Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue.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 0.002323/0.002323, allocations: 105.5 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 0.002787/0.002787, allocations: 226.9 kB / 22.25 MB, free: 3.586 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 1.824/1.824, 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 3.732/3.732, allocations: 335.2 MB / 0.6325 GB, free: 7.301 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.PBPK_SingleDoseVenousArteryTissue,tolerance=1e-06,outputFormat="empty",numberOfIntervals=7200,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue")
translateModel(Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue,tolerance=1e-06,outputFormat="empty",numberOfIntervals=7200,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue") [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 0.003923/0.003923, allocations: 71.89 kB / 0.868 GB, free: 5.977 MB / 0.573 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.2592/0.2632, allocations: 112.8 MB / 0.9782 GB, free: 4.895 MB / 0.6824 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue): time 0.004787/0.2679, allocations: 2.744 MB / 0.9809 GB, free: 2.137 MB / 0.6824 GB
Notification: Performance of NFInst.instExpressions: time 0.001567/0.2695, allocations: 0.7361 MB / 0.9816 GB, free: 1.398 MB / 0.6824 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001324/0.2696, allocations: 4 kB / 0.9816 GB, free: 1.395 MB / 0.6824 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001743/0.2698, allocations: 43.56 kB / 0.9816 GB, free: 1.352 MB / 0.6824 GB
Notification: Performance of NFTyping.typeBindings: time 0.000311/0.2701, allocations: 115.1 kB / 0.9817 GB, free: 1.238 MB / 0.6824 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0003037/0.2704, allocations: 95.81 kB / 0.9818 GB, free: 1.145 MB / 0.6824 GB
Notification: Performance of NFFlatten.flatten: time 0.0004982/0.2709, allocations: 418.1 kB / 0.9822 GB, free: 0.7344 MB / 0.6824 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0003889/0.2713, allocations: 212.1 kB / 0.9824 GB, free: 0.5273 MB / 0.6824 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002268/0.2715, allocations: 171.5 kB / 0.9826 GB, free: 368 kB / 0.6824 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0003186/0.2719, allocations: 183.2 kB / 0.9828 GB, free: 184 kB / 0.6824 GB
Notification: Performance of NFPackage.collectConstants: time 8.639e-05/0.2719, allocations: 40 kB / 0.9828 GB, free: 144 kB / 0.6824 GB
Notification: Performance of NFFlatten.collectFunctions: time 7.886e-05/0.272, allocations: 36 kB / 0.9828 GB, free: 108 kB / 0.6824 GB
Notification: Performance of NFScalarize.scalarize: time 9.462e-05/0.2721, allocations: 83.75 kB / 0.9829 GB, free: 24 kB / 0.6824 GB
Notification: Performance of NFVerifyModel.verify: time 0.0002255/0.2723, allocations: 159.5 kB / 0.9831 GB, free: 15.86 MB / 0.698 GB
Notification: Performance of NFConvertDAE.convert: time 0.000498/0.2728, allocations: 382.5 kB / 0.9834 GB, free: 15.49 MB / 0.698 GB
Notification: Performance of FrontEnd - DAE generated: time 4.459e-06/0.2728, allocations: 0 / 0.9834 GB, free: 15.49 MB / 0.698 GB
Notification: Performance of FrontEnd: time 1.342e-06/0.2729, allocations: 0 / 0.9834 GB, free: 15.49 MB / 0.698 GB
Notification: Performance of Transformations before backend: time 7.294e-06/0.2729, allocations: 0 / 0.9834 GB, free: 15.49 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: 68
 * Number of variables: 68
Notification: Performance of Generate backend data structure: time 0.001272/0.2741, allocations: 0.5578 MB / 0.984 GB, free: 14.89 MB / 0.698 GB
Notification: Performance of prepare preOptimizeDAE: time 4.166e-05/0.2742, allocations: 10.11 kB / 0.984 GB, free: 14.89 MB / 0.698 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 9.279e-05/0.2743, allocations: 40.69 kB / 0.984 GB, free: 14.85 MB / 0.698 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0005054/0.2748, allocations: 237 kB / 0.9843 GB, free: 14.59 MB / 0.698 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.71e-05/0.2748, allocations: 25.02 kB / 0.9843 GB, free: 14.57 MB / 0.698 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 7.396e-05/0.2749, allocations: 36.08 kB / 0.9843 GB, free: 14.53 MB / 0.698 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0007244/0.2756, allocations: 388.1 kB / 0.9847 GB, free: 14.13 MB / 0.698 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.96e-05/0.2756, allocations: 0 / 0.9847 GB, free: 14.13 MB / 0.698 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.482e-05/0.2757, allocations: 12 kB / 0.9847 GB, free: 14.12 MB / 0.698 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.977e-06/0.2757, allocations: 4 kB / 0.9847 GB, free: 14.12 MB / 0.698 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0005995/0.2763, allocations: 241.8 kB / 0.9849 GB, free: 13.88 MB / 0.698 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001753/0.278, allocations: 0.8114 MB / 0.9857 GB, free: 13.04 MB / 0.698 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0006111/0.2786, allocations: 206.7 kB / 0.9859 GB, free: 12.82 MB / 0.698 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002551/0.2789, allocations: 80.81 kB / 0.986 GB, free: 12.74 MB / 0.698 GB
