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 0.001793/0.001793, 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 0.001901/0.001901, allocations: 169.9 kB / 22.45 MB, free: 2.105 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 1.586/1.586, allocations: 177.1 MB / 202.8 MB, free: 5.746 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 3.617/3.617, allocations: 274 MB / 0.5207 GB, free: 14.94 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.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver,tolerance=1e-06,outputFormat="empty",numberOfIntervals=494,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver")
translateModel(Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver,tolerance=1e-06,outputFormat="empty",numberOfIntervals=494,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.533e-06/1.533e-06, allocations: 0 / 0.7563 GB, free: 9.961 MB / 0.5887 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.818e-05/2.972e-05, allocations: 4.531 kB / 0.7563 GB, free: 9.957 MB / 0.5887 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver): time 0.005927/0.005956, allocations: 3.702 MB / 0.7599 GB, free: 6.297 MB / 0.5887 GB
Notification: Performance of NFInst.instExpressions: time 0.002086/0.008043, allocations: 0.9501 MB / 0.7608 GB, free: 5.352 MB / 0.5887 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001632/0.008206, allocations: 8 kB / 0.7608 GB, free: 5.344 MB / 0.5887 GB
Notification: Performance of NFTyping.typeComponents: time 0.000218/0.008424, allocations: 71.27 kB / 0.7609 GB, free: 5.273 MB / 0.5887 GB
Notification: Performance of NFTyping.typeBindings: time 0.0005202/0.008944, allocations: 222.1 kB / 0.7611 GB, free: 5.055 MB / 0.5887 GB
Notification: Performance of NFTyping.typeClassSections: time 0.000366/0.00931, allocations: 155.6 kB / 0.7613 GB, free: 4.902 MB / 0.5887 GB
Notification: Performance of NFFlatten.flatten: time 0.0008469/0.01016, allocations: 0.7152 MB / 0.7619 GB, free: 4.184 MB / 0.5887 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0007311/0.01089, allocations: 469.7 kB / 0.7624 GB, free: 3.723 MB / 0.5887 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0006754/0.01156, allocations: 495.2 kB / 0.7629 GB, free: 3.238 MB / 0.5887 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0006528/0.01222, allocations: 351.2 kB / 0.7632 GB, free: 2.895 MB / 0.5887 GB
Notification: Performance of NFPackage.collectConstants: time 0.000132/0.01235, allocations: 80 kB / 0.7633 GB, free: 2.816 MB / 0.5887 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001519/0.0125, allocations: 76 kB / 0.7634 GB, free: 2.742 MB / 0.5887 GB
Notification: Performance of NFScalarize.scalarize: time 0.0002236/0.01272, allocations: 183.5 kB / 0.7635 GB, free: 2.562 MB / 0.5887 GB
Notification: Performance of NFVerifyModel.verify: time 0.0004783/0.0132, allocations: 271.4 kB / 0.7638 GB, free: 2.297 MB / 0.5887 GB
Notification: Performance of NFConvertDAE.convert: time 0.0009544/0.01416, allocations: 0.7518 MB / 0.7645 GB, free: 1.543 MB / 0.5887 GB
Notification: Performance of FrontEnd - DAE generated: time 3.166e-06/0.01416, allocations: 4 kB / 0.7645 GB, free: 1.539 MB / 0.5887 GB
Notification: Performance of FrontEnd: time 1.322e-06/0.01416, allocations: 4 kB / 0.7645 GB, free: 1.535 MB / 0.5887 GB
Notification: Performance of Transformations before backend: time 8.025e-06/0.01417, allocations: 0 / 0.7645 GB, free: 1.535 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: 124
 * Number of variables: 124
Notification: Performance of Generate backend data structure: time 0.001874/0.01604, allocations: 0.7699 MB / 0.7653 GB, free: 0.7266 MB / 0.5887 GB
Notification: Performance of prepare preOptimizeDAE: time 3.674e-05/0.01608, allocations: 12.03 kB / 0.7653 GB, free: 0.7148 MB / 0.5887 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.00014/0.01622, allocations: 68.44 kB / 0.7654 GB, free: 0.6484 MB / 0.5887 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0006703/0.01689, allocations: 327 kB / 0.7657 GB, free: 304 kB / 0.5887 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 4.755e-05/0.01694, allocations: 37.38 kB / 0.7657 GB, free: 268 kB / 0.5887 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001134/0.01705, allocations: 48.38 kB / 0.7658 GB, free: 220 kB / 0.5887 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.00139/0.01844, allocations: 0.7468 MB / 0.7665 GB, free: 15.44 MB / 0.6043 GB
