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 0.00185/0.00185, allocations: 105.5 kB / 18.95 MB, free: 1.176 MB / 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 0.001938/0.001938, allocations: 217.7 kB / 22.25 MB, free: 3.582 MB / 13.93 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 1.729/1.729, allocations: 230.6 MB / 256 MB, free: 9.609 MB / 202.7 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 3.994/3.994, allocations: 335.2 MB / 0.6325 GB, free: 7.266 MB / 442.7 MB
"
[Timeout remaining time 176]
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: Pharmacolibrary requested package Modelica of version 4.0.0. Modelica 4.1.0 is used instead which states that it is fully compatible without conversion script needed.
Notification: Performance of FrontEnd - loaded program: time 0.003902/0.003902, allocations: 67.89 kB / 0.868 GB, free: 5.836 MB / 0.573 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.249/0.2529, allocations: 112.8 MB / 0.9782 GB, free: 4.754 MB / 0.6824 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKPG_1C_Gentamicin): time 0.004271/0.2572, allocations: 2.37 MB / 0.9805 GB, free: 2.371 MB / 0.6824 GB
Notification: Performance of NFInst.instExpressions: time 0.001735/0.2589, allocations: 0.8916 MB / 0.9814 GB, free: 1.477 MB / 0.6824 GB
Notification: Performance of NFInst.updateImplicitVariability: time 9.597e-05/0.259, allocations: 4 kB / 0.9814 GB, free: 1.473 MB / 0.6824 GB
Notification: Performance of NFTyping.typeComponents: time 0.0004424/0.2595, allocations: 107.3 kB / 0.9815 GB, free: 1.367 MB / 0.6824 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001649/0.2596, allocations: 87.39 kB / 0.9816 GB, free: 1.281 MB / 0.6824 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0004006/0.2601, allocations: 143.6 kB / 0.9817 GB, free: 1.141 MB / 0.6824 GB
Notification: Performance of NFFlatten.flatten: time 0.0003923/0.2604, allocations: 270.9 kB / 0.982 GB, free: 0.875 MB / 0.6824 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001526/0.2606, allocations: 45.08 kB / 0.982 GB, free: 0.8242 MB / 0.6824 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001563/0.2608, allocations: 99.64 kB / 0.9821 GB, free: 0.7266 MB / 0.6824 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002129/0.261, allocations: 111.4 kB / 0.9822 GB, free: 0.6172 MB / 0.6824 GB
Notification: Performance of NFPackage.collectConstants: time 4.572e-05/0.261, allocations: 20 kB / 0.9822 GB, free: 0.5977 MB / 0.6824 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.0002801/0.2613, allocations: 163.4 kB / 0.9824 GB, free: 448 kB / 0.6824 GB
Notification: Performance of NFScalarize.scalarize: time 0.0001129/0.2614, allocations: 67.75 kB / 0.9824 GB, free: 380 kB / 0.6824 GB
Notification: Performance of NFVerifyModel.verify: time 0.0001413/0.2615, allocations: 103.4 kB / 0.9825 GB, free: 276 kB / 0.6824 GB
Notification: Performance of NFConvertDAE.convert: time 0.0005786/0.2621, allocations: 406.4 kB / 0.9829 GB, free: 15.87 MB / 0.698 GB
Notification: Performance of FrontEnd - DAE generated: time 5.04e-06/0.2621, allocations: 4 kB / 0.9829 GB, free: 15.87 MB / 0.698 GB
Notification: Performance of FrontEnd: time 1.453e-06/0.2621, allocations: 0 / 0.9829 GB, free: 15.87 MB / 0.698 GB
Notification: Performance of Transformations before backend: time 6.502e-06/0.2621, allocations: 3.938 kB / 0.9829 GB, free: 15.86 MB / 0.698 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 0.001167/0.2633, allocations: 0.5977 MB / 0.9835 GB, free: 15.21 MB / 0.698 GB
Notification: Performance of prepare preOptimizeDAE: time 3.629e-05/0.2633, allocations: 14.11 kB / 0.9835 GB, free: 15.2 MB / 0.698 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0002283/0.2636, allocations: 48.73 kB / 0.9836 GB, free: 15.15 MB / 0.698 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0004717/0.264, allocations: 233 kB / 0.9838 GB, free: 14.9 MB / 0.698 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.871e-05/0.2641, allocations: 12.38 kB / 0.9838 GB, free: 14.89 MB / 0.698 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 6.34e-05/0.2641, allocations: 31.86 kB / 0.9839 GB, free: 14.86 MB / 0.698 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0006428/0.2648, allocations: 371.5 kB / 0.9842 GB, free: 14.47 MB / 0.698 GB
