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 0.0009155/0.0009155, allocations: 92.2 kB / 20.19 MB, free: 4.355 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 0.0009325/0.0009325, allocations: 177 kB / 23.5 MB, free: 1.047 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 0.9206/0.9206, allocations: 177.1 MB / 203.8 MB, free: 5.633 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 1.566/1.566, allocations: 273.5 MB / 0.5213 GB, free: 14.84 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 / 0.6462 GB, free: 39.09 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.989e-05/2.141e-05, allocations: 9.516 kB / 0.6462 GB, free: 39.09 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue): time 0.002433/0.002454, allocations: 2.976 MB / 0.6491 GB, free: 37.16 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.0008199/0.003274, allocations: 0.7519 MB / 0.6498 GB, free: 36.66 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 8.862e-05/0.003363, allocations: 4 kB / 0.6498 GB, free: 36.66 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001185/0.003481, allocations: 45.64 kB / 0.6499 GB, free: 36.64 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001986/0.00368, allocations: 124.7 kB / 0.65 GB, free: 36.59 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.000197/0.003877, allocations: 95.69 kB / 0.6501 GB, free: 36.53 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002782/0.004155, allocations: 437.3 kB / 0.6505 GB, free: 36.3 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002597/0.004415, allocations: 222.5 kB / 0.6507 GB, free: 36.18 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.000189/0.004604, allocations: 258 kB / 0.651 GB, free: 36.07 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001763/0.00478, allocations: 161.6 kB / 0.6511 GB, free: 36.02 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 4.615e-05/0.004826, allocations: 37.84 kB / 0.6512 GB, free: 36.02 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 3.818e-05/0.004864, allocations: 38.5 kB / 0.6512 GB, free: 36.02 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 4.695e-05/0.004911, allocations: 87.28 kB / 0.6513 GB, free: 35.97 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 0.0001006/0.005012, allocations: 137.4 kB / 0.6514 GB, free: 35.91 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002276/0.00524, allocations: 276.4 kB / 0.6517 GB, free: 35.77 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 2.765e-06/0.005242, allocations: 0 / 0.6517 GB, free: 35.77 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 9.42e-07/0.005243, allocations: 1.281 kB / 0.6517 GB, free: 35.77 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 5.8e-06/0.005249, allocations: 2.156 kB / 0.6517 GB, free: 35.77 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 0.0006542/0.005903, allocations: 0.6479 MB / 0.6523 GB, free: 35.24 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.448e-05/0.005938, allocations: 11.22 kB / 0.6523 GB, free: 35.24 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 8.211e-05/0.00602, allocations: 54.41 kB / 0.6524 GB, free: 35.21 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002477/0.006268, allocations: 239.1 kB / 0.6526 GB, free: 35.02 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.648e-05/0.006284, allocations: 20.81 kB / 0.6526 GB, free: 35.01 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.314e-05/0.006327, allocations: 37.42 kB / 0.6527 GB, free: 34.99 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003424/0.00667, allocations: 337.3 kB / 0.653 GB, free: 34.8 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.429e-05/0.006684, allocations: 3.938 kB / 0.653 GB, free: 34.8 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.351e-05/0.006707, allocations: 11.44 kB / 0.653 GB, free: 34.79 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.897e-06/0.006716, allocations: 9.812 kB / 0.653 GB, free: 34.79 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001909/0.006907, allocations: 134.1 kB / 0.6531 GB, free: 34.77 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0008888/0.007796, allocations: 0.8553 MB / 0.654 GB, free: 34.17 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002556/0.008052, allocations: 136.4 kB / 0.6541 GB, free: 34.11 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 7.26e-05/0.008124, allocations: 52.62 kB / 0.6541 GB, free: 34.09 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 2.132e-05/0.008146, allocations: 5 kB / 0.6542 GB, free: 34.09 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001639/0.008309, allocations: 132.1 kB / 0.6543 GB, free: 34.02 MB / 0.5262 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.0001096/0.008419, allocations: 38.84 kB / 0.6543 GB, free: 34.01 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=25): time 1.383e-06/0.00842, allocations: 1.156 kB / 0.6543 GB, free: 34.01 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=25): time 0.0003461/0.008767, allocations: 212.3 kB / 0.6545 GB, free: 33.93 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.609e-05/0.008793, allocations: 71.47 kB / 0.6546 GB, free: 33.86 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001032/0.008896, allocations: 234.8 kB / 0.6548 GB, free: 33.68 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.501e-05/0.008911, allocations: 33.11 kB / 0.6548 GB, free: 33.64 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 6.49e-05/0.008976, allocations: 226 kB / 0.6551 GB, free: 33.44 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 4.921e-05/0.009025, allocations: 