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 0.0009527/0.0009527, allocations: 92.2 kB / 20.19 MB, free: 4.363 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 0.00113/0.00113, allocations: 173 kB / 23.5 MB, free: 1.055 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 0.9462/0.9462, allocations: 177.1 MB / 203.8 MB, free: 5.594 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 1.583/1.583, allocations: 273.5 MB / 0.5213 GB, free: 14.91 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 1.252e-06/1.252e-06, allocations: 0 / 0.647 GB, free: 38.68 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.536e-05/1.661e-05, allocations: 2.312 kB / 0.647 GB, free: 38.67 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_LithiumCarbonate): time 0.002091/0.002107, allocations: 2.127 MB / 0.6491 GB, free: 37.29 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.0006479/0.002755, allocations: 0.5454 MB / 0.6496 GB, free: 36.93 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 6.598e-05/0.002821, allocations: 8.188 kB / 0.6496 GB, free: 36.93 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 9.797e-05/0.002919, allocations: 15.14 kB / 0.6496 GB, free: 36.92 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001217/0.003041, allocations: 56.39 kB / 0.6497 GB, free: 36.89 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001451/0.003186, allocations: 47.95 kB / 0.6497 GB, free: 36.87 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0001981/0.003384, allocations: 203.3 kB / 0.6499 GB, free: 36.81 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001104/0.003494, allocations: 31.3 kB / 0.6499 GB, free: 36.79 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001074/0.003602, allocations: 108.5 kB / 0.65 GB, free: 36.74 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001053/0.003707, allocations: 63.86 kB / 0.6501 GB, free: 36.72 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 2.721e-05/0.003734, allocations: 14.22 kB / 0.6501 GB, free: 36.72 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 2.001e-05/0.003754, allocations: 18.09 kB / 0.6501 GB, free: 36.72 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 2.927e-05/0.003783, allocations: 25.23 kB / 0.6501 GB, free: 36.7 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 6.068e-05/0.003844, allocations: 60.5 kB / 0.6502 GB, free: 36.68 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0001584/0.004002, allocations: 127.9 kB / 0.6503 GB, free: 36.61 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 1.814e-06/0.004004, allocations: 0 / 0.6503 GB, free: 36.61 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 4.91e-07/0.004005, allocations: 0 / 0.6503 GB, free: 36.61 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 4.158e-06/0.004009, allocations: 1.969 kB / 0.6503 GB, free: 36.61 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 0.0004984/0.004507, allocations: 0.5378 MB / 0.6509 GB, free: 36.11 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.392e-05/0.004541, allocations: 9.406 kB / 0.6509 GB, free: 36.11 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 5.542e-05/0.004597, allocations: 26.16 kB / 0.6509 GB, free: 36.1 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.000141/0.004738, allocations: 158.6 kB / 0.651 GB, free: 35.94 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.228e-05/0.00475, allocations: 7.438 kB / 0.651 GB, free: 35.94 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 2.956e-05/0.004779, allocations: 16.42 kB / 0.6511 GB, free: 35.93 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0001817/0.004961, allocations: 140.7 kB / 0.6512 GB, free: 35.84 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.177e-05/0.004973, allocations: 11.42 kB / 0.6512 GB, free: 35.83 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.351e-05/0.004986, allocations: 7.234 kB / 0.6512 GB, free: 35.83 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.025e-06/0.004995, allocations: 3.531 kB / 0.6512 GB, free: 35.83 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001002/0.005095, allocations: 77.52 kB / 0.6513 GB, free: 35.79 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0004081/0.005503, allocations: 404.9 kB / 0.6517 GB, free: 35.46 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001534/0.005656, allocations: 124 kB / 0.6518 GB, free: 35.38 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 5.8e-05/0.005714, allocations: 66.66 kB / 0.6519 GB, free: 35.32 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 9.919e-06/0.005724, allocations: 4.312 kB / 0.6519 GB, free: 35.32 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001512/0.005875, allocations: 193.1 kB / 0.652 GB, free: 35.16 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=20): time 1.292e-06/0.005877, allocations: 0 / 0.652 GB, free: 35.16 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=21): time 0.0006634/0.00654, allocations: 0.5814 MB / 0.6526 GB, free: 34.74 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.829e-05/0.006578, allocations: 131.9 kB / 0.6527 GB, free: 34.59 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 9.007e-05/0.006668, allocations: 216.4 kB / 0.6529 GB, free: 34.4 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.33e-05/0.006682, allocations: 38.64 kB / 0.653 GB, free: 34.36 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 4.289e-05/0.006725, allocations: 154.1 kB / 0.6531 GB, free: 34.22 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 3.223e-05/0.006757, allocations: 66.34 kB / 0.6532 GB, free: 34.17 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 4.962e-05/0.006806, allocations: 