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 0.001435/0.001435, allocations: 92.2 kB / 20.19 MB, free: 4.359 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 0.001767/0.001767, allocations: 173 kB / 23.49 MB, free: 1.055 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 0.9044/0.9044, allocations: 177.1 MB / 203.8 MB, free: 5.602 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 1.481/1.481, allocations: 273.5 MB / 0.5213 GB, free: 14.92 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 1.984e-06/1.984e-06, allocations: 0 / 0.647 GB, free: 38.57 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 1.564e-05/1.762e-05, allocations: 5.406 kB / 0.647 GB, free: 38.57 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue): time 0.003207/0.003224, allocations: 2.966 MB / 0.6499 GB, free: 36.64 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.000996/0.00422, allocations: 0.7547 MB / 0.6506 GB, free: 36.14 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001092/0.004329, allocations: 3.594 kB / 0.6506 GB, free: 36.14 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001177/0.004447, allocations: 46.39 kB / 0.6507 GB, free: 36.12 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0002062/0.004653, allocations: 125 kB / 0.6508 GB, free: 36.07 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.000209/0.004862, allocations: 91.22 kB / 0.6509 GB, free: 36.02 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0002857/0.005148, allocations: 443.6 kB / 0.6513 GB, free: 35.79 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.000252/0.0054, allocations: 227.4 kB / 0.6515 GB, free: 35.66 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001934/0.005593, allocations: 254.6 kB / 0.6517 GB, free: 35.55 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001775/0.005771, allocations: 163.7 kB / 0.6519 GB, free: 35.5 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 4.482e-05/0.005816, allocations: 38.97 kB / 0.6519 GB, free: 35.5 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 4.161e-05/0.005857, allocations: 39.88 kB / 0.652 GB, free: 35.5 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 4.474e-05/0.005902, allocations: 79.88 kB / 0.652 GB, free: 35.45 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 0.0001025/0.006005, allocations: 145.2 kB / 0.6522 GB, free: 35.39 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002188/0.006223, allocations: 264.8 kB / 0.6524 GB, free: 35.26 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 2.124e-06/0.006225, allocations: 5.656 kB / 0.6524 GB, free: 35.26 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 6.72e-07/0.006226, allocations: 0 / 0.6524 GB, free: 35.26 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 5.871e-06/0.006232, allocations: 0 / 0.6524 GB, free: 35.26 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 0.0006379/0.00687, allocations: 0.6542 MB / 0.6531 GB, free: 34.72 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.237e-05/0.006902, allocations: 9.312 kB / 0.6531 GB, free: 34.72 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 7.904e-05/0.006981, allocations: 57.53 kB / 0.6531 GB, free: 34.7 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002348/0.007216, allocations: 228.8 kB / 0.6534 GB, free: 34.5 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.504e-05/0.007231, allocations: 20.66 kB / 0.6534 GB, free: 34.49 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.957e-05/0.007271, allocations: 47.22 kB / 0.6534 GB, free: 34.47 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003349/0.007606, allocations: 328.5 kB / 0.6537 GB, free: 34.29 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.363e-05/0.007619, allocations: 7 kB / 0.6537 GB, free: 34.29 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.147e-05/0.007641, allocations: 12.16 kB / 0.6538 GB, free: 34.28 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.556e-06/0.007649, allocations: 5.75 kB / 0.6538 GB, free: 34.28 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002063/0.007856, allocations: 135.4 kB / 0.6539 GB, free: 34.26 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0008372/0.008693, allocations: 0.8574 MB / 0.6547 GB, free: 33.65 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002487/0.008941, allocations: 137.3 kB / 0.6549 GB, free: 33.6 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 7.622e-05/0.009018, allocations: 57.38 kB / 0.6549 GB, free: 33.57 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.743e-05/0.009035, allocations: 3.969 kB / 0.6549 GB, free: 33.57 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001431/0.009178, allocations: 128 kB / 0.655 GB, free: 33.51 MB / 0.5262 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.0001079/0.009286, allocations: 38.62 kB / 0.6551 GB, free: 33.49 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=25): time 1.233e-06/0.009287, allocations: 0.5625 kB / 0.6551 GB, free: 33.49 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=25): time 0.0003284/0.009616, allocations: 222 kB / 0.6553 GB, free: 33.41 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 1.58e-05/0.009631, allocations: 63.28 kB / 0.6554 GB, free: 33.34 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001181/0.009749, allocations: 240.2 kB / 0.6556 GB, free: 33.16 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 1.471e-05/0.009764, allocations: 32.08 kB / 0.6556 GB, free: 33.12 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 5.156e-05/0.009816, allocations: 216.9 kB / 0.6558 GB, free: 32.93 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 