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 0.001863/0.001863, allocations: 105.5 kB / 18.95 MB, free: 1.176 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 0.002094/0.002094, allocations: 214.2 kB / 22.25 MB, free: 3.566 MB / 13.93 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 1.681/1.681, allocations: 230.6 MB / 256 MB, free: 9.578 MB / 202.7 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 3.779/3.779, allocations: 335.2 MB / 0.6325 GB, free: 7.16 MB / 442.7 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: Pharmacolibrary requested package Modelica of version 4.0.0. Modelica 4.1.0 is used instead which states that it is fully compatible without conversion script needed.
Notification: Performance of FrontEnd - loaded program: time 0.00373/0.00373, allocations: 72.16 kB / 0.868 GB, free: 5.637 MB / 0.573 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.2633/0.267, allocations: 112.8 MB / 0.9782 GB, free: 4.562 MB / 0.6824 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver): time 0.006169/0.2732, allocations: 3.702 MB / 0.9818 GB, free: 0.8438 MB / 0.6824 GB
Notification: Performance of NFInst.instExpressions: time 0.002974/0.2762, allocations: 0.9427 MB / 0.9827 GB, free: 15.9 MB / 0.698 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.000313/0.2765, allocations: 4 kB / 0.9827 GB, free: 15.89 MB / 0.698 GB
Notification: Performance of NFTyping.typeComponents: time 0.0002815/0.2768, allocations: 79.27 kB / 0.9828 GB, free: 15.82 MB / 0.698 GB
Notification: Performance of NFTyping.typeBindings: time 0.0006514/0.2774, allocations: 198.4 kB / 0.983 GB, free: 15.62 MB / 0.698 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0004634/0.2779, allocations: 151.8 kB / 0.9831 GB, free: 15.47 MB / 0.698 GB
Notification: Performance of NFFlatten.flatten: time 0.0009096/0.2788, allocations: 0.6805 MB / 0.9838 GB, free: 14.79 MB / 0.698 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0008116/0.2796, allocations: 482 kB / 0.9843 GB, free: 14.31 MB / 0.698 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0005062/0.2801, allocations: 335.2 kB / 0.9846 GB, free: 13.98 MB / 0.698 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0007303/0.2808, allocations: 390.6 kB / 0.985 GB, free: 13.6 MB / 0.698 GB
Notification: Performance of NFPackage.collectConstants: time 0.0001368/0.281, allocations: 76 kB / 0.985 GB, free: 13.53 MB / 0.698 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.000153/0.2811, allocations: 80 kB / 0.9851 GB, free: 13.45 MB / 0.698 GB
Notification: Performance of NFScalarize.scalarize: time 0.0002413/0.2814, allocations: 179.4 kB / 0.9853 GB, free: 13.27 MB / 0.698 GB
Notification: Performance of NFVerifyModel.verify: time 0.0004027/0.2818, allocations: 299 kB / 0.9856 GB, free: 12.98 MB / 0.698 GB
Notification: Performance of NFConvertDAE.convert: time 0.0009524/0.2827, allocations: 0.7163 MB / 0.9863 GB, free: 12.26 MB / 0.698 GB
Notification: Performance of FrontEnd - DAE generated: time 4.379e-06/0.2827, allocations: 0 / 0.9863 GB, free: 12.26 MB / 0.698 GB
Notification: Performance of FrontEnd: time 2.194e-06/0.2827, allocations: 0 / 0.9863 GB, free: 12.26 MB / 0.698 GB
Notification: Performance of Transformations before backend: time 1.105e-05/0.2827, allocations: 3.938 kB / 0.9863 GB, free: 12.26 MB / 0.698 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 0.00227/0.285, allocations: 0.7854 MB / 0.987 GB, free: 11.43 MB / 0.698 GB
Notification: Performance of prepare preOptimizeDAE: time 5.318e-05/0.2851, allocations: 18.05 kB / 0.987 GB, free: 11.42 MB / 0.698 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001737/0.2852, allocations: 60.56 kB / 0.9871 GB, free: 11.36 MB / 0.698 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0007338/0.286, allocations: 317.6 kB / 0.9874 GB, free: 11.02 MB / 0.698 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 0.5375/0.8234, allocations: 43.22 kB / 0.9874 GB, free: 27.04 MB / 0.698 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 0.0002916/0.8237, allocations: 53.41 kB / 0.9875 GB, free: 27.04 MB / 0.698 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.001329/0.8251, allocations: 0.7398 MB / 0.9882 GB, free: 26.86 MB / 0.698 GB
