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 0.001074/0.001074, allocations: 100.4 kB / 19.71 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 0.001161/0.001161, allocations: 212.9 kB / 23 MB, free: 2.957 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 1.025/1.025, allocations: 230.6 MB / 256.8 MB, free: 9.637 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 1.76/1.76, allocations: 334.2 MB / 0.6323 GB, free: 7.973 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.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: 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 0.004799/0.004799, allocations: 63.91 kB / 0.867 GB, free: 8.203 MB / 0.573 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1973/0.2021, allocations: 112.8 MB / 0.9772 GB, free: 7.113 MB / 0.6824 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue): time 0.002898/0.205, allocations: 2.752 MB / 0.9799 GB, free: 4.348 MB / 0.6824 GB
Notification: Performance of NFInst.instExpressions: time 0.001267/0.2062, allocations: 0.7284 MB / 0.9806 GB, free: 3.617 MB / 0.6824 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001753/0.2064, allocations: 4 kB / 0.9806 GB, free: 3.613 MB / 0.6824 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001979/0.2066, allocations: 39.56 kB / 0.9806 GB, free: 3.574 MB / 0.6824 GB
Notification: Performance of NFTyping.typeBindings: time 0.0002723/0.2069, allocations: 115 kB / 0.9807 GB, free: 3.461 MB / 0.6824 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0002775/0.2072, allocations: 103.8 kB / 0.9808 GB, free: 3.359 MB / 0.6824 GB
Notification: Performance of NFFlatten.flatten: time 0.0003495/0.2075, allocations: 414.2 kB / 0.9812 GB, free: 2.953 MB / 0.6824 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0003125/0.2078, allocations: 207.8 kB / 0.9814 GB, free: 2.75 MB / 0.6824 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001644/0.208, allocations: 179.5 kB / 0.9816 GB, free: 2.574 MB / 0.6824 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002079/0.2082, allocations: 171.3 kB / 0.9818 GB, free: 2.406 MB / 0.6824 GB
Notification: Performance of NFPackage.collectConstants: time 4.532e-05/0.2082, allocations: 36 kB / 0.9818 GB, free: 2.371 MB / 0.6824 GB
Notification: Performance of NFFlatten.collectFunctions: time 4.626e-05/0.2083, allocations: 44 kB / 0.9818 GB, free: 2.328 MB / 0.6824 GB
Notification: Performance of NFScalarize.scalarize: time 5.78e-05/0.2083, allocations: 91.67 kB / 0.9819 GB, free: 2.238 MB / 0.6824 GB
Notification: Performance of NFVerifyModel.verify: time 0.0001144/0.2084, allocations: 151.4 kB / 0.9821 GB, free: 2.09 MB / 0.6824 GB
Notification: Performance of NFConvertDAE.convert: time 0.000299/0.2087, allocations: 382.5 kB / 0.9824 GB, free: 1.715 MB / 0.6824 GB
Notification: Performance of FrontEnd - DAE generated: time 4.408e-06/0.2088, allocations: 0 / 0.9824 GB, free: 1.715 MB / 0.6824 GB
Notification: Performance of FrontEnd: time 1.993e-06/0.2088, allocations: 0 / 0.9824 GB, free: 1.715 MB / 0.6824 GB
Notification: Performance of Transformations before backend: time 6.983e-06/0.2088, allocations: 0 / 0.9824 GB, free: 1.715 MB / 0.6824 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 0.0008288/0.2096, allocations: 0.5617 MB / 0.983 GB, free: 1.117 MB / 0.6824 GB
Notification: Performance of prepare preOptimizeDAE: time 3.772e-05/0.2096, allocations: 10.11 kB / 0.983 GB, free: 1.109 MB / 0.6824 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.701e-05/0.2097, allocations: 36.7 kB / 0.983 GB, free: 1.074 MB / 0.6824 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.000331/0.21, allocations: 237.1 kB / 0.9833 GB, free: 0.8164 MB / 0.6824 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.85e-05/0.21, allocations: 21.03 kB / 0.9833 GB, free: 0.7969 MB / 0.6824 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.906e-05/0.2101, allocations: 36.08 kB / 0.9833 GB, free: 0.7617 MB / 0.6824 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004582/0.2106, allocations: 392 kB / 0.9837 GB, free: 368 kB / 0.6824 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.611e-05/0.2106, allocations: 4 kB / 0.9837 GB, free: 364 kB / 0.6824 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.479e-05/0.2106, allocations: 12 kB / 0.9837 GB, free: 352 kB / 0.6824 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.015e-06/0.2106, allocations: 11.94 kB / 0.9837 GB, free: 340 kB / 0.6824 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003507/0.211, allocations: 233.8 kB / 0.9839 GB, free: 108 kB / 0.6824 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001085/0.212, allocations: 0.8079 MB / 0.9847 GB, free: 15.26 MB / 0.698 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0004/0.2124, allocations: 210.6 kB / 0.9849 GB, free: 15.04 MB / 0.698 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001342/0.2126, allocations: 80.81 kB / 0.985 GB, free: 14.96 MB / 0.698 GB