92.48 kB / 0.6551 GB, free: 33.36 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 8.303e-05/0.009108, allocations: 74.86 kB / 0.6552 GB, free: 33.32 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 5.358e-05/0.009162, allocations: 0.4974 MB / 0.6557 GB, free: 32.82 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001039/0.009266, allocations: 100.6 kB / 0.6558 GB, free: 32.76 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.000131/0.009397, allocations: 216.6 kB / 0.656 GB, free: 32.54 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002127/0.009609, allocations: 264.1 kB / 0.6563 GB, free: 32.32 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.304e-06/0.009612, allocations: 0 / 0.6563 GB, free: 32.32 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=41) (initialization): time 0.00032/0.009932, allocations: 325.1 kB / 0.6566 GB, free: 32.16 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 2.899e-05/0.009961, allocations: 38.7 kB / 0.6566 GB, free: 32.12 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 4.769e-06/0.009965, allocations: 0 / 0.6566 GB, free: 32.12 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.816e-05/0.009983, allocations: 4.312 kB / 0.6566 GB, free: 32.12 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002291/0.01021, allocations: 84.83 kB / 0.6567 GB, free: 32.12 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.018e-05/0.01022, allocations: 7.469 kB / 0.6567 GB, free: 32.12 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.000103/0.01033, allocations: 15.92 kB / 0.6567 GB, free: 32.11 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.743e-05/0.01035, allocations: 15.53 kB / 0.6567 GB, free: 32.11 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 0.0001396/0.01049, allocations: 197.8 kB / 0.6569 GB, free: 31.93 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 4.057e-05/0.01053, allocations: 25.75 kB / 0.6569 GB, free: 31.91 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0003067/0.01084, allocations: 202 kB / 0.6571 GB, free: 31.82 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.519e-06/0.01084, allocations: 2.812 kB / 0.6571 GB, free: 31.82 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.066e-06/0.01085, allocations: 2.406 kB / 0.6571 GB, free: 31.82 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.849e-06/0.01085, allocations: 3.891 kB / 0.6571 GB, free: 31.82 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0001669/0.01102, allocations: 221.2 kB / 0.6574 GB, free: 31.64 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.304e-06/0.01102, allocations: 0.5312 kB / 0.6574 GB, free: 31.64 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001591/0.01118, allocations: 43.61 kB / 0.6574 GB, free: 31.64 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 3.597e-06/0.01118, allocations: 0.5625 kB / 0.6574 GB, free: 31.64 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.926e-05/0.0112, allocations: 11.8 kB / 0.6574 GB, free: 31.63 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.916e-06/0.01121, allocations: 1.125 kB / 0.6574 GB, free: 31.63 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.022e-06/0.01121, allocations: 0.5625 kB / 0.6574 GB, free: 31.63 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003379/0.01155, allocations: 272.2 kB / 0.6577 GB, free: 31.5 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.083e-05/0.01157, allocations: 21.61 kB / 0.6577 GB, free: 31.48 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.48e-05/0.01159, allocations: 10.72 kB / 0.6577 GB, free: 31.48 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.152e-05/0.01166, allocations: 16.42 kB / 0.6577 GB, free: 31.47 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.648e-05/0.01171, allocations: 21.7 kB / 0.6577 GB, free: 31.46 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.165e-05/0.01172, allocations: 6.531 kB / 0.6577 GB, free: 31.46 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 6.135e-05/0.01178, allocations: 178.5 kB / 0.6579 GB, free: 31.34 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 5e-08/0.01178, allocations: 0 / 0.6579 GB, free: 31.34 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0001971/0.01198, allocations: 90.62 kB / 0.658 GB, free: 31.32 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 7.21e-05/0.01205, allocations: 104 kB / 0.6581 GB, free: 31.22 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.000254/0.01231, allocations: 249.2 kB / 0.6583 GB, free: 31.09 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.302e-06/0.01231, allocations: 0 / 0.6583 GB, free: 31.09 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 9.098e-05/0.0124, allocations: 82.7 kB / 0.6584 GB, free: 31.06 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002593/0.01266, allocations: 83.09 kB / 0.6585 GB, free: 31.03 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001501/0.01416, allocations: 0.8756 MB / 0.6593 GB, free: 30.46 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 7.97e-05/0.01424, allocations: 158 kB / 0.6595 GB, free: 30.38 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 8.139e-05/0.01432, allocations: 30.23 kB / 0.6595 GB, free: 30.37 MB / 0.5262 GB
Notification: Performance of SimCode: time 7.51e-07/0.01432, allocations: 0 / 0.6595 GB, free: 30.37 MB / 0.5262 GB
Notification: Performance of Templates: time 0.003606/0.01793, allocations: 3.658 MB / 0.6631 GB, free: 30.07 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 > Pharmacolibrary_Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 6.246572549920529]