Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.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 0.001047/0.001047, allocations: 93.06 kB / 19.65 MB, free: 276 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 0.001137/0.001137, allocations: 165 kB / 23.02 MB, free: 1.547 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 1.013/1.013, allocations: 177.1 MB / 203.4 MB, free: 5.191 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 1.589/1.589, allocations: 273.5 MB / 0.5209 GB, free: 14.75 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.DevModels.SingleDoseDiffusion,tolerance=1e-06,outputFormat="empty",numberOfIntervals=500,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion")
translateModel(Pharmacolibrary.DevModels.SingleDoseDiffusion,tolerance=1e-06,outputFormat="empty",numberOfIntervals=500,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 2.465e-06/2.465e-06, allocations: 0 / 0.6469 GB, free: 38.71 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 3.044e-05/3.29e-05, allocations: 3.812 kB / 0.6469 GB, free: 38.71 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.SingleDoseDiffusion): time 0.003761/0.003794, allocations: 2.907 MB / 0.6498 GB, free: 36.83 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.001263/0.005057, allocations: 0.7421 MB / 0.6505 GB, free: 36.34 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001147/0.005172, allocations: 5 kB / 0.6505 GB, free: 36.34 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 9.359e-05/0.005265, allocations: 39.7 kB / 0.6506 GB, free: 36.32 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0003195/0.005585, allocations: 116.7 kB / 0.6507 GB, free: 36.27 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0002909/0.005876, allocations: 91.88 kB / 0.6508 GB, free: 36.22 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.000407/0.006283, allocations: 409.6 kB / 0.6511 GB, free: 36.02 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0003779/0.006661, allocations: 220 kB / 0.6514 GB, free: 35.89 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002917/0.006952, allocations: 246 kB / 0.6516 GB, free: 35.79 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002692/0.007222, allocations: 153.9 kB / 0.6517 GB, free: 35.74 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 6.506e-05/0.007287, allocations: 36.59 kB / 0.6518 GB, free: 35.74 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 6.645e-05/0.007353, allocations: 36.84 kB / 0.6518 GB, free: 35.74 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 6.776e-05/0.007421, allocations: 80.27 kB / 0.6519 GB, free: 35.68 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 0.0001596/0.00758, allocations: 132.8 kB / 0.652 GB, free: 35.63 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0003311/0.007912, allocations: 267.2 kB / 0.6523 GB, free: 35.5 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 2.515e-06/0.007914, allocations: 0 / 0.6523 GB, free: 35.5 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 9.71e-07/0.007915, allocations: 2.375 kB / 0.6523 GB, free: 35.5 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 5.52e-06/0.007921, allocations: 0 / 0.6523 GB, free: 35.5 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: 65
 * Number of variables: 65
Notification: Performance of Generate backend data structure: time 0.00092/0.008841, allocations: 0.6653 MB / 0.6529 GB, free: 34.94 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 4.419e-05/0.008885, allocations: 15.12 kB / 0.6529 GB, free: 34.94 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001156/0.009, allocations: 53.78 kB / 0.653 GB, free: 34.91 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0003541/0.009354, allocations: 219.8 kB / 0.6532 GB, free: 34.73 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.738e-05/0.009382, allocations: 20.78 kB / 0.6532 GB, free: 34.72 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 6.803e-05/0.00945, allocations: 34.39 kB / 0.6532 GB, free: 34.71 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0005561/0.01001, allocations: 355.9 kB / 0.6536 GB, free: 34.49 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 2.163e-05/0.01003, allocations: 9.062 kB / 0.6536 GB, free: 34.48 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.663e-05/0.01006, allocations: 14.3 kB / 0.6536 GB, free: 34.47 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.519e-05/0.01008, allocations: 6.75 kB / 0.6536 GB, free: 34.47 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003726/0.01045, allocations: 164.2 kB / 0.6538 GB, free: 34.43 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001389/0.01184, allocations: 0.8288 MB / 0.6546 GB, free: 33.83 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0004988/0.01234, allocations: 176.3 kB / 0.6547 GB, free: 33.74 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001831/0.01252, allocations: 85.08 kB / 0.6548 GB, free: 33.68 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 3.664e-05/0.01256, allocations: 9.25 kB / 0.6548 GB, free: 33.68 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0003948/0.01295, allocations: 238.6 kB / 0.6551 GB, free: 33.51 MB / 0.5262 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.0002364/0.01319, allocations: 46.3 kB / 0.6551 GB, free: 33.49 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=30): time 2.154e-06/0.01319, allocations: 0.5625 kB / 0.6551 GB, free: 33.49 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=31): time 0.001691/0.01488, allocations: 0.7353 MB / 0.6558 GB, free: 33.02 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.652e-05/0.01493, allocations: 135.4 kB / 0.656 GB, free: 32.87 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001669/0.0151, allocations: 241.2 kB / 0.6562 GB, free: 32.67 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 2.719e-05/0.01512, allocations: 35.95 kB / 0.6562 GB, free: 32.64 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 8.446e-05/0.01521, allocations: 208.6 kB / 0.6564 GB, free: 32.45 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 8.252e-05/0.01529, allocations: 110.5 kB / 0.6565 GB, free: 32.36 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001206/0.01541, allocations: 77.73 kB / 0.6566 GB, free: 32.31 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 8.018e-05/0.01549, allocations: 0.5027 MB / 0.6571 GB, free: 31.81 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001814/0.01567, allocations: 134.1 kB / 0.6572 GB, free: 31.71 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002179/0.01589, allocations: 269.7 kB / 0.6575 GB, free: 31.45 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0005024/0.01639, allocations: 451.4 