Notification: Performance of preOpt findStateOrder (simulation): time 2.931e-05/0.8251, allocations: 9.484 kB / 0.9882 GB, free: 26.86 MB / 0.698 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 5.571e-05/0.8251, allocations: 19.84 kB / 0.9882 GB, free: 26.86 MB / 0.698 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 3.809e-05/0.8252, allocations: 22.77 kB / 0.9883 GB, free: 26.86 MB / 0.698 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0009805/0.8262, allocations: 0.531 MB / 0.9888 GB, free: 26.85 MB / 0.698 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.002847/0.829, allocations: 1.356 MB / 0.9901 GB, free: 26.46 MB / 0.698 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0007881/0.8298, allocations: 361.2 kB / 0.9905 GB, free: 26.44 MB / 0.698 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0004329/0.8302, allocations: 205.1 kB / 0.9907 GB, free: 26.43 MB / 0.698 GB
Notification: Performance of preOpt evalFunc (simulation): time 3.932e-05/0.8303, allocations: 8.656 kB / 0.9907 GB, free: 26.43 MB / 0.698 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0006624/0.8309, allocations: 338.8 kB / 0.991 GB, free: 26.35 MB / 0.698 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.0008315/0.8318, allocations: 149.7 kB / 0.9911 GB, free: 26.34 MB / 0.698 GB
Notification: Performance of pre-optimization done (n=46): time 2.745e-06/0.8318, allocations: 0 / 0.9911 GB, free: 26.34 MB / 0.698 GB
Notification: Performance of matching and sorting (n=46): time 0.00144/0.8332, allocations: 0.6403 MB / 0.9918 GB, free: 26.28 MB / 0.698 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.024e-05/0.8333, allocations: 58.08 kB / 0.9918 GB, free: 26.22 MB / 0.698 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003101/0.8336, allocations: 257.5 kB / 0.9921 GB, free: 26.12 MB / 0.698 GB
Notification: Performance of collectPreVariables (initialization): time 4.518e-05/0.8336, allocations: 36 kB / 0.9921 GB, free: 26.09 MB / 0.698 GB
Notification: Performance of collectInitialEqns (initialization): time 0.0001594/0.8338, allocations: 242.8 kB / 0.9923 GB, free: 25.95 MB / 0.698 GB
Notification: Performance of collectInitialBindings (initialization): time 0.0001478/0.8339, allocations: 181.7 kB / 0.9925 GB, free: 25.83 MB / 0.698 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002021/0.8341, allocations: 121.4 kB / 0.9926 GB, free: 25.81 MB / 0.698 GB
Notification: Performance of setup shared object (initialization): time 8.91e-05/0.8342, allocations: 350 kB / 0.9929 GB, free: 25.5 MB / 0.698 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0004859/0.8347, allocations: 265.5 kB / 0.9932 GB, free: 25.45 MB / 0.698 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0005456/0.8352, allocations: 400.1 kB / 0.9936 GB, free: 25.25 MB / 0.698 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.001/0.8362, allocations: 0.5797 MB / 0.9941 GB, free: 25.09 MB / 0.698 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.338e-06/0.8362, allocations: 1.219 kB / 0.9941 GB, free: 25.09 MB / 0.698 GB
Notification: Performance of matching and sorting (n=72) (initialization): time 0.001232/0.8375, allocations: 0.7136 MB / 0.9948 GB, free: 24.88 MB / 0.698 GB
Notification: Performance of prepare postOptimizeDAE: time 4.016e-05/0.8375, allocations: 37.44 kB / 0.9949 GB, free: 24.84 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.246e-05/0.8375, allocations: 5.219 kB / 0.9949 GB, free: 24.84 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (initialization): time 2.539e-05/0.8376, allocations: 5.781 kB / 0.9949 GB, free: 24.84 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0007277/0.8383, allocations: 171.1 kB / 0.995 GB, free: 24.83 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.512e-05/0.8383, allocations: 9.344 kB / 0.9951 GB, free: 24.82 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0004251/0.8387, allocations: 26.47 kB / 0.9951 GB, free: 24.82 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 6.079e-05/0.8388, allocations: 33.75 kB / 0.9951 GB, free: 24.81 MB / 0.698 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 0.0003547/0.8391, allocations: 217.3 kB / 0.9953 GB, free: 24.65 MB / 0.698 