Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver.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 0.001335/0.001335, 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 0.001056/0.001056, allocations: 173 kB / 23.49 MB, free: 1.059 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 0.9365/0.9365, allocations: 177.1 MB / 203.8 MB, free: 5.621 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 1.565/1.565, allocations: 273.5 MB / 0.5213 GB, free: 14.79 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.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver,tolerance=1e-06,outputFormat="empty",numberOfIntervals=495,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver")
translateModel(Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver,tolerance=1e-06,outputFormat="empty",numberOfIntervals=495,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.363e-06/1.363e-06, allocations: 0 / 0.6462 GB, free: 39.12 MB / 0.5262 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.065e-05/2.201e-05, allocations: 3.625 kB / 0.6462 GB, free: 39.12 MB / 0.5262 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver): time 0.003306/0.003328, allocations: 4.105 MB / 0.6502 GB, free: 36.47 MB / 0.5262 GB
Notification: Performance of NFInst.instExpressions: time 0.001194/0.004522, allocations: 0.9606 MB / 0.6511 GB, free: 35.82 MB / 0.5262 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001194/0.004642, allocations: 5.875 kB / 0.6512 GB, free: 35.82 MB / 0.5262 GB
Notification: Performance of NFTyping.typeComponents: time 0.000143/0.004785, allocations: 75.27 kB / 0.6512 GB, free: 35.78 MB / 0.5262 GB
Notification: Performance of NFTyping.typeBindings: time 0.0003435/0.005128, allocations: 213.6 kB / 0.6514 GB, free: 35.65 MB / 0.5262 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0002207/0.005349, allocations: 151.4 kB / 0.6516 GB, free: 35.56 MB / 0.5262 GB
Notification: Performance of NFFlatten.flatten: time 0.0004015/0.00575, allocations: 0.7203 MB / 0.6523 GB, free: 35.18 MB / 0.5262 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0004333/0.006184, allocations: 0.4921 MB / 0.6528 GB, free: 34.89 MB / 0.5262 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0003472/0.006531, allocations: 496.8 kB / 0.6532 GB, free: 34.69 MB / 0.5262 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0004196/0.006951, allocations: 355.9 kB / 0.6536 GB, free: 34.59 MB / 0.5262 GB
Notification: Performance of NFPackage.collectConstants: time 8.986e-05/0.00704, allocations: 75.75 kB / 0.6536 GB, free: 34.59 MB / 0.5262 GB
Notification: Performance of NFFlatten.collectFunctions: time 8.497e-05/0.007125, allocations: 77.53 kB / 0.6537 GB, free: 34.59 MB / 0.5262 GB
Notification: Performance of NFScalarize.scalarize: time 0.0001175/0.007243, allocations: 185.8 kB / 0.6539 GB, free: 34.47 MB / 0.5262 GB
Notification: Performance of NFVerifyModel.verify: time 0.0001853/0.007428, allocations: 267.4 kB / 0.6541 GB, free: 34.36 MB / 0.5262 GB
Notification: Performance of NFConvertDAE.convert: time 0.0004166/0.007845, allocations: 0.5332 MB / 0.6547 GB, free: 34.09 MB / 0.5262 GB
Notification: Performance of FrontEnd - DAE generated: time 2.995e-06/0.007848, allocations: 0.5625 kB / 0.6547 GB, free: 34.09 MB / 0.5262 GB
Notification: Performance of FrontEnd: time 1.843e-06/0.00785, allocations: 0 / 0.6547 GB, free: 34.09 MB / 0.5262 GB
Notification: Performance of Transformations before backend: time 6.943e-06/0.007857, allocations: 1.906 kB / 0.6547 GB, free: 34.09 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: 124
 * Number of variables: 124
Notification: Performance of Generate backend data structure: time 0.001077/0.008934, allocations: 0.8769 MB / 0.6555 GB, free: 33.45 MB / 0.5262 GB
Notification: Performance of prepare preOptimizeDAE: time 4.12e-05/0.008975, allocations: 15.88 kB / 0.6555 GB, free: 33.44 MB / 0.5262 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001907/0.009166, allocations: 99.44 kB / 0.6556 GB, free: 33.39 MB / 0.5262 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0003627/0.009528, allocations: 310.2 kB / 0.6559 GB, free: 33.16 MB / 0.5262 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.71e-05/0.009566, allocations: 37.34 kB / 0.656 GB, free: 33.14 MB / 0.5262 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 9.739e-05/0.009663, allocations: 52.31 kB / 0.656 GB, free: 33.12 MB / 0.5262 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0008352/0.0105, allocations: 0.6237 MB / 0.6566 GB, free: 32.83 MB / 0.5262 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.867e-05/0.01052, allocations: 9.016 kB / 0.6566 GB, free: 32.82 MB / 0.5262 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 4.052e-05/0.01056, allocations: 18.25 kB / 0.6567 GB, free: 32.81 MB / 0.5262 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 4.865e-05/0.01061, allocations: 23.77 kB / 0.6567 GB, free: 32.81 MB / 0.5262 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0004788/0.01108, allocations: 315.8 kB / 0.657 GB, free: 32.77 MB / 0.5262 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001678/0.01276, allocations: 1.376 MB / 0.6583 GB, free: 31.92 MB / 0.5262 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0004088/0.01317, allocations: 244.2 kB / 0.6586 GB, free: 31.85 MB / 0.5262 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001813/0.01335, allocations: 117.7 kB / 0.6587 GB, free: 31.82 MB / 0.5262 GB