kB / 0.6579 GB, free: 31.07 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.877e-06/0.0164, allocations: 2.438 kB / 0.6579 GB, free: 31.07 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=49) (initialization): time 0.0006058/0.017, allocations: 425.4 kB / 0.6583 GB, free: 30.83 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 4.472e-05/0.01705, allocations: 65.5 kB / 0.6584 GB, free: 30.76 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 9.879e-06/0.01706, allocations: 2.781 kB / 0.6584 GB, free: 30.76 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 2.624e-05/0.01708, allocations: 5.562 kB / 0.6584 GB, free: 30.76 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003614/0.01745, allocations: 84.67 kB / 0.6585 GB, free: 30.76 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.303e-05/0.01746, allocations: 12.58 kB / 0.6585 GB, free: 30.75 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001739/0.01763, allocations: 16.41 kB / 0.6585 GB, free: 30.75 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 3.294e-05/0.01767, allocations: 20.78 kB / 0.6585 GB, free: 30.74 MB / 0.5262 GB
Warning: Assuming fixed start value for the following 8 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
         artery.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         tissueCompartment.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         RBC.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         RBC.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         RBC.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         RBC.rising:DISCRETE(fixed = true protected = true )  type: Boolean
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 12
 * Number of states: 0 ()
 * Number of discrete variables: 13 ($PRE.RBC.Cmin,RBC.Cmin,$PRE.RBC.Cmax,RBC.Cmax,$PRE.RBC.rising,$PRE.singleDose.pulse.count,$PRE.singleDose.pulse.T_start,RBC.rising,singleDose.pulse.count,singleDose.pulse.T_start,$whenCondition2,$whenCondition1,$whenCondition3)
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (47):
 * Single equations (assignments): 45
 * 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 0.0002083/0.01787, allocations: 235.3 kB / 0.6587 GB, free: 30.53 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 5.716e-05/0.01793, allocations: 38.12 kB / 0.6588 GB, free: 30.51 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0005138/0.01845, allocations: 319.1 kB / 0.6591 GB, free: 30.34 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.929e-06/0.01845, allocations: 2.719 kB / 0.6591 GB, free: 30.34 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.799e-06/0.01845, allocations: 3.5 kB / 0.6591 GB, free: 30.34 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.112e-06/0.01846, allocations: 3.703 kB / 0.6591 GB, free: 30.34 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0007373/0.0192, allocations: 0.6304 MB / 0.6597 GB, free: 29.9 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.066e-06/0.0192, allocations: 0 / 0.6597 GB, free: 29.9 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002705/0.01947, allocations: 49.03 kB / 0.6597 GB, free: 29.89 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 3.747e-06/0.01948, allocations: 2.5 kB / 0.6597 GB, free: 29.89 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.592e-05/0.0195, allocations: 6.781 kB / 0.6598 GB, free: 29.89 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.968e-06/0.01951, allocations: 7.781 kB / 0.6598 GB, free: 29.89 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.482e-06/0.01951, allocations: 1.219 kB / 0.6598 GB, free: 29.89 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0006195/0.02013, allocations: 0.5394 MB / 0.6603 GB, free: 29.53 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 3.13e-05/0.02016, allocations: 21.53 kB / 0.6603 GB, free: 29.51 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.089e-05/0.02021, allocations: 14.94 kB / 0.6603 GB, free: 29.5 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001709/0.02038, allocations: 13.22 kB / 0.6603 GB, free: 29.5 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 7.758e-05/0.02046, allocations: 22.61 kB / 0.6604 GB, free: 29.5 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.336e-05/0.02048, allocations: 10.05 kB / 0.6604 GB, free: 29.5 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 9.708e-05/0.02058, allocations: 176 kB / 0.6605 GB, free: 29.36 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 1e-07/0.02058, allocations: 0 / 0.6605 GB, free: 29.36 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.000394/0.02097, allocations: 79.38 kB / 0.6606 GB, free: 29.36 MB / 0.5262 GB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 8 (singleDose.TotalCumulativeMass,singleDose.variableDose.TotalCumulativeMass,artery.M,artery.AUC,tissueCompartment.M,tissueCompartment.AUC,RBC.C,RBC.AUC)
 * Number of discrete variables: 8 ($whenCondition3,$whenCondition1,$whenCondition2,singleDose.pulse.T_start,singleDose.pulse.count,RBC.Cmax,RBC.Cmin,RBC.rising)
 * Number of discrete states: 6 (singleDose.pulse.count,RBC.Cmin,$whenCondition2,RBC.Cmax,$whenCondition1,RBC.rising)
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (28):
 * Single equations (assignments): 25
 * 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 0.0001099/0.02108, allocations: 113.8 kB / 0.6607 GB, free: 29.26 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0004936/0.02158, allocations: 395.4 kB / 0.6611 GB, free: 28.99 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.944e-06/0.02158, allocations: 0 / 0.6611 GB, free: 28.99 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.0002073/0.02178, allocations: 188.4 kB / 0.6613 GB, free: 28.86 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005044/0.02229, allocations: 86.77 kB / 0.6614 GB, free: 28.84 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001633/0.02392, allocations: 0.8504 MB / 0.6622 GB, free: 28.29 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 5.471e-05/0.02398, allocations: 101.4 kB / 0.6623 GB, free: 28.21 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 8.508e-05/0.02406, allocations: 33.31 kB / 0.6623 GB, free: 28.2 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 8.099e-05/0.02414, allocations: 30.09 kB / 0.6623 GB, free: 28.19 MB / 0.5262 GB
Notification: Performance of SimCode: time 1.142e-06/0.02414, allocations: 4 kB / 0.6624 GB, free: 28.19 MB / 0.5262 GB
Notification: Performance of Templates: time 0.005929/0.03007, allocations: 4.028 MB / 0.6663 GB, free: 27.84 MB / 0.5262 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.sim & ./Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 5.627443589735776]