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 0.001068/0.001068, allocations: 89.08 kB / 19.42 MB, free: 492 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 0.001072/0.001072, allocations: 169 kB / 22.72 MB, free: 1.828 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 0.9919/0.9919, allocations: 177.1 MB / 203.1 MB, free: 5.34 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 1.691/1.691, allocations: 273.5 MB / 0.5205 GB, free: 14.87 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.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 1.623e-06/1.623e-06, allocations: 1.469 kB / 0.6462 GB, free: 38.74 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.83e-05/1.992e-05, allocations: 4.281 kB / 0.6462 GB, free: 38.74 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_Digoxin): time 0.002395/0.002415, allocations: 2.071 MB / 0.6482 GB, free: 37.39 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.000612/0.003027, allocations: 0.5514 MB / 0.6488 GB, free: 37.03 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 5.683e-05/0.003084, allocations: 3.938 kB / 0.6488 GB, free: 37.03 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 8.123e-05/0.003165, allocations: 14.27 kB / 0.6488 GB, free: 37.02 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001029/0.003268, allocations: 48.56 kB / 0.6488 GB, free: 37 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001268/0.003394, allocations: 49.53 kB / 0.6489 GB, free: 36.97 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0001751/0.00357, allocations: 197.9 kB / 0.6491 GB, free: 36.92 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 9.34e-05/0.003663, allocations: 29.66 kB / 0.6491 GB, free: 36.89 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001052/0.003768, allocations: 98.78 kB / 0.6492 GB, free: 36.85 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 8.97e-05/0.003858, allocations: 61.58 kB / 0.6493 GB, free: 36.83 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 2.408e-05/0.003882, allocations: 15.06 kB / 0.6493 GB, free: 36.83 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 2.15e-05/0.003903, allocations: 15.94 kB / 0.6493 GB, free: 36.83 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 2.535e-05/0.003929, allocations: 23.16 kB / 0.6493 GB, free: 36.82 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 5.839e-05/0.003987, allocations: 61.94 kB / 0.6494 GB, free: 36.79 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0001392/0.004126, allocations: 114.2 kB / 0.6495 GB, free: 36.73 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 1.603e-06/0.004128, allocations: 0 / 0.6495 GB, free: 36.73 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 6.91e-07/0.004129, allocations: 0 / 0.6495 GB, free: 36.73 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 3.576e-06/0.004132, allocations: 1.719 kB / 0.6495 GB, free: 36.73 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 0.0004463/0.004579, allocations: 0.5183 MB / 0.65 GB, free: 36.24 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.015e-05/0.004609, allocations: 12.5 kB / 0.65 GB, free: 36.24 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 4.996e-05/0.004659, allocations: 29.61 kB / 0.65 GB, free: 36.23 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001318/0.004791, allocations: 167.9 kB / 0.6502 GB, free: 36.06 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.802e-05/0.004809, allocations: 6.25 kB / 0.6502 GB, free: 36.06 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 2.98e-05/0.004838, allocations: 11.72 kB / 0.6502 GB, free: 36.06 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.000173/0.005011, allocations: 143.6 kB / 0.6503 GB, free: 35.96 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.136e-05/0.005023, allocations: 11.53 kB / 0.6504 GB, free: 35.96 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.242e-05/0.005035, allocations: 6.219 kB / 0.6504 GB, free: 35.95 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.715e-06/0.005043, allocations: 1.469 kB / 0.6504 GB, free: 35.95 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 9.748e-05/0.00514, allocations: 79.84 kB / 0.6504 GB, free: 35.92 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0003752/0.005516, allocations: 405.2 kB / 0.6508 GB, free: 35.58 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001384/0.005654, allocations: 130.1 kB / 0.651 GB, free: 35.5 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 4.934e-05/0.005703, allocations: 60.05 kB / 0.651 GB, free: 35.45 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 8.276e-06/0.005712, allocations: 2.438 kB / 0.651 GB, free: 35.45 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001419/0.005853, allocations: 196.3 kB / 0.6512 GB, free: 35.29 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=20): time 1.543e-06/0.005855, allocations: 0 / 0.6512 GB, free: 35.29 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=21): time 0.0006252/0.00648, allocations: 0.5799 MB / 0.6518 GB, free: 34.88 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.795e-05/0.006508, allocations: 132.4 kB / 0.6519 GB, free: 34.72 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 7.91e-05/0.006587, allocations: 209.2 kB / 0.6521 GB, free: 34.54 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.345e-05/0.006601, allocations: 36.55 kB / 0.6521 GB, free: 34.5 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 3.773e-05/0.006638, allocations: 161.5 kB / 0.6523 GB, free: 34.35 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 3.136e-05/0.00667, allocations: 66.83 kB / 0.6523 GB, free: 