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 0.001084/0.001084, allocations: 104.3 kB / 19.7 MB, free: 440 kB / 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 0.001321/0.001321, allocations: 208.2 kB / 22.99 MB, free: 2.98 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 0.9801/0.9801, allocations: 230.6 MB / 256.8 MB, free: 9.602 MB / 202.7 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 1.692/1.692, allocations: 334.3 MB / 0.6323 GB, free: 7.922 MB / 442.7 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=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 0.001594/0.001594, allocations: 67.91 kB / 0.867 GB, free: 8.129 MB / 0.573 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1869/0.1885, allocations: 112.8 MB / 0.9772 GB, free: 7.047 MB / 0.6824 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver): time 0.004181/0.1926, allocations: 3.705 MB / 0.9808 GB, free: 3.324 MB / 0.6824 GB
Notification: Performance of NFInst.instExpressions: time 0.00185/0.1945, allocations: 0.9388 MB / 0.9817 GB, free: 2.383 MB / 0.6824 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0002324/0.1947, allocations: 7.938 kB / 0.9817 GB, free: 2.375 MB / 0.6824 GB
Notification: Performance of NFTyping.typeComponents: time 0.0002189/0.1949, allocations: 75.27 kB / 0.9818 GB, free: 2.301 MB / 0.6824 GB
Notification: Performance of NFTyping.typeBindings: time 0.000468/0.1954, allocations: 202.4 kB / 0.982 GB, free: 2.102 MB / 0.6824 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0003493/0.1958, allocations: 151.7 kB / 0.9821 GB, free: 1.953 MB / 0.6824 GB
Notification: Performance of NFFlatten.flatten: time 0.0005958/0.1964, allocations: 0.6882 MB / 0.9828 GB, free: 1.262 MB / 0.6824 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0005482/0.1969, allocations: 470.2 kB / 0.9833 GB, free: 0.7969 MB / 0.6824 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0004063/0.1973, allocations: 351.1 kB / 0.9836 GB, free: 464 kB / 0.6824 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0005544/0.1979, allocations: 378.6 kB / 0.984 GB, free: 84 kB / 0.6824 GB
Notification: Performance of NFPackage.collectConstants: time 9.319e-05/0.198, allocations: 79.94 kB / 0.984 GB, free: 4 kB / 0.6824 GB
Notification: Performance of NFFlatten.collectFunctions: time 0.0001134/0.1981, allocations: 80.05 kB / 0.9841 GB, free: 15.92 MB / 0.698 GB
Notification: Performance of NFScalarize.scalarize: time 0.0001363/0.1982, allocations: 171.5 kB / 0.9843 GB, free: 15.76 MB / 0.698 GB
Notification: Performance of NFVerifyModel.verify: time 0.0002611/0.1985, allocations: 314.8 kB / 0.9846 GB, free: 15.45 MB / 0.698 GB
Notification: Performance of NFConvertDAE.convert: time 0.0005959/0.1991, allocations: 0.7085 MB / 0.9853 GB, free: 14.74 MB / 0.698 GB
Notification: Performance of FrontEnd - DAE generated: time 4.779e-06/0.1991, allocations: 0 / 0.9853 GB, free: 14.74 MB / 0.698 GB
Notification: Performance of FrontEnd: time 1.934e-06/0.1991, allocations: 0 / 0.9853 GB, free: 14.74 MB / 0.698 GB
Notification: Performance of Transformations before backend: time 1.577e-05/0.1991, allocations: 0 / 0.9853 GB, free: 14.74 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 0.00133/0.2004, allocations: 0.7777 MB / 0.986 GB, free: 13.92 MB / 0.698 GB
Notification: Performance of prepare preOptimizeDAE: time 4.358e-05/0.2005, allocations: 14.11 kB / 0.986 GB, free: 13.91 MB / 0.698 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001106/0.2006, allocations: 60.56 kB / 0.9861 GB, free: 13.85 MB / 0.698 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0004917/0.2011, allocations: 325.6 kB / 0.9864 GB, free: 13.5 MB / 0.698 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.814e-05/0.2011, allocations: 37.38 kB / 0.9864 GB, free: 13.47 MB / 0.698 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 8.455e-05/0.2012, allocations: 52.12 kB / 0.9865 GB, free: 13.42 MB / 0.698 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0008646/0.202, allocations: 0.7583 MB / 0.9872 GB, free: 12.62 MB / 0.698 GB
