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 0.002444/0.002444, allocations: 80.44 kB / 19.17 MB, free: 0.7422 MB / 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 0.003279/0.003279, allocations: 165.9 kB / 22.45 MB, free: 2.109 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 1.724/1.724, allocations: 177.1 MB / 202.8 MB, free: 5.754 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 3.577/3.577, allocations: 274 MB / 0.5207 GB, free: 14.91 MB / 458.7 MB
"
[Timeout remaining time 176]
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 1.433e-06/1.433e-06, allocations: 0 / 0.7563 GB, free: 9.934 MB / 0.5887 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.539e-05/2.682e-05, allocations: 4.391 kB / 0.7563 GB, free: 9.93 MB / 0.5887 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue): time 0.004359/0.004386, allocations: 2.757 MB / 0.759 GB, free: 7.195 MB / 0.5887 GB
Notification: Performance of NFInst.instExpressions: time 0.001643/0.006028, allocations: 0.7295 MB / 0.7597 GB, free: 6.469 MB / 0.5887 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001118/0.00614, allocations: 8 kB / 0.7597 GB, free: 6.461 MB / 0.5887 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001513/0.006291, allocations: 43.56 kB / 0.7597 GB, free: 6.418 MB / 0.5887 GB
Notification: Performance of NFTyping.typeBindings: time 0.0002896/0.006581, allocations: 130.4 kB / 0.7598 GB, free: 6.312 MB / 0.5887 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0003029/0.006884, allocations: 95.75 kB / 0.7599 GB, free: 6.219 MB / 0.5887 GB
Notification: Performance of NFFlatten.flatten: time 0.0005158/0.0074, allocations: 421.9 kB / 0.7603 GB, free: 5.805 MB / 0.5887 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0004105/0.00781, allocations: 223.7 kB / 0.7606 GB, free: 5.59 MB / 0.5887 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0003532/0.008163, allocations: 263.5 kB / 0.7608 GB, free: 5.332 MB / 0.5887 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.000292/0.008455, allocations: 155.6 kB / 0.761 GB, free: 5.18 MB / 0.5887 GB
Notification: Performance of NFPackage.collectConstants: time 7.709e-05/0.008532, allocations: 36 kB / 0.761 GB, free: 5.145 MB / 0.5887 GB
Notification: Performance of NFFlatten.collectFunctions: time 9.143e-05/0.008624, allocations: 40 kB / 0.761 GB, free: 5.105 MB / 0.5887 GB
Notification: Performance of NFScalarize.scalarize: time 9.907e-05/0.008723, allocations: 83.72 kB / 0.7611 GB, free: 5.023 MB / 0.5887 GB
Notification: Performance of NFVerifyModel.verify: time 0.0002014/0.008924, allocations: 143.7 kB / 0.7612 GB, free: 4.883 MB / 0.5887 GB
Notification: Performance of NFConvertDAE.convert: time 0.0004926/0.009417, allocations: 383 kB / 0.7616 GB, free: 4.508 MB / 0.5887 GB
Notification: Performance of FrontEnd - DAE generated: time 2.504e-06/0.009419, allocations: 3.938 kB / 0.7616 GB, free: 4.504 MB / 0.5887 GB
Notification: Performance of FrontEnd: time 1.212e-06/0.009421, allocations: 4 kB / 0.7616 GB, free: 4.5 MB / 0.5887 GB
Notification: Performance of Transformations before backend: time 6.502e-06/0.009427, allocations: 0 / 0.7616 GB, free: 4.5 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 0.001233/0.01066, allocations: 0.5577 MB / 0.7622 GB, free: 3.906 MB / 0.5887 GB
Notification: Performance of prepare preOptimizeDAE: time 4.2e-05/0.0107, allocations: 12.03 kB / 0.7622 GB, free: 3.895 MB / 0.5887 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 9.01e-05/0.01079, allocations: 40.69 kB / 0.7622 GB, free: 3.855 MB / 0.5887 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0004779/0.01127, allocations: 226 kB / 0.7624 GB, free: 3.605 MB / 0.5887 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.072e-05/0.0113, allocations: 25.02 kB / 0.7624 GB, free: 3.582 MB / 0.5887 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 7.303e-05/0.01137, allocations: 32.33 kB / 0.7625 GB, free: 3.551 MB / 0.5887 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0007283/0.0121, allocations: 388.3 kB / 0.7628 GB, free: 3.156 MB / 0.5887 GB
