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 0.001007/0.001007, allocations: 84.44 kB / 19.93 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 0.001403/0.001403, allocations: 173.9 kB / 23.21 MB, free: 1.332 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 0.9665/0.9665, allocations: 177.1 MB / 203.5 MB, free: 5.754 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 1.557/1.557, allocations: 273.5 MB / 0.5209 GB, free: 15.11 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 1.703e-06/1.703e-06, allocations: 0 / 0.7558 GB, free: 10.85 MB / 0.5887 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 3.027e-05/3.197e-05, allocations: 2.281 kB / 0.7558 GB, free: 10.85 MB / 0.5887 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue): time 0.003993/0.004025, allocations: 2.764 MB / 0.7585 GB, free: 8.105 MB / 0.5887 GB
Notification: Performance of NFInst.instExpressions: time 0.001273/0.005298, allocations: 0.7299 MB / 0.7592 GB, free: 7.379 MB / 0.5887 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.000137/0.005435, allocations: 4 kB / 0.7592 GB, free: 7.375 MB / 0.5887 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001931/0.005628, allocations: 44.88 kB / 0.7592 GB, free: 7.332 MB / 0.5887 GB
Notification: Performance of NFTyping.typeBindings: time 0.0003065/0.005935, allocations: 125.5 kB / 0.7593 GB, free: 7.238 MB / 0.5887 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0002981/0.006233, allocations: 91.75 kB / 0.7594 GB, free: 7.148 MB / 0.5887 GB
Notification: Performance of NFFlatten.flatten: time 0.0004411/0.006674, allocations: 429.9 kB / 0.7598 GB, free: 6.727 MB / 0.5887 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0003745/0.007048, allocations: 219.8 kB / 0.76 GB, free: 6.516 MB / 0.5887 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002912/0.007339, allocations: 259.5 kB / 0.7603 GB, free: 6.262 MB / 0.5887 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002607/0.0076, allocations: 151.6 kB / 0.7604 GB, free: 6.113 MB / 0.5887 GB
Notification: Performance of NFPackage.collectConstants: time 5.039e-05/0.007651, allocations: 36 kB / 0.7605 GB, free: 6.078 MB / 0.5887 GB
Notification: Performance of NFFlatten.collectFunctions: time 5.023e-05/0.007701, allocations: 40 kB / 0.7605 GB, free: 6.039 MB / 0.5887 GB
Notification: Performance of NFScalarize.scalarize: time 5.712e-05/0.007758, allocations: 87.66 kB / 0.7606 GB, free: 5.953 MB / 0.5887 GB
Notification: Performance of NFVerifyModel.verify: time 0.0001155/0.007873, allocations: 143.7 kB / 0.7607 GB, free: 5.812 MB / 0.5887 GB
Notification: Performance of NFConvertDAE.convert: time 0.0003186/0.008192, allocations: 390.9 kB / 0.7611 GB, free: 5.43 MB / 0.5887 GB
Notification: Performance of FrontEnd - DAE generated: time 2.685e-06/0.008195, allocations: 0 / 0.7611 GB, free: 5.43 MB / 0.5887 GB
Notification: Performance of FrontEnd: time 2.084e-06/0.008197, allocations: 4 kB / 0.7611 GB, free: 5.426 MB / 0.5887 GB
Notification: Performance of Transformations before backend: time 6.402e-06/0.008203, allocations: 0 / 0.7611 GB, free: 5.426 MB / 0.5887 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 0.0007916/0.008995, allocations: 0.5539 MB / 0.7616 GB, free: 4.836 MB / 0.5887 GB
Notification: Performance of prepare preOptimizeDAE: time 3.677e-05/0.009032, allocations: 12.03 kB / 0.7617 GB, free: 4.824 MB / 0.5887 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 5.971e-05/0.009091, allocations: 36.7 kB / 0.7617 GB, free: 4.789 MB / 0.5887 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0003126/0.009404, allocations: 241.9 kB / 0.7619 GB, free: 4.527 MB / 0.5887 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.104e-05/0.009425, allocations: 25.02 kB / 0.7619 GB, free: 4.504 MB / 0.5887 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.772e-05/0.009473, allocations: 32.33 kB / 0.762 GB, free: 4.473 MB / 0.5887 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004487/0.009921, allocations: 384.7 kB / 0.7623 GB, free: 4.078 MB / 0.5887 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.933e-05/0.009941, allocations: 3.938 kB / 