Notification: Performance of preOpt findStateOrder (simulation): time 2.99e-05/0.01847, allocations: 7.891 kB / 0.7665 GB, free: 15.43 MB / 0.6043 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 6.154e-05/0.01853, allocations: 20 kB / 0.7665 GB, free: 15.41 MB / 0.6043 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 3.769e-05/0.01857, allocations: 25 kB / 0.7665 GB, free: 15.39 MB / 0.6043 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.001163/0.01973, allocations: 0.5113 MB / 0.767 GB, free: 14.88 MB / 0.6043 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.00315/0.02288, allocations: 1.36 MB / 0.7684 GB, free: 13.48 MB / 0.6043 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0009324/0.02382, allocations: 361.4 kB / 0.7687 GB, free: 13.12 MB / 0.6043 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0005073/0.02432, allocations: 201.5 kB / 0.7689 GB, free: 12.92 MB / 0.6043 GB
Notification: Performance of preOpt evalFunc (simulation): time 3.629e-05/0.02436, allocations: 12.38 kB / 0.7689 GB, free: 12.91 MB / 0.6043 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0007162/0.02507, allocations: 344.2 kB / 0.7692 GB, free: 12.55 MB / 0.6043 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.0008481/0.02592, allocations: 147.7 kB / 0.7694 GB, free: 12.41 MB / 0.6043 GB
Notification: Performance of pre-optimization done (n=46): time 1.984e-06/0.02592, allocations: 0 / 0.7694 GB, free: 12.41 MB / 0.6043 GB
Notification: Performance of matching and sorting (n=46): time 0.00167/0.02759, allocations: 0.6356 MB / 0.77 GB, free: 11.77 MB / 0.6043 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 6.953e-05/0.02766, allocations: 63.41 kB / 0.7701 GB, free: 11.7 MB / 0.6043 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003235/0.02799, allocations: 257.9 kB / 0.7703 GB, free: 11.44 MB / 0.6043 GB
Notification: Performance of collectPreVariables (initialization): time 5.663e-05/0.02804, allocations: 37.7 kB / 0.7703 GB, free: 11.39 MB / 0.6043 GB
Notification: Performance of collectInitialEqns (initialization): time 0.0003497/0.02839, allocations: 241 kB / 0.7706 GB, free: 11.16 MB / 0.6043 GB
Notification: Performance of collectInitialBindings (initialization): time 0.000182/0.02858, allocations: 174.5 kB / 0.7707 GB, free: 10.98 MB / 0.6043 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002159/0.02879, allocations: 118.3 kB / 0.7708 GB, free: 10.86 MB / 0.6043 GB
Notification: Performance of setup shared object (initialization): time 0.0002007/0.02899, allocations: 346.8 kB / 0.7712 GB, free: 10.52 MB / 0.6043 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0005783/0.02957, allocations: 272.6 kB / 0.7714 GB, free: 10.24 MB / 0.6043 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0006894/0.03026, allocations: 392.9 kB / 0.7718 GB, free: 9.793 MB / 0.6043 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001187/0.03145, allocations: 0.5809 MB / 0.7724 GB, free: 9.16 MB / 0.6043 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.038e-06/0.03145, allocations: 0 / 0.7724 GB, free: 9.16 MB / 0.6043 GB
Notification: Performance of matching and sorting (n=72) (initialization): time 0.001582/0.03303, allocations: 0.7269 MB / 0.7731 GB, free: 8.418 MB / 0.6043 GB
Notification: Performance of prepare postOptimizeDAE: time 7.672e-05/0.03311, allocations: 33.7 kB / 0.7731 GB, free: 8.379 MB / 0.6043 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.381e-05/0.03312, allocations: 4 kB / 0.7731 GB, free: 8.375 MB / 0.6043 GB
Notification: Performance of postOpt tearingSystem (initialization): time 2.747e-05/0.03315, allocations: 4 kB / 0.7731 GB, free: 8.371 MB / 0.6043 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.001062/0.03421, allocations: 171.7 kB / 0.7733 GB, free: 8.203 MB / 0.6043 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 2.775e-05/0.03424, allocations: 11.94 kB / 0.7733 GB, free: 8.191 MB / 0.6043 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0005536/0.03479, allocations: 24.27 kB / 0.7733 GB, free: 8.168 MB / 0.6043 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 9.466e-05/0.03489, allocations: 35.97 kB / 0.7734 GB, free: 8.133 MB / 0.6043 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 0.0004702/0.03536, allocations: 207.1 kB / 0.7736 GB, free: 7.922 MB / 0.6043 