Notification: Performance of preOpt findStateOrder (simulation): time 2.085e-05/0.2021, allocations: 0 / 0.9872 GB, free: 12.62 MB / 0.698 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 4.092e-05/0.2021, allocations: 16 kB / 0.9872 GB, free: 12.61 MB / 0.698 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 3.147e-05/0.2021, allocations: 28.98 kB / 0.9873 GB, free: 12.58 MB / 0.698 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0007124/0.2029, allocations: 0.527 MB / 0.9878 GB, free: 12.05 MB / 0.698 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001966/0.2048, allocations: 1.352 MB / 0.9891 GB, free: 10.66 MB / 0.698 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.4195/0.6243, allocations: 358.5 kB / 0.9894 GB, free: 22.56 MB / 0.698 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0004259/0.6247, allocations: 205.2 kB / 0.9896 GB, free: 22.55 MB / 0.698 GB
Notification: Performance of preOpt evalFunc (simulation): time 3.928e-05/0.6248, allocations: 12.58 kB / 0.9897 GB, free: 22.55 MB / 0.698 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0005236/0.6253, allocations: 341.2 kB / 0.99 GB, free: 22.47 MB / 0.698 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.0006464/0.6259, allocations: 147.3 kB / 0.9901 GB, free: 22.47 MB / 0.698 GB
Notification: Performance of pre-optimization done (n=46): time 4.058e-06/0.626, allocations: 0.8438 kB / 0.9901 GB, free: 22.47 MB / 0.698 GB
Notification: Performance of matching and sorting (n=46): time 0.001168/0.6271, allocations: 0.6382 MB / 0.9907 GB, free: 22.43 MB / 0.698 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 2.821e-05/0.6271, allocations: 62.55 kB / 0.9908 GB, free: 22.36 MB / 0.698 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002212/0.6274, allocations: 265.3 kB / 0.9911 GB, free: 22.26 MB / 0.698 GB
Notification: Performance of collectPreVariables (initialization): time 3.618e-05/0.6274, allocations: 33.73 kB / 0.9911 GB, free: 22.23 MB / 0.698 GB
Notification: Performance of collectInitialEqns (initialization): time 0.0001248/0.6275, allocations: 242.3 kB / 0.9913 GB, free: 22.11 MB / 0.698 GB
Notification: Performance of collectInitialBindings (initialization): time 9.629e-05/0.6276, allocations: 175.7 kB / 0.9915 GB, free: 22.02 MB / 0.698 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001565/0.6278, allocations: 124.7 kB / 0.9916 GB, free: 22 MB / 0.698 GB
Notification: Performance of setup shared object (initialization): time 5.665e-05/0.6278, allocations: 348.5 kB / 0.9919 GB, free: 21.68 MB / 0.698 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003894/0.6282, allocations: 262.2 kB / 0.9922 GB, free: 21.64 MB / 0.698 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0004437/0.6287, allocations: 401.3 kB / 0.9926 GB, free: 21.44 MB / 0.698 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0008251/0.6295, allocations: 0.5775 MB / 0.9931 GB, free: 21.27 MB / 0.698 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.929e-06/0.6295, allocations: 2.297 kB / 0.9931 GB, free: 21.27 MB / 0.698 GB
Notification: Performance of matching and sorting (n=72) (initialization): time 0.001024/0.6305, allocations: 0.7176 MB / 0.9938 GB, free: 21.15 MB / 0.698 GB
Notification: Performance of prepare postOptimizeDAE: time 3.537e-05/0.6306, allocations: 34.47 kB / 0.9939 GB, free: 21.12 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 9.808e-06/0.6306, allocations: 6.266 kB / 0.9939 GB, free: 21.12 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (initialization): time 2.248e-05/0.6306, allocations: 5.5 kB / 0.9939 GB, free: 21.12 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0005442/0.6311, allocations: 167.6 kB / 0.994 GB, free: 21.12 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.604e-05/0.6312, allocations: 15.67 kB / 0.9941 GB, free: 21.12 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0002853/0.6314, allocations: 23.67 kB / 0.9941 GB, free: 21.12 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.918e-05/0.6315, allocations: 37.88 kB / 0.9941 GB, free: 21.12 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 0.0002927/0.6318, allocations: 206.9 kB / 0.9943 GB, free: 