0.7623 GB, free: 4.074 MB / 0.5887 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.433e-05/0.009965, allocations: 12 kB / 0.7624 GB, free: 4.062 MB / 0.5887 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.024e-06/0.009972, allocations: 8 kB / 0.7624 GB, free: 4.055 MB / 0.5887 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003263/0.0103, allocations: 237.8 kB / 0.7626 GB, free: 3.824 MB / 0.5887 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0009908/0.01129, allocations: 0.7963 MB / 0.7634 GB, free: 2.988 MB / 0.5887 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0003839/0.01167, allocations: 206.5 kB / 0.7636 GB, free: 2.777 MB / 0.5887 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001337/0.01181, allocations: 80.81 kB / 0.7636 GB, free: 2.695 MB / 0.5887 GB
Notification: Performance of preOpt evalFunc (simulation): time 2.268e-05/0.01183, allocations: 8 kB / 0.7637 GB, free: 2.688 MB / 0.5887 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002439/0.01207, allocations: 171.9 kB / 0.7638 GB, free: 2.508 MB / 0.5887 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.0001061/0.01218, allocations: 35.81 kB / 0.7639 GB, free: 2.473 MB / 0.5887 GB
Notification: Performance of pre-optimization done (n=25): time 1.282e-06/0.01218, allocations: 0 / 0.7639 GB, free: 2.473 MB / 0.5887 GB
Notification: Performance of matching and sorting (n=25): time 0.0005239/0.0127, allocations: 312.3 kB / 0.7642 GB, free: 2.164 MB / 0.5887 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.145e-05/0.01275, allocations: 67.33 kB / 0.7642 GB, free: 2.086 MB / 0.5887 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.000136/0.01288, allocations: 195.8 kB / 0.7644 GB, free: 1.887 MB / 0.5887 GB
Notification: Performance of collectPreVariables (initialization): time 2.307e-05/0.01291, allocations: 33.7 kB / 0.7644 GB, free: 1.848 MB / 0.5887 GB
Notification: Performance of collectInitialEqns (initialization): time 8.294e-05/0.01299, allocations: 172.5 kB / 0.7646 GB, free: 1.672 MB / 0.5887 GB
Notification: Performance of collectInitialBindings (initialization): time 5.605e-05/0.01304, allocations: 99.3 kB / 0.7647 GB, free: 1.574 MB / 0.5887 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 6.94e-05/0.01311, allocations: 61.69 kB / 0.7648 GB, free: 1.508 MB / 0.5887 GB
Notification: Performance of setup shared object (initialization): time 8.923e-05/0.0132, allocations: 330.8 kB / 0.7651 GB, free: 1.176 MB / 0.5887 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001762/0.01338, allocations: 147.1 kB / 0.7652 GB, free: 1.02 MB / 0.5887 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002128/0.01359, allocations: 238.2 kB / 0.7654 GB, free: 0.7344 MB / 0.5887 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0003317/0.01392, allocations: 308.5 kB / 0.7657 GB, free: 408 kB / 0.5887 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.775e-06/0.01393, allocations: 4 kB / 0.7657 GB, free: 404 kB / 0.5887 GB
Notification: Performance of matching and sorting (n=41) (initialization): time 0.0004456/0.01437, allocations: 404.6 kB / 0.7661 GB, free: 15.98 MB / 0.6043 GB
Notification: Performance of prepare postOptimizeDAE: time 3.049e-05/0.0144, allocations: 33.7 kB / 0.7662 GB, free: 15.94 MB / 0.6043 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.062e-06/0.01441, allocations: 4 kB / 0.7662 GB, free: 15.94 MB / 0.6043 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.876e-05/0.01443, allocations: 4.312 kB / 0.7662 GB, free: 15.93 MB / 0.6043 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001819/0.01461, allocations: 87.88 kB / 0.7662 GB, free: 15.85 MB / 0.6043 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.526e-06/0.01462, allocations: 7.938 kB / 0.7662 GB, free: 15.84 MB / 0.6043 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001016/0.01472, allocations: 19.98 kB / 0.7663 GB, free: 15.82 MB / 0.6043 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.683e-05/0.01474, allocations: 12 kB / 0.7663 GB, free: 15.81 MB / 0.6043 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 0.0001721/0.01491, allocations: 179.9 kB / 0.7665 GB, free: 15.63 MB / 0.6043 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 2.245e-05/0.01493, allocations: 19.91 kB / 0.7665 GB, free: 15.61 MB / 0.6043 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.000366/0.0153, allocations: 262.7 kB / 0.7667 GB, free: 15.35 MB / 0.6043 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.453e-06/0.0153, allocations: 0 / 0.7667 GB, free: 15.35 MB / 0.6043 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 3.076e-06/0.0153, allocations: 0 / 0.7667 GB, free: 15.35 MB / 0.6043 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.617e-06/0.0153, allocations: 0 / 0.7667 GB, free: 15.35 MB / 0.6043 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0001735/0.01548, allocations: 217.2 kB / 0.7669 GB, free: 15.11 MB / 0.6043 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.144e-06/0.01548, allocations: 4 kB / 0.7669 GB, free: 15.11 MB / 0.6043 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001488/0.01563, allocations: 47.91 kB / 0.767 GB, free: 15.06 MB / 0.6043 GB
Notification: Performance of postOpt tearingSystem (simulation): time 1.333e-06/0.01563, allocations: 3.938 kB / 0.767 GB, free: 15.05 MB / 0.6043 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.766e-05/0.01565, allocations: 11.98 kB / 0.767 GB, free: 15.04 MB / 0.6043 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.102e-06/0.01565, allocations: 0 / 0.767 GB, free: 15.04 MB / 0.6043 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 5.71e-07/0.01565, allocations: 0 / 0.767 GB, free: 15.04 MB / 0.6043 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004842/0.01613, allocations: 381.5 kB / 0.7674 GB, free: 14.65 MB / 0.6043 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.519e-05/0.01616, allocations: 27.64 kB / 0.7674 GB, free: 14.63 MB / 0.6043 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.366e-05/0.01618, allocations: 8 kB / 0.7674 GB, free: 14.62 MB / 0.6043 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.718e-05/0.01626, allocations: 23.92 kB / 0.7674 GB, free: 14.6 MB / 0.6043 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.136e-05/0.01632, allocations: 19.97 kB / 0.7674 GB, free: 14.58 MB / 0.6043 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.091e-05/0.01633, allocations: 4 kB / 0.7674 GB, free: 14.57 MB / 0.6043 GB
Notification: Performance of sorting global known variables: time 9.191e-05/0.01642, allocations: 147 kB / 0.7676 GB, free: 14.43 MB / 0.6043 GB
Notification: Performance of sort global known variables: time 8e-08/0.01642, allocations: 0 / 0.7676 GB, free: 14.43 MB / 0.6043 GB
Notification: Performance of remove unused functions: time 0.0002006/0.01663, allocations: 91.78 kB / 0.7677 GB, free: 14.34 MB / 0.6043 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 9.832e-05/0.01672, allocations: 110.5 kB / 0.7678 GB, free: 14.23 MB / 0.6043 GB
Notification: Performance of simCode: created initialization part: time 0.0004046/0.01713, allocations: 320.8 kB / 0.7681 GB, free: 13.89 MB / 0.6043 GB
Notification: Performance of simCode: created event and clocks part: time 1.873e-06/0.01713, allocations: 0 / 0.7681 GB, free: 13.89 MB / 0.6043 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001443/0.01727, allocations: 98.94 kB / 0.7682 GB, free: 13.8 MB / 0.6043 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002587/0.01753, allocations: 60.52 kB / 0.7682 GB, free: 13.74 MB / 0.6043 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001129/0.01866, allocations: 0.8226 MB / 0.769 GB, free: 12.91 MB / 0.6043 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001118/0.01877, allocations: 159.3 kB / 0.7692 GB, free: 12.73 MB / 0.6043 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 8.006e-05/0.01885, allocations: 32.48 kB / 0.7692 GB, free: 12.7 MB / 0.6043 GB
Notification: Performance of SimCode: time 6.31e-07/0.01885, allocations: 11.88 kB / 0.7692 GB, free: 12.69 MB / 0.6043 GB
Notification: Performance of Templates: time 0.00399/0.02284, allocations: 3.642 MB / 0.7728 GB, free: 9.129 MB / 0.6043 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: 6.520992072997615]