Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PK_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 0.002259/0.002259, allocations: 101.5 kB / 18.95 MB, free: 1.18 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 0.002519/0.002519, allocations: 218.8 kB / 22.25 MB, free: 3.574 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 1.836/1.836, allocations: 230.6 MB / 256 MB, free: 9.586 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 3.729/3.729, allocations: 335.2 MB / 0.6325 GB, free: 7.238 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.PK_1C_Gentamicin,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin")
translateModel(Pharmacolibrary.Examples.PK_1C_Gentamicin,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_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 0.003665/0.003665, allocations: 67.89 kB / 0.868 GB, free: 5.754 MB / 0.573 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.2729/0.2766, allocations: 112.8 MB / 0.9782 GB, free: 4.68 MB / 0.6824 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_Gentamicin): time 0.004017/0.2806, allocations: 2.018 MB / 0.9802 GB, free: 2.648 MB / 0.6824 GB
Notification: Performance of NFInst.instExpressions: time 0.001182/0.2818, allocations: 0.5221 MB / 0.9807 GB, free: 2.125 MB / 0.6824 GB
Notification: Performance of NFInst.updateImplicitVariability: time 9.077e-05/0.2819, allocations: 0 / 0.9807 GB, free: 2.125 MB / 0.6824 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001415/0.282, allocations: 27.78 kB / 0.9807 GB, free: 2.098 MB / 0.6824 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001734/0.2822, allocations: 51.56 kB / 0.9807 GB, free: 2.047 MB / 0.6824 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0002012/0.2824, allocations: 47.94 kB / 0.9808 GB, free: 2 MB / 0.6824 GB
Notification: Performance of NFFlatten.flatten: time 0.0003159/0.2827, allocations: 195.1 kB / 0.981 GB, free: 1.809 MB / 0.6824 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001519/0.2829, allocations: 29.95 kB / 0.981 GB, free: 1.773 MB / 0.6824 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001269/0.283, allocations: 67.72 kB / 0.9811 GB, free: 1.707 MB / 0.6824 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001553/0.2831, allocations: 67.69 kB / 0.9811 GB, free: 1.641 MB / 0.6824 GB
Notification: Performance of NFPackage.collectConstants: time 3.83e-05/0.2832, allocations: 16 kB / 0.9812 GB, free: 1.625 MB / 0.6824 GB
Notification: Performance of NFFlatten.collectFunctions: time 3.994e-05/0.2832, allocations: 16 kB / 0.9812 GB, free: 1.609 MB / 0.6824 GB
Notification: Performance of NFScalarize.scalarize: time 5.317e-05/0.2833, allocations: 39.84 kB / 0.9812 GB, free: 1.57 MB / 0.6824 GB
Notification: Performance of NFVerifyModel.verify: time 0.0001068/0.2834, allocations: 67.72 kB / 0.9813 GB, free: 1.504 MB / 0.6824 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002743/0.2837, allocations: 163.4 kB / 0.9814 GB, free: 1.344 MB / 0.6824 GB
Notification: Performance of FrontEnd - DAE generated: time 5.16e-06/0.2837, allocations: 0 / 0.9814 GB, free: 1.344 MB / 0.6824 GB
Notification: Performance of FrontEnd: time 1.843e-06/0.2837, allocations: 0 / 0.9814 GB, free: 1.344 MB / 0.6824 GB
Notification: Performance of Transformations before backend: time 5.861e-06/0.2837, allocations: 0 / 0.9814 GB, free: 1.344 MB / 0.6824 GB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 26
 * Number of variables: 26
Notification: Performance of Generate backend data structure: time 0.0009674/0.2846, allocations: 445 kB / 0.9818 GB, free: 0.8672 MB / 0.6824 GB
Notification: Performance of prepare preOptimizeDAE: time 4.43e-05/0.2847, allocations: 14.11 kB / 0.9819 GB, free: 0.8555 MB / 0.6824 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 5.723e-05/0.2847, allocations: 16.84 kB / 0.9819 GB, free: 0.8398 MB / 0.6824 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0004072/0.2852, allocations: 188.2 kB / 0.9821 GB, free: 0.6328 MB / 0.6824 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.822e-05/0.2852, allocations: 11.94 kB / 0.9821 GB, free: 0.6211 MB / 0.6824 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.489e-05/0.2852, allocations: 15.94 kB / 0.9821 GB, free: 0.6055 MB / 0.6824 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004959/0.2857, allocations: 154.6 kB / 0.9822 GB, free: 456 kB / 0.6824 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.931e-05/0.2857, allocations: 3.953 kB / 