Notification: Performance of preOpt findStateOrder (simulation): time 2.09e-05/0.2648, allocations: 3.953 kB / 0.9842 GB, free: 14.46 MB / 0.698 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.498e-05/0.2648, allocations: 8 kB / 0.9842 GB, free: 14.46 MB / 0.698 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.875e-06/0.2648, allocations: 4 kB / 0.9842 GB, free: 14.45 MB / 0.698 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0006266/0.2654, allocations: 332.9 kB / 0.9845 GB, free: 14.11 MB / 0.698 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0009439/0.2664, allocations: 464.6 kB / 0.985 GB, free: 13.62 MB / 0.698 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0006449/0.267, allocations: 359.6 kB / 0.9853 GB, free: 13.25 MB / 0.698 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.000394/0.2674, allocations: 281.7 kB / 0.9856 GB, free: 12.95 MB / 0.698 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.657e-05/0.2674, allocations: 0 / 0.9856 GB, free: 12.95 MB / 0.698 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0005864/0.268, allocations: 411.8 kB / 0.986 GB, free: 12.5 MB / 0.698 GB
Notification: Performance of pre-optimization done (n=26): time 1.753e-06/0.268, allocations: 0 / 0.986 GB, free: 12.5 MB / 0.698 GB
Notification: Performance of matching and sorting (n=27): time 0.002727/0.2708, allocations: 1.643 MB / 0.9876 GB, free: 10.74 MB / 0.698 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001422/0.2709, allocations: 187.9 kB / 0.9878 GB, free: 10.51 MB / 0.698 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003293/0.2712, allocations: 269.8 kB / 0.988 GB, free: 10.25 MB / 0.698 GB
Notification: Performance of collectPreVariables (initialization): time 3.792e-05/0.2713, allocations: 33.7 kB / 0.9881 GB, free: 10.21 MB / 0.698 GB
Notification: Performance of collectInitialEqns (initialization): time 0.0001359/0.2714, allocations: 148.6 kB / 0.9882 GB, free: 10.06 MB / 0.698 GB
Notification: Performance of collectInitialBindings (initialization): time 9.195e-05/0.2715, allocations: 87.33 kB / 0.9883 GB, free: 9.973 MB / 0.698 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001071/0.2716, allocations: 57.92 kB / 0.9883 GB, free: 9.91 MB / 0.698 GB
Notification: Performance of setup shared object (initialization): time 0.0001961/0.2718, allocations: 342.8 kB / 0.9887 GB, free: 9.566 MB / 0.698 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0004535/0.2723, allocations: 316.3 kB / 0.989 GB, free: 9.23 MB / 0.698 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0005174/0.2728, allocations: 401.5 kB / 0.9894 GB, free: 8.785 MB / 0.698 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.3857/0.6584, allocations: 1.251 MB / 0.9906 GB, free: 26.02 MB / 0.698 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.617e-06/0.6584, allocations: 0 / 0.9906 GB, free: 26.02 MB / 0.698 GB
Notification: Performance of matching and sorting (n=38) (initialization): time 0.0008647/0.6593, allocations: 0.7503 MB / 0.9913 GB, free: 25.73 MB / 0.698 GB
Notification: Performance of prepare postOptimizeDAE: time 5.275e-05/0.6594, allocations: 122.8 kB / 0.9914 GB, free: 25.61 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.915e-06/0.6594, allocations: 2.031 kB / 0.9914 GB, free: 25.61 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (initialization): time 2.326e-05/0.6594, allocations: 4.375 kB / 0.9914 GB, free: 25.61 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002225/0.6596, allocations: 47.86 kB / 0.9915 GB, free: 25.61 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.005e-05/0.6596, allocations: 5.344 kB / 0.9915 GB, free: 25.61 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001824/0.6598, allocations: 20.42 kB / 0.9915 GB, free: 25.61 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 7.684e-05/0.6599, allocations: 52.33 kB / 0.9915 GB, free: 25.61 MB / 0.698 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 0.0002465/0.6601, allocations: 279.1 kB / 0.9918 GB, free: 25.4 MB / 0.698 