Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.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 0.001957/0.001957, 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 0.002146/0.002146, allocations: 214.8 kB / 22.25 MB, free: 3.566 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 1.758/1.758, allocations: 230.6 MB / 256 MB, free: 9.605 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 3.817/3.817, allocations: 335.2 MB / 0.6325 GB, free: 7.32 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.PKOneCompartmentModel,tolerance=1e-09,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel")
translateModel(Pharmacolibrary.Examples.PKOneCompartmentModel,tolerance=1e-09,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel") [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 0.003679/0.003679, allocations: 71.89 kB / 0.868 GB, free: 5.867 MB / 0.573 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.2479/0.2516, allocations: 112.8 MB / 0.9782 GB, free: 4.793 MB / 0.6824 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKOneCompartmentModel): time 0.003465/0.2551, allocations: 1.954 MB / 0.9801 GB, free: 2.828 MB / 0.6824 GB
Notification: Performance of NFInst.instExpressions: time 0.001081/0.2561, allocations: 0.5299 MB / 0.9806 GB, free: 2.297 MB / 0.6824 GB
Notification: Performance of NFInst.updateImplicitVariability: time 7.742e-05/0.2562, allocations: 3.938 kB / 0.9806 GB, free: 2.293 MB / 0.6824 GB
Notification: Performance of NFTyping.typeComponents: time 9.558e-05/0.2563, allocations: 11.86 kB / 0.9806 GB, free: 2.281 MB / 0.6824 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001455/0.2565, allocations: 51.56 kB / 0.9807 GB, free: 2.23 MB / 0.6824 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001752/0.2566, allocations: 51.94 kB / 0.9807 GB, free: 2.18 MB / 0.6824 GB
Notification: Performance of NFFlatten.flatten: time 0.0002612/0.2569, allocations: 187.2 kB / 0.9809 GB, free: 1.996 MB / 0.6824 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001146/0.257, allocations: 21.91 kB / 0.9809 GB, free: 1.965 MB / 0.6824 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.000121/0.2571, allocations: 75.77 kB / 0.981 GB, free: 1.891 MB / 0.6824 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001299/0.2573, allocations: 63.69 kB / 0.9811 GB, free: 1.828 MB / 0.6824 GB
Notification: Performance of NFPackage.collectConstants: time 3.778e-05/0.2573, allocations: 16 kB / 0.9811 GB, free: 1.812 MB / 0.6824 GB
Notification: Performance of NFFlatten.collectFunctions: time 3.595e-05/0.2573, allocations: 16 kB / 0.9811 GB, free: 1.797 MB / 0.6824 GB
Notification: Performance of NFScalarize.scalarize: time 3.908e-05/0.2574, allocations: 31.8 kB / 0.9811 GB, free: 1.766 MB / 0.6824 GB
Notification: Performance of NFVerifyModel.verify: time 9.702e-05/0.2575, allocations: 67.77 kB / 0.9812 GB, free: 1.699 MB / 0.6824 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002318/0.2577, allocations: 155.4 kB / 0.9813 GB, free: 1.547 MB / 0.6824 GB
Notification: Performance of FrontEnd - DAE generated: time 3.126e-06/0.2577, allocations: 0 / 0.9813 GB, free: 1.547 MB / 0.6824 GB
Notification: Performance of FrontEnd: time 8.61e-07/0.2577, allocations: 7.938 kB / 0.9813 GB, free: 1.539 MB / 0.6824 GB
Notification: Performance of Transformations before backend: time 4.859e-06/0.2577, allocations: 0 / 0.9813 GB, free: 1.539 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 0.0008261/0.2585, allocations: 437.1 kB / 0.9818 GB, free: 1.07 MB / 0.6824 GB
Notification: Performance of prepare preOptimizeDAE: time 3.474e-05/0.2586, allocations: 14.09 kB / 0.9818 GB, free: 1.059 MB / 0.6824 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 5.012e-05/0.2586, allocations: 16.89 kB / 0.9818 GB, free: 1.043 MB / 0.6824 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0003657/0.259, allocations: 182.2 kB / 0.982 GB, free: 0.8398 MB / 0.6824 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.411e-05/0.259, allocations: 8.375 kB / 0.982 GB, free: 0.832 MB / 0.6824 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.577e-05/0.2591, allocations: 24.08 kB / 0.982 GB, free: 