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 0.001304/0.001304, allocations: 89.08 kB / 19.42 MB, free: 496 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 0.001417/0.001417, allocations: 169.3 kB / 22.72 MB, free: 1.828 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 0.9707/0.9707, allocations: 177.1 MB / 203.1 MB, free: 5.656 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 1.783/1.783, allocations: 273.5 MB / 0.5205 GB, free: 14.9 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 1.753e-06/1.753e-06, allocations: 0 / 0.6462 GB, free: 38.73 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.464e-05/2.639e-05, allocations: 3.625 kB / 0.6462 GB, free: 38.73 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue): time 0.006363/0.00639, allocations: 2.986 MB / 0.6491 GB, free: 36.8 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.004189/0.01058, allocations: 0.7506 MB / 0.6499 GB, free: 36.3 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001662/0.01074, allocations: 2.156 kB / 0.6499 GB, free: 36.3 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.00014/0.01088, allocations: 46.66 kB / 0.6499 GB, free: 36.28 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0002637/0.01115, allocations: 133.7 kB / 0.65 GB, free: 36.22 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.000276/0.01142, allocations: 92.42 kB / 0.6501 GB, free: 36.16 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0003628/0.01179, allocations: 435.6 kB / 0.6505 GB, free: 35.94 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0003218/0.01211, allocations: 229.6 kB / 0.6508 GB, free: 35.81 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002496/0.01236, allocations: 262.3 kB / 0.651 GB, free: 35.7 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.000223/0.01258, allocations: 150.5 kB / 0.6512 GB, free: 35.66 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 5.125e-05/0.01263, allocations: 36.16 kB / 0.6512 GB, free: 35.66 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 5.422e-05/0.01269, allocations: 38.69 kB / 0.6512 GB, free: 35.66 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 5.248e-05/0.01274, allocations: 85.36 kB / 0.6513 GB, free: 35.6 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 0.0001163/0.01286, allocations: 135.1 kB / 0.6514 GB, free: 35.55 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002744/0.01313, allocations: 269.3 kB / 0.6517 GB, free: 35.41 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 4.118e-06/0.01313, allocations: 0 / 0.6517 GB, free: 35.41 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 1.352e-06/0.01314, allocations: 2.156 kB / 0.6517 GB, free: 35.41 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 5.951e-06/0.01314, allocations: 0 / 0.6517 GB, free: 35.41 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 0.003742/0.01688, allocations: 0.649 MB / 0.6523 GB, free: 34.88 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.608e-05/0.01692, allocations: 10.03 kB / 0.6523 GB, free: 34.88 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 8.884e-05/0.01701, allocations: 52.94 kB / 0.6524 GB, free: 34.85 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002235/0.01723, allocations: 219.1 kB / 0.6526 GB, free: 34.66 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.699e-05/0.01726, allocations: 22.28 kB / 0.6526 GB, free: 34.65 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 5.297e-05/0.01731, allocations: 35.89 kB / 0.6527 GB, free: 34.64 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004201/0.01773, allocations: 339.3 kB / 0.653 GB, free: 34.45 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.517e-05/0.01775, allocations: 3.938 kB / 0.653 GB, free: 34.44 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.594e-05/0.01777, allocations: 12.94 kB / 0.653 GB, free: 34.43 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.02e-05/0.01778, allocations: 5.75 kB / 0.653 GB, free: 34.43 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.000244/0.01803, allocations: 131.8 kB / 0.6531 GB, free: 34.42 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0009412/0.01897, allocations: 0.8464 MB / 0.654 GB, free: 33.82 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002813/0.01925, allocations: 145.6 kB / 0.6541 GB, free: 33.76 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.000102/0.01935, allocations: 49.06 kB / 0.6541 GB, free: 33.74 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 2.79e-05/0.01938, allocations: 4.5 kB / 0.6541 GB, free: 33.74 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.000174/0.01955, allocations: 132.3 kB / 0.6543 GB, free: 33.67 MB / 0.5262 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.0001082/0.01966, allocations: 40.95 kB / 0.6543 GB, free: 33.66 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=25): time 1.433e-06/0.01966, allocations: 0 / 0.6543 GB, free: 33.66 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=25): time 0.0003331/0.02, allocations: 222.7 kB / 0.6545 GB, free: 33.58 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.426e-05/0.02002, allocations: 65.75 kB / 0.6546 GB, free: 33.51 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001128/0.02013, allocations: 240.6 kB / 0.6548 GB, free: 33.32 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.437e-05/0.02015, allocations: 33.27 kB / 0.6548 GB, free: 33.28 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 6.18e-05/0.02021, allocations: 225.3 kB / 0.6551 GB, free: 33.08 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 4.118e-05/0.02025, allocations: 95.39 