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 0.0009544/0.0009544, allocations: 93.06 kB / 19.65 MB, free: 280 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 0.001135/0.001135, allocations: 169 kB / 23.02 MB, free: 1.551 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 0.9512/0.9512, allocations: 177.1 MB / 203.4 MB, free: 5.652 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 1.62/1.62, allocations: 273.5 MB / 0.5209 GB, free: 14.79 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.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: Performance of FrontEnd - loaded program: time 1.202e-06/1.202e-06, allocations: 0 / 0.6469 GB, free: 38.66 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.21e-05/2.33e-05, allocations: 2.312 kB / 0.6469 GB, free: 38.66 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKOneCompartmentModel): time 0.002264/0.002287, allocations: 2.064 MB / 0.649 GB, free: 37.32 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.0007519/0.003039, allocations: 0.5443 MB / 0.6495 GB, free: 36.96 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 6.752e-05/0.003107, allocations: 1.125 kB / 0.6495 GB, free: 36.96 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001189/0.003226, allocations: 21.36 kB / 0.6495 GB, free: 36.95 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001653/0.003391, allocations: 48.53 kB / 0.6496 GB, free: 36.93 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001715/0.003562, allocations: 46.25 kB / 0.6496 GB, free: 36.91 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002214/0.003784, allocations: 196.2 kB / 0.6498 GB, free: 36.85 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001228/0.003907, allocations: 27.11 kB / 0.6498 GB, free: 36.83 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.000144/0.004051, allocations: 108.3 kB / 0.6499 GB, free: 36.78 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001115/0.004162, allocations: 56.94 kB / 0.65 GB, free: 36.76 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 3.14e-05/0.004193, allocations: 17.19 kB / 0.65 GB, free: 36.76 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 2.404e-05/0.004218, allocations: 15.34 kB / 0.65 GB, free: 36.76 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 3.304e-05/0.004251, allocations: 34.23 kB / 0.65 GB, free: 36.74 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 7.095e-05/0.004322, allocations: 65.19 kB / 0.6501 GB, free: 36.71 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0001778/0.004499, allocations: 108 kB / 0.6502 GB, free: 36.66 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 3.376e-06/0.004503, allocations: 1.594 kB / 0.6502 GB, free: 36.66 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 1.413e-06/0.004504, allocations: 1.688 kB / 0.6502 GB, free: 36.66 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 4.879e-06/0.004509, allocations: 0 / 0.6502 GB, free: 36.66 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 0.0005816/0.005091, allocations: 0.5231 MB / 0.6507 GB, free: 36.16 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 4.096e-05/0.005132, allocations: 9.375 kB / 0.6507 GB, free: 36.16 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.135e-05/0.005193, allocations: 25.19 kB / 0.6508 GB, free: 36.16 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002018/0.005395, allocations: 170.8 kB / 0.6509 GB, free: 36 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.363e-05/0.005408, allocations: 10.12 kB / 0.6509 GB, free: 35.99 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.336e-05/0.005442, allocations: 15.11 kB / 0.6509 GB, free: 35.99 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0001855/0.005627, allocations: 139.4 kB / 0.6511 GB, free: 35.89 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.393e-05/0.005641, allocations: 16.48 kB / 0.6511 GB, free: 35.88 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.396e-05/0.005655, allocations: 5.719 kB / 0.6511 GB, free: 35.88 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.564e-06/0.005663, allocations: 2.344 kB / 0.6511 GB, free: 35.88 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001085/0.005771, allocations: 82.64 kB / 0.6512 GB, free: 35.84 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0005816/0.006353, allocations: 397.3 kB / 0.6516 GB, free: 35.51 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001811/0.006534, allocations: 120.8 kB / 0.6517 GB, free: 35.43 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 6.11e-05/0.006595, allocations: 64.52 kB / 0.6517 GB, free: 35.38 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.086e-05/0.006606, allocations: 2.438 kB / 0.6517 GB, free: 35.38 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001827/0.006788, allocations: 206.5 kB / 0.6519 GB, free: 35.21 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=20): time 1.703e-06/0.00679, allocations: 0 / 0.6519 GB, free: 35.21 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=21): time 0.0007842/0.007574, allocations: 0.5756 MB / 0.6525 GB, free: 34.8 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.946e-05/0.007614, allocations: 137.2 kB / 0.6526 GB, free: 34.64 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 9.483e-05/0.007709, allocations: 202.7 kB / 0.6528 GB, free: 34.46 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.456e-05/0.007723, allocations: 33.11 kB / 0.6528 GB, free: 34.43 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 4.969e-05/0.007773, allocations: 158.9 kB / 0.653 GB, free: 34.28 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 3.675e-05/0.00781, allocations: 72.62 kB / 0.6531 