Notification: Performance of preOpt evalFunc (simulation): time 2.639e-05/0.2126, allocations: 3.984 kB / 0.985 GB, free: 14.96 MB / 0.698 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002463/0.2128, allocations: 162.3 kB / 0.9852 GB, free: 14.79 MB / 0.698 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.0001214/0.213, allocations: 43.88 kB / 0.9852 GB, free: 14.75 MB / 0.698 GB
Notification: Performance of pre-optimization done (n=25): time 2.485e-06/0.213, allocations: 0 / 0.9852 GB, free: 14.75 MB / 0.698 GB
Notification: Performance of matching and sorting (n=25): time 0.0005272/0.2135, allocations: 309.3 kB / 0.9855 GB, free: 14.44 MB / 0.698 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 3.357e-05/0.2135, allocations: 63.33 kB / 0.9856 GB, free: 14.36 MB / 0.698 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001375/0.2137, allocations: 198.2 kB / 0.9857 GB, free: 14.16 MB / 0.698 GB
Notification: Performance of collectPreVariables (initialization): time 1.967e-05/0.2137, allocations: 25.7 kB / 0.9858 GB, free: 14.13 MB / 0.698 GB
Notification: Performance of collectInitialEqns (initialization): time 8.454e-05/0.2138, allocations: 180.6 kB / 0.9859 GB, free: 13.95 MB / 0.698 GB
Notification: Performance of collectInitialBindings (initialization): time 5.385e-05/0.2138, allocations: 95.17 kB / 0.986 GB, free: 13.85 MB / 0.698 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 7.453e-05/0.2139, allocations: 69.69 kB / 0.9861 GB, free: 13.78 MB / 0.698 GB
Notification: Performance of setup shared object (initialization): time 7.994e-05/0.214, allocations: 334.8 kB / 0.9864 GB, free: 13.44 MB / 0.698 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001897/0.2142, allocations: 139.1 kB / 0.9866 GB, free: 13.29 MB / 0.698 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002074/0.2144, allocations: 238.2 kB / 0.9868 GB, free: 13.01 MB / 0.698 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0003521/0.2147, allocations: 322.4 kB / 0.9871 GB, free: 12.66 MB / 0.698 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.545e-06/0.2147, allocations: 0 / 0.9871 GB, free: 12.66 MB / 0.698 GB
Notification: Performance of matching and sorting (n=41) (initialization): time 0.0005534/0.2153, allocations: 408.6 kB / 0.9875 GB, free: 12.24 MB / 0.698 GB
Notification: Performance of prepare postOptimizeDAE: time 3.105e-05/0.2153, allocations: 33.7 kB / 0.9875 GB, free: 12.2 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.841e-06/0.2153, allocations: 0 / 0.9875 GB, free: 12.2 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.578e-05/0.2153, allocations: 4 kB / 0.9875 GB, free: 12.2 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002034/0.2155, allocations: 87.88 kB / 0.9876 GB, free: 12.11 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 9.047e-06/0.2155, allocations: 7.984 kB / 0.9876 GB, free: 12.1 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001146/0.2157, allocations: 16.27 kB / 0.9876 GB, free: 12.09 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.079e-05/0.2157, allocations: 27.92 kB / 0.9876 GB, free: 12.06 MB / 0.698 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 0.0001741/0.2159, allocations: 164.3 kB / 0.9878 GB, free: 11.89 MB / 0.698 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 2.229e-05/0.2159, allocations: 23.84 kB / 0.9878 GB, free: 11.87 MB / 0.698 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0004011/0.2163, allocations: 263.6 kB / 0.9881 GB, free: 11.6 MB / 0.698 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.626e-06/0.2163, allocations: 4 kB / 0.9881 GB, free: 11.6 MB / 0.698 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.398e-06/0.2163, allocations: 0 / 0.9881 GB, free: 11.6 MB / 0.698 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.663e-06/0.2163, allocations: 3.984 kB / 0.9881 GB, free: 11.59 MB / 0.698 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0001776/0.2165, allocations: 225 kB / 0.9883 GB, free: 11.34 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.194e-06/0.2165, allocations: 0 / 0.9883 GB, free: 11.34 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001639/0.2166, allocations: 47.91 kB / 0.9883 GB, free: 11.3 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (simulation): time 3.907e-06/0.2166, allocations: 4 kB / 0.9883 GB, free: 11.29 MB / 0.698 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.535e-05/0.2167, allocations: