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 0.00139/0.00139, allocations: 85.08 kB / 19.87 MB, free: 4.617 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 0.001526/0.001526, allocations: 169 kB / 23.27 MB, free: 1.223 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 0.9448/0.9448, allocations: 177.1 MB / 203.7 MB, free: 5.516 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 1.645/1.645, allocations: 273.5 MB / 0.5212 GB, free: 14.77 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 1.783e-06/1.783e-06, allocations: 0 / 0.6474 GB, free: 38.53 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.172e-05/1.351e-05, allocations: 3.438 kB / 0.6474 GB, free: 38.53 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue): time 0.003134/0.003147, allocations: 2.953 MB / 0.6503 GB, free: 36.61 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.001016/0.004163, allocations: 0.7532 MB / 0.651 GB, free: 36.1 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001212/0.004285, allocations: 2.125 kB / 0.651 GB, free: 36.1 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001443/0.004429, allocations: 44.58 kB / 0.6511 GB, free: 36.08 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0002616/0.00469, allocations: 119.6 kB / 0.6512 GB, free: 36.03 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0002473/0.004938, allocations: 97.3 kB / 0.6513 GB, free: 35.98 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.000362/0.0053, allocations: 441.1 kB / 0.6517 GB, free: 35.75 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0002975/0.005597, allocations: 233.9 kB / 0.6519 GB, free: 35.61 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002609/0.005858, allocations: 257.1 kB / 0.6521 GB, free: 35.51 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002249/0.006083, allocations: 156.4 kB / 0.6523 GB, free: 35.46 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 5.625e-05/0.006139, allocations: 37.19 kB / 0.6523 GB, free: 35.46 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 6.018e-05/0.006199, allocations: 38.09 kB / 0.6524 GB, free: 35.46 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 5.565e-05/0.006255, allocations: 81.31 kB / 0.6524 GB, free: 35.41 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 0.0001203/0.006375, allocations: 137.5 kB / 0.6526 GB, free: 35.35 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002731/0.006648, allocations: 273.6 kB / 0.6528 GB, free: 35.21 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 2.295e-06/0.006651, allocations: 0 / 0.6528 GB, free: 35.21 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 6.11e-07/0.006651, allocations: 0 / 0.6528 GB, free: 35.21 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 4.779e-06/0.006656, allocations: 1.469 kB / 0.6528 GB, free: 35.21 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 0.0007422/0.007398, allocations: 0.6538 MB / 0.6535 GB, free: 34.67 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.561e-05/0.007434, allocations: 8.125 kB / 0.6535 GB, free: 34.67 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 9.18e-05/0.007526, allocations: 56.22 kB / 0.6535 GB, free: 34.65 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002062/0.007732, allocations: 209.7 kB / 0.6537 GB, free: 34.46 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.736e-05/0.007759, allocations: 20.34 kB / 0.6538 GB, free: 34.45 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 5.116e-05/0.00781, allocations: 37.72 kB / 0.6538 GB, free: 34.44 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004155/0.008226, allocations: 311.5 kB / 0.6541 GB, free: 34.26 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.71e-05/0.008243, allocations: 6.219 kB / 0.6541 GB, free: 34.26 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.793e-05/0.008271, allocations: 10.72 kB / 0.6541 GB, free: 34.25 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.439e-05/0.008285, allocations: 10.62 kB / 0.6541 GB, free: 34.25 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002077/0.008493, allocations: 115.9 kB / 0.6542 GB, free: 34.24 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001101/0.009594, allocations: 0.8187 MB / 0.655 GB, free: 33.66 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0003112/0.009905, allocations: 130.2 kB / 0.6552 GB, free: 33.61 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001001/0.01001, allocations: 41.36 kB / 0.6552 GB, free: 33.59 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 2.363e-05/0.01003, allocations: 12.91 kB / 0.6552 GB, free: 33.59 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001997/0.01023, allocations: 119 kB / 0.6553 GB, free: 33.53 MB / 0.5262 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.0001699/0.0104, allocations: 42.59 kB / 0.6554 GB, free: 33.51 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=25): time 2.044e-06/0.0104, allocations: 0.5625 kB / 0.6554 GB, free: 33.51 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=25): time 0.0004454/0.01085, allocations: 198.1 kB / 0.6555 GB, free: 33.45 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.534e-05/0.01087, allocations: 68.59 kB / 0.6556 GB, free: 33.37 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001568/0.01103, allocations: 238.5 kB / 0.6558 GB, free: 33.18 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.942e-05/0.01105, allocations: 33.77 kB / 0.6559 GB, free: 33.15 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 8.144e-05/0.01113, allocations: 223 kB / 0.6561 GB, free: 32.95 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 6.544e-05/0.01119, allocations: 