34.29 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 4.859e-05/0.006718, allocations: 52.5 kB / 0.6524 GB, free: 34.26 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 4.433e-05/0.006763, allocations: 0.4968 MB / 0.6529 GB, free: 33.76 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 6.83e-05/0.006831, allocations: 103.3 kB / 0.653 GB, free: 33.68 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 8.987e-05/0.006921, allocations: 197 kB / 0.6532 GB, free: 33.47 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0001873/0.007108, allocations: 325 kB / 0.6535 GB, free: 33.18 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.305e-06/0.00711, allocations: 1.938 kB / 0.6535 GB, free: 33.18 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0002306/0.007341, allocations: 311 kB / 0.6538 GB, free: 32.98 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 2.384e-05/0.007365, allocations: 62.66 kB / 0.6538 GB, free: 32.91 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.25e-06/0.00737, allocations: 1.812 kB / 0.6538 GB, free: 32.91 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.518e-05/0.007385, allocations: 4.062 kB / 0.6538 GB, free: 32.91 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001361/0.007521, allocations: 48.86 kB / 0.6539 GB, free: 32.91 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 6.442e-06/0.007528, allocations: 7.094 kB / 0.6539 GB, free: 32.9 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 7.034e-05/0.007598, allocations: 17.08 kB / 0.6539 GB, free: 32.9 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.36e-05/0.007612, allocations: 16.06 kB / 0.6539 GB, free: 32.89 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 0.000116/0.007728, allocations: 223.8 kB / 0.6541 GB, free: 32.68 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 2.358e-05/0.007751, allocations: 24.31 kB / 0.6542 GB, free: 32.67 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.146e-05/0.007783, allocations: 20.05 kB / 0.6542 GB, free: 32.66 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.076e-06/0.007786, allocations: 6.141 kB / 0.6542 GB, free: 32.66 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.526e-06/0.007789, allocations: 0 / 0.6542 GB, free: 32.66 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.719e-06/0.007794, allocations: 7.562 kB / 0.6542 GB, free: 32.66 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003224/0.008117, allocations: 0.5163 MB / 0.6547 GB, free: 32.24 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.583e-06/0.008118, allocations: 0 / 0.6547 GB, free: 32.24 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001059/0.008224, allocations: 31.16 kB / 0.6547 GB, free: 32.23 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 3.236e-06/0.008227, allocations: 6.078 kB / 0.6547 GB, free: 32.23 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.359e-05/0.008241, allocations: 5.469 kB / 0.6547 GB, free: 32.23 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.555e-06/0.008243, allocations: 2.031 kB / 0.6547 GB, free: 32.23 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 9.62e-07/0.008244, allocations: 0 / 0.6547 GB, free: 32.23 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0002753/0.00852, allocations: 459.8 kB / 0.6552 GB, free: 31.9 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 1.728e-05/0.008537, allocations: 15.78 kB / 0.6552 GB, free: 31.89 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.257e-05/0.00856, allocations: 11.5 kB / 0.6552 GB, free: 31.88 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7e-05/0.00863, allocations: 11.34 kB / 0.6552 GB, free: 31.88 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.814e-05/0.008678, allocations: 14.27 kB / 0.6552 GB, free: 31.88 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.433e-05/0.008692, allocations: 12.58 kB / 0.6552 GB, free: 31.88 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 4.701e-05/0.008739, allocations: 149.2 kB / 0.6554 GB, free: 31.75 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 5e-08/0.008739, allocations: 4.5 kB / 0.6554 GB, free: 31.75 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0001955/0.008935, allocations: 45.38 kB / 0.6554 GB, free: 31.75 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 6.443e-05/0.008999, allocations: 111.1 kB / 0.6555 GB, free: 31.65 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0002137/0.009213, allocations: 326.3 kB / 0.6558 GB, free: 31.39 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.153e-06/0.009214, allocations: 0 / 0.6558 GB, free: 31.39 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 8.009e-05/0.009294, allocations: 152.7 kB / 0.656 GB, free: 31.27 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002388/0.009533, allocations: 34.8 kB / 0.656 GB, free: 31.27 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001196/0.01073, allocations: 0.5801 MB / 0.6566 GB, free: 30.9 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 4.038e-05/0.01077, allocations: 81.42 kB / 0.6567 GB, free: 30.82 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 5.773e-05/0.01083, allocations: 17.36 kB / 0.6567 GB, free: 30.82 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.559e-05/0.01087, allocations: 22.61 kB / 0.6567 GB, free: 30.81 MB / 0.5262 GB
Notification: Performance of SimCode: time 6.41e-07/0.01087, allocations: 0.5625 kB / 0.6567 GB, free: 30.81 MB / 0.5262 GB
Notification: Performance of Templates: time 0.003921/0.01479, allocations: 2.442 MB / 0.6591 GB, free: 30.61 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: 5.062098081689328]