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 0.001856/0.001856, allocations: 89.48 kB / 19.44 MB, free: 336 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 0.002066/0.002066, allocations: 169.6 kB / 22.76 MB, free: 1.664 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 1.676/1.676, allocations: 177.1 MB / 203.1 MB, free: 5.617 MB / 186.7 MB
"
[Timeout remaining time 178]
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 5.762/5.762, allocations: 274.5 MB / 0.5215 GB, free: 14.21 MB / 458.7 MB
"
[Timeout remaining time 173]
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 1.723e-06/1.723e-06, allocations: 0 / 0.6472 GB, free: 39.09 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.594e-05/2.766e-05, allocations: 4.969 kB / 0.6472 GB, free: 39.08 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue): time 0.003709/0.003736, allocations: 2.948 MB / 0.6501 GB, free: 37.15 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.001281/0.005018, allocations: 0.7433 MB / 0.6508 GB, free: 36.66 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001159/0.005134, allocations: 8.5 kB / 0.6508 GB, free: 36.65 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001333/0.005267, allocations: 40.34 kB / 0.6509 GB, free: 36.63 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.000252/0.005519, allocations: 120.9 kB / 0.651 GB, free: 36.58 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0002427/0.005762, allocations: 103.9 kB / 0.6511 GB, free: 36.53 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0003531/0.006115, allocations: 437.9 kB / 0.6515 GB, free: 36.3 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0003193/0.006434, allocations: 231.7 kB / 0.6517 GB, free: 36.16 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.000249/0.006683, allocations: 255 kB / 0.652 GB, free: 36.06 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002482/0.006931, allocations: 164.6 kB / 0.6521 GB, free: 36.01 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 6.241e-05/0.006994, allocations: 38.25 kB / 0.6522 GB, free: 36.01 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 6.857e-05/0.007062, allocations: 38.53 kB / 0.6522 GB, free: 36.01 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 6.119e-05/0.007123, allocations: 80.14 kB / 0.6523 GB, free: 35.95 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 0.000143/0.007266, allocations: 140.9 kB / 0.6524 GB, free: 35.89 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0003632/0.00763, allocations: 387.8 kB / 0.6528 GB, free: 35.73 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 4.258e-06/0.007634, allocations: 4.875 kB / 0.6528 GB, free: 35.73 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 8.72e-07/0.007635, allocations: 0 / 0.6528 GB, free: 35.73 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 5.711e-06/0.00764, allocations: 0 / 0.6528 GB, free: 35.73 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 0.0009482/0.008589, allocations: 0.6742 MB / 0.6534 GB, free: 35.18 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 3.505e-05/0.008624, allocations: 10.22 kB / 0.6535 GB, free: 35.18 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001143/0.008738, allocations: 53.53 kB / 0.6535 GB, free: 35.16 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0003373/0.009075, allocations: 231.3 kB / 0.6537 GB, free: 34.96 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.223e-05/0.009098, allocations: 23.84 kB / 0.6537 GB, free: 34.96 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 5.504e-05/0.009153, allocations: 36.45 kB / 0.6538 GB, free: 34.94 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0005961/0.009749, allocations: 404.7 kB / 0.6542 GB, free: 34.72 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.825e-05/0.009767, allocations: 3.938 kB / 0.6542 GB, free: 34.72 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.906e-05/0.009796, allocations: 9.625 kB / 0.6542 GB, free: 34.71 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.689e-06/0.009806, allocations: 9.406 kB / 0.6542 GB, free: 34.71 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0004401/0.01025, allocations: 214.5 kB / 0.6544 GB, free: 34.66 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001485/0.01173, allocations: 0.9476 MB / 0.6553 GB, free: 34 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0005662/0.0123, allocations: 212.6 kB / 0.6555 GB, free: 33.91 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002124/0.01251, allocations: 80.7 kB / 0.6556 GB, free: 33.88 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 4.136e-05/0.01255, allocations: 11.88 kB / 0.6556 GB, free: 33.88 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0003601/0.01291, allocations: 165.3 kB / 0.6558 GB, free: 33.79 MB / 0.5262 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.0002203/0.01313, allocations: 35.19 kB / 0.6558 GB, free: 33.78 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=25): time 1.532e-06/0.01313, allocations: 0 / 0.6558 GB, free: 33.78 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=25): time 0.0006896/0.01382, allocations: 303.9 kB / 0.6561 GB, free: 33.67 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.569e-05/0.01385, allocations: 58.25 kB / 0.6561 GB, free: 33.6 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001903/0.01404, allocations: 275.2 kB / 0.6564 GB, free: 33.39 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 2.368e-05/0.01406, allocations: 32.45 kB / 0.6564 GB, free: 33.36 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 8.629e-05/0.01415, allocations: 229.4 kB / 0.6567 GB, free: 33.16 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 