Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.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 0.002253/0.002253, allocations: 84.44 kB / 19.93 MB, free: 4.602 MB / 18.57 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 0.001992/0.001992, allocations: 173.9 kB / 23.21 MB, free: 1.32 MB / 18.57 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 1.018/1.018, allocations: 177.1 MB / 203.5 MB, free: 5.75 MB / 186.7 MB
"
[Timeout remaining time 179]
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 1.627/1.627, allocations: 273.5 MB / 0.5209 GB, free: 14.93 MB / 458.7 MB
"
[Timeout remaining time 178]
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.DevModels.PKTwoCompartmentModel,tolerance=1e-06,outputFormat="empty",numberOfIntervals=500,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel")
translateModel(Pharmacolibrary.DevModels.PKTwoCompartmentModel,tolerance=1e-06,outputFormat="empty",numberOfIntervals=500,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 2.625e-06/2.625e-06, allocations: 4 kB / 0.7558 GB, free: 10.69 MB / 0.5887 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.314e-05/2.577e-05, allocations: 2.281 kB / 0.7558 GB, free: 10.69 MB / 0.5887 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.PKTwoCompartmentModel): time 0.0025/0.002526, allocations: 2.25 MB / 0.758 GB, free: 8.453 MB / 0.5887 GB
Notification: Performance of NFInst.instExpressions: time 0.0008186/0.003345, allocations: 0.5923 MB / 0.7585 GB, free: 7.863 MB / 0.5887 GB
Notification: Performance of NFInst.updateImplicitVariability: time 8.382e-05/0.003428, allocations: 4 kB / 0.7585 GB, free: 7.859 MB / 0.5887 GB
Notification: Performance of NFTyping.typeComponents: time 6.32e-05/0.003492, allocations: 23.72 kB / 0.7586 GB, free: 7.836 MB / 0.5887 GB
Notification: Performance of NFTyping.typeBindings: time 0.0002078/0.003699, allocations: 85.95 kB / 0.7586 GB, free: 7.777 MB / 0.5887 GB
Notification: Performance of NFTyping.typeClassSections: time 0.000193/0.003892, allocations: 67.84 kB / 0.7587 GB, free: 7.711 MB / 0.5887 GB
Notification: Performance of NFFlatten.flatten: time 0.0002465/0.004139, allocations: 292.4 kB / 0.759 GB, free: 7.438 MB / 0.5887 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001542/0.004293, allocations: 48.73 kB / 0.759 GB, free: 7.391 MB / 0.5887 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.000174/0.004467, allocations: 151.7 kB / 0.7592 GB, free: 7.242 MB / 0.5887 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001246/0.004592, allocations: 91.69 kB / 0.7593 GB, free: 7.152 MB / 0.5887 GB
Notification: Performance of NFPackage.collectConstants: time 3.739e-05/0.004629, allocations: 27.94 kB / 0.7593 GB, free: 7.125 MB / 0.5887 GB
Notification: Performance of NFFlatten.collectFunctions: time 2.814e-05/0.004657, allocations: 20 kB / 0.7593 GB, free: 7.105 MB / 0.5887 GB
Notification: Performance of NFScalarize.scalarize: time 4.414e-05/0.004701, allocations: 47.83 kB / 0.7594 GB, free: 7.059 MB / 0.5887 GB
Notification: Performance of NFVerifyModel.verify: time 8.464e-05/0.004786, allocations: 83.83 kB / 0.7594 GB, free: 6.977 MB / 0.5887 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002398/0.005026, allocations: 251.3 kB / 0.7597 GB, free: 6.73 MB / 0.5887 GB
Notification: Performance of FrontEnd - DAE generated: time 1.874e-06/0.005028, allocations: 0 / 0.7597 GB, free: 6.73 MB / 0.5887 GB
Notification: Performance of FrontEnd: time 1.041e-06/0.005029, allocations: 0 / 0.7597 GB, free: 6.73 MB / 0.5887 GB
Notification: Performance of Transformations before backend: time 4.799e-06/0.005033, allocations: 0 / 0.7597 GB, free: 6.73 MB / 0.5887 GB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 45
 * Number of variables: 45