0.8086 MB / 0.6824 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003351/0.2594, allocations: 159.2 kB / 0.9821 GB, free: 0.6406 MB / 0.6824 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.58e-05/0.2594, allocations: 3.984 kB / 0.9821 GB, free: 0.6367 MB / 0.6824 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.609e-05/0.2594, allocations: 4 kB / 0.9821 GB, free: 0.6328 MB / 0.6824 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 3.838e-06/0.2594, allocations: 0 / 0.9821 GB, free: 0.6328 MB / 0.6824 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003335/0.2598, allocations: 137.6 kB / 0.9823 GB, free: 0.4922 MB / 0.6824 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0006843/0.2604, allocations: 360.1 kB / 0.9826 GB, free: 112 kB / 0.6824 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0004215/0.2609, allocations: 160.3 kB / 0.9828 GB, free: 15.94 MB / 0.698 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001943/0.2611, allocations: 86.53 kB / 0.9829 GB, free: 15.84 MB / 0.698 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.802e-05/0.2611, allocations: 4 kB / 0.9829 GB, free: 15.84 MB / 0.698 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0003818/0.2615, allocations: 224.4 kB / 0.9831 GB, free: 15.59 MB / 0.698 GB
Notification: Performance of pre-optimization done (n=20): time 1.333e-06/0.2615, allocations: 0 / 0.9831 GB, free: 15.59 MB / 0.698 GB
Notification: Performance of matching and sorting (n=21): time 0.001538/0.263, allocations: 0.6771 MB / 0.9837 GB, free: 14.86 MB / 0.698 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001096/0.2631, allocations: 140.5 kB / 0.9839 GB, free: 14.69 MB / 0.698 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001663/0.2633, allocations: 156 kB / 0.984 GB, free: 14.53 MB / 0.698 GB
Notification: Performance of collectPreVariables (initialization): time 3.367e-05/0.2633, allocations: 33.7 kB / 0.9841 GB, free: 14.49 MB / 0.698 GB
Notification: Performance of collectInitialEqns (initialization): time 7.973e-05/0.2634, allocations: 104.5 kB / 0.9842 GB, free: 14.38 MB / 0.698 GB
Notification: Performance of collectInitialBindings (initialization): time 7.624e-05/0.2635, allocations: 79.41 kB / 0.9842 GB, free: 14.3 MB / 0.698 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 8.242e-05/0.2635, allocations: 45.7 kB / 0.9843 GB, free: 14.25 MB / 0.698 GB
Notification: Performance of setup shared object (initialization): time 0.0001762/0.2637, allocations: 334.8 kB / 0.9846 GB, free: 13.92 MB / 0.698 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002487/0.264, allocations: 132.6 kB / 0.9847 GB, free: 13.77 MB / 0.698 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0004146/0.2644, allocations: 218.7 kB / 0.9849 GB, free: 13.52 MB / 0.698 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0009852/0.2654, allocations: 0.5023 MB / 0.9854 GB, free: 12.96 MB / 0.698 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.553e-06/0.2654, allocations: 0 / 0.9854 GB, free: 12.96 MB / 0.698 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0006595/0.266, allocations: 380 kB / 0.9858 GB, free: 12.55 MB / 0.698 GB
Notification: Performance of prepare postOptimizeDAE: time 6.018e-05/0.2661, allocations: 63.39 kB / 0.9858 GB, free: 12.48 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.693e-06/0.2661, allocations: 3.938 kB / 0.9858 GB, free: 12.48 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.328e-05/0.2661, allocations: 4 kB / 0.9858 GB, free: 12.47 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002167/0.2663, allocations: 47.91 kB / 0.9859 GB, free: 12.43 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 5.37e-06/0.2663, allocations: 4 kB / 0.9859 GB, free: 12.42 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001554/0.2665, allocations: 16.17 kB / 0.9859 GB, free: 12.41 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.895e-05/0.2665, allocations: 15.94 kB / 0.9859 GB, free: 12.39 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 0.0002372/0.2667, allocations: 177.1 kB / 0.9861 GB, free: 12.2 MB / 0.698 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.559e-05/0.2668, allocations: 