6.787e-05/0.01422, allocations: 106.1 kB / 0.6568 GB, free: 33.07 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001082/0.01432, allocations: 82.3 kB / 0.6568 GB, free: 33.02 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 0.0001183/0.01444, allocations: 0.5146 MB / 0.6573 GB, free: 32.52 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002408/0.01468, allocations: 147.8 kB / 0.6575 GB, free: 32.44 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002719/0.01496, allocations: 277.1 kB / 0.6577 GB, free: 32.19 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0004443/0.0154, allocations: 345 kB / 0.6581 GB, free: 31.93 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.836e-06/0.0154, allocations: 0 / 0.6581 GB, free: 31.93 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=41) (initialization): time 0.0006276/0.01603, allocations: 406.4 kB / 0.6585 GB, free: 31.73 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 2.937e-05/0.01606, allocations: 36.83 kB / 0.6585 GB, free: 31.7 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.231e-06/0.01607, allocations: 2.781 kB / 0.6585 GB, free: 31.7 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.561e-05/0.01608, allocations: 8.188 kB / 0.6585 GB, free: 31.69 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003194/0.0164, allocations: 80.02 kB / 0.6586 GB, free: 31.69 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.335e-06/0.01641, allocations: 7.5 kB / 0.6586 GB, free: 31.69 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001983/0.01661, allocations: 16.5 kB / 0.6586 GB, free: 31.68 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.887e-05/0.01664, allocations: 18.95 kB / 0.6586 GB, free: 31.68 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 0.0001864/0.01682, allocations: 223 kB / 0.6588 GB, free: 31.48 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 4.966e-05/0.01687, allocations: 25.91 kB / 0.6589 GB, free: 31.47 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0006014/0.01747, allocations: 254.9 kB / 0.6591 GB, free: 31.36 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.558e-06/0.01748, allocations: 2.781 kB / 0.6591 GB, free: 31.36 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.485e-06/0.01748, allocations: 1.438 kB / 0.6591 GB, free: 31.36 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.959e-06/0.01749, allocations: 3.703 kB / 0.6591 GB, free: 31.36 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0002635/0.01775, allocations: 256.7 kB / 0.6594 GB, free: 31.16 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.473e-06/0.01775, allocations: 2.812 kB / 0.6594 GB, free: 31.16 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002467/0.018, allocations: 39.41 kB / 0.6594 GB, free: 31.16 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 5.611e-06/0.018, allocations: 4.922 kB / 0.6594 GB, free: 31.16 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.268e-05/0.01803, allocations: 14.14 kB / 0.6594 GB, free: 31.15 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.465e-06/0.01803, allocations: 1.438 kB / 0.6594 GB, free: 31.15 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.052e-06/0.01803, allocations: 0 / 0.6594 GB, free: 31.15 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.000821/0.01885, allocations: 378.7 kB / 0.6598 GB, free: 30.96 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 3.113e-05/0.01888, allocations: 17.48 kB / 0.6598 GB, free: 30.95 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 4.014e-05/0.01892, allocations: 10.38 kB / 0.6598 GB, free: 30.95 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001435/0.01906, allocations: 8.188 kB / 0.6598 GB, free: 30.95 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 4.979e-05/0.01911, allocations: 22.17 kB / 0.6598 GB, free: 30.94 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.749e-05/0.01913, allocations: 5.594 kB / 0.6598 GB, free: 30.94 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 0.0001298/0.01926, allocations: 199.5 kB / 0.66 GB, free: 30.8 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 5e-08/0.01926, allocations: 1.656 kB / 0.66 GB, free: 30.8 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0003432/0.01961, allocations: 89.02 kB / 0.6601 GB, free: 30.78 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 0.0007646/0.02037, allocations: 104.3 kB / 0.6602 GB, free: 30.69 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.001014/0.02138, allocations: 339.4 kB / 0.6605 GB, free: 30.51 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.523e-06/0.02139, allocations: 1.406 kB / 0.6605 GB, free: 30.51 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.0002209/0.02161, allocations: 111.6 kB / 0.6606 GB, free: 30.47 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004187/0.02202, allocations: 80.78 kB / 0.6607 GB, free: 30.45 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001327/0.02335, allocations: 0.8172 MB / 0.6615 GB, free: 29.92 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001187/0.02347, allocations: 157.3 kB / 0.6617 GB, free: 29.84 MB / 0.5262 GB
Notification: Performance of simCode: alias equations: time 0.0001365/0.02361, allocations: 31.45 kB / 0.6617 GB, free: 29.83 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 8.973e-05/0.0237, allocations: 28.61 kB / 0.6617 GB, free: 29.82 MB / 0.5262 GB
Notification: Performance of SimCode: time 7.91e-07/0.0237, allocations: 0 / 0.6617 GB, free: 29.82 MB / 0.5262 GB
Notification: Performance of Templates: time 0.01231/0.03601, allocations: 3.688 MB / 0.6653 GB, free: 29.49 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: 11.09056999196764]