0.9822 GB, free: 452 kB / 0.6824 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.194e-05/0.2858, allocations: 11.98 kB / 0.9822 GB, free: 440 kB / 0.6824 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 5.64e-06/0.2858, allocations: 0 / 0.9822 GB, free: 440 kB / 0.6824 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003469/0.2861, allocations: 137.5 kB / 0.9824 GB, free: 296 kB / 0.6824 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0007694/0.2869, allocations: 360.2 kB / 0.9827 GB, free: 15.91 MB / 0.698 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0004259/0.2873, allocations: 164.2 kB / 0.9829 GB, free: 15.73 MB / 0.698 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002046/0.2875, allocations: 82.53 kB / 0.983 GB, free: 15.64 MB / 0.698 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.998e-05/0.2875, allocations: 3.984 kB / 0.983 GB, free: 15.64 MB / 0.698 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.000416/0.2879, allocations: 228.5 kB / 0.9832 GB, free: 15.38 MB / 0.698 GB
Notification: Performance of pre-optimization done (n=20): time 1.362e-06/0.2879, allocations: 4 kB / 0.9832 GB, free: 15.38 MB / 0.698 GB
Notification: Performance of matching and sorting (n=21): time 0.001643/0.2896, allocations: 0.6716 MB / 0.9838 GB, free: 14.64 MB / 0.698 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 0.000111/0.2897, allocations: 140.4 kB / 0.984 GB, free: 14.48 MB / 0.698 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001918/0.2899, allocations: 162.4 kB / 0.9841 GB, free: 14.31 MB / 0.698 GB
Notification: Performance of collectPreVariables (initialization): time 3.74e-05/0.2899, allocations: 33.7 kB / 0.9842 GB, free: 14.27 MB / 0.698 GB
Notification: Performance of collectInitialEqns (initialization): time 0.0001081/0.29, allocations: 112.5 kB / 0.9843 GB, free: 14.16 MB / 0.698 GB
Notification: Performance of collectInitialBindings (initialization): time 6.979e-05/0.2901, allocations: 63.44 kB / 0.9843 GB, free: 14.09 MB / 0.698 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 9.155e-05/0.2902, allocations: 49.69 kB / 0.9844 GB, free: 14.04 MB / 0.698 GB
Notification: Performance of setup shared object (initialization): time 0.0001857/0.2904, allocations: 330.8 kB / 0.9847 GB, free: 13.71 MB / 0.698 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002644/0.2906, allocations: 136.6 kB / 0.9848 GB, free: 13.55 MB / 0.698 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003038/0.2909, allocations: 202.8 kB / 0.985 GB, free: 13.32 MB / 0.698 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0009767/0.2919, allocations: 0.5099 MB / 0.9855 GB, free: 12.75 MB / 0.698 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.068e-06/0.2919, allocations: 4 kB / 0.9855 GB, free: 12.74 MB / 0.698 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0006755/0.2926, allocations: 379.9 kB / 0.9859 GB, free: 12.34 MB / 0.698 GB
Notification: Performance of prepare postOptimizeDAE: time 6.906e-05/0.2927, allocations: 65.42 kB / 0.9859 GB, free: 12.27 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.623e-06/0.2927, allocations: 0 / 0.9859 GB, free: 12.27 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (initialization): time 2.616e-05/0.2927, allocations: 7.984 kB / 0.9859 GB, free: 12.26 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002335/0.2929, allocations: 60.09 kB / 0.986 GB, free: 12.2 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.133e-05/0.293, allocations: 4 kB / 0.986 GB, free: 12.2 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.000158/0.2931, allocations: 15.98 kB / 0.986 GB, free: 12.18 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.035e-05/0.2931, allocations: 8 kB / 0.986 GB, free: 12.17 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: 13 ($PRE.central.Cmin,central.Cmin,$PRE.central.Cmax,central.Cmax,$PRE.central.rising,$PRE.singleDose.pulse.count,$PRE.singleDose.pulse.T_start,central.rising,singleDose.pulse.count,singleDose.pulse.T_start,$whenCondition3,$whenCondition2,$whenCondition1)
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (30):
 * Single equations (assignments): 28
 * Array equations: 0
 * Algorithm blocks: 2