4.396e-05/0.00986, allocations: 105.5 kB / 0.6559 GB, free: 32.84 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.954e-05/0.009919, allocations: 65.94 kB / 0.656 GB, free: 32.8 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 4.779e-05/0.009967, allocations: 0.501 MB / 0.6565 GB, free: 32.3 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 9.591e-05/0.01006, allocations: 94.09 kB / 0.6566 GB, free: 32.25 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.000116/0.01018, allocations: 228.8 kB / 0.6568 GB, free: 32.02 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.000224/0.0104, allocations: 265.4 kB / 0.657 GB, free: 31.8 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.166e-06/0.01041, allocations: 1.125 kB / 0.657 GB, free: 31.8 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=41) (initialization): time 0.0004108/0.01082, allocations: 318.2 kB / 0.6573 GB, free: 31.64 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 2.625e-05/0.01084, allocations: 32.86 kB / 0.6574 GB, free: 31.61 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.955e-06/0.01085, allocations: 5.375 kB / 0.6574 GB, free: 31.61 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.881e-05/0.01087, allocations: 4.406 kB / 0.6574 GB, free: 31.61 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002189/0.01109, allocations: 84.53 kB / 0.6575 GB, free: 31.6 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.022e-05/0.0111, allocations: 4.5 kB / 0.6575 GB, free: 31.6 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.939e-05/0.0112, allocations: 16.23 kB / 0.6575 GB, free: 31.59 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.231e-05/0.01122, allocations: 18.67 kB / 0.6575 GB, free: 31.59 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 0.0001326/0.01135, allocations: 212.1 kB / 0.6577 GB, free: 31.4 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.78e-05/0.01139, allocations: 26.44 kB / 0.6577 GB, free: 31.39 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0002773/0.01167, allocations: 197.5 kB / 0.6579 GB, free: 31.3 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.375e-06/0.01167, allocations: 2.688 kB / 0.6579 GB, free: 31.3 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.456e-06/0.01167, allocations: 0 / 0.6579 GB, free: 31.3 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.576e-06/0.01168, allocations: 0 / 0.6579 GB, free: 31.3 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0001359/0.01181, allocations: 224.5 kB / 0.6581 GB, free: 31.12 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.713e-06/0.01182, allocations: 0 / 0.6581 GB, free: 31.12 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001425/0.01196, allocations: 43.3 kB / 0.6582 GB, free: 31.12 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.314e-06/0.01196, allocations: 1.406 kB / 0.6582 GB, free: 31.12 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.558e-05/0.01198, allocations: 8.594 kB / 0.6582 GB, free: 31.11 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.182e-06/0.01198, allocations: 1.406 kB / 0.6582 GB, free: 31.11 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 7.91e-07/0.01198, allocations: 0 / 0.6582 GB, free: 31.11 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0002954/0.01227, allocations: 279 kB / 0.6584 GB, free: 30.97 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 1.862e-05/0.01229, allocations: 19.44 kB / 0.6585 GB, free: 30.96 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.57e-05/0.01232, allocations: 6.844 kB / 0.6585 GB, free: 30.96 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 6.944e-05/0.01239, allocations: 13.16 kB / 0.6585 GB, free: 30.95 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.535e-05/0.01243, allocations: 16.61 kB / 0.6585 GB, free: 30.95 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.047e-05/0.01244, allocations: 9.312 kB / 0.6585 GB, free: 30.95 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 6.444e-05/0.01251, allocations: 175.2 kB / 0.6587 GB, free: 30.82 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 5e-08/0.01251, allocations: 7.188 kB / 0.6587 GB, free: 30.82 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0002008/0.01271, allocations: 90.41 kB / 0.6588 GB, free: 30.8 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 7.069e-05/0.01278, allocations: 111.7 kB / 0.6589 GB, free: 30.7 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.0002646/0.01304, allocations: 241.3 kB / 0.6591 GB, free: 30.57 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.713e-06/0.01304, allocations: 0 / 0.6591 GB, free: 30.57 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 9.243e-05/0.01314, allocations: 77.14 kB / 0.6592 GB, free: 30.54 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002477/0.01339, allocations: 86.78 kB / 0.6593 GB, free: 30.52 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001456/0.01484, allocations: 0.8542 MB / 0.6601 GB, free: 29.98 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 4.215e-05/0.01488, allocations: 90.8 kB / 0.6602 GB, free: 29.91 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 9.523e-05/0.01498, allocations: 31.66 kB / 0.6602 GB, free: 29.9 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 6.415e-05/0.01504, allocations: 25.28 kB / 0.6602 GB, free: 29.89 MB / 0.5262 GB
Notification: Performance of SimCode: time 9.32e-07/0.01504, allocations: 0 / 0.6602 GB, free: 29.89 MB / 0.5262 GB
Notification: Performance of Templates: time 0.005374/0.02042, allocations: 3.676 MB / 0.6638 GB, free: 29.56 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: 4.496051486814395]