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 0.001666/0.001666, allocations: 80.81 kB / 19.94 MB, free: 4.543 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 0.002044/0.002044, allocations: 173 kB / 23.36 MB, free: 1.129 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 0.9517/0.9517, allocations: 177.1 MB / 203.8 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 1.666/1.666, allocations: 273.5 MB / 0.5213 GB, free: 14.64 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 8.92e-07/8.92e-07, allocations: 0 / 0.5954 GB, free: 2.73 MB / 0.5105 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 8.877e-06/9.769e-06, allocations: 2.312 kB / 0.5954 GB, free: 2.727 MB / 0.5105 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue): time 0.002539/0.002548, allocations: 2.973 MB / 0.5983 GB, free: 15.78 MB / 0.5261 GB
Notification: Performance of NFInst.instExpressions: time 0.00128/0.003828, allocations: 0.7616 MB / 0.599 GB, free: 15.02 MB / 0.5261 GB
Notification: Performance of NFInst.updateImplicitVariability: time 8.704e-05/0.003915, allocations: 7.938 kB / 0.599 GB, free: 15.02 MB / 0.5261 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001059/0.004021, allocations: 47.56 kB / 0.5991 GB, free: 14.97 MB / 0.5261 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001989/0.00422, allocations: 127.4 kB / 0.5992 GB, free: 14.88 MB / 0.5261 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0002/0.00442, allocations: 99.73 kB / 0.5993 GB, free: 14.79 MB / 0.5261 GB
Notification: Performance of NFFlatten.flatten: time 0.0003201/0.00474, allocations: 424.4 kB / 0.5997 GB, free: 14.39 MB / 0.5261 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.000231/0.004971, allocations: 230.7 kB / 0.5999 GB, free: 14.17 MB / 0.5261 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002072/0.005178, allocations: 263.5 kB / 0.6002 GB, free: 13.91 MB / 0.5261 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001745/0.005353, allocations: 151.6 kB / 0.6003 GB, free: 13.76 MB / 0.5261 GB
Notification: Performance of NFPackage.collectConstants: time 3.889e-05/0.005392, allocations: 36 kB / 0.6004 GB, free: 13.73 MB / 0.5261 GB
Notification: Performance of NFFlatten.collectFunctions: time 3.787e-05/0.005429, allocations: 40 kB / 0.6004 GB, free: 13.69 MB / 0.5261 GB
Notification: Performance of NFScalarize.scalarize: time 5.404e-05/0.005483, allocations: 83.67 kB / 0.6005 GB, free: 13.61 MB / 0.5261 GB
Notification: Performance of NFVerifyModel.verify: time 9.584e-05/0.005579, allocations: 139.7 kB / 0.6006 GB, free: 13.47 MB / 0.5261 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002213/0.005801, allocations: 271 kB / 0.6009 GB, free: 13.2 MB / 0.5261 GB
Notification: Performance of FrontEnd - DAE generated: time 1.443e-06/0.005802, allocations: 0 / 0.6009 GB, free: 13.2 MB / 0.5261 GB
Notification: Performance of FrontEnd: time 4.71e-07/0.005802, allocations: 0 / 0.6009 GB, free: 13.2 MB / 0.5261 GB
Notification: Performance of Transformations before backend: time 3.396e-06/0.005806, allocations: 8 kB / 0.6009 GB, free: 13.2 MB / 0.5261 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 0.0005684/0.006374, allocations: 0.5173 MB / 0.6014 GB, free: 12.65 MB / 0.5261 GB
Notification: Performance of prepare preOptimizeDAE: time 2.783e-05/0.006402, allocations: 11.97 kB / 0.6014 GB, free: 12.64 MB / 0.5261 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.149e-05/0.006464, allocations: 48.89 kB / 0.6014 GB, free: 12.59 MB / 0.5261 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001737/0.006637, allocations: 169.3 kB / 0.6016 GB, free: 12.4 MB / 0.5261 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.475e-05/0.006662, allocations: 21.03 kB / 0.6016 GB, free: 12.38 MB / 0.5261 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.182e-05/0.006704, allocations: 36.36 kB / 0.6017 GB, free: 12.34 MB / 0.5261 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003945/0.007098, allocations: 317.2 kB / 0.602 GB, free: 12.01 MB / 0.5261 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.408e-05/0.007112, allocations: 3.938 kB / 0.602 GB, free: 12 MB / 0.5261 