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 0.0009182/0.0009182, 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 0.000906/0.000906, allocations: 169 kB / 23.03 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 0.8952/0.8952, allocations: 177.1 MB / 203.4 MB, free: 5.621 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 1.513/1.513, allocations: 273.5 MB / 0.5209 GB, free: 14.81 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 1.523e-06/1.523e-06, allocations: 0 / 0.6469 GB, free: 38.7 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.547e-05/1.699e-05, allocations: 3.625 kB / 0.647 GB, free: 38.7 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue): time 0.002364/0.002381, allocations: 2.989 MB / 0.6499 GB, free: 36.77 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.0007651/0.003146, allocations: 0.7468 MB / 0.6506 GB, free: 36.28 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 8.642e-05/0.003232, allocations: 7.375 kB / 0.6506 GB, free: 36.27 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001204/0.003353, allocations: 48.83 kB / 0.6507 GB, free: 36.25 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.000197/0.00355, allocations: 124.8 kB / 0.6508 GB, free: 36.2 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001915/0.003741, allocations: 97.23 kB / 0.6509 GB, free: 36.14 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002699/0.004011, allocations: 436.8 kB / 0.6513 GB, free: 35.91 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002579/0.004269, allocations: 233.3 kB / 0.6515 GB, free: 35.78 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001824/0.004451, allocations: 251.5 kB / 0.6517 GB, free: 35.68 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001678/0.004619, allocations: 160.2 kB / 0.6519 GB, free: 35.63 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 4.551e-05/0.004665, allocations: 36.16 kB / 0.6519 GB, free: 35.63 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 4.133e-05/0.004706, allocations: 36.81 kB / 0.652 GB, free: 35.63 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 4.49e-05/0.004751, allocations: 83.27 kB / 0.652 GB, free: 35.57 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 9.411e-05/0.004845, allocations: 137.7 kB / 0.6522 GB, free: 35.52 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002058/0.005051, allocations: 268.6 kB / 0.6524 GB, free: 35.39 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 2.425e-06/0.005053, allocations: 0 / 0.6524 GB, free: 35.39 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 7.12e-07/0.005054, allocations: 1.469 kB / 0.6524 GB, free: 35.39 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 4.889e-06/0.005059, allocations: 0 / 0.6524 GB, free: 35.39 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 0.0006213/0.00568, allocations: 0.6482 MB / 0.6531 GB, free: 34.85 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.225e-05/0.005713, allocations: 9.438 kB / 0.6531 GB, free: 34.85 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 7.767e-05/0.00579, allocations: 59.78 kB / 0.6531 GB, free: 34.82 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.000185/0.005975, allocations: 211 kB / 0.6533 GB, free: 34.63 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.418e-05/0.005999, allocations: 23.88 kB / 0.6534 GB, free: 34.62 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.024e-05/0.00604, allocations: 37.23 kB / 0.6534 GB, free: 34.61 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003748/0.006414, allocations: 333.8 kB / 0.6537 GB, free: 34.42 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.654e-05/0.006431, allocations: 4.5 kB / 0.6537 GB, free: 34.41 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.485e-05/0.006456, allocations: 16.38 kB / 0.6537 GB, free: 34.4 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.484e-05/0.006471, allocations: 6.75 kB / 0.6537 GB, free: 34.4 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002251/0.006696, allocations: 128.2 kB / 0.6539 GB, free: 34.39 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0008725/0.007568, allocations: 0.8556 MB / 0.6547 GB, free: 33.79 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002814/0.00785, allocations: 138.4 kB / 0.6548 GB, free: 33.73 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 8.7e-05/0.007937, allocations: 50.52 kB / 0.6549 GB, free: 33.71 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 2.322e-05/0.00796, allocations: 4.469 kB / 0.6549 GB, free: 33.71 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001876/0.008147, allocations: 130.9 kB / 0.655 GB, free: 33.64 MB / 0.5262 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.0001219/0.008269, allocations: 38.91 kB / 0.655 GB, free: 33.62 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=25): time 1.473e-06/0.008271, allocations: 0 / 0.655 GB, free: 33.62 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=25): time 0.0004179/0.008689, allocations: 216.1 kB / 0.6552 GB, free: 33.55 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.638e-05/0.008715, allocations: 67.09 kB / 0.6553 GB, free: 33.48 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001339/0.008849, allocations: 242.6 kB / 0.6555 GB, free: 33.29 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.548e-05/0.008864, allocations: 33.39 kB / 0.6556 GB, free: 33.25 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 7.878e-05/0.008943, allocations: 219.5 kB / 0.6558 GB, free: 33.05 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 5.798e-05/0.009001, allocations: 97.98 kB / 0.6559 