Notification: Performance of preOpt findStateOrder (simulation): time 2.071e-05/0.01212, allocations: 7.875 kB / 0.7629 GB, free: 3.148 MB / 0.5887 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.662e-05/0.01216, allocations: 12 kB / 0.7629 GB, free: 3.137 MB / 0.5887 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.646e-06/0.01217, allocations: 4 kB / 0.7629 GB, free: 3.133 MB / 0.5887 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0006077/0.01278, allocations: 241.8 kB / 0.7631 GB, free: 2.898 MB / 0.5887 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001717/0.01449, allocations: 0.8001 MB / 0.7639 GB, free: 2.059 MB / 0.5887 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0006109/0.0151, allocations: 202.7 kB / 0.7641 GB, free: 1.852 MB / 0.5887 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0002529/0.01536, allocations: 88.81 kB / 0.7642 GB, free: 1.762 MB / 0.5887 GB
Notification: Performance of preOpt evalFunc (simulation): time 2.534e-05/0.01538, allocations: 4.094 kB / 0.7642 GB, free: 1.758 MB / 0.5887 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0004103/0.01579, allocations: 163.2 kB / 0.7643 GB, free: 1.586 MB / 0.5887 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.0002079/0.016, allocations: 35.88 kB / 0.7644 GB, free: 1.551 MB / 0.5887 GB
Notification: Performance of pre-optimization done (n=25): time 1.463e-06/0.016, allocations: 3.938 kB / 0.7644 GB, free: 1.547 MB / 0.5887 GB
Notification: Performance of matching and sorting (n=25): time 0.0009013/0.0169, allocations: 308.8 kB / 0.7647 GB, free: 1.242 MB / 0.5887 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.383e-05/0.01697, allocations: 67.33 kB / 0.7647 GB, free: 1.164 MB / 0.5887 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002263/0.01719, allocations: 195.7 kB / 0.7649 GB, free: 0.9648 MB / 0.5887 GB
Notification: Performance of collectPreVariables (initialization): time 3.566e-05/0.01723, allocations: 29.7 kB / 0.7649 GB, free: 0.9297 MB / 0.5887 GB
Notification: Performance of collectInitialEqns (initialization): time 0.000149/0.01738, allocations: 176.5 kB / 0.7651 GB, free: 0.75 MB / 0.5887 GB
Notification: Performance of collectInitialBindings (initialization): time 0.0001038/0.01748, allocations: 103.2 kB / 0.7652 GB, free: 0.6484 MB / 0.5887 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.000115/0.0176, allocations: 61.69 kB / 0.7653 GB, free: 0.582 MB / 0.5887 GB
Notification: Performance of setup shared object (initialization): time 0.0001792/0.01778, allocations: 330.8 kB / 0.7656 GB, free: 256 kB / 0.5887 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.000313/0.01809, allocations: 139.1 kB / 0.7657 GB, free: 104 kB / 0.5887 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0004156/0.0185, allocations: 242.3 kB / 0.7659 GB, free: 15.81 MB / 0.6043 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001102/0.01961, allocations: 305.6 kB / 0.7662 GB, free: 15.48 MB / 0.6043 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.876e-06/0.01961, allocations: 0 / 0.7662 GB, free: 15.48 MB / 0.6043 GB
Notification: Performance of matching and sorting (n=41) (initialization): time 0.0008313/0.02044, allocations: 408 kB / 0.7666 GB, free: 15.06 MB / 0.6043 GB
Notification: Performance of prepare postOptimizeDAE: time 4.591e-05/0.02049, allocations: 34.02 kB / 0.7666 GB, free: 15.02 MB / 0.6043 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.633e-06/0.02049, allocations: 4 kB / 0.7667 GB, free: 15.02 MB / 0.6043 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.736e-05/0.02051, allocations: 4 kB / 0.7667 GB, free: 15.02 MB / 0.6043 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003741/0.02088, allocations: 87.88 kB / 0.7667 GB, free: 14.93 MB / 0.6043 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.244e-05/0.0209, allocations: 7.938 kB / 0.7667 GB, free: 14.92 MB / 0.6043 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0002123/0.02111, allocations: 15.98 kB / 0.7668 GB, free: 14.91 MB / 0.6043 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 3.173e-05/0.02114, allocations: 16 kB / 0.7668 GB, free: 14.89 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 0.0002521/0.02139, allocations: 177.2 kB / 0.7669 GB, free: 14.71 MB / 0.6043 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 3.825e-05/0.02143, allocations: 15.91 kB / 0.767 GB, free: 