Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModelPeriodic.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 0.002287/0.002287, allocations: 101.5 kB / 18.94 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 0.008716/0.008716, allocations: 211.6 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 1.666/1.666, allocations: 230.6 MB / 256 MB, free: 9.594 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 3.778/3.778, allocations: 335.2 MB / 0.6325 GB, free: 7.227 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.PKOneCompartmentModelPeriodic,tolerance=1e-09,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModelPeriodic")
translateModel(Pharmacolibrary.Examples.PKOneCompartmentModelPeriodic,tolerance=1e-09,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModelPeriodic") [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 0.003873/0.003873, allocations: 67.91 kB / 0.868 GB, free: 5.789 MB / 0.573 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.2934/0.2973, allocations: 112.8 MB / 0.9782 GB, free: 4.707 MB / 0.6824 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKOneCompartmentModelPeriodic): time 0.003879/0.3012, allocations: 1.94 MB / 0.9801 GB, free: 2.754 MB / 0.6824 GB
Notification: Performance of NFInst.instExpressions: time 0.001189/0.3024, allocations: 0.526 MB / 0.9806 GB, free: 2.227 MB / 0.6824 GB
Notification: Performance of NFInst.updateImplicitVariability: time 8.693e-05/0.3025, allocations: 4 kB / 0.9806 GB, free: 2.223 MB / 0.6824 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001318/0.3026, allocations: 19.78 kB / 0.9806 GB, free: 2.203 MB / 0.6824 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001875/0.3028, allocations: 55.5 kB / 0.9807 GB, free: 2.148 MB / 0.6824 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001894/0.303, allocations: 43.94 kB / 0.9807 GB, free: 2.105 MB / 0.6824 GB
Notification: Performance of NFFlatten.flatten: time 0.0002974/0.3033, allocations: 183.2 kB / 0.9809 GB, free: 1.926 MB / 0.6824 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.000156/0.3034, allocations: 29.89 kB / 0.9809 GB, free: 1.887 MB / 0.6824 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001216/0.3035, allocations: 67.78 kB / 0.981 GB, free: 1.82 MB / 0.6824 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001617/0.3037, allocations: 67.69 kB / 0.981 GB, free: 1.754 MB / 0.6824 GB
Notification: Performance of NFPackage.collectConstants: time 3.771e-05/0.3037, allocations: 16 kB / 0.9811 GB, free: 1.738 MB / 0.6824 GB
Notification: Performance of NFFlatten.collectFunctions: time 3.712e-05/0.3038, allocations: 16 kB / 0.9811 GB, free: 1.723 MB / 0.6824 GB
Notification: Performance of NFScalarize.scalarize: time 4.791e-05/0.3038, allocations: 35.84 kB / 0.9811 GB, free: 1.688 MB / 0.6824 GB
Notification: Performance of NFVerifyModel.verify: time 9.976e-05/0.3039, allocations: 59.73 kB / 0.9812 GB, free: 1.629 MB / 0.6824 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002679/0.3042, allocations: 167.4 kB / 0.9813 GB, free: 1.465 MB / 0.6824 GB
Notification: Performance of FrontEnd - DAE generated: time 3.978e-06/0.3042, allocations: 0 / 0.9813 GB, free: 1.465 MB / 0.6824 GB
Notification: Performance of FrontEnd: time 1.223e-06/0.3042, allocations: 0 / 0.9813 GB, free: 1.465 MB / 0.6824 GB
Notification: Performance of Transformations before backend: time 5.68e-06/0.3042, allocations: 0 / 0.9813 GB, free: 1.465 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 0.0009747/0.3052, allocations: 429.1 kB / 0.9817 GB, free: 1.004 MB / 0.6824 GB
Notification: Performance of prepare preOptimizeDAE: time 4.173e-05/0.3052, allocations: 18.05 kB / 0.9817 GB, free: 0.9883 MB / 0.6824 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.013e-05/0.3053, allocations: 20.78 kB / 0.9818 GB, free: 0.9688 MB / 0.6824 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002831/0.3056, allocations: 152.5 kB / 0.9819 GB, free: 0.7969 MB / 0.6824 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.808e-05/0.3056, allocations: 12.38 kB / 0.9819 GB, free: 0.7852 MB / 0.6824 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.596e-05/0.3056, allocations: 16.12 kB / 0.9819 GB, free: 0.7695 MB / 0.6824 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003837/0.306, allocations: 166.5 kB / 0.9821 GB, free: 0.5977 MB / 0.6824 GB
