Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin.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 0.002104/0.002104, allocations: 81.5 kB / 19.44 MB, free: 344 kB / 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 0.002068/0.002068, allocations: 173.2 kB / 22.76 MB, free: 1.664 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 1.66/1.66, allocations: 177.1 MB / 203.1 MB, free: 5.621 MB / 186.7 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 5.776/5.776, allocations: 274.5 MB / 0.5215 GB, free: 14.23 MB / 458.7 MB
"
[Timeout remaining time 173]
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_Digoxin,tolerance=1e-09,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin")
translateModel(Pharmacolibrary.Examples.PK_1C_Digoxin,tolerance=1e-09,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.974e-06/1.974e-06, allocations: 0 / 0.6472 GB, free: 39.15 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 3.239e-05/3.437e-05, allocations: 2.312 kB / 0.6472 GB, free: 39.15 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_Digoxin): time 0.003134/0.003169, allocations: 2.046 MB / 0.6492 GB, free: 37.8 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.0009274/0.004096, allocations: 0.5445 MB / 0.6497 GB, free: 37.44 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 8.177e-05/0.004178, allocations: 1.812 kB / 0.6497 GB, free: 37.44 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001238/0.004302, allocations: 21.56 kB / 0.6498 GB, free: 37.43 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001504/0.004452, allocations: 48.42 kB / 0.6498 GB, free: 37.41 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001926/0.004645, allocations: 45.77 kB / 0.6499 GB, free: 37.39 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002614/0.004906, allocations: 194.1 kB / 0.65 GB, free: 37.33 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001288/0.005035, allocations: 31.94 kB / 0.6501 GB, free: 37.3 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001484/0.005183, allocations: 100 kB / 0.6502 GB, free: 37.27 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001269/0.00531, allocations: 59.17 kB / 0.6502 GB, free: 37.25 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 3.906e-05/0.005349, allocations: 18 kB / 0.6502 GB, free: 37.24 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 3.416e-05/0.005383, allocations: 15.81 kB / 0.6503 GB, free: 37.24 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 3.95e-05/0.005423, allocations: 33.25 kB / 0.6503 GB, free: 37.22 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 9.259e-05/0.005516, allocations: 56.27 kB / 0.6503 GB, free: 37.2 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002337/0.005749, allocations: 170.2 kB / 0.6505 GB, free: 37.12 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 5.531e-06/0.005755, allocations: 2.156 kB / 0.6505 GB, free: 37.12 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 6.91e-07/0.005755, allocations: 0 / 0.6505 GB, free: 37.12 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 6.482e-06/0.005762, allocations: 1.281 kB / 0.6505 GB, free: 37.12 MB / 0.5262 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 0.0007193/0.006481, allocations: 0.5206 MB / 0.651 GB, free: 36.63 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.345e-05/0.006515, allocations: 9.781 kB / 0.651 GB, free: 36.63 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 7.222e-05/0.006587, allocations: 28.41 kB / 0.6511 GB, free: 36.62 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0009835/0.00757, allocations: 174.5 kB / 0.6512 GB, free: 36.46 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.905e-05/0.007589, allocations: 10.25 kB / 0.6512 GB, free: 36.46 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0003843/0.007974, allocations: 19.11 kB / 0.6512 GB, free: 36.45 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0008392/0.008813, allocations: 149.5 kB / 0.6514 GB, free: 36.36 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 0.0003159/0.009129, allocations: 11.83 kB / 0.6514 GB, free: 36.36 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.821e-05/0.009147, allocations: 5.312 kB / 0.6514 GB, free: 36.35 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.923e-06/0.009154, allocations: 3.875 kB / 0.6514 GB, free: 36.35 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.000673/0.009827, allocations: 115.3 kB / 0.6515 GB, free: 36.3 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001497/0.01132, allocations: 432.4 kB / 0.6519 GB, free: 35.95 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0003263/0.01165, allocations: 175.6 kB / 0.6521 GB, free: 35.84 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001299/0.01178, allocations: 87.59 kB / 0.6522 GB, free: 35.79 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 2.031e-05/0.0118, allocations: 4.719 kB / 0.6522 GB, free: 35.79 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.000574/0.01237, allocations: 230.1 kB / 0.6524 GB, free: 35.61 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=20): time 1.983e-06/0.01238, allocations: 0 / 0.6524 GB, free: 35.61 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=21): time 0.002937/0.01531, allocations: 0.6661 MB / 0.6531 GB, free: 35.16 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.938e-05/0.01537, allocations: 133.6 kB / 0.6532 GB, free: 35 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001473/0.01552, allocations: 226.4 kB / 0.6534 GB, free: 34.81 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 2.048e-05/0.01554, allocations: 33.92 kB / 0.6534 GB, free: 34.78 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 6.129e-05/0.0156, allocations: 164.5 kB / 0.6536 GB, free: 34.62 