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 7.942e-05/0.6602, allocations: 32.02 kB / 0.9918 GB, free: 25.4 MB / 0.698 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 5.9e-05/0.6603, allocations: 32.97 kB / 0.9919 GB, free: 25.39 MB / 0.698 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.236e-06/0.6603, allocations: 1 kB / 0.9919 GB, free: 25.39 MB / 0.698 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.781e-06/0.6603, allocations: 0.5312 kB / 0.9919 GB, free: 25.39 MB / 0.698 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.679e-06/0.6603, allocations: 4.562 kB / 0.9919 GB, free: 25.39 MB / 0.698 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0009841/0.6613, allocations: 0.9585 MB / 0.9928 GB, free: 24.97 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.036e-06/0.6613, allocations: 7.594 kB / 0.9928 GB, free: 24.96 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001969/0.6615, allocations: 41.31 kB / 0.9929 GB, free: 24.96 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.134e-06/0.6615, allocations: 0 / 0.9929 GB, free: 24.96 MB / 0.698 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.23e-05/0.6615, allocations: 7.156 kB / 0.9929 GB, free: 24.96 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.723e-06/0.6615, allocations: 3.219 kB / 0.9929 GB, free: 24.96 MB / 0.698 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.162e-06/0.6615, allocations: 3.688 kB / 0.9929 GB, free: 24.96 MB / 0.698 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001089/0.6626, allocations: 1.136 MB / 0.994 GB, free: 24.54 MB / 0.698 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.951e-05/0.6626, allocations: 18.92 kB / 0.994 GB, free: 24.54 MB / 0.698 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 4.477e-05/0.6627, allocations: 7.391 kB / 0.994 GB, free: 24.54 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001701/0.6628, allocations: 17.89 kB / 0.994 GB, free: 24.54 MB / 0.698 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 8.338e-05/0.6629, allocations: 26.06 kB / 0.9941 GB, free: 24.54 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 5.271e-05/0.663, allocations: 52.41 kB / 0.9941 GB, free: 24.54 MB / 0.698 GB
Notification: Performance of sorting global known variables: time 0.0001381/0.6631, allocations: 197.1 kB / 0.9943 GB, free: 24.46 MB / 0.698 GB
Notification: Performance of sort global known variables: time 8e-08/0.6631, allocations: 0 / 0.9943 GB, free: 24.46 MB / 0.698 GB
Notification: Performance of remove unused functions: time 0.0003527/0.6634, allocations: 74.64 kB / 0.9944 GB, free: 24.46 MB / 0.698 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 0.0002186/0.6637, allocations: 160.5 kB / 0.9945 GB, free: 24.37 MB / 0.698 GB
Notification: Performance of simCode: created initialization part: time 0.0008019/0.6645, allocations: 0.8418 MB / 0.9953 GB, free: 23.89 MB / 0.698 GB
Notification: Performance of simCode: created event and clocks part: time 2.836e-06/0.6645, allocations: 9.359 kB / 0.9953 GB, free: 23.89 MB / 0.698 GB
Notification: Performance of simCode: created simulation system equations: time 0.0003665/0.6648, allocations: 468.7 kB / 0.9958 GB, free: 23.6 MB / 0.698 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004558/0.6653, allocations: 71.44 kB / 0.9959 GB, free: 23.6 MB / 0.698 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001352/0.6666, allocations: 1.047 MB / 0.9969 GB, free: 23.06 MB / 0.698 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001658/0.6668, allocations: 165.1 kB / 0.997 GB, free: 22.97 MB / 0.698 GB
Notification: Performance of simCode: alias equations: time 8.468e-05/0.6669, allocations: 17.66 kB / 0.9971 GB, free: 22.97 MB / 0.698 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.304e-05/0.6669, allocations: 21.22 kB / 0.9971 GB, free: 22.96 MB / 0.698 GB
Notification: Performance of SimCode: time 3.31e-07/0.6669, allocations: 0 / 0.9971 GB, free: 22.96 MB / 0.698 GB
Notification: Performance of Templates: time 0.01012/0.6771, allocations: 4.85 MB / 1.002 GB, free: 22.53 MB / 0.698 GB
"
[Timeout remaining time 659]
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: 10.755165094975382]