Notification: Performance of preOpt evalFunc (simulation): time 3.751e-05/0.2789, allocations: 8 kB / 0.986 GB, free: 12.73 MB / 0.698 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0004052/0.2793, allocations: 170.4 kB / 0.9862 GB, free: 12.56 MB / 0.698 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.0002107/0.2795, allocations: 39.86 kB / 0.9862 GB, free: 12.52 MB / 0.698 GB
Notification: Performance of pre-optimization done (n=25): time 6.352e-06/0.2795, allocations: 3.984 kB / 0.9862 GB, free: 12.52 MB / 0.698 GB
Notification: Performance of matching and sorting (n=25): time 0.0009875/0.2805, allocations: 301.3 kB / 0.9865 GB, free: 12.21 MB / 0.698 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.799e-05/0.2806, allocations: 63.34 kB / 0.9866 GB, free: 12.14 MB / 0.698 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002413/0.2808, allocations: 194.3 kB / 0.9867 GB, free: 11.94 MB / 0.698 GB
Notification: Performance of collectPreVariables (initialization): time 3.928e-05/0.2809, allocations: 37.7 kB / 0.9868 GB, free: 11.9 MB / 0.698 GB
Notification: Performance of collectInitialEqns (initialization): time 0.0001488/0.281, allocations: 172.5 kB / 0.9869 GB, free: 11.72 MB / 0.698 GB
Notification: Performance of collectInitialBindings (initialization): time 9.808e-05/0.2811, allocations: 95.23 kB / 0.987 GB, free: 11.63 MB / 0.698 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001166/0.2812, allocations: 61.69 kB / 0.9871 GB, free: 11.56 MB / 0.698 GB
Notification: Performance of setup shared object (initialization): time 0.0001874/0.2814, allocations: 338.7 kB / 0.9874 GB, free: 11.22 MB / 0.698 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.000327/0.2818, allocations: 143.1 kB / 0.9876 GB, free: 11.07 MB / 0.698 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003825/0.2821, allocations: 234.3 kB / 0.9878 GB, free: 10.79 MB / 0.698 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0006096/0.2827, allocations: 306.4 kB / 0.9881 GB, free: 10.45 MB / 0.698 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.517e-06/0.2827, allocations: 0 / 0.9881 GB, free: 10.45 MB / 0.698 GB
Notification: Performance of matching and sorting (n=41) (initialization): time 0.0008239/0.2836, allocations: 412.5 kB / 0.9885 GB, free: 10.03 MB / 0.698 GB
Notification: Performance of prepare postOptimizeDAE: time 6.055e-05/0.2836, allocations: 37.69 kB / 0.9885 GB, free: 9.988 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.059e-05/0.2836, allocations: 4 kB / 0.9885 GB, free: 9.984 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (initialization): time 2.504e-05/0.2837, allocations: 4 kB / 0.9885 GB, free: 9.98 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003736/0.284, allocations: 88.19 kB / 0.9886 GB, free: 9.895 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.675e-05/0.2841, allocations: 11.92 kB / 0.9886 GB, free: 9.883 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0002215/0.2843, allocations: 19.98 kB / 0.9886 GB, free: 9.863 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 3.013e-05/0.2843, allocations: 12 kB / 0.9886 GB, free: 9.852 MB / 0.698 GB
Warning: Assuming fixed start value for the following 5 variables:
         tissue.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         arteries.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         veins.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         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
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 11
 * Number of states: 0 ()
 * Number of discrete variables: 5 (singleDose.pulse.count,$PRE.singleDose.pulse.count,singleDose.pulse.T_start,$PRE.singleDose.pulse.T_start,$whenCondition1)
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (40):
 * Single equations (assignments): 39
 * Array equations: 0
 * Algorithm blocks: 1