27.89 kB / 0.9861 GB, free: 12.18 MB / 0.698 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 5.308e-05/0.2668, allocations: 21.22 kB / 0.9861 GB, free: 12.16 MB / 0.698 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.679e-06/0.2668, allocations: 3.984 kB / 0.9861 GB, free: 12.15 MB / 0.698 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.018e-06/0.2668, allocations: 0 / 0.9861 GB, free: 12.15 MB / 0.698 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 2.835e-06/0.2668, allocations: 0 / 0.9861 GB, free: 12.15 MB / 0.698 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.000828/0.2677, allocations: 0.5095 MB / 0.9866 GB, free: 11.59 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.964e-06/0.2677, allocations: 0 / 0.9866 GB, free: 11.59 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002031/0.2679, allocations: 31.97 kB / 0.9867 GB, free: 11.56 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (simulation): time 5.39e-06/0.2679, allocations: 4 kB / 0.9867 GB, free: 11.55 MB / 0.698 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.813e-05/0.2679, allocations: 8 kB / 0.9867 GB, free: 11.55 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 8.256e-06/0.2679, allocations: 7.938 kB / 0.9867 GB, free: 11.54 MB / 0.698 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.236e-06/0.2679, allocations: 3.984 kB / 0.9867 GB, free: 11.54 MB / 0.698 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0007977/0.2687, allocations: 480.8 kB / 0.9872 GB, free: 11.03 MB / 0.698 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.269e-05/0.2687, allocations: 11.91 kB / 0.9872 GB, free: 11.02 MB / 0.698 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.348e-05/0.2688, allocations: 8.062 kB / 0.9872 GB, free: 11.01 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001517/0.2689, allocations: 15.98 kB / 0.9872 GB, free: 11 MB / 0.698 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.856e-05/0.269, allocations: 19.97 kB / 0.9872 GB, free: 10.98 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.784e-05/0.269, allocations: 8 kB / 0.9872 GB, free: 10.97 MB / 0.698 GB
Notification: Performance of sorting global known variables: time 0.0001073/0.2691, allocations: 115.2 kB / 0.9873 GB, free: 10.86 MB / 0.698 GB
Notification: Performance of sort global known variables: time 7e-08/0.2691, allocations: 3.938 kB / 0.9873 GB, free: 10.85 MB / 0.698 GB
Notification: Performance of remove unused functions: time 0.0002841/0.2694, allocations: 44 kB / 0.9874 GB, free: 10.81 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 0.0001214/0.2695, allocations: 108 kB / 0.9875 GB, free: 10.7 MB / 0.698 GB
Notification: Performance of simCode: created initialization part: time 0.0006085/0.2701, allocations: 375.8 kB / 0.9878 GB, free: 10.29 MB / 0.698 GB
Notification: Performance of simCode: created event and clocks part: time 1.463e-06/0.2701, allocations: 0 / 0.9878 GB, free: 10.29 MB / 0.698 GB
Notification: Performance of simCode: created simulation system equations: time 0.0002679/0.2704, allocations: 173 kB / 0.988 GB, free: 10.1 MB / 0.698 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003903/0.2708, allocations: 39.98 kB / 0.988 GB, free: 10.06 MB / 0.698 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001303/0.2721, allocations: 0.6706 MB / 0.9887 GB, free: 9.355 MB / 0.698 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001228/0.2722, allocations: 103.5 kB / 0.9888 GB, free: 9.23 MB / 0.698 GB
Notification: Performance of simCode: alias equations: time 8.009e-05/0.2723, allocations: 17.48 kB / 0.9888 GB, free: 9.215 MB / 0.698 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.741e-05/0.2723, allocations: 19.44 kB / 0.9888 GB, free: 9.199 MB / 0.698 GB
Notification: Performance of SimCode: time 6.41e-07/0.2723, allocations: 0 / 0.9888 GB, free: 9.199 MB / 0.698 GB
Notification: Performance of Templates: time 0.5352/0.8076, allocations: 2.586 MB / 0.9913 GB, free: 26.14 MB / 0.698 GB
"
[Timeout remaining time 659]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModel.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 10.754635453922674]