Notification: Performance of preOpt evalFunc (simulation): time 3.026e-05/0.01338, allocations: 10.72 kB / 0.6587 GB, free: 31.82 MB / 0.5262 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0003074/0.01369, allocations: 267.2 kB / 0.6589 GB, free: 31.7 MB / 0.5262 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.0004258/0.01412, allocations: 155.6 kB / 0.6591 GB, free: 31.66 MB / 0.5262 GB
Notification: Performance of pre-optimization done (n=46): time 2.194e-06/0.01412, allocations: 0 / 0.6591 GB, free: 31.66 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=46): time 0.0007134/0.01483, allocations: 432.2 kB / 0.6595 GB, free: 31.55 MB / 0.5262 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.077e-05/0.01486, allocations: 68.84 kB / 0.6596 GB, free: 31.48 MB / 0.5262 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001648/0.01503, allocations: 296.5 kB / 0.6598 GB, free: 31.28 MB / 0.5262 GB
Notification: Performance of collectPreVariables (initialization): time 3.209e-05/0.01506, allocations: 39.86 kB / 0.6599 GB, free: 31.24 MB / 0.5262 GB
Notification: Performance of collectInitialEqns (initialization): time 8.551e-05/0.01515, allocations: 291.6 kB / 0.6602 GB, free: 30.99 MB / 0.5262 GB
Notification: Performance of collectInitialBindings (initialization): time 8.286e-05/0.01523, allocations: 175.6 kB / 0.6603 GB, free: 30.85 MB / 0.5262 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001259/0.01535, allocations: 122.5 kB / 0.6604 GB, free: 30.79 MB / 0.5262 GB
Notification: Performance of setup shared object (initialization): time 6.494e-05/0.01542, allocations: 0.5147 MB / 0.6609 GB, free: 30.28 MB / 0.5262 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0002142/0.01563, allocations: 176.8 kB / 0.6611 GB, free: 30.21 MB / 0.5262 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002553/0.01589, allocations: 351.5 kB / 0.6614 GB, free: 29.93 MB / 0.5262 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0004594/0.01635, allocations: 474 kB / 0.6619 GB, free: 29.61 MB / 0.5262 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.356e-06/0.01635, allocations: 1.406 kB / 0.6619 GB, free: 29.61 MB / 0.5262 GB
Notification: Performance of matching and sorting (n=72) (initialization): time 0.0006736/0.01702, allocations: 0.5736 MB / 0.6625 GB, free: 29.38 MB / 0.5262 GB
Notification: Performance of prepare postOptimizeDAE: time 3.368e-05/0.01706, allocations: 34.45 kB / 0.6625 GB, free: 29.35 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.605e-06/0.01707, allocations: 4.219 kB / 0.6625 GB, free: 29.35 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.879e-05/0.01709, allocations: 5.625 kB / 0.6625 GB, free: 29.35 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0004007/0.01749, allocations: 170.4 kB / 0.6627 GB, free: 29.34 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.062e-05/0.0175, allocations: 5.719 kB / 0.6627 GB, free: 29.34 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001831/0.01768, allocations: 27.27 kB / 0.6627 GB, free: 29.32 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.098e-05/0.01772, allocations: 31.73 kB / 0.6627 GB, free: 29.32 MB / 0.5262 GB
Warning: Assuming fixed start value for the following 8 variables:
         singleDose1.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         singleDose1.variableDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         artery.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         gut.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         vein.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         spleen.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         liver.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         lungs.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 16
 * Number of states: 0 ()
 * Number of discrete variables: 5 (singleDose1.pulse.count,$PRE.singleDose1.pulse.count,singleDose1.pulse.T_start,$PRE.singleDose1.pulse.T_start,$whenCondition1)
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (71):
 * Single equations (assignments): 70