kB / 0.6552 GB, free: 33 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 8.098e-05/0.02033, allocations: 72.62 kB / 0.6552 GB, free: 32.96 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 6.276e-05/0.02039, allocations: 0.5 MB / 0.6557 GB, free: 32.46 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001216/0.02052, allocations: 95.86 kB / 0.6558 GB, free: 32.4 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001558/0.02067, allocations: 216.3 kB / 0.656 GB, free: 32.18 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.000268/0.02094, allocations: 267.8 kB / 0.6563 GB, free: 31.96 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.306e-06/0.02094, allocations: 1.125 kB / 0.6563 GB, free: 31.96 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=41) (initialization): time 0.0004291/0.02137, allocations: 319.1 kB / 0.6566 GB, free: 31.8 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 3.448e-05/0.02141, allocations: 40.61 kB / 0.6566 GB, free: 31.77 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.476e-06/0.02142, allocations: 2.781 kB / 0.6566 GB, free: 31.77 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 2.149e-05/0.02144, allocations: 3.906 kB / 0.6566 GB, free: 31.77 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002161/0.02165, allocations: 84.38 kB / 0.6567 GB, free: 31.76 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.126e-06/0.02166, allocations: 4.812 kB / 0.6567 GB, free: 31.76 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.659e-05/0.02176, allocations: 22.05 kB / 0.6567 GB, free: 31.75 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.756e-05/0.02178, allocations: 12.44 kB / 0.6567 GB, free: 31.75 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 0.000146/0.02192, allocations: 210.6 kB / 0.6569 GB, free: 31.56 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.63e-05/0.02196, allocations: 27.03 kB / 0.657 GB, free: 31.55 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0002732/0.02223, allocations: 197.6 kB / 0.6571 GB, free: 31.46 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.599e-06/0.02224, allocations: 6.297 kB / 0.6572 GB, free: 31.46 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.467e-06/0.02224, allocations: 3.906 kB / 0.6572 GB, free: 31.46 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.479e-06/0.02224, allocations: 3.422 kB / 0.6572 GB, free: 31.46 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0001497/0.02239, allocations: 216.2 kB / 0.6574 GB, free: 31.28 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.313e-06/0.02239, allocations: 0 / 0.6574 GB, free: 31.28 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001475/0.02254, allocations: 47.3 kB / 0.6574 GB, free: 31.27 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 3.086e-06/0.02254, allocations: 1.406 kB / 0.6574 GB, free: 31.27 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.776e-05/0.02256, allocations: 13.59 kB / 0.6574 GB, free: 31.27 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.615e-06/0.02257, allocations: 1.406 kB / 0.6574 GB, free: 31.27 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.022e-06/0.02257, allocations: 0 / 0.6574 GB, free: 31.27 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.000321/0.02289, allocations: 269 kB / 0.6577 GB, free: 31.13 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.133e-05/0.02291, allocations: 25.42 kB / 0.6577 GB, free: 31.11 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.57e-05/0.02293, allocations: 10.41 kB / 0.6577 GB, free: 31.11 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.11e-05/0.02301, allocations: 9.062 kB / 0.6577 GB, free: 31.11 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.838e-05/0.02305, allocations: 20.97 kB / 0.6577 GB, free: 31.11 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.172e-05/0.02307, allocations: 13.5 kB / 0.6578 GB, free: 31.1 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 6.74e-05/0.02313, allocations: 176.4 kB / 0.6579 GB, free: 30.97 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 6e-08/0.02313, allocations: 0 / 0.6579 GB, free: 30.97 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0002195/0.02335, allocations: 86.33 kB / 0.658 GB, free: 30.96 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 7.946e-05/0.02343, allocations: 101.8 kB / 0.6581 GB, free: 30.87 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0002743/0.02371, allocations: 253.6 kB / 0.6583 GB, free: 30.73 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.242e-06/0.02371, allocations: 0 / 0.6583 GB, free: 30.73 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 9.72e-05/0.0238, allocations: 76.39 kB / 0.6584 GB, free: 30.7 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002777/0.02408, allocations: 72.25 kB / 0.6585 GB, free: 30.68 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001529/0.02561, allocations: 0.8439 MB / 0.6593 GB, free: 30.15 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 4.012e-05/0.02565, allocations: 91.47 kB / 0.6594 GB, free: 30.08 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 8.97e-05/0.02574, allocations: 31.38 kB / 0.6594 GB, free: 30.07 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 6.616e-05/0.02581, allocations: 32.52 kB / 0.6595 GB, free: 30.05 MB / 0.5262 GB
Notification: Performance of SimCode: time 5.01e-07/0.02581, allocations: 0 / 0.6595 GB, free: 30.05 MB / 0.5262 GB
Notification: Performance of Templates: time 0.005547/0.03136, allocations: 3.672 MB / 0.663 GB, free: 29.73 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: 5.170937680639327]