 * 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 0.000269/0.2934, allocations: 189 kB / 0.9862 GB, free: 11.97 MB / 0.698 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.592e-05/0.2934, allocations: 19.84 kB / 0.9862 GB, free: 11.95 MB / 0.698 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 6.108e-05/0.2935, allocations: 21.27 kB / 0.9863 GB, free: 11.93 MB / 0.698 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.382e-06/0.2935, allocations: 4 kB / 0.9863 GB, free: 11.93 MB / 0.698 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.121e-06/0.2935, allocations: 0 / 0.9863 GB, free: 11.93 MB / 0.698 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.977e-06/0.2935, allocations: 3.938 kB / 0.9863 GB, free: 11.93 MB / 0.698 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0008789/0.2944, allocations: 0.5131 MB / 0.9868 GB, free: 11.36 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.823e-06/0.2944, allocations: 4 kB / 0.9868 GB, free: 11.36 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002034/0.2946, allocations: 35.91 kB / 0.9868 GB, free: 11.32 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (simulation): time 5.441e-06/0.2946, allocations: 4 kB / 0.9868 GB, free: 11.32 MB / 0.698 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.416e-05/0.2946, allocations: 7.938 kB / 0.9868 GB, free: 11.31 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.178e-06/0.2946, allocations: 4 kB / 0.9868 GB, free: 11.31 MB / 0.698 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 8.82e-07/0.2946, allocations: 0 / 0.9868 GB, free: 11.31 MB / 0.698 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0008351/0.2955, allocations: 484.8 kB / 0.9873 GB, free: 10.8 MB / 0.698 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.73e-05/0.2955, allocations: 15.91 kB / 0.9873 GB, free: 10.79 MB / 0.698 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.885e-05/0.2955, allocations: 8.062 kB / 0.9873 GB, free: 10.78 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001519/0.2957, allocations: 11.98 kB / 0.9873 GB, free: 10.77 MB / 0.698 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 8.533e-05/0.2958, allocations: 19.97 kB / 0.9873 GB, free: 10.75 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.424e-05/0.2958, allocations: 4 kB / 0.9873 GB, free: 10.74 MB / 0.698 GB
Notification: Performance of sorting global known variables: time 0.0001201/0.2959, allocations: 125.4 kB / 0.9875 GB, free: 10.62 MB / 0.698 GB
Notification: Performance of sort global known variables: time 8e-08/0.2959, allocations: 0 / 0.9875 GB, free: 10.62 MB / 0.698 GB
Notification: Performance of remove unused functions: time 0.0002917/0.2962, allocations: 48 kB / 0.9875 GB, free: 10.57 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: 8 ($whenCondition1,$whenCondition2,$whenCondition3,singleDose.pulse.T_start,singleDose.pulse.count,central.Cmax,central.Cmin,central.rising)
 * Number of discrete states: 6 (singleDose.pulse.count,central.Cmin,$whenCondition3,central.Cmax,$whenCondition2,central.rising)
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (18):
 * Single equations (assignments): 15
 * Array equations: 0
 * Algorithm blocks: 1
 * 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 0.000153/0.2963, allocations: 117.7 kB / 0.9876 GB, free: 10.45 MB / 0.698 GB
Notification: Performance of simCode: created initialization part: time 0.0006473/0.297, allocations: 365.4 kB / 0.988 GB, free: 10.05 MB / 0.698 GB
Notification: Performance of simCode: created event and clocks part: time 1.934e-06/0.297, allocations: 0 / 0.988 GB, free: 10.05 MB / 0.698 GB
Notification: Performance of simCode: created simulation system equations: time 0.0002757/0.2973, allocations: 169 kB / 0.9881 GB, free: 9.871 MB / 0.698 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004259/0.2977, allocations: 56.34 kB / 0.9882 GB, free: 9.816 MB / 0.698 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001365/0.2991, allocations: 0.6591 MB / 0.9888 GB, free: 9.121 MB / 0.698 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0002616/0.2993, allocations: 119.4 kB / 0.9889 GB, free: 8.984 MB / 0.698 GB
Notification: Performance of simCode: alias equations: time 7.943e-05/0.2994, allocations: 13.64 kB / 0.9889 GB, free: 8.969 MB / 0.698 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 5.386e-05/0.2995, allocations: 19.44 kB / 0.989 GB, free: 8.949 MB / 0.698 GB
Notification: Performance of SimCode: time 7.01e-07/0.2995, allocations: 0 / 0.989 GB, free: 8.949 MB / 0.698 GB
Notification: Performance of Templates: time 0.4963/0.7958, allocations: 2.792 MB / 0.9917 GB, free: 26.22 MB / 0.698 GB
"
[Timeout remaining time 659]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 10.570671119960025]