Notification: Performance of Generate backend data structure: time 0.0007298/0.005763, allocations: 0.5224 MB / 0.7602 GB, free: 6.16 MB / 0.5887 GB
Notification: Performance of prepare preOptimizeDAE: time 4.143e-05/0.005805, allocations: 8.031 kB / 0.7602 GB, free: 6.152 MB / 0.5887 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 5.758e-05/0.005862, allocations: 28.78 kB / 0.7602 GB, free: 6.125 MB / 0.5887 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001158/0.005978, allocations: 153.2 kB / 0.7604 GB, free: 5.953 MB / 0.5887 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.926e-05/0.005997, allocations: 12.38 kB / 0.7604 GB, free: 5.941 MB / 0.5887 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.159e-05/0.006039, allocations: 28.31 kB / 0.7604 GB, free: 5.914 MB / 0.5887 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003176/0.006357, allocations: 246.4 kB / 0.7606 GB, free: 5.652 MB / 0.5887 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.472e-05/0.006371, allocations: 4 kB / 0.7607 GB, free: 5.648 MB / 0.5887 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.677e-05/0.006388, allocations: 4 kB / 0.7607 GB, free: 5.645 MB / 0.5887 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.835e-06/0.006396, allocations: 8 kB / 0.7607 GB, free: 5.637 MB / 0.5887 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002695/0.006665, allocations: 227.6 kB / 0.7609 GB, free: 5.402 MB / 0.5887 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0006761/0.007341, allocations: 476.5 kB / 0.7613 GB, free: 4.906 MB / 0.5887 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0003176/0.007659, allocations: 250.7 kB / 0.7616 GB, free: 4.641 MB / 0.5887 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001395/0.007798, allocations: 140.2 kB / 0.7617 GB, free: 4.488 MB / 0.5887 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.329e-05/0.007812, allocations: 4 kB / 0.7617 GB, free: 4.484 MB / 0.5887 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0003201/0.008132, allocations: 349.4 kB / 0.762 GB, free: 4.094 MB / 0.5887 GB
Notification: Performance of pre-optimization done (n=31): time 2.134e-06/0.008134, allocations: 3.938 kB / 0.762 GB, free: 4.09 MB / 0.5887 GB
Notification: Performance of matching and sorting (n=33): time 0.001322/0.009456, allocations: 1.047 MB / 0.7631 GB, free: 2.949 MB / 0.5887 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 8.801e-05/0.009544, allocations: 217.6 kB / 0.7633 GB, free: 2.688 MB / 0.5887 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001206/0.009665, allocations: 173.1 kB / 0.7634 GB, free: 2.512 MB / 0.5887 GB
Notification: Performance of collectPreVariables (initialization): time 2.192e-05/0.009687, allocations: 37.69 kB / 0.7635 GB, free: 2.469 MB / 0.5887 GB
Notification: Performance of collectInitialEqns (initialization): time 6.755e-05/0.009754, allocations: 128.9 kB / 0.7636 GB, free: 2.34 MB / 0.5887 GB
Notification: Performance of collectInitialBindings (initialization): time 6.424e-05/0.009818, allocations: 111.1 kB / 0.7637 GB, free: 2.23 MB / 0.5887 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 7.185e-05/0.00989, allocations: 61.69 kB / 0.7638 GB, free: 2.164 MB / 0.5887 GB
Notification: Performance of setup shared object (initialization): time 0.0001082/0.009998, allocations: 334.8 kB / 0.7641 GB, free: 1.828 MB / 0.5887 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001833/0.01018, allocations: 195 kB / 0.7643 GB, free: 1.617 MB / 0.5887 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002031/0.01038, allocations: 279 kB / 0.7645 GB, free: 1.289 MB / 0.5887 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0007637/0.01115, allocations: 0.7441 MB / 0.7653 GB, free: 464 kB / 0.5887 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.063e-06/0.01115, allocations: 0 / 0.7653 GB, free: 464 kB / 0.5887 GB