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.883e-05/0.007131, allocations: 12 kB / 0.602 GB, free: 11.99 MB / 0.5261 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.424e-06/0.007139, allocations: 8 kB / 0.602 GB, free: 11.98 MB / 0.5261 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001319/0.007271, allocations: 97.42 kB / 0.6021 GB, free: 11.89 MB / 0.5261 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0007823/0.008053, allocations: 0.6171 MB / 0.6027 GB, free: 11.25 MB / 0.5261 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0001768/0.00823, allocations: 102.5 kB / 0.6028 GB, free: 11.14 MB / 0.5261 GB
Notification: Performance of preOpt resolveLoops (simulation): time 4.849e-05/0.008278, allocations: 40.83 kB / 0.6028 GB, free: 11.1 MB / 0.5261 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.664e-05/0.008295, allocations: 4 kB / 0.6028 GB, free: 11.1 MB / 0.5261 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001262/0.008421, allocations: 121.4 kB / 0.6029 GB, free: 10.97 MB / 0.5261 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.0001044/0.008525, allocations: 43.91 kB / 0.603 GB, free: 10.93 MB / 0.5261 GB
Notification: Performance of pre-optimization done (n=25): time 1.944e-06/0.008527, allocations: 3.609 kB / 0.603 GB, free: 10.93 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=25): time 0.0002077/0.008735, allocations: 142.2 kB / 0.6031 GB, free: 10.78 MB / 0.5261 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.733e-05/0.008762, allocations: 59.41 kB / 0.6032 GB, free: 10.71 MB / 0.5261 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 9.642e-05/0.008859, allocations: 184 kB / 0.6033 GB, free: 10.52 MB / 0.5261 GB
Notification: Performance of collectPreVariables (initialization): time 1.962e-05/0.008878, allocations: 33.64 kB / 0.6034 GB, free: 10.48 MB / 0.5261 GB
Notification: Performance of collectInitialEqns (initialization): time 6.045e-05/0.008939, allocations: 164.5 kB / 0.6035 GB, free: 10.32 MB / 0.5261 GB
Notification: Performance of collectInitialBindings (initialization): time 5.078e-05/0.00899, allocations: 99.14 kB / 0.6036 GB, free: 10.22 MB / 0.5261 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 6.711e-05/0.009057, allocations: 73.61 kB / 0.6037 GB, free: 10.14 MB / 0.5261 GB
Notification: Performance of setup shared object (initialization): time 7.957e-05/0.009136, allocations: 334.8 kB / 0.604 GB, free: 9.805 MB / 0.5261 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 6.973e-05/0.009206, allocations: 75.11 kB / 0.6041 GB, free: 9.723 MB / 0.5261 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.000101/0.009307, allocations: 178.1 kB / 0.6043 GB, free: 9.5 MB / 0.5261 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.000158/0.009465, allocations: 210.1 kB / 0.6045 GB, free: 9.258 MB / 0.5261 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.254e-06/0.009467, allocations: 0 / 0.6045 GB, free: 9.258 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=41) (initialization): time 0.0002158/0.009683, allocations: 252.9 kB / 0.6047 GB, free: 8.992 MB / 0.5261 GB
Notification: Performance of prepare postOptimizeDAE: time 2.231e-05/0.009705, allocations: 33.7 kB / 0.6047 GB, free: 8.953 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 3.918e-06/0.009709, allocations: 0 / 0.6047 GB, free: 8.953 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.27e-05/0.009722, allocations: 4 kB / 0.6047 GB, free: 8.949 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001778/0.0099, allocations: 87.83 kB / 0.6048 GB, free: 8.863 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 6.562e-06/0.009906, allocations: 7.984 kB / 0.6048 GB, free: 8.855 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 8.822e-05/0.009994, allocations: 12 kB / 0.6048 GB, free: 8.844 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.695e-05/0.01001, allocations: 15.98 kB / 0.6049 GB, free: 8.828 MB / 0.5261 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 0.0001164/0.01013, allocations: 145.8 kB / 0.605 GB, free: 8.68 MB / 0.5261 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 2.588e-05/0.01015, allocations: 