Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue.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 0.0009436/0.0009436, allocations: 73.09 kB / 20.65 MB, free: 3.848 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 0.001012/0.001012, allocations: 169 kB / 24.06 MB, free: 456 kB / 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 0.9987/0.9987, allocations: 177.1 MB / 204.5 MB, free: 5.484 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 1.574/1.574, allocations: 273.5 MB / 0.522 GB, free: 14.65 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.PBPK_SingleDoseVenousArteryTissue,tolerance=1e-06,outputFormat="empty",numberOfIntervals=7200,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue")
translateModel(Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue,tolerance=1e-06,outputFormat="empty",numberOfIntervals=7200,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.332e-06/1.332e-06, allocations: 0 / 0.6482 GB, free: 38.6 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.187e-05/1.321e-05, allocations: 3.562 kB / 0.6482 GB, free: 38.6 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue): time 0.002315/0.002328, allocations: 2.959 MB / 0.6511 GB, free: 36.68 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.0008019/0.00313, allocations: 0.7508 MB / 0.6518 GB, free: 36.18 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 9.542e-05/0.003226, allocations: 7.406 kB / 0.6518 GB, free: 36.17 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001175/0.003343, allocations: 45.17 kB / 0.6518 GB, free: 36.15 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001894/0.003532, allocations: 124.1 kB / 0.652 GB, free: 36.1 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001958/0.003728, allocations: 92.12 kB / 0.652 GB, free: 36.05 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002761/0.004004, allocations: 444.5 kB / 0.6525 GB, free: 35.82 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.000232/0.004236, allocations: 227.7 kB / 0.6527 GB, free: 35.69 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001916/0.004428, allocations: 255.6 kB / 0.6529 GB, free: 35.59 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001781/0.004606, allocations: 157.5 kB / 0.6531 GB, free: 35.54 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 4.437e-05/0.00465, allocations: 35.12 kB / 0.6531 GB, free: 35.54 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 4.699e-05/0.004697, allocations: 40.16 kB / 0.6532 GB, free: 35.54 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 4.784e-05/0.004745, allocations: 77.53 kB / 0.6532 GB, free: 35.48 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 9.54e-05/0.004841, allocations: 140.3 kB / 0.6534 GB, free: 35.43 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002084/0.005049, allocations: 270.7 kB / 0.6536 GB, free: 35.29 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 2.475e-06/0.005051, allocations: 1.781 kB / 0.6536 GB, free: 35.29 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 5.31e-07/0.005052, allocations: 0 / 0.6536 GB, free: 35.29 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 4.418e-06/0.005056, allocations: 0 / 0.6536 GB, free: 35.29 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: 68
 * Number of variables: 68
Notification: Performance of Generate backend data structure: time 0.0005543/0.005611, allocations: 0.6479 MB / 0.6543 GB, free: 34.75 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.247e-05/0.005643, allocations: 10.53 kB / 0.6543 GB, free: 34.75 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 7.356e-05/0.005717, allocations: 57.53 kB / 0.6543 GB, free: 34.73 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001835/0.0059, allocations: 209 kB / 0.6545 GB, free: 34.54 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.126e-05/0.005931, allocations: 22.28 kB / 0.6545 GB, free: 34.53 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 5.139e-05/0.005983, allocations: 36.7 kB / 0.6546 GB, free: 34.52 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002991/0.006282, allocations: 316.4 kB / 0.6549 GB, free: 34.34 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.48e-05/0.006297, allocations: 10.11 kB / 0.6549 GB, free: 34.33 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.893e-05/0.006316, allocations: 10.94 kB / 0.6549 GB, free: 34.32 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.444e-06/0.006323, allocations: 5.875 kB / 0.6549 GB, free: 34.32 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001368/0.00646, allocations: 110.3 kB / 0.655 GB, free: 34.32 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0008308/0.007291, allocations: 0.8205 MB / 0.6558 GB, free: 33.74 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002526/0.007543, allocations: 124.8 kB / 0.6559 GB, free: 33.69 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 8.452e-05/0.007628, allocations: 47.25 kB / 0.656 GB, free: 33.67 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 2.135e-05/0.007649, allocations: 8.406 kB / 0.656 GB, free: 33.67 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001689/0.007818, allocations: 120.7 kB / 0.6561 GB, free: 33.6 MB / 0.5262 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.0001197/0.007938, allocations: 34.67 kB / 0.6561 GB, free: 33.59 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=25): time 2.275e-06/0.00794, allocations: 4.875 kB / 0.6561 GB, free: 33.59 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=25): time 0.0003675/0.008308, allocations: 201.5 kB / 0.6563 GB, free: 33.52 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.52e-05/0.008333, allocations: 65.28 kB / 0.6564 GB, free: 33.45 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001282/0.008461, allocations: 239 kB / 0.6566 GB, free: 33.26 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.558e-05/0.008477, allocations: 33.39 kB / 0.6566 GB, free: 33.23 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 6.261e-05/0.008539, allocations: 218.4 kB / 0.6569 GB, free: 33.03 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 5.16e-05/0.008591, allocations: 100.2 kB / 0.6569 GB, free: 32.95 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 6.697e-05/0.008658, allocations: 69.17 kB / 0.657 GB, free: 32.9 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 5.92e-05/0.008717, allocations: 0.5099 MB / 0.6575 GB, free: 32.4 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 7.309e-05/0.00879, allocations: 85.02 kB / 0.6576 GB, free: 