59.33 kB / 0.6533 GB, free: 34.12 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 4.83e-05/0.006855, allocations: 0.4974 MB / 0.6537 GB, free: 33.62 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 7.658e-05/0.006931, allocations: 106.3 kB / 0.6538 GB, free: 33.54 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 9.05e-05/0.007022, allocations: 197.7 kB / 0.654 GB, free: 33.33 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0001979/0.00722, allocations: 324.2 kB / 0.6543 GB, free: 33.04 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.122e-06/0.007221, allocations: 0 / 0.6543 GB, free: 33.04 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0002358/0.007457, allocations: 309.3 kB / 0.6546 GB, free: 32.84 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 2.53e-05/0.007482, allocations: 67 kB / 0.6547 GB, free: 32.77 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.13e-06/0.007487, allocations: 2.438 kB / 0.6547 GB, free: 32.77 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.205e-05/0.007499, allocations: 3.25 kB / 0.6547 GB, free: 32.77 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.000141/0.00764, allocations: 50.98 kB / 0.6548 GB, free: 32.77 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 6.783e-06/0.007647, allocations: 7.406 kB / 0.6548 GB, free: 32.77 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 7.053e-05/0.007717, allocations: 13.19 kB / 0.6548 GB, free: 32.76 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.384e-05/0.007731, allocations: 19.31 kB / 0.6548 GB, free: 32.76 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 0.0001226/0.007854, allocations: 222.7 kB / 0.655 GB, free: 32.55 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 2.554e-05/0.007879, allocations: 26.81 kB / 0.655 GB, free: 32.54 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 2.91e-05/0.007908, allocations: 26.92 kB / 0.6551 GB, free: 32.52 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.034e-06/0.007911, allocations: 1.75 kB / 0.6551 GB, free: 32.52 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.266e-06/0.007914, allocations: 1.469 kB / 0.6551 GB, free: 32.52 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.328e-06/0.007918, allocations: 3.938 kB / 0.6551 GB, free: 32.52 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003337/0.008252, allocations: 0.5188 MB / 0.6556 GB, free: 32.1 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.463e-06/0.008253, allocations: 0 / 0.6556 GB, free: 32.1 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001064/0.00836, allocations: 36.64 kB / 0.6556 GB, free: 32.09 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 1.783e-06/0.008361, allocations: 0 / 0.6556 GB, free: 32.09 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.287e-05/0.008374, allocations: 8.938 kB / 0.6556 GB, free: 32.09 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.122e-06/0.008375, allocations: 0 / 0.6556 GB, free: 32.09 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.104e-06/0.008378, allocations: 5.422 kB / 0.6556 GB, free: 32.09 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0002973/0.008675, allocations: 458.7 kB / 0.6561 GB, free: 31.76 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 1.767e-05/0.008693, allocations: 15.62 kB / 0.6561 GB, free: 31.75 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.611e-05/0.008719, allocations: 12.7 kB / 0.6561 GB, free: 31.74 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.39e-05/0.008793, allocations: 10.75 kB / 0.6561 GB, free: 31.74 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.964e-05/0.008852, allocations: 21.03 kB / 0.6561 GB, free: 31.73 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.204e-05/0.008864, allocations: 5.938 kB / 0.6561 GB, free: 31.73 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 5.093e-05/0.008915, allocations: 156.4 kB / 0.6563 GB, free: 31.61 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 5e-08/0.008915, allocations: 0.5 kB / 0.6563 GB, free: 31.61 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0001976/0.009113, allocations: 48.91 kB / 0.6563 GB, free: 31.61 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 6.313e-05/0.009176, allocations: 109.7 kB / 0.6564 GB, free: 31.51 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0002221/0.009398, allocations: 330.7 kB / 0.6567 GB, free: 31.25 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.694e-06/0.0094, allocations: 0 / 0.6567 GB, free: 31.25 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 9.279e-05/0.009493, allocations: 154 kB / 0.6569 GB, free: 31.13 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002557/0.009748, allocations: 61.2 kB / 0.6569 GB, free: 31.11 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001299/0.01105, allocations: 0.6063 MB / 0.6575 GB, free: 30.74 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 4.842e-05/0.0111, allocations: 78.36 kB / 0.6576 GB, free: 30.66 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 5.698e-05/0.01115, allocations: 18.2 kB / 0.6576 GB, free: 30.66 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.834e-05/0.0112, allocations: 18.84 kB / 0.6576 GB, free: 30.65 MB / 0.5262 GB
Notification: Performance of SimCode: time 1.032e-06/0.0112, allocations: 0.5625 kB / 0.6576 GB, free: 30.65 MB / 0.5262 GB
Notification: Performance of Templates: time 0.004023/0.01523, allocations: 2.729 MB / 0.6603 GB, free: 30.41 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 -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_LithiumCarbonate.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 5.902844961965457]