GB, free: 34.22 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 6.308e-05/0.007873, allocations: 52.38 kB / 0.6531 GB, free: 34.18 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 6.795e-05/0.007941, allocations: 0.4994 MB / 0.6536 GB, free: 33.68 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 8.124e-05/0.008022, allocations: 103.7 kB / 0.6537 GB, free: 33.6 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001015/0.008123, allocations: 197.2 kB / 0.6539 GB, free: 33.4 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002145/0.008338, allocations: 321.6 kB / 0.6542 GB, free: 33.11 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.444e-06/0.00834, allocations: 2.875 kB / 0.6542 GB, free: 33.11 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0002619/0.008602, allocations: 310.9 kB / 0.6545 GB, free: 32.9 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 3.359e-05/0.008636, allocations: 66.72 kB / 0.6546 GB, free: 32.84 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.913e-06/0.008643, allocations: 3.844 kB / 0.6546 GB, free: 32.84 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.961e-05/0.008662, allocations: 8.797 kB / 0.6546 GB, free: 32.83 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001654/0.008828, allocations: 49.16 kB / 0.6546 GB, free: 32.83 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.065e-05/0.008838, allocations: 6.656 kB / 0.6546 GB, free: 32.82 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 8.099e-05/0.008919, allocations: 16.45 kB / 0.6546 GB, free: 32.82 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.23e-05/0.008942, allocations: 16.11 kB / 0.6547 GB, free: 32.81 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 0.0001618/0.009103, allocations: 218.9 kB / 0.6549 GB, free: 32.61 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.223e-05/0.009136, allocations: 25.77 kB / 0.6549 GB, free: 32.6 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.003e-05/0.009166, allocations: 21.22 kB / 0.6549 GB, free: 32.58 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.528e-06/0.00917, allocations: 1.688 kB / 0.6549 GB, free: 32.58 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.169e-06/0.009175, allocations: 0.5 kB / 0.6549 GB, free: 32.58 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.009e-06/0.00918, allocations: 4.5 kB / 0.6549 GB, free: 32.58 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003881/0.009568, allocations: 0.5169 MB / 0.6554 GB, free: 32.16 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.756e-06/0.009571, allocations: 2.375 kB / 0.6554 GB, free: 32.16 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001124/0.009684, allocations: 33.95 kB / 0.6555 GB, free: 32.16 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 1.964e-06/0.009686, allocations: 0.5 kB / 0.6555 GB, free: 32.16 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.413e-05/0.0097, allocations: 10.47 kB / 0.6555 GB, free: 32.15 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.985e-06/0.009703, allocations: 2.25 kB / 0.6555 GB, free: 32.15 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.062e-06/0.009704, allocations: 3.969 kB / 0.6555 GB, free: 32.15 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.000317/0.01002, allocations: 454.6 kB / 0.6559 GB, free: 31.82 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.001e-05/0.01004, allocations: 21.81 kB / 0.6559 GB, free: 31.81 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.632e-05/0.01007, allocations: 6.25 kB / 0.6559 GB, free: 31.8 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.424e-05/0.01014, allocations: 9.719 kB / 0.6559 GB, free: 31.8 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.223e-05/0.0102, allocations: 16.44 kB / 0.656 GB, free: 31.8 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.531e-05/0.01022, allocations: 8.562 kB / 0.656 GB, free: 31.8 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 5.857e-05/0.01028, allocations: 150.9 kB / 0.6561 GB, free: 31.68 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 5e-08/0.01028, allocations: 0 / 0.6561 GB, free: 31.68 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.000219/0.0105, allocations: 44.41 kB / 0.6562 GB, free: 31.67 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 9.822e-05/0.01059, allocations: 118.9 kB / 0.6563 GB, free: 31.58 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0003445/0.01094, allocations: 321.8 kB / 0.6566 GB, free: 31.32 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.933e-06/0.01094, allocations: 0.5625 kB / 0.6566 GB, free: 31.32 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001274/0.01107, allocations: 157.4 kB / 0.6567 GB, free: 31.2 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002842/0.01135, allocations: 43.75 kB / 0.6568 GB, free: 31.19 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001398/0.01275, allocations: 0.5815 MB / 0.6573 GB, free: 30.82 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 4.181e-05/0.01279, allocations: 81.02 kB / 0.6574 GB, free: 30.74 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 5.638e-05/0.01285, allocations: 16.33 kB / 0.6574 GB, free: 30.73 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.406e-05/0.01289, allocations: 26.8 kB / 0.6575 GB, free: 30.72 MB / 0.5262 GB
Notification: Performance of SimCode: time 7.52e-07/0.01289, allocations: 0 / 0.6575 GB, free: 30.72 MB / 0.5262 GB
Notification: Performance of Templates: time 0.004356/0.01725, allocations: 2.447 MB / 0.6598 GB, free: 30.52 MB / 0.5262 GB
"
[Timeout remaining time 660]
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: 4.968696030788124]