23.92 kB / 0.605 GB, free: 8.656 MB / 0.5261 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001787/0.01033, allocations: 154.6 kB / 0.6052 GB, free: 8.5 MB / 0.5261 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.066e-06/0.01034, allocations: 3.984 kB / 0.6052 GB, free: 8.496 MB / 0.5261 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 1.834e-06/0.01034, allocations: 4 kB / 0.6052 GB, free: 8.492 MB / 0.5261 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.559e-06/0.01034, allocations: 7.656 kB / 0.6052 GB, free: 8.488 MB / 0.5261 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0001305/0.01047, allocations: 145.8 kB / 0.6053 GB, free: 8.328 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.633e-06/0.01047, allocations: 0 / 0.6053 GB, free: 8.328 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001293/0.0106, allocations: 35.98 kB / 0.6053 GB, free: 8.293 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (simulation): time 3.597e-06/0.01061, allocations: 7.984 kB / 0.6054 GB, free: 8.285 MB / 0.5261 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.51e-05/0.01062, allocations: 11.62 kB / 0.6054 GB, free: 8.277 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.282e-06/0.01062, allocations: 0 / 0.6054 GB, free: 8.277 MB / 0.5261 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.072e-06/0.01062, allocations: 0 / 0.6054 GB, free: 8.277 MB / 0.5261 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0002074/0.01083, allocations: 209.9 kB / 0.6056 GB, free: 8.055 MB / 0.5261 GB
Notification: Performance of postOpt removeConstants (simulation): time 1.939e-05/0.01085, allocations: 19.86 kB / 0.6056 GB, free: 8.035 MB / 0.5261 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.402e-05/0.01088, allocations: 7.938 kB / 0.6056 GB, free: 8.027 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 6.465e-05/0.01094, allocations: 19.92 kB / 0.6056 GB, free: 8.008 MB / 0.5261 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.5e-05/0.01097, allocations: 11.97 kB / 0.6056 GB, free: 7.996 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 9.387e-06/0.01098, allocations: 8 kB / 0.6056 GB, free: 7.988 MB / 0.5261 GB
Notification: Performance of sorting global known variables: time 4.258e-05/0.01103, allocations: 56.84 kB / 0.6057 GB, free: 7.934 MB / 0.5261 GB
Notification: Performance of sort global known variables: time 5e-08/0.01103, allocations: 0 / 0.6057 GB, free: 7.934 MB / 0.5261 GB
Notification: Performance of remove unused functions: time 0.0001768/0.0112, allocations: 87.83 kB / 0.6058 GB, free: 7.848 MB / 0.5261 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 6.768e-05/0.01127, allocations: 92.36 kB / 0.6059 GB, free: 7.75 MB / 0.5261 GB
Notification: Performance of simCode: created initialization part: time 0.0004661/0.01174, allocations: 221.2 kB / 0.6061 GB, free: 7.516 MB / 0.5261 GB
Notification: Performance of simCode: created event and clocks part: time 4.819e-06/0.01174, allocations: 4 kB / 0.6061 GB, free: 7.512 MB / 0.5261 GB
Notification: Performance of simCode: created simulation system equations: time 7.041e-05/0.01181, allocations: 64.7 kB / 0.6061 GB, free: 7.445 MB / 0.5261 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0001858/0.012, allocations: 84.22 kB / 0.6062 GB, free: 7.367 MB / 0.5261 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0012/0.0132, allocations: 0.6783 MB / 0.6069 GB, free: 6.664 MB / 0.5261 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 4.937e-05/0.01325, allocations: 92.31 kB / 0.607 GB, free: 6.551 MB / 0.5261 GB
Notification: Performance of simCode: alias equations: time 8.801e-05/0.01334, allocations: 33.66 kB / 0.607 GB, free: 6.52 MB / 0.5261 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001468/0.01348, allocations: 115.3 kB / 0.6071 GB, free: 6.406 MB / 0.5261 GB
Notification: Performance of SimCode: time 4.31e-07/0.01348, allocations: 0 / 0.6071 GB, free: 6.406 MB / 0.5261 GB
Notification: Performance of Templates: time 0.005197/0.01868, allocations: 3.936 MB / 0.611 GB, free: 2.672 MB / 0.5261 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: 4.6230043838731945]