Notification: Performance of preOpt findStateOrder (simulation): time 2.176e-05/0.306, allocations: 3.953 kB / 0.9821 GB, free: 0.5938 MB / 0.6824 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.937e-05/0.3061, allocations: 12 kB / 0.9821 GB, free: 0.582 MB / 0.6824 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 5.26e-06/0.3061, allocations: 0 / 0.9821 GB, free: 0.582 MB / 0.6824 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003601/0.3064, allocations: 137.6 kB / 0.9822 GB, free: 452 kB / 0.6824 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0007671/0.3072, allocations: 360.1 kB / 0.9826 GB, free: 60 kB / 0.6824 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0004561/0.3076, allocations: 160.2 kB / 0.9827 GB, free: 15.89 MB / 0.698 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002017/0.3078, allocations: 98.52 kB / 0.9828 GB, free: 15.78 MB / 0.698 GB
Notification: Performance of preOpt evalFunc (simulation): time 2.018e-05/0.3079, allocations: 3.984 kB / 0.9828 GB, free: 15.78 MB / 0.698 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0004158/0.3083, allocations: 236.4 kB / 0.9831 GB, free: 15.52 MB / 0.698 GB
Notification: Performance of pre-optimization done (n=20): time 1.383e-06/0.3083, allocations: 0 / 0.9831 GB, free: 15.52 MB / 0.698 GB
Notification: Performance of matching and sorting (n=21): time 0.001672/0.31, allocations: 0.6794 MB / 0.9837 GB, free: 14.77 MB / 0.698 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001186/0.3101, allocations: 136.5 kB / 0.9839 GB, free: 14.61 MB / 0.698 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001871/0.3103, allocations: 152.4 kB / 0.984 GB, free: 14.45 MB / 0.698 GB
Notification: Performance of collectPreVariables (initialization): time 4.053e-05/0.3103, allocations: 33.7 kB / 0.984 GB, free: 14.41 MB / 0.698 GB
Notification: Performance of collectInitialEqns (initialization): time 0.0001213/0.3104, allocations: 112.4 kB / 0.9841 GB, free: 14.3 MB / 0.698 GB
Notification: Performance of collectInitialBindings (initialization): time 0.0002778/0.3107, allocations: 67.42 kB / 0.9842 GB, free: 14.23 MB / 0.698 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 9.77e-05/0.3108, allocations: 49.7 kB / 0.9843 GB, free: 14.18 MB / 0.698 GB
Notification: Performance of setup shared object (initialization): time 0.0002176/0.311, allocations: 334.8 kB / 0.9846 GB, free: 13.84 MB / 0.698 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002748/0.3113, allocations: 140.6 kB / 0.9847 GB, free: 13.69 MB / 0.698 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0003369/0.3116, allocations: 217.5 kB / 0.9849 GB, free: 13.44 MB / 0.698 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001076/0.3127, allocations: 0.5071 MB / 0.9854 GB, free: 12.87 MB / 0.698 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.338e-06/0.3127, allocations: 4 kB / 0.9854 GB, free: 12.87 MB / 0.698 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0007235/0.3134, allocations: 378.8 kB / 0.9858 GB, free: 12.47 MB / 0.698 GB
Notification: Performance of prepare postOptimizeDAE: time 6.811e-05/0.3135, allocations: 63.58 kB / 0.9858 GB, free: 12.39 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.627e-05/0.3135, allocations: 11.94 kB / 0.9858 GB, free: 12.38 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (initialization): time 2.01e-05/0.3135, allocations: 4 kB / 0.9859 GB, free: 12.38 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002315/0.3138, allocations: 47.91 kB / 0.9859 GB, free: 12.33 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.085e-06/0.3138, allocations: 0 / 0.9859 GB, free: 12.33 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001711/0.3139, allocations: 19.98 kB / 0.9859 GB, free: 12.31 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.426e-05/0.314, allocations: 12 kB / 0.9859 GB, free: 12.3 MB / 0.698 GB
Warning: Assuming fixed start value for the following 6 variables:
         central.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         periodicDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         periodicDose.variableDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" 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,$PRE.periodicDose.pulse.count,$PRE.periodicDose.pulse.T_start,$PRE.central.rising,periodicDose.pulse.count,periodicDose.pulse.T_start,central.rising,$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 0.0002726/0.3142, allocations: 187 kB / 0.9861 GB, free: 12.11 MB / 0.698 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.536e-05/0.3143, allocations: 15.91 kB / 0.9861 GB, free: 12.09 MB / 0.698 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 6.183e-05/0.3143, allocations: 21.22 kB / 0.9861 GB, free: 12.07 MB / 0.698 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.905e-06/0.3143, allocations: 0 / 0.9861 GB, free: 12.07 MB / 0.698 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 