32.35 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 9.661e-05/0.008887, allocations: 213.1 kB / 0.6578 GB, free: 32.13 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0001556/0.009042, allocations: 236.6 kB / 0.658 GB, free: 31.93 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.806e-06/0.009045, allocations: 1.406 kB / 0.658 GB, free: 31.93 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=41) (initialization): time 0.0002615/0.009307, allocations: 303.4 kB / 0.6583 GB, free: 31.77 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 2.236e-05/0.009329, allocations: 39.36 kB / 0.6584 GB, free: 31.73 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.991e-06/0.009335, allocations: 6.844 kB / 0.6584 GB, free: 31.73 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.087e-05/0.009346, allocations: 4.094 kB / 0.6584 GB, free: 31.73 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001855/0.009531, allocations: 81.06 kB / 0.6584 GB, free: 31.73 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 5.23e-06/0.009537, allocations: 4.219 kB / 0.6584 GB, free: 31.73 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.801e-05/0.009635, allocations: 19.56 kB / 0.6585 GB, free: 31.72 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.717e-05/0.009652, allocations: 14.22 kB / 0.6585 GB, free: 31.72 MB / 0.5262 GB
Warning: Assuming fixed start value for the following 5 variables:
         tissue.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         arteries.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         veins.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         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
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 11
 * Number of states: 0 ()
 * Number of discrete variables: 5 (singleDose.pulse.count,$PRE.singleDose.pulse.count,singleDose.pulse.T_start,$PRE.singleDose.pulse.T_start,$whenCondition1)
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (40):
 * Single equations (assignments): 39
 * Array equations: 0
 * Algorithm blocks: 1
 * 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 0.0001173/0.009769, allocations: 212.9 kB / 0.6587 GB, free: 31.52 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3e-05/0.009799, allocations: 25.84 kB / 0.6587 GB, free: 31.51 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0002137/0.01001, allocations: 186.2 kB / 0.6589 GB, free: 31.43 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.665e-06/0.01002, allocations: 2.781 kB / 0.6589 GB, free: 31.43 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.422e-06/0.01002, allocations: 1.438 kB / 0.6589 GB, free: 31.43 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.328e-06/0.01002, allocations: 3.469 kB / 0.6589 GB, free: 31.43 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0001252/0.01015, allocations: 172.3 kB / 0.6591 GB, free: 31.29 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.283e-06/0.01015, allocations: 0 / 0.6591 GB, free: 31.29 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.000137/0.01028, allocations: 50.62 kB / 0.6591 GB, free: 31.28 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.054e-06/0.01029, allocations: 3.938 kB / 0.6591 GB, free: 31.28 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.441e-05/0.0103, allocations: 10.31 kB / 0.6591 GB, free: 31.27 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.703e-06/0.0103, allocations: 1.375 kB / 0.6591 GB, free: 31.27 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 6.11e-07/0.0103, allocations: 0 / 0.6591 GB, free: 31.27 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0002774/0.01058, allocations: 254.8 kB / 0.6594 GB, free: 31.14 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.002e-05/0.0106, allocations: 18.92 kB / 0.6594 GB, free: 31.13 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.472e-05/0.01063, allocations: 10.78 kB / 0.6594 GB, free: 31.12 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.267e-05/0.0107, allocations: 17.31 kB / 0.6594 GB, free: 31.12 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.849e-05/0.01074, allocations: 21.45 kB / 0.6594 GB, free: 31.11 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 8.997e-06/0.01075, allocations: 2.75 kB / 0.6594 GB, free: 31.11 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 5.142e-05/0.0108, allocations: 170.3 kB / 0.6596 GB, free: 30.99 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 6e-08/0.0108, allocations: 0 / 0.6596 GB, free: 30.99 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0001951/0.01099, allocations: 89.17 kB / 0.6597 GB, free: 30.97 MB / 0.5262 GB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 9 (tissue.M,tissue.AUC,arteries.M,arteries.AUC,veins.M,veins.AUC,singleDose.TotalCumulativeMass,singleDose.variableDose.TotalCumulativeMass,kidneyElim.MExc)
 * Number of discrete variables: 3 ($whenCondition1,singleDose.pulse.T_start,singleDose.pulse.count)
 * Number of discrete states: 1 (singleDose.pulse.count)
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (25):
 * Single equations (assignments): 23
 * Array equations: 0
 * Algorithm blocks: 0
 * 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 7.185e-05/0.01106, allocations: 101.9 kB / 0.6598 GB, free: 30.88 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0002188/0.01128, allocations: 234.3 kB / 0.66 GB, free: 30.75 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.112e-06/0.01128, allocations: 0.7812 kB / 0.66 GB, free: 30.75 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 8.174e-05/0.01137, allocations: 74.36 kB / 0.6601 GB, free: 30.73 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002609/0.01163, allocations: 71.75 kB / 0.6601 GB, free: 30.71 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001327/0.01295, allocations: 0.8486 MB / 0.661 GB, free: 30.18 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 5.091e-05/0.013, allocations: 91.08 kB / 0.6611 GB, free: 30.11 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 8.754e-05/0.01309, allocations: 29.66 kB / 0.6611 GB, free: 30.09 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.000164/0.01326, allocations: 142.8 kB / 0.6612 GB, free: 30.02 MB / 0.5262 GB
Notification: Performance of SimCode: time 7.41e-07/0.01326, allocations: 0 / 0.6612 GB, free: 30.02 MB / 0.5262 GB
Notification: Performance of Templates: time 0.005873/0.01913, allocations: 4.105 MB / 0.6652 GB, free: 29.63 MB / 0.5262 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 4.679058697074652]