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 0.001009/0.001009, allocations: 89.06 kB / 19.64 MB, free: 272 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 0.001074/0.001074, allocations: 169 kB / 23.02 MB, free: 1.543 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 0.9627/0.9627, allocations: 177.1 MB / 203.4 MB, free: 5.637 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 1.639/1.639, allocations: 273.5 MB / 0.5209 GB, free: 14.79 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 1.272e-06/1.272e-06, allocations: 0 / 0.6469 GB, free: 38.46 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.165e-05/2.292e-05, allocations: 6.234 kB / 0.6469 GB, free: 38.46 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue): time 0.002779/0.002802, allocations: 2.984 MB / 0.6499 GB, free: 36.54 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.0009253/0.003728, allocations: 0.7584 MB / 0.6506 GB, free: 36.04 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 9.878e-05/0.003826, allocations: 1.688 kB / 0.6506 GB, free: 36.04 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001389/0.003965, allocations: 43.17 kB / 0.6506 GB, free: 36.01 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.000217/0.004182, allocations: 123.6 kB / 0.6508 GB, free: 35.96 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0002212/0.004403, allocations: 98.62 kB / 0.6509 GB, free: 35.91 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002916/0.004695, allocations: 438.4 kB / 0.6513 GB, free: 35.68 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002986/0.004994, allocations: 230.3 kB / 0.6515 GB, free: 35.55 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001968/0.00519, allocations: 256.7 kB / 0.6517 GB, free: 35.44 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001924/0.005383, allocations: 153.5 kB / 0.6519 GB, free: 35.4 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 4.93e-05/0.005432, allocations: 42.02 kB / 0.6519 GB, free: 35.39 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 4.646e-05/0.005479, allocations: 40.09 kB / 0.652 GB, free: 35.39 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 5.016e-05/0.005529, allocations: 85.7 kB / 0.652 GB, free: 35.34 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 0.0001079/0.005637, allocations: 141.5 kB / 0.6522 GB, free: 35.27 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002593/0.005896, allocations: 264.3 kB / 0.6524 GB, free: 35.15 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 2.215e-06/0.005898, allocations: 0 / 0.6524 GB, free: 35.15 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 7.61e-07/0.005899, allocations: 0 / 0.6524 GB, free: 35.15 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 6.362e-06/0.005905, allocations: 3.938 kB / 0.6524 GB, free: 35.15 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 0.0007261/0.006631, allocations: 0.6564 MB / 0.6531 GB, free: 34.61 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.674e-05/0.006668, allocations: 7.875 kB / 0.6531 GB, free: 34.61 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 8.241e-05/0.006751, allocations: 61.44 kB / 0.6531 GB, free: 34.58 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002645/0.007015, allocations: 230.6 kB / 0.6534 GB, free: 34.39 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.97e-05/0.007035, allocations: 20.91 kB / 0.6534 GB, free: 34.38 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 5.015e-05/0.007085, allocations: 35.95 kB / 0.6534 GB, free: 34.37 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.000348/0.007433, allocations: 335.7 kB / 0.6537 GB, free: 34.18 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.53e-05/0.007448, allocations: 5.406 kB / 0.6537 GB, free: 34.18 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.224e-05/0.00747, allocations: 15.5 kB / 0.6538 GB, free: 34.16 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.083e-05/0.007481, allocations: 8.125 kB / 0.6538 GB, free: 34.16 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002084/0.00769, allocations: 127.4 kB / 0.6539 GB, free: 34.15 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0009936/0.008683, allocations: 0.8622 MB / 0.6547 GB, free: 33.54 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002792/0.008962, allocations: 137.1 kB / 0.6549 GB, free: 33.49 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 7.464e-05/0.009037, allocations: 51.25 kB / 0.6549 GB, free: 33.47 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 2.523e-05/0.009062, allocations: 3.656 kB / 0.6549 GB, free: 33.47 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001655/0.009228, allocations: 136.7 kB / 0.655 GB, free: 33.39 MB / 0.5262 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.0001143/0.009342, allocations: 35.5 kB / 0.6551 GB, free: 33.38 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=25): time 1.613e-06/0.009344, allocations: 0 / 0.6551 GB, free: 33.38 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=25): time 0.0004172/0.009761, allocations: 217.6 kB / 0.6553 GB, free: 33.31 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.224e-05/0.009803, allocations: 71.16 kB / 0.6554 GB, free: 33.23 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001798/0.009983, allocations: 240.1 kB / 0.6556 GB, free: 33.04 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.915e-05/0.01, allocations: 31.92 kB / 0.6556 GB, free: 33.01 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 7.892e-05/0.01008, allocations: 219.9 kB / 0.6558 GB, free: 32.81 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 