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 5.329e-05/0.01566, allocations: 79.94 kB / 0.6537 GB, free: 34.56 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 7.62e-05/0.01573, allocations: 57.45 kB / 0.6537 GB, free: 34.52 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 9.86e-05/0.01583, allocations: 0.5088 MB / 0.6542 GB, free: 34.02 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.000166/0.016, allocations: 141.8 kB / 0.6544 GB, free: 33.92 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.000195/0.01619, allocations: 229.9 kB / 0.6546 GB, free: 33.7 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0005327/0.01672, allocations: 406 kB / 0.655 GB, free: 33.38 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.346e-06/0.01673, allocations: 2.125 kB / 0.655 GB, free: 33.38 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0004931/0.01722, allocations: 373.7 kB / 0.6553 GB, free: 33.14 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 5.059e-05/0.01727, allocations: 66.81 kB / 0.6554 GB, free: 33.07 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.906e-06/0.01728, allocations: 2.625 kB / 0.6554 GB, free: 33.07 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 0.000835/0.01811, allocations: 2.312 kB / 0.6554 GB, free: 33.07 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002226/0.01834, allocations: 51.03 kB / 0.6554 GB, free: 33.07 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.061e-05/0.01835, allocations: 15.75 kB / 0.6555 GB, free: 33.06 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001383/0.01849, allocations: 15.02 kB / 0.6555 GB, free: 33.05 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.1e-05/0.01851, allocations: 6.906 kB / 0.6555 GB, free: 33.05 MB / 0.5262 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 0.0006535/0.01916, allocations: 236.6 kB / 0.6557 GB, free: 32.84 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 4.317e-05/0.0192, allocations: 25.66 kB / 0.6557 GB, free: 32.83 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 7.124e-05/0.01928, allocations: 22.12 kB / 0.6557 GB, free: 32.82 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.867e-06/0.01928, allocations: 2.375 kB / 0.6557 GB, free: 32.82 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.281e-06/0.01929, allocations: 0 / 0.6557 GB, free: 32.82 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.292e-06/0.01929, allocations: 9.453 kB / 0.6558 GB, free: 32.81 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.000749/0.02004, allocations: 0.5668 MB / 0.6563 GB, free: 32.37 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.914e-06/0.02004, allocations: 0.5625 kB / 0.6563 GB, free: 32.37 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002018/0.02024, allocations: 39.11 kB / 0.6563 GB, free: 32.36 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 4.759e-06/0.02025, allocations: 1.094 kB / 0.6563 GB, free: 32.36 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.136e-05/0.02027, allocations: 5.469 kB / 0.6564 GB, free: 32.36 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.485e-06/0.02027, allocations: 0.5 kB / 0.6564 GB, free: 32.36 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.062e-06/0.02027, allocations: 0.5625 kB / 0.6564 GB, free: 32.36 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.000737/0.02101, allocations: 0.5198 MB / 0.6569 GB, free: 32 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 3.126e-05/0.02104, allocations: 23.44 kB / 0.6569 GB, free: 31.99 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.859e-05/0.02108, allocations: 10.47 kB / 0.6569 GB, free: 31.98 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001496/0.02123, allocations: 11.08 kB / 0.6569 GB, free: 31.98 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0003615/0.02159, allocations: 15.73 kB / 0.6569 GB, free: 31.98 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.122e-05/0.02161, allocations: 8.719 kB / 0.6569 GB, free: 31.98 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 9.541e-05/0.02171, allocations: 168.3 kB / 0.6571 GB, free: 31.84 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 5e-08/0.02171, allocations: 0 / 0.6571 GB, free: 31.84 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0002889/0.022, allocations: 48.02 kB / 0.6571 GB, free: 31.84 MB / 0.5262 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 0.001137/0.02313, allocations: 101.5 kB / 0.6572 GB, free: 31.75 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0009402/0.02407, allocations: 393.6 kB / 0.6576 GB, free: 31.46 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 2.775e-06/0.02408, allocations: 1.375 kB / 0.6576 GB, free: 31.46 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.000217/0.02429, allocations: 183.9 kB / 0.6578 GB, free: 31.33 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004312/0.02473, allocations: 44.33 kB / 0.6578 GB, free: 31.32 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001049/0.02577, allocations: 0.5546 MB / 0.6584 GB, free: 30.95 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001009/0.02587, allocations: 113.9 kB / 0.6585 GB, free: 30.86 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 7.462e-05/0.02595, allocations: 18.39 kB / 0.6585 GB, free: 30.86 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 5.386e-05/0.026, allocations: 18.38 kB / 0.6585 GB, free: 30.86 MB / 0.5262 GB
Notification: Performance of SimCode: time 7.82e-07/0.026, allocations: 0 / 0.6585 GB, free: 30.86 MB / 0.5262 GB
Notification: Performance of Templates: time 0.01236/0.03836, allocations: 2.443 MB / 0.6609 GB, free: 30.66 MB / 0.5262 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Digoxin.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 11.103309442987666]