Notification: Performance of matching and sorting (n=48) (initialization): time 0.0004836/0.01163, allocations: 0.524 MB / 0.7658 GB, free: 15.89 MB / 0.6043 GB
Notification: Performance of prepare postOptimizeDAE: time 4.742e-05/0.01168, allocations: 89.09 kB / 0.7659 GB, free: 15.78 MB / 0.6043 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.142e-06/0.01169, allocations: 4 kB / 0.7659 GB, free: 15.78 MB / 0.6043 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.521e-05/0.0117, allocations: 4 kB / 0.7659 GB, free: 15.77 MB / 0.6043 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001701/0.01187, allocations: 67.91 kB / 0.7659 GB, free: 15.71 MB / 0.6043 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 9.719e-06/0.01188, allocations: 7.984 kB / 0.7659 GB, free: 15.7 MB / 0.6043 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.552e-05/0.01198, allocations: 15.98 kB / 0.766 GB, free: 15.68 MB / 0.6043 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.719e-05/0.012, allocations: 16 kB / 0.766 GB, free: 15.67 MB / 0.6043 GB
Warning: Assuming fixed start value for the following 10 variables:
         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
         intestine.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         blood.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         intestine.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         intestine.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         blood.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         blood.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         blood.rising:DISCRETE(fixed = true protected = true )  type: Boolean
         intestine.rising:DISCRETE(fixed = true protected = true )  type: Boolean
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 9
 * Number of states: 0 ()
 * Number of discrete variables: 21 ($PRE.intestine.Cmin,intestine.Cmin,$PRE.intestine.Cmax,intestine.Cmax,$PRE.blood.Cmin,blood.Cmin,$PRE.blood.Cmax,blood.Cmax,$PRE.blood.rising,$PRE.intestine.rising,$PRE.periodicDose.pulse.count,$PRE.periodicDose.pulse.T_start,blood.rising,intestine.rising,periodicDose.pulse.count,periodicDose.pulse.T_start,$whenCondition5,$whenCondition4,$whenCondition3,$whenCondition2,$whenCondition1)
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (45):
 * Single equations (assignments): 42
 * Array equations: 0
 * Algorithm blocks: 3
 * 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 0.0002092/0.0122, allocations: 253 kB / 0.7662 GB, free: 15.4 MB / 0.6043 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 2.259e-05/0.01223, allocations: 19.86 kB / 0.7662 GB, free: 15.38 MB / 0.6043 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 4.374e-05/0.01227, allocations: 33.89 kB / 0.7663 GB, free: 15.35 MB / 0.6043 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.046e-06/0.01227, allocations: 4 kB / 0.7663 GB, free: 15.34 MB / 0.6043 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.54e-06/0.01228, allocations: 0 / 0.7663 GB, free: 15.34 MB / 0.6043 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.348e-06/0.01228, allocations: 0 / 0.7663 GB, free: 15.34 MB / 0.6043 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.000673/0.01296, allocations: 0.7291 MB / 0.767 GB, free: 14.55 MB / 0.6043 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.653e-06/0.01296, allocations: 4 kB / 0.767 GB, free: 14.55 MB / 0.6043 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002947/0.01325, allocations: 59.89 kB / 0.767 GB, free: 14.49 MB / 0.6043 GB