GB, free: 32.98 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 8.789e-05/0.009089, allocations: 70.17 kB / 0.6559 GB, free: 32.93 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 6.066e-05/0.00915, allocations: 0.5052 MB / 0.6564 GB, free: 32.43 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001192/0.009269, allocations: 94.69 kB / 0.6565 GB, free: 32.38 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001247/0.009394, allocations: 221.7 kB / 0.6567 GB, free: 32.15 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002029/0.009596, allocations: 267.8 kB / 0.657 GB, free: 31.93 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.775e-06/0.009599, allocations: 0 / 0.657 GB, free: 31.93 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=41) (initialization): time 0.0003131/0.009912, allocations: 320.1 kB / 0.6573 GB, free: 31.77 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 2.531e-05/0.009938, allocations: 32.83 kB / 0.6573 GB, free: 31.74 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.564e-06/0.009945, allocations: 7.859 kB / 0.6573 GB, free: 31.73 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.769e-05/0.009963, allocations: 7.656 kB / 0.6573 GB, free: 31.73 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001986/0.01016, allocations: 82.69 kB / 0.6574 GB, free: 31.73 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 6.843e-06/0.01017, allocations: 8.125 kB / 0.6574 GB, free: 31.73 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.341e-05/0.01026, allocations: 15.58 kB / 0.6574 GB, free: 31.72 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.772e-05/0.01028, allocations: 15.34 kB / 0.6575 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 0.0001258/0.01041, allocations: 207.2 kB / 0.6577 GB, free: 31.53 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.208e-05/0.01044, allocations: 31.86 kB / 0.6577 GB, free: 31.52 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0002525/0.01069, allocations: 196.8 kB / 0.6579 GB, free: 31.43 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.236e-06/0.01069, allocations: 2.812 kB / 0.6579 GB, free: 31.43 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.765e-06/0.0107, allocations: 0 / 0.6579 GB, free: 31.43 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.898e-06/0.0107, allocations: 1.406 kB / 0.6579 GB, free: 31.43 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0001424/0.01084, allocations: 222.3 kB / 0.6581 GB, free: 31.25 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.903e-06/0.01084, allocations: 1.375 kB / 0.6581 GB, free: 31.25 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001525/0.011, allocations: 43.33 kB / 0.6581 GB, free: 31.25 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.706e-06/0.011, allocations: 1.375 kB / 0.6581 GB, free: 31.25 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.651e-05/0.01102, allocations: 9.016 kB / 0.6581 GB, free: 31.24 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.044e-06/0.01102, allocations: 1.406 kB / 0.6582 GB, free: 31.24 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.183e-06/0.01102, allocations: 0.7812 kB / 0.6582 GB, free: 31.24 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003077/0.01133, allocations: 272.8 kB / 0.6584 GB, free: 31.11 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 1.965e-05/0.01135, allocations: 20 kB / 0.6584 GB, free: 31.09 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.615e-05/0.01137, allocations: 8.219 kB / 0.6584 GB, free: 31.09 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 6.674e-05/0.01144, allocations: 13.66 kB / 0.6585 GB, free: 31.08 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.817e-05/0.01149, allocations: 19.8 kB / 0.6585 GB, free: 31.08 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.123e-05/0.0115, allocations: 13.05 kB / 0.6585 GB, free: 31.07 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 6.199e-05/0.01156, allocations: 176.7 kB / 0.6587 GB, free: 30.95 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 5.1e-08/0.01156, allocations: 0 / 0.6587 GB, free: 30.95 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0001919/0.01175, allocations: 86.58 kB / 0.6587 GB, free: 30.93 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 7.051e-05/0.01182, allocations: 105.9 kB / 0.6588 GB, free: 30.84 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0002732/0.0121, allocations: 250.2 kB / 0.6591 GB, free: 30.7 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.212e-06/0.0121, allocations: 0.9688 kB / 0.6591 GB, free: 30.7 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 9.161e-05/0.01219, allocations: 79.69 kB / 0.6591 GB, free: 30.68 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002563/0.01245, allocations: 85.12 kB / 0.6592 GB, free: 30.65 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001394/0.01384, allocations: 0.8449 MB / 0.6601 GB, free: 30.11 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 4.256e-05/0.01388, allocations: 86.91 kB / 0.6601 GB, free: 30.04 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 8.423e-05/0.01397, allocations: 35.52 kB / 0.6602 GB, free: 30.03 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 6.855e-05/0.01403, allocations: 28.55 kB / 0.6602 GB, free: 30.02 MB / 0.5262 GB
Notification: Performance of SimCode: time 6.01e-07/0.01403, allocations: 0 / 0.6602 GB, free: 30.02 MB / 0.5262 GB
Notification: Performance of Templates: time 0.005422/0.01946, allocations: 3.858 MB / 0.664 GB, free: 29.68 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: 4.545924311969429]