5.876e-05/0.01014, allocations: 102.1 kB / 0.6559 GB, free: 32.73 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 9.093e-05/0.01023, allocations: 66.86 kB / 0.656 GB, free: 32.69 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 6.959e-05/0.0103, allocations: 0.5048 MB / 0.6565 GB, free: 32.18 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001443/0.01044, allocations: 91.42 kB / 0.6566 GB, free: 32.13 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001784/0.01062, allocations: 223.6 kB / 0.6568 GB, free: 31.91 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002944/0.01092, allocations: 262.2 kB / 0.657 GB, free: 31.69 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.278e-06/0.01092, allocations: 1.906 kB / 0.657 GB, free: 31.69 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=41) (initialization): time 0.0003716/0.01129, allocations: 324.3 kB / 0.6573 GB, free: 31.53 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 2.55e-05/0.01132, allocations: 32.77 kB / 0.6574 GB, free: 31.5 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.921e-06/0.01132, allocations: 2.875 kB / 0.6574 GB, free: 31.5 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.777e-05/0.01134, allocations: 5.75 kB / 0.6574 GB, free: 31.5 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.000203/0.01155, allocations: 85.25 kB / 0.6575 GB, free: 31.49 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.966e-06/0.01155, allocations: 4.25 kB / 0.6575 GB, free: 31.49 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.445e-05/0.01165, allocations: 19.7 kB / 0.6575 GB, free: 31.48 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.934e-05/0.01167, allocations: 15.25 kB / 0.6575 GB, free: 31.48 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 0.0001453/0.01181, allocations: 207.9 kB / 0.6577 GB, free: 31.29 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.265e-05/0.01185, allocations: 32.23 kB / 0.6577 GB, free: 31.28 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0002719/0.01212, allocations: 196.8 kB / 0.6579 GB, free: 31.18 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.767e-06/0.01212, allocations: 2.812 kB / 0.6579 GB, free: 31.18 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.757e-06/0.01213, allocations: 0 / 0.6579 GB, free: 31.18 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.98e-06/0.01213, allocations: 4.766 kB / 0.6579 GB, free: 31.18 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0001515/0.01228, allocations: 216.1 kB / 0.6581 GB, free: 31 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.024e-06/0.01228, allocations: 0 / 0.6581 GB, free: 31 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001498/0.01243, allocations: 43.28 kB / 0.6582 GB, free: 31 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 3.837e-06/0.01244, allocations: 7.938 kB / 0.6582 GB, free: 31 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.987e-05/0.01246, allocations: 10.14 kB / 0.6582 GB, free: 31 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.844e-06/0.01246, allocations: 1.438 kB / 0.6582 GB, free: 31 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 9.92e-07/0.01246, allocations: 3.938 kB / 0.6582 GB, free: 30.99 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003291/0.01279, allocations: 271.8 kB / 0.6584 GB, free: 30.86 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.368e-05/0.01281, allocations: 23.17 kB / 0.6585 GB, free: 30.84 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.624e-05/0.01284, allocations: 6.844 kB / 0.6585 GB, free: 30.84 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.001e-05/0.01291, allocations: 8.219 kB / 0.6585 GB, free: 30.84 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.098e-05/0.01296, allocations: 24.95 kB / 0.6585 GB, free: 30.83 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.253e-05/0.01297, allocations: 9.188 kB / 0.6585 GB, free: 30.83 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 6.617e-05/0.01304, allocations: 178.8 kB / 0.6587 GB, free: 30.7 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 5e-08/0.01304, allocations: 1.406 kB / 0.6587 GB, free: 30.7 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0002094/0.01325, allocations: 89.09 kB / 0.6588 GB, free: 30.68 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 8.076e-05/0.01333, allocations: 102.6 kB / 0.6589 GB, free: 30.59 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0002934/0.01362, allocations: 253.3 kB / 0.6591 GB, free: 30.45 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.533e-06/0.01362, allocations: 0.7812 kB / 0.6591 GB, free: 30.45 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001101/0.01373, allocations: 76.28 kB / 0.6592 GB, free: 30.43 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.000288/0.01402, allocations: 77.42 kB / 0.6593 GB, free: 30.41 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001563/0.01559, allocations: 0.8507 MB / 0.6601 GB, free: 29.87 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 5.14e-05/0.01564, allocations: 93.12 kB / 0.6602 GB, free: 29.8 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 8.689e-05/0.01572, allocations: 31.86 kB / 0.6602 GB, free: 29.79 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 7.149e-05/0.0158, allocations: 25.31 kB / 0.6602 GB, free: 29.78 MB / 0.5262 GB
Notification: Performance of SimCode: time 1.082e-06/0.0158, allocations: 0 / 0.6602 GB, free: 29.78 MB / 0.5262 GB
Notification: Performance of Templates: time 0.005833/0.02163, allocations: 3.677 MB / 0.6638 GB, free: 29.46 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: 4.943744453135878]