Notification: Performance of postOpt tearingSystem (simulation): time 7.093e-06/0.01326, allocations: 4 kB / 0.767 GB, free: 14.49 MB / 0.6043 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.961e-05/0.0133, allocations: 8 kB / 0.7671 GB, free: 14.48 MB / 0.6043 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.236e-06/0.0133, allocations: 0 / 0.7671 GB, free: 14.48 MB / 0.6043 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.733e-06/0.0133, allocations: 0 / 0.7671 GB, free: 14.48 MB / 0.6043 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0009707/0.01428, allocations: 0.7119 MB / 0.7677 GB, free: 13.71 MB / 0.6043 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.181e-05/0.0143, allocations: 11.91 kB / 0.7678 GB, free: 13.7 MB / 0.6043 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.035e-05/0.01433, allocations: 12.06 kB / 0.7678 GB, free: 13.69 MB / 0.6043 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 8.73e-05/0.01442, allocations: 23.92 kB / 0.7678 GB, free: 13.67 MB / 0.6043 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 8.059e-05/0.0145, allocations: 35.55 kB / 0.7678 GB, free: 13.64 MB / 0.6043 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.537e-05/0.01451, allocations: 8 kB / 0.7678 GB, free: 13.63 MB / 0.6043 GB
Notification: Performance of sorting global known variables: time 6.897e-05/0.01458, allocations: 126.3 kB / 0.768 GB, free: 13.51 MB / 0.6043 GB
Notification: Performance of sort global known variables: time 1.3e-07/0.01458, allocations: 0 / 0.768 GB, free: 13.51 MB / 0.6043 GB
Notification: Performance of remove unused functions: time 0.0002079/0.01479, allocations: 75.94 kB / 0.768 GB, free: 13.43 MB / 0.6043 GB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 6 (periodicDose.TotalCumulativeMass,periodicDose.variableDose.TotalCumulativeMass,intestine.C,intestine.AUC,blood.C,blood.AUC)
 * Number of discrete variables: 13 ($whenCondition1,$whenCondition2,$whenCondition3,$whenCondition4,$whenCondition5,periodicDose.pulse.T_start,periodicDose.pulse.count,intestine.Cmax,intestine.Cmin,intestine.rising,blood.Cmax,blood.Cmin,blood.rising)
 * Number of discrete states: 11 (periodicDose.pulse.count,blood.Cmin,$whenCondition3,blood.Cmax,$whenCondition2,blood.rising,intestine.Cmin,$whenCondition5,intestine.Cmax,$whenCondition4,intestine.rising)
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (27):
 * Single equations (assignments): 23
 * Array equations: 0
 * Algorithm blocks: 2
 * 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 0.0001033/0.01489, allocations: 115.2 kB / 0.7681 GB, free: 13.31 MB / 0.6043 GB
Notification: Performance of simCode: created initialization part: time 0.0004897/0.01538, allocations: 0.5492 MB / 0.7687 GB, free: 12.7 MB / 0.6043 GB
Notification: Performance of simCode: created event and clocks part: time 2.295e-06/0.01538, allocations: 0 / 0.7687 GB, free: 12.7 MB / 0.6043 GB
Notification: Performance of simCode: created simulation system equations: time 0.0002143/0.0156, allocations: 297.4 kB / 0.769 GB, free: 12.37 MB / 0.6043 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002909/0.01589, allocations: 70.34 kB / 0.769 GB, free: 12.3 MB / 0.6043 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0009311/0.01682, allocations: 0.7363 MB / 0.7697 GB, free: 11.54 MB / 0.6043 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 9.561e-05/0.01692, allocations: 138.7 kB / 0.7699 GB, free: 11.38 MB / 0.6043 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 5.984e-05/0.01698, allocations: 24.5 kB / 0.7699 GB, free: 11.36 MB / 0.6043 GB
Notification: Performance of SimCode: time 8.82e-07/0.01698, allocations: 0 / 0.7699 GB, free: 11.36 MB / 0.6043 GB
Notification: Performance of Templates: time 0.003647/0.02062, allocations: 3.152 MB / 0.773 GB, free: 8.27 MB / 0.6043 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.sim & ./Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel > Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 6.9233474330976605]