Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.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 0.001038/0.001038, allocations: 92.2 kB / 20.19 MB, free: 4.355 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 0.001117/0.001117, allocations: 169 kB / 23.49 MB, free: 1.059 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 1/1, allocations: 177.1 MB / 203.8 MB, free: 5.629 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 1.517/1.517, allocations: 273.5 MB / 0.5213 GB, free: 14.8 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_LithiumCarbonate,tolerance=1e-09,outputFormat="empty",numberOfIntervals=864000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate")
translateModel(Pharmacolibrary.Examples.PK_1C_LithiumCarbonate,tolerance=1e-09,outputFormat="empty",numberOfIntervals=864000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.553e-06/1.553e-06, allocations: 0 / 0.6462 GB, free: 39.01 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.683e-05/1.839e-05, allocations: 5.266 kB / 0.6462 GB, free: 39 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_LithiumCarbonate): time 0.001956/0.001975, allocations: 2.114 MB / 0.6483 GB, free: 37.63 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.000662/0.002637, allocations: 0.5511 MB / 0.6488 GB, free: 37.27 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 6.728e-05/0.002704, allocations: 4.062 kB / 0.6488 GB, free: 37.27 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 9.951e-05/0.002803, allocations: 18.38 kB / 0.6488 GB, free: 37.25 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001191/0.002922, allocations: 58.3 kB / 0.6489 GB, free: 37.23 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001403/0.003063, allocations: 49.64 kB / 0.6489 GB, free: 37.2 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002062/0.003269, allocations: 198.5 kB / 0.6491 GB, free: 37.14 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001102/0.003379, allocations: 34.8 kB / 0.6492 GB, free: 37.12 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001086/0.003488, allocations: 104 kB / 0.6493 GB, free: 37.08 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001013/0.003589, allocations: 68.25 kB / 0.6493 GB, free: 37.05 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 2.68e-05/0.003616, allocations: 15.28 kB / 0.6493 GB, free: 37.05 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 2.183e-05/0.003637, allocations: 16.09 kB / 0.6494 GB, free: 37.05 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 2.866e-05/0.003666, allocations: 27 kB / 0.6494 GB, free: 37.04 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 6.483e-05/0.003731, allocations: 59.75 kB / 0.6494 GB, free: 37.01 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0001598/0.003891, allocations: 124.4 kB / 0.6496 GB, free: 36.95 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 1.773e-06/0.003892, allocations: 3.938 kB / 0.6496 GB, free: 36.95 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 1.663e-06/0.003894, allocations: 2.844 kB / 0.6496 GB, free: 36.95 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 4.278e-06/0.003898, allocations: 0 / 0.6496 GB, free: 36.95 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 0.000519/0.004417, allocations: 0.5296 MB / 0.6501 GB, free: 36.45 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.658e-05/0.004454, allocations: 11.12 kB / 0.6501 GB, free: 36.45 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 5.58e-05/0.00451, allocations: 25.88 kB / 0.6501 GB, free: 36.44 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001339/0.004644, allocations: 162.8 kB / 0.6503 GB, free: 36.28 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.214e-05/0.004656, allocations: 7.406 kB / 0.6503 GB, free: 36.28 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 2.717e-05/0.004683, allocations: 17.66 kB / 0.6503 GB, free: 36.27 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0001828/0.004866, allocations: 146.8 kB / 0.6504 GB, free: 36.18 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.218e-05/0.004878, allocations: 9.766 kB / 0.6504 GB, free: 36.17 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.307e-05/0.004891, allocations: 6.25 kB / 0.6505 GB, free: 36.16 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.672e-06/0.004898, allocations: 1.938 kB / 0.6505 GB, free: 36.16 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 9.717e-05/0.004995, allocations: 79.27 kB / 0.6505 GB, free: 36.13 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0004134/0.005408, allocations: 404.4 kB / 0.6509 GB, free: 35.8 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001359/0.005544, allocations: 117.8 kB / 0.651 GB, free: 35.71 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 5.166e-05/0.005596, allocations: 64.36 kB / 0.6511 GB, free: 35.66 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.003e-05/0.005606, allocations: 4.75 kB / 0.6511 GB, free: 35.66 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001501/0.005756, allocations: 197.6 kB / 0.6513 GB, free: 35.5 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=20): time 1.323e-06/0.005757, allocations: 1.469 kB / 0.6513 GB, free: 35.5 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=21): time 0.0006966/0.006454, allocations: 0.5731 MB / 0.6518 GB, free: 35.08 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.987e-05/0.006504, allocations: 143.6 kB / 0.652 GB, free: 34.92 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001038/0.006608, allocations: 215.9 kB / 0.6522 GB, free: 34.74 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.466e-05/0.006622, allocations: 29.33 kB / 0.6522 GB, free: 34.71 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 