97.34 kB / 0.6562 GB, free: 32.87 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001096/0.0113, allocations: 70.59 kB / 0.6562 GB, free: 32.82 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 6.841e-05/0.01137, allocations: 0.5056 MB / 0.6567 GB, free: 32.32 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.000112/0.01148, allocations: 91.3 kB / 0.6568 GB, free: 32.27 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001466/0.01163, allocations: 210 kB / 0.657 GB, free: 32.05 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002386/0.01187, allocations: 241.5 kB / 0.6573 GB, free: 31.84 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.118e-06/0.01187, allocations: 1.406 kB / 0.6573 GB, free: 31.84 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=41) (initialization): time 0.0003939/0.01227, allocations: 302.5 kB / 0.6575 GB, free: 31.69 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 2.376e-05/0.01229, allocations: 36.77 kB / 0.6576 GB, free: 31.65 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.582e-06/0.0123, allocations: 2.844 kB / 0.6576 GB, free: 31.65 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.638e-05/0.01231, allocations: 4.312 kB / 0.6576 GB, free: 31.65 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002826/0.0126, allocations: 85.39 kB / 0.6577 GB, free: 31.64 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 7.054e-06/0.0126, allocations: 11.58 kB / 0.6577 GB, free: 31.64 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001504/0.01275, allocations: 16.53 kB / 0.6577 GB, free: 31.64 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.24e-05/0.01278, allocations: 11.81 kB / 0.6577 GB, free: 31.64 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 0.0001355/0.01291, allocations: 204.8 kB / 0.6579 GB, free: 31.45 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 4.295e-05/0.01296, allocations: 25.97 kB / 0.6579 GB, free: 31.44 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0002941/0.01325, allocations: 190.5 kB / 0.6581 GB, free: 31.35 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.745e-06/0.01325, allocations: 1.562 kB / 0.6581 GB, free: 31.35 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.054e-06/0.01325, allocations: 5.031 kB / 0.6581 GB, free: 31.35 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.897e-06/0.01326, allocations: 0 / 0.6581 GB, free: 31.35 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0001779/0.01344, allocations: 175 kB / 0.6583 GB, free: 31.21 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.713e-06/0.01344, allocations: 1.406 kB / 0.6583 GB, free: 31.21 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.000204/0.01364, allocations: 43.62 kB / 0.6583 GB, free: 31.2 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.594e-06/0.01364, allocations: 5.469 kB / 0.6583 GB, free: 31.2 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.048e-05/0.01367, allocations: 13.7 kB / 0.6583 GB, free: 31.2 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.254e-06/0.01367, allocations: 1.406 kB / 0.6583 GB, free: 31.2 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 7.61e-07/0.01367, allocations: 3.938 kB / 0.6583 GB, free: 31.19 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003455/0.01401, allocations: 254.5 kB / 0.6586 GB, free: 31.07 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.564e-05/0.01404, allocations: 17.42 kB / 0.6586 GB, free: 31.05 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.315e-05/0.01407, allocations: 10.75 kB / 0.6586 GB, free: 31.05 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001105/0.01418, allocations: 12.86 kB / 0.6586 GB, free: 31.04 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.574e-05/0.01423, allocations: 19.73 kB / 0.6587 GB, free: 31.04 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.488e-05/0.01424, allocations: 4.219 kB / 0.6587 GB, free: 31.04 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 7.598e-05/0.01432, allocations: 175.8 kB / 0.6588 GB, free: 30.91 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 1e-07/0.01432, allocations: 3 kB / 0.6588 GB, free: 30.91 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0003311/0.01465, allocations: 85.89 kB / 0.6589 GB, free: 30.89 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 7.646e-05/0.01473, allocations: 106.6 kB / 0.659 GB, free: 30.8 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0002817/0.01501, allocations: 230.1 kB / 0.6592 GB, free: 30.68 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.743e-06/0.01501, allocations: 4 kB / 0.6592 GB, free: 30.67 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001083/0.01512, allocations: 71.48 kB / 0.6593 GB, free: 30.65 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003558/0.01547, allocations: 73.92 kB / 0.6594 GB, free: 30.64 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001893/0.01737, allocations: 0.8424 MB / 0.6602 GB, free: 30.11 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 4.625e-05/0.01741, allocations: 89.77 kB / 0.6603 GB, free: 30.04 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 0.00013/0.01754, allocations: 34.53 kB / 0.6603 GB, free: 30.03 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0002087/0.01775, allocations: 146 kB / 0.6605 GB, free: 29.95 MB / 0.5262 GB
Notification: Performance of SimCode: time 4.51e-07/0.01775, allocations: 0 / 0.6605 GB, free: 29.95 MB / 0.5262 GB
Notification: Performance of Templates: time 0.007557/0.02531, allocations: 4.005 MB / 0.6644 GB, free: 29.57 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: 4.716643060091883]