 226.3 kB / 0.6533 GB, free: 35.38 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.261e-05/0.008536, allocations: 12.12 kB / 0.6533 GB, free: 35.38 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.65e-05/0.008582, allocations: 17.84 kB / 0.6533 GB, free: 35.37 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003846/0.008967, allocations: 274.8 kB / 0.6536 GB, free: 35.2 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.644e-05/0.008983, allocations: 0 / 0.6536 GB, free: 35.2 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.021e-05/0.009004, allocations: 9.344 kB / 0.6536 GB, free: 35.19 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.432e-06/0.00901, allocations: 4.094 kB / 0.6536 GB, free: 35.19 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003316/0.009342, allocations: 232.2 kB / 0.6538 GB, free: 35.05 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0007805/0.01012, allocations: 0.5729 MB / 0.6544 GB, free: 34.65 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0004702/0.01059, allocations: 262.5 kB / 0.6546 GB, free: 34.48 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002237/0.01082, allocations: 181 kB / 0.6548 GB, free: 34.34 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 2.457e-05/0.01084, allocations: 4.594 kB / 0.6548 GB, free: 34.34 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0003949/0.01124, allocations: 322.7 kB / 0.6551 GB, free: 34.09 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=26): time 1.443e-06/0.01124, allocations: 2.125 kB / 0.6551 GB, free: 34.09 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=27): time 0.00176/0.013, allocations: 1.211 MB / 0.6563 GB, free: 33.21 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.385e-05/0.01305, allocations: 194.5 kB / 0.6565 GB, free: 32.99 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002704/0.01332, allocations: 365.8 kB / 0.6568 GB, free: 32.76 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 2.186e-05/0.01334, allocations: 35.58 kB / 0.6569 GB, free: 32.72 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 0.0001107/0.01345, allocations: 219.5 kB / 0.6571 GB, free: 32.53 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 5.706e-05/0.01351, allocations: 96.98 kB / 0.6572 GB, free: 32.46 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 9.569e-05/0.01361, allocations: 71.75 kB / 0.6572 GB, free: 32.41 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 0.0001061/0.01371, allocations: 0.534 MB / 0.6578 GB, free: 31.9 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002296/0.01394, allocations: 236.6 kB / 0.658 GB, free: 31.72 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002486/0.01419, allocations: 318.5 kB / 0.6583 GB, free: 31.43 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0006153/0.01481, allocations: 0.6593 MB / 0.6589 GB, free: 30.88 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.154e-06/0.01481, allocations: 1.375 kB / 0.6589 GB, free: 30.88 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=38) (initialization): time 0.0007115/0.01552, allocations: 0.6139 MB / 0.6595 GB, free: 30.47 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 5.199e-05/0.01557, allocations: 121.2 kB / 0.6596 GB, free: 30.34 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.574e-06/0.01558, allocations: 5.344 kB / 0.6597 GB, free: 30.34 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.831e-05/0.0156, allocations: 2.938 kB / 0.6597 GB, free: 30.34 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002118/0.01581, allocations: 55.88 kB / 0.6597 GB, free: 30.34 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 9.428e-06/0.01582, allocations: 2.906 kB / 0.6597 GB, free: 30.34 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001525/0.01597, allocations: 17.25 kB / 0.6597 GB, free: 30.33 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 7.029e-05/0.01604, allocations: 54.44 kB / 0.6598 GB, free: 30.32 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 0.0002134/0.01625, allocations: 301.5 kB / 0.6601 GB, free: 30.04 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.000142/0.0164, allocations: 90.98 kB / 0.6602 GB, free: 30.01 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 5.813e-05/0.01645, allocations: 33.47 kB / 0.6602 GB, free: 29.99 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.297e-06/0.01646, allocations: 1.344 kB / 0.6602 GB, free: 29.99 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.953e-06/0.01646, allocations: 1.438 kB / 0.6602 GB, free: 29.99 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.21e-06/0.01647, allocations: 4.234 kB / 0.6602 GB, free: 29.99 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0009103/0.01738, allocations: 0.8766 MB / 0.6611 GB, free: 29.35 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.896e-06/0.01738, allocations: 10.66 kB / 0.6611 GB, free: 29.35 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.000179/0.01756, allocations: 33.64 kB / 0.6611 GB, free: 29.35 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.384e-06/0.01756, allocations: 1.438 kB / 0.6611 GB, free: 29.35 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.497e-05/0.01759, allocations: 12.98 kB / 0.6611 GB, free: 29.34 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.934e-06/0.01759, allocations: 0 / 0.6611 GB, free: 29.34 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.543e-06/0.01759, allocations: 1.438 kB / 0.6611 GB, free: 29.34 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0009412/0.01853, allocations: 0.9028 MB / 0.662 GB, free: 28.71 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 3.726e-05/0.01857, allocations: 22.81 kB / 0.662 GB, free: 28.7 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 4.612e-05/0.01862, allocations: 9.562 kB / 0.662 GB, free: 28.7 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.00015/0.01877, allocations: 15.86 kB / 0.662 GB, free: 28.69 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 8.872e-05/0.01886, allocations: 28.47 kB / 0.6621 GB, free: 28.68 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 5.94e-05/0.01892, allocations: 47.34 kB / 0.6621 GB, free: 28.68 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 0.0001707/0.01909, allocations: 241.6 kB / 0.6623 GB, free: 28.52 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 7.1e-08/0.01909, allocations: 0 / 0.6623 GB, free: 28.52 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0003709/0.01946, allocations: 75.53 kB / 0.6624 GB, free: 28.52 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 0.0002416/0.0197, allocations: 158.1 kB / 0.6626 GB, free: 28.42 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0006388/0.02034, allocations: 0.6789 MB / 0.6632 GB, free: 27.85 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 2.294e-06/0.02034, allocations: 0.9375 kB / 0.6632 GB, free: 27.85 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.000289/0.02063, allocations: 400.4 kB / 0.6636 GB, free: 27.52 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004679/0.0211, allocations: 85.58 kB / 0.6637 GB, free: 27.49 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.00119/0.02229, allocations: 0.8264 MB / 0.6645 GB, free: 26.93 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001338/0.02242, allocations: 169.7 kB / 0.6647 GB, free: 26.84 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 8.044e-05/0.0225, allocations: 15.05 kB / 0.6647 GB, free: 26.84 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 5.395e-05/0.02255, allocations: 28.42 kB / 0.6647 GB, free: 26.83 MB / 0.5262 GB
Notification: Performance of SimCode: time 6.51e-07/0.02256, allocations: 0 / 0.6647 GB, free: 26.83 MB / 0.5262 GB
Notification: Performance of Templates: time 0.009095/0.03165, allocations: 4.595 MB / 0.6692 GB, free: 26.42 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: 11.358191107981838]