5.172e-05/0.006674, allocations: 160.8 kB / 0.6524 GB, free: 34.55 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 3.513e-05/0.006709, allocations: 71.33 kB / 0.6524 GB, free: 34.5 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.685e-05/0.006766, allocations: 52.98 kB / 0.6525 GB, free: 34.46 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 6.517e-05/0.006831, allocations: 0.4996 MB / 0.653 GB, free: 33.96 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 8.261e-05/0.006914, allocations: 104.8 kB / 0.6531 GB, free: 33.87 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001014/0.007015, allocations: 198.6 kB / 0.6533 GB, free: 33.67 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002325/0.007248, allocations: 323.6 kB / 0.6536 GB, free: 33.38 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.725e-06/0.00725, allocations: 1 kB / 0.6536 GB, free: 33.38 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.000266/0.007516, allocations: 309.8 kB / 0.6539 GB, free: 33.18 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 3.549e-05/0.007552, allocations: 65.77 kB / 0.6539 GB, free: 33.11 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.342e-06/0.007558, allocations: 7.25 kB / 0.6539 GB, free: 33.11 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.798e-05/0.007576, allocations: 3.438 kB / 0.6539 GB, free: 33.11 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001607/0.007737, allocations: 52.06 kB / 0.654 GB, free: 33.11 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 6.732e-06/0.007744, allocations: 3.938 kB / 0.654 GB, free: 33.1 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 7.504e-05/0.007819, allocations: 13.22 kB / 0.654 GB, free: 33.1 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.596e-05/0.007835, allocations: 14.14 kB / 0.654 GB, free: 33.1 MB / 0.5262 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 0.0001554/0.00799, allocations: 228.2 kB / 0.6542 GB, free: 32.88 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 2.745e-05/0.008017, allocations: 23.78 kB / 0.6543 GB, free: 32.88 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.47e-05/0.008052, allocations: 22.12 kB / 0.6543 GB, free: 32.86 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.705e-06/0.008055, allocations: 3.562 kB / 0.6543 GB, free: 32.86 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.088e-06/0.008059, allocations: 0 / 0.6543 GB, free: 32.86 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.681e-06/0.008065, allocations: 5.125 kB / 0.6543 GB, free: 32.86 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.000393/0.008458, allocations: 0.526 MB / 0.6548 GB, free: 32.43 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.533e-06/0.008459, allocations: 0 / 0.6548 GB, free: 32.43 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001214/0.008581, allocations: 32.33 kB / 0.6548 GB, free: 32.43 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 3.807e-06/0.008584, allocations: 2.094 kB / 0.6548 GB, free: 32.43 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.524e-05/0.0086, allocations: 5.719 kB / 0.6548 GB, free: 32.43 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.745e-06/0.008602, allocations: 7.125 kB / 0.6549 GB, free: 32.42 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.383e-06/0.008604, allocations: 0 / 0.6549 GB, free: 32.42 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003212/0.008925, allocations: 457.5 kB / 0.6553 GB, free: 32.09 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 1.678e-05/0.008942, allocations: 14.88 kB / 0.6553 GB, free: 32.08 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.831e-05/0.00897, allocations: 14.59 kB / 0.6553 GB, free: 32.08 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.26e-05/0.009043, allocations: 12.53 kB / 0.6553 GB, free: 32.07 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 7.322e-05/0.009116, allocations: 19.19 kB / 0.6553 GB, free: 32.07 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.189e-05/0.009128, allocations: 5.781 kB / 0.6554 GB, free: 32.07 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 5.371e-05/0.009181, allocations: 159.8 kB / 0.6555 GB, free: 31.95 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 6e-08/0.009182, allocations: 1.062 kB / 0.6555 GB, free: 31.95 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0001901/0.009372, allocations: 47.16 kB / 0.6555 GB, free: 31.94 MB / 0.5262 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 8.185e-05/0.009453, allocations: 113 kB / 0.6557 GB, free: 31.85 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0002589/0.009712, allocations: 327.1 kB / 0.656 GB, free: 31.59 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.323e-06/0.009714, allocations: 0 / 0.656 GB, free: 31.59 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 9.451e-05/0.009808, allocations: 149.2 kB / 0.6561 GB, free: 31.47 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003025/0.01011, allocations: 60.94 kB / 0.6562 GB, free: 31.45 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001368/0.01148, allocations: 0.6272 MB / 0.6568 GB, free: 31.04 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 6.776e-05/0.01155, allocations: 117.9 kB / 0.6569 GB, free: 30.96 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.949e-05/0.0116, allocations: 24 kB / 0.6569 GB, free: 30.95 MB / 0.5262 GB
Notification: Performance of SimCode: time 9.42e-07/0.0116, allocations: 0 / 0.6569 GB, free: 30.95 MB / 0.5262 GB
Notification: Performance of Templates: time 0.003034/0.01463, allocations: 2.415 MB / 0.6593 GB, free: 30.77 MB / 0.5262 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate > Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 6.579458954976872]