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 6.493e-05/0.8392, allocations: 33.27 kB / 0.9954 GB, free: 24.63 MB / 0.698 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.001131/0.8403, allocations: 0.5154 MB / 0.9959 GB, free: 24.42 MB / 0.698 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 7.674e-06/0.8403, allocations: 5.281 kB / 0.9959 GB, free: 24.42 MB / 0.698 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 6.342e-06/0.8403, allocations: 1.031 kB / 0.9959 GB, free: 24.42 MB / 0.698 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.035e-05/0.8404, allocations: 7.781 kB / 0.9959 GB, free: 24.42 MB / 0.698 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001373/0.8417, allocations: 0.8109 MB / 0.9967 GB, free: 23.97 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.268e-06/0.8417, allocations: 1.984 kB / 0.9967 GB, free: 23.97 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0005311/0.8423, allocations: 87.12 kB / 0.9967 GB, free: 23.96 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (simulation): time 6.983e-06/0.8423, allocations: 2.562 kB / 0.9968 GB, free: 23.96 MB / 0.698 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 4.357e-05/0.8423, allocations: 24.05 kB / 0.9968 GB, free: 23.95 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.508e-06/0.8423, allocations: 2.188 kB / 0.9968 GB, free: 23.95 MB / 0.698 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.166e-06/0.8423, allocations: 5.156 kB / 0.9968 GB, free: 23.95 MB / 0.698 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001373/0.8437, allocations: 0.7667 MB / 0.9975 GB, free: 23.55 MB / 0.698 GB
Notification: Performance of postOpt removeConstants (simulation): time 7.027e-05/0.8438, allocations: 26.33 kB / 0.9976 GB, free: 23.54 MB / 0.698 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 7.564e-05/0.8438, allocations: 24.91 kB / 0.9976 GB, free: 23.52 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0003352/0.8442, allocations: 16.95 kB / 0.9976 GB, free: 23.52 MB / 0.698 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001036/0.8443, allocations: 36.72 kB / 0.9976 GB, free: 23.51 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.815e-05/0.8443, allocations: 18.12 kB / 0.9976 GB, free: 23.5 MB / 0.698 GB
Notification: Performance of sorting global known variables: time 0.0001892/0.8445, allocations: 204.7 kB / 0.9978 GB, free: 23.39 MB / 0.698 GB
Notification: Performance of sort global known variables: time 6e-08/0.8445, allocations: 0 / 0.9978 GB, free: 23.39 MB / 0.698 GB
Notification: Performance of remove unused functions: time 0.0005986/0.8451, allocations: 166.9 kB / 0.998 GB, free: 23.35 MB / 0.698 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 0.0001474/0.8453, allocations: 113.8 kB / 0.9981 GB, free: 23.25 MB / 0.698 GB
Notification: Performance of simCode: created initialization part: time 0.001161/0.8464, allocations: 0.5449 MB / 0.9986 GB, free: 23 MB / 0.698 GB
Notification: Performance of simCode: created event and clocks part: time 2.315e-06/0.8464, allocations: 0.9688 kB / 0.9986 GB, free: 23 MB / 0.698 GB
Notification: Performance of simCode: created simulation system equations: time 0.0004463/0.8469, allocations: 199.7 kB / 0.9988 GB, free: 22.94 MB / 0.698 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0007184/0.8476, allocations: 125.8 kB / 0.999 GB, free: 22.9 MB / 0.698 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002625/0.8502, allocations: 1.617 MB / 1.001 GB, free: 21.83 MB / 0.698 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0002646/0.8505, allocations: 237.7 kB / 1.001 GB, free: 21.74 MB / 0.698 GB
Notification: Performance of simCode: alias equations: time 0.0004138/0.8509, allocations: 67.88 kB / 1.001 GB, free: 21.72 MB / 0.698 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0002504/0.8511, allocations: 59.98 kB / 1.001 GB, free: 21.71 MB / 0.698 GB
Notification: Performance of SimCode: time 1.072e-06/0.8511, allocations: 0.5625 kB / 1.001 GB, free: 21.71 MB / 0.698 GB
Notification: Performance of Templates: time 0.02155/0.8727, allocations: 8.694 MB / 1.009 GB, free: 20.76 MB / 0.698 GB
"
[Timeout remaining time 659]
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: 11.916212053969502]