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001077/0.03547, allocations: 39.75 kB / 0.7736 GB, free: 7.883 MB / 0.6043 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.001856/0.03732, allocations: 0.514 MB / 0.7741 GB, free: 7.375 MB / 0.6043 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 1.013e-05/0.03733, allocations: 4 kB / 0.7741 GB, free: 7.371 MB / 0.6043 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.772e-06/0.03734, allocations: 0 / 0.7741 GB, free: 7.371 MB / 0.6043 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.356e-05/0.03735, allocations: 3.984 kB / 0.7741 GB, free: 7.367 MB / 0.6043 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.00227/0.03962, allocations: 0.8302 MB / 0.7749 GB, free: 6.496 MB / 0.6043 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.988e-06/0.03963, allocations: 0 / 0.7749 GB, free: 6.496 MB / 0.6043 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.000815/0.04044, allocations: 83.88 kB / 0.775 GB, free: 6.414 MB / 0.6043 GB
Notification: Performance of postOpt tearingSystem (simulation): time 6.372e-06/0.04045, allocations: 0 / 0.775 GB, free: 6.414 MB / 0.6043 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 7.115e-05/0.04052, allocations: 19.98 kB / 0.775 GB, free: 6.395 MB / 0.6043 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 5.17e-06/0.04052, allocations: 0 / 0.775 GB, free: 6.395 MB / 0.6043 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.764e-06/0.04053, allocations: 0 / 0.775 GB, free: 6.395 MB / 0.6043 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.002381/0.04291, allocations: 0.7745 MB / 0.7758 GB, free: 5.602 MB / 0.6043 GB
Notification: Performance of postOpt removeConstants (simulation): time 9.349e-05/0.043, allocations: 31.8 kB / 0.7758 GB, free: 5.57 MB / 0.6043 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001043/0.04311, allocations: 15.98 kB / 0.7758 GB, free: 5.555 MB / 0.6043 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0005097/0.04361, allocations: 15.98 kB / 0.7758 GB, free: 5.539 MB / 0.6043 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001247/0.04374, allocations: 31.94 kB / 0.7759 GB, free: 5.508 MB / 0.6043 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 6.462e-05/0.0438, allocations: 19.98 kB / 0.7759 GB, free: 5.488 MB / 0.6043 GB
Notification: Performance of sorting global known variables: time 0.0003541/0.04416, allocations: 203 kB / 0.7761 GB, free: 5.293 MB / 0.6043 GB
Notification: Performance of sort global known variables: time 1.2e-07/0.04416, allocations: 0 / 0.7761 GB, free: 5.293 MB / 0.6043 GB
Notification: Performance of remove unused functions: time 0.0009142/0.04507, allocations: 163.7 kB / 0.7762 GB, free: 5.133 MB / 0.6043 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 0.0002344/0.04531, allocations: 123.5 kB / 0.7764 GB, free: 5.008 MB / 0.6043 GB
Notification: Performance of simCode: created initialization part: time 0.001788/0.04709, allocations: 0.5462 MB / 0.7769 GB, free: 4.441 MB / 0.6043 GB
Notification: Performance of simCode: created event and clocks part: time 2.986e-06/0.0471, allocations: 0 / 0.7769 GB, free: 4.441 MB / 0.6043 GB
Notification: Performance of simCode: created simulation system equations: time 0.0007127/0.04781, allocations: 204.4 kB / 0.7771 GB, free: 4.242 MB / 0.6043 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.001135/0.04895, allocations: 128.9 kB / 0.7772 GB, free: 4.113 MB / 0.6043 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003703/0.05265, allocations: 1.305 MB / 0.7785 GB, free: 2.805 MB / 0.6043 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0003773/0.05303, allocations: 237 kB / 0.7787 GB, free: 2.551 MB / 0.6043 GB
Notification: Performance of simCode: alias equations: time 0.0004467/0.05347, allocations: 70.16 kB / 0.7788 GB, free: 2.492 MB / 0.6043 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003218/0.05379, allocations: 64.44 kB / 0.7788 GB, free: 2.43 MB / 0.6043 GB
Notification: Performance of SimCode: time 6.51e-07/0.0538, allocations: 0 / 0.7788 GB, free: 2.43 MB / 0.6043 GB
Notification: Performance of Templates: time 0.02234/0.07614, allocations: 7.848 MB / 0.7865 GB, free: 10.91 MB / 0.6199 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 -abortSlowSimulation -alarm=240  -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 10.879607638344169]