21 MB / 0.698 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 5.742e-05/0.6318, allocations: 33.53 kB / 0.9943 GB, free: 20.98 MB / 0.698 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0009275/0.6328, allocations: 0.5234 MB / 0.9949 GB, free: 20.93 MB / 0.698 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 8.787e-06/0.6328, allocations: 7.719 kB / 0.9949 GB, free: 20.92 MB / 0.698 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.52e-06/0.6328, allocations: 1.562 kB / 0.9949 GB, free: 20.92 MB / 0.698 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 7.614e-06/0.6328, allocations: 4.234 kB / 0.9949 GB, free: 20.92 MB / 0.698 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001198/0.634, allocations: 0.8078 MB / 0.9957 GB, free: 20.68 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.617e-06/0.634, allocations: 5.406 kB / 0.9957 GB, free: 20.68 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0003802/0.6344, allocations: 95.97 kB / 0.9958 GB, free: 20.67 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (simulation): time 4.899e-06/0.6344, allocations: 0 / 0.9958 GB, free: 20.67 MB / 0.698 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.558e-05/0.6344, allocations: 17.36 kB / 0.9958 GB, free: 20.67 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.557e-06/0.6344, allocations: 0.7031 kB / 0.9958 GB, free: 20.67 MB / 0.698 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.623e-06/0.6344, allocations: 0 / 0.9958 GB, free: 20.67 MB / 0.698 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.00108/0.6355, allocations: 0.7768 MB / 0.9965 GB, free: 20.49 MB / 0.698 GB
Notification: Performance of postOpt removeConstants (simulation): time 4.793e-05/0.6355, allocations: 26.94 kB / 0.9966 GB, free: 20.48 MB / 0.698 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.735e-05/0.6356, allocations: 25.39 kB / 0.9966 GB, free: 20.47 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0002438/0.6358, allocations: 18.77 kB / 0.9966 GB, free: 20.47 MB / 0.698 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 9.919e-05/0.6359, allocations: 31.12 kB / 0.9966 GB, free: 20.47 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.444e-05/0.636, allocations: 16.62 kB / 0.9966 GB, free: 20.47 MB / 0.698 GB
Notification: Performance of sorting global known variables: time 0.0001855/0.6362, allocations: 200.1 kB / 0.9968 GB, free: 20.39 MB / 0.698 GB
Notification: Performance of sort global known variables: time 9e-08/0.6362, allocations: 1.125 kB / 0.9968 GB, free: 20.39 MB / 0.698 GB
Notification: Performance of remove unused functions: time 0.0005846/0.6367, allocations: 167 kB / 0.997 GB, free: 20.38 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 0.0001538/0.6369, allocations: 116.1 kB / 0.9971 GB, free: 20.29 MB / 0.698 GB
Notification: Performance of simCode: created initialization part: time 0.0009426/0.6378, allocations: 0.5439 MB / 0.9976 GB, free: 20.18 MB / 0.698 GB
Notification: Performance of simCode: created event and clocks part: time 2.736e-06/0.6378, allocations: 2.656 kB / 0.9976 GB, free: 20.18 MB / 0.698 GB
Notification: Performance of simCode: created simulation system equations: time 0.0003383/0.6382, allocations: 200.5 kB / 0.9978 GB, free: 20.18 MB / 0.698 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004785/0.6387, allocations: 131.4 kB / 0.998 GB, free: 20.16 MB / 0.698 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001996/0.6407, allocations: 1.639 MB / 0.9996 GB, free: 19.17 MB / 0.698 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0002246/0.6409, allocations: 237.8 kB / 0.9998 GB, free: 19.08 MB / 0.698 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001772/0.6411, allocations: 60.06 kB / 0.9998 GB, free: 19.07 MB / 0.698 GB
Notification: Performance of SimCode: time 7.41e-07/0.6411, allocations: 0 / 0.9998 GB, free: 19.07 MB / 0.698 GB
Notification: Performance of Templates: time 0.01113/0.6522, allocations: 6.619 MB / 1.006 GB, free: 18.48 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 > Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 8.121158146997914]