8.185e-06/0.3144, allocations: 4 kB / 0.9861 GB, free: 12.07 MB / 0.698 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.903e-06/0.3144, allocations: 7.984 kB / 0.9862 GB, free: 12.06 MB / 0.698 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0009263/0.3153, allocations: 0.5152 MB / 0.9867 GB, free: 11.5 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.214e-06/0.3153, allocations: 0 / 0.9867 GB, free: 11.5 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002137/0.3155, allocations: 39.91 kB / 0.9867 GB, free: 11.46 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (simulation): time 5.53e-06/0.3155, allocations: 4 kB / 0.9867 GB, free: 11.45 MB / 0.698 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.103e-05/0.3155, allocations: 4 kB / 0.9867 GB, free: 11.45 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 9.238e-06/0.3155, allocations: 7.938 kB / 0.9867 GB, free: 11.44 MB / 0.698 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.022e-06/0.3155, allocations: 0 / 0.9867 GB, free: 11.44 MB / 0.698 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.00091/0.3164, allocations: 495.2 kB / 0.9872 GB, free: 10.93 MB / 0.698 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.873e-05/0.3165, allocations: 11.91 kB / 0.9872 GB, free: 10.91 MB / 0.698 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 4.444e-05/0.3165, allocations: 12.05 kB / 0.9872 GB, free: 10.9 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001559/0.3167, allocations: 11.98 kB / 0.9872 GB, free: 10.89 MB / 0.698 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 9.374e-05/0.3168, allocations: 23.91 kB / 0.9872 GB, free: 10.87 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.128e-05/0.3168, allocations: 11.94 kB / 0.9872 GB, free: 10.86 MB / 0.698 GB
Notification: Performance of sorting global known variables: time 0.0001307/0.3169, allocations: 115.2 kB / 0.9874 GB, free: 10.74 MB / 0.698 GB
Notification: Performance of sort global known variables: time 6e-08/0.3169, allocations: 0 / 0.9874 GB, free: 10.74 MB / 0.698 GB
Notification: Performance of remove unused functions: time 0.0003219/0.3172, allocations: 48 kB / 0.9874 GB, free: 10.7 MB / 0.698 GB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 5 (central.C,central.AUC,elim.MExc,periodicDose.TotalCumulativeMass,periodicDose.variableDose.TotalCumulativeMass)
 * Number of discrete variables: 8 ($whenCondition1,$whenCondition2,$whenCondition3,central.Cmax,central.Cmin,central.rising,periodicDose.pulse.T_start,periodicDose.pulse.count)
 * Number of discrete states: 6 (periodicDose.pulse.count,central.Cmin,$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 0.0001386/0.3174, allocations: 110.2 kB / 0.9875 GB, free: 10.58 MB / 0.698 GB
Notification: Performance of simCode: created initialization part: time 0.0006725/0.3181, allocations: 383 kB / 0.9879 GB, free: 10.17 MB / 0.698 GB
Notification: Performance of simCode: created event and clocks part: time 4.649e-06/0.3181, allocations: 4 kB / 0.9879 GB, free: 10.16 MB / 0.698 GB
Notification: Performance of simCode: created simulation system equations: time 0.0003139/0.3184, allocations: 169.4 kB / 0.988 GB, free: 9.98 MB / 0.698 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004065/0.3188, allocations: 51.83 kB / 0.9881 GB, free: 9.93 MB / 0.698 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001746/0.3205, allocations: 0.6463 MB / 0.9887 GB, free: 9.25 MB / 0.698 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001327/0.3207, allocations: 111.4 kB / 0.9888 GB, free: 9.117 MB / 0.698 GB
Notification: Performance of simCode: alias equations: time 8.464e-05/0.3207, allocations: 17.47 kB / 0.9888 GB, free: 9.102 MB / 0.698 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 5.672e-05/0.3208, allocations: 19.44 kB / 0.9889 GB, free: 9.086 MB / 0.698 GB
Notification: Performance of SimCode: time 6.81e-07/0.3208, allocations: 4 kB / 0.9889 GB, free: 9.082 MB / 0.698 GB
Notification: Performance of Templates: time 0.4455/0.7663, allocations: 2.624 MB / 0.9914 GB, free: 26.19 MB / 0.698 GB
"
[Timeout remaining time 659]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModelPeriodic.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModelPeriodic.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModelPeriodic.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModelPeriodic.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModelPeriodic.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModelPeriodic -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PKOneCompartmentModelPeriodic.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 10.461470221867785]