14.7 MB / 0.6043 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.000673/0.0221, allocations: 259.6 kB / 0.7672 GB, free: 14.44 MB / 0.6043 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.211e-06/0.02211, allocations: 4 kB / 0.7672 GB, free: 14.43 MB / 0.6043 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 8.125e-06/0.02212, allocations: 11.88 kB / 0.7672 GB, free: 14.42 MB / 0.6043 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.047e-06/0.02212, allocations: 4 kB / 0.7672 GB, free: 14.42 MB / 0.6043 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003043/0.02243, allocations: 217.2 kB / 0.7674 GB, free: 14.18 MB / 0.6043 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.493e-06/0.02243, allocations: 0 / 0.7674 GB, free: 14.18 MB / 0.6043 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002889/0.02272, allocations: 43.97 kB / 0.7675 GB, free: 14.13 MB / 0.6043 GB
Notification: Performance of postOpt tearingSystem (simulation): time 6.883e-06/0.02272, allocations: 3.984 kB / 0.7675 GB, free: 14.13 MB / 0.6043 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.474e-05/0.02275, allocations: 11.94 kB / 0.7675 GB, free: 14.12 MB / 0.6043 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.873e-06/0.02275, allocations: 0 / 0.7675 GB, free: 14.12 MB / 0.6043 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 8.61e-07/0.02275, allocations: 0 / 0.7675 GB, free: 14.12 MB / 0.6043 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0008879/0.02364, allocations: 388.6 kB / 0.7679 GB, free: 13.72 MB / 0.6043 GB
Notification: Performance of postOpt removeConstants (simulation): time 3.857e-05/0.02368, allocations: 19.84 kB / 0.7679 GB, free: 13.7 MB / 0.6043 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 4.209e-05/0.02372, allocations: 8 kB / 0.7679 GB, free: 13.7 MB / 0.6043 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001795/0.0239, allocations: 15.98 kB / 0.7679 GB, free: 13.68 MB / 0.6043 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.565e-05/0.02397, allocations: 15.97 kB / 0.7679 GB, free: 13.66 MB / 0.6043 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.514e-05/0.02399, allocations: 11.98 kB / 0.7679 GB, free: 13.65 MB / 0.6043 GB
Notification: Performance of sorting global known variables: time 0.0001524/0.02414, allocations: 142.8 kB / 0.7681 GB, free: 13.51 MB / 0.6043 GB
Notification: Performance of sort global known variables: time 8e-08/0.02414, allocations: 0 / 0.7681 GB, free: 13.51 MB / 0.6043 GB
Notification: Performance of remove unused functions: time 0.0003384/0.02448, allocations: 95.83 kB / 0.7682 GB, free: 13.42 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 0.0001467/0.02463, allocations: 111.5 kB / 0.7683 GB, free: 13.3 MB / 0.6043 GB
Notification: Performance of simCode: created initialization part: time 0.0007142/0.02534, allocations: 315 kB / 0.7686 GB, free: 12.98 MB / 0.6043 GB
Notification: Performance of simCode: created event and clocks part: time 1.603e-06/0.02534, allocations: 0 / 0.7686 GB, free: 12.98 MB / 0.6043 GB
Notification: Performance of simCode: created simulation system equations: time 0.0002667/0.02561, allocations: 103.8 kB / 0.7687 GB, free: 12.88 MB / 0.6043 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004351/0.02605, allocations: 79.08 kB / 0.7687 GB, free: 12.8 MB / 0.6043 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001617/0.02766, allocations: 0.7918 MB / 0.7695 GB, free: 12.01 MB / 0.6043 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.000176/0.02784, allocations: 159.3 kB / 0.7697 GB, free: 11.83 MB / 0.6043 GB
Notification: Performance of simCode: alias equations: time 0.0001405/0.02798, allocations: 34.17 kB / 0.7697 GB, free: 11.8 MB / 0.6043 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 9.558e-05/0.02807, allocations: 32.48 kB / 0.7697 GB, free: 11.77 MB / 0.6043 GB
Notification: Performance of SimCode: time 4.6e-07/0.02808, allocations: 4 kB / 0.7697 GB, free: 11.77 MB / 0.6043 GB
Notification: Performance of Templates: time 0.008994/0.03707, allocations: 3.621 MB / 0.7733 GB, free: 8.336 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 -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 9.204409555066377]