 * 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 0.556/0.8403, allocations: 166.7 kB / 0.9888 GB, free: 26.46 MB / 0.698 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 7.239e-05/0.8404, allocations: 20.11 kB / 0.9888 GB, free: 26.46 MB / 0.698 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0007282/0.8411, allocations: 258.5 kB / 0.9891 GB, free: 26.42 MB / 0.698 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.131e-06/0.8411, allocations: 4.344 kB / 0.9891 GB, free: 26.42 MB / 0.698 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.829e-06/0.8411, allocations: 1.469 kB / 0.9891 GB, free: 26.42 MB / 0.698 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.62e-06/0.8411, allocations: 4.672 kB / 0.9891 GB, free: 26.42 MB / 0.698 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0002703/0.8414, allocations: 219.1 kB / 0.9893 GB, free: 26.3 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.775e-06/0.8414, allocations: 0 / 0.9893 GB, free: 26.3 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0003197/0.8417, allocations: 50.97 kB / 0.9893 GB, free: 26.3 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (simulation): time 6.312e-06/0.8417, allocations: 1.094 kB / 0.9893 GB, free: 26.3 MB / 0.698 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.524e-05/0.8417, allocations: 7.672 kB / 0.9893 GB, free: 26.3 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.957e-06/0.8417, allocations: 2.125 kB / 0.9893 GB, free: 26.3 MB / 0.698 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.944e-06/0.8417, allocations: 3.984 kB / 0.9893 GB, free: 26.3 MB / 0.698 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0007931/0.8425, allocations: 382.2 kB / 0.9897 GB, free: 26.23 MB / 0.698 GB
Notification: Performance of postOpt removeConstants (simulation): time 4.28e-05/0.8426, allocations: 18.66 kB / 0.9897 GB, free: 26.23 MB / 0.698 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 4.588e-05/0.8426, allocations: 7.703 kB / 0.9897 GB, free: 26.23 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001723/0.8428, allocations: 12.92 kB / 0.9897 GB, free: 26.23 MB / 0.698 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 7.923e-05/0.8429, allocations: 19.58 kB / 0.9898 GB, free: 26.23 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.027e-05/0.8429, allocations: 13.17 kB / 0.9898 GB, free: 26.23 MB / 0.698 GB
Notification: Performance of sorting global known variables: time 0.0001131/0.843, allocations: 144.2 kB / 0.9899 GB, free: 26.16 MB / 0.698 GB
Notification: Performance of sort global known variables: time 7e-08/0.843, allocations: 2.969 kB / 0.9899 GB, free: 26.16 MB / 0.698 GB
Notification: Performance of remove unused functions: time 0.0003643/0.8434, allocations: 90.58 kB / 0.99 GB, free: 26.16 MB / 0.698 GB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 9 (tissue.M,tissue.AUC,arteries.M,arteries.AUC,veins.M,veins.AUC,singleDose.TotalCumulativeMass,singleDose.variableDose.TotalCumulativeMass,kidneyElim.MExc)
 * Number of discrete variables: 3 ($whenCondition1,singleDose.pulse.T_start,singleDose.pulse.count)
 * Number of discrete states: 1 (singleDose.pulse.count)
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (25):
 * Single equations (assignments): 23
 * Array equations: 0
 * Algorithm blocks: 0
 * 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 0.0001212/0.8435, allocations: 101.2 kB / 0.9901 GB, free: 26.07 MB / 0.698 GB
Notification: Performance of simCode: created initialization part: time 0.0006594/0.8442, allocations: 321.5 kB / 0.9904 GB, free: 25.97 MB / 0.698 GB
Notification: Performance of simCode: created event and clocks part: time 2.034e-06/0.8442, allocations: 0 / 0.9904 GB, free: 25.97 MB / 0.698 GB
Notification: Performance of simCode: created simulation system equations: time 0.0002365/0.8444, allocations: 106.2 kB / 0.9905 GB, free: 25.97 MB / 0.698 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004345/0.8448, allocations: 73.89 kB / 0.9906 GB, free: 25.97 MB / 0.698 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001629/0.8465, allocations: 0.994 MB / 0.9915 GB, free: 25.43 MB / 0.698 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001257/0.8466, allocations: 159.1 kB / 0.9917 GB, free: 25.35 MB / 0.698 GB
Notification: Performance of simCode: alias equations: time 0.0001382/0.8467, allocations: 39.55 kB / 0.9917 GB, free: 25.34 MB / 0.698 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 8.301e-05/0.8468, allocations: 34.56 kB / 0.9918 GB, free: 25.32 MB / 0.698 GB
Notification: Performance of SimCode: time 7.81e-07/0.8468, allocations: 0 / 0.9918 GB, free: 25.32 MB / 0.698 GB
Notification: Performance of Templates: time 0.009131/0.8559, allocations: 4.094 MB / 0.9958 GB, free: 24.94 MB / 0.698 GB
"
[Timeout remaining time 659]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 10.555165928089991]