 * 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 0.0002092/0.01793, allocations: 217.4 kB / 0.6629 GB, free: 29.13 MB / 0.5262 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 6.609e-05/0.018, allocations: 51.84 kB / 0.663 GB, free: 29.1 MB / 0.5262 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0005578/0.01855, allocations: 412.5 kB / 0.6634 GB, free: 28.95 MB / 0.5262 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.659e-06/0.01856, allocations: 4.219 kB / 0.6634 GB, free: 28.95 MB / 0.5262 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.007e-06/0.01856, allocations: 1.312 kB / 0.6634 GB, free: 28.95 MB / 0.5262 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.643e-06/0.01857, allocations: 4.844 kB / 0.6634 GB, free: 28.95 MB / 0.5262 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0007075/0.01928, allocations: 0.7254 MB / 0.6641 GB, free: 28.51 MB / 0.5262 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.444e-06/0.01928, allocations: 0.75 kB / 0.6641 GB, free: 28.51 MB / 0.5262 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002882/0.01957, allocations: 84.16 kB / 0.6642 GB, free: 28.5 MB / 0.5262 GB
Notification: Performance of postOpt tearingSystem (simulation): time 4.479e-06/0.01957, allocations: 5.781 kB / 0.6642 GB, free: 28.5 MB / 0.5262 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.835e-05/0.0196, allocations: 16.98 kB / 0.6642 GB, free: 28.5 MB / 0.5262 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.586e-06/0.0196, allocations: 2.188 kB / 0.6642 GB, free: 28.5 MB / 0.5262 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.375e-06/0.01961, allocations: 5.219 kB / 0.6642 GB, free: 28.5 MB / 0.5262 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0006364/0.02024, allocations: 0.5952 MB / 0.6648 GB, free: 28.18 MB / 0.5262 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.985e-05/0.02027, allocations: 32.2 kB / 0.6648 GB, free: 28.16 MB / 0.5262 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 4.267e-05/0.02031, allocations: 13.66 kB / 0.6648 GB, free: 28.15 MB / 0.5262 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001555/0.02047, allocations: 12.91 kB / 0.6648 GB, free: 28.14 MB / 0.5262 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.018e-05/0.02053, allocations: 32.97 kB / 0.6649 GB, free: 28.14 MB / 0.5262 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.578e-05/0.02056, allocations: 17.36 kB / 0.6649 GB, free: 28.14 MB / 0.5262 GB
Notification: Performance of sorting global known variables: time 0.0001076/0.02066, allocations: 227.1 kB / 0.6651 GB, free: 28 MB / 0.5262 GB
Notification: Performance of sort global known variables: time 7e-08/0.02066, allocations: 0 / 0.6651 GB, free: 28 MB / 0.5262 GB
Notification: Performance of remove unused functions: time 0.0003432/0.02101, allocations: 170.8 kB / 0.6653 GB, free: 27.96 MB / 0.5262 GB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 2
 * Number of states: 14 (singleDose1.TotalCumulativeMass,singleDose1.variableDose.TotalCumulativeMass,artery.M,artery.AUC,gut.M,gut.AUC,vein.M,vein.AUC,spleen.M,spleen.AUC,liver.M,liver.AUC,lungs.M,lungs.AUC)
 * Number of discrete variables: 3 ($whenCondition1,singleDose1.pulse.T_start,singleDose1.pulse.count)
 * Number of discrete states: 1 (singleDose1.pulse.count)
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (46):
 * Single equations (assignments): 44
 * 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 0.0001076/0.02111, allocations: 110.9 kB / 0.6654 GB, free: 27.86 MB / 0.5262 GB
Notification: Performance of simCode: created initialization part: time 0.000492/0.02161, allocations: 429 kB / 0.6658 GB, free: 27.7 MB / 0.5262 GB
Notification: Performance of simCode: created event and clocks part: time 1.653e-06/0.02161, allocations: 4.312 kB / 0.6658 GB, free: 27.69 MB / 0.5262 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001863/0.02179, allocations: 144.5 kB / 0.6659 GB, free: 27.66 MB / 0.5262 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004486/0.02224, allocations: 141.5 kB / 0.6661 GB, free: 27.61 MB / 0.5262 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002028/0.02427, allocations: 1.362 MB / 0.6674 GB, free: 26.74 MB / 0.5262 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.000144/0.02441, allocations: 235.7 kB / 0.6676 GB, free: 26.65 MB / 0.5262 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001773/0.02459, allocations: 62.77 kB / 0.6677 GB, free: 26.64 MB / 0.5262 GB
Notification: Performance of SimCode: time 8.02e-07/0.02459, allocations: 0 / 0.6677 GB, free: 26.64 MB / 0.5262 GB
Notification: Performance of Templates: time 0.007393/0.03199, allocations: 6.632 MB / 0.6742 GB, free: 25.32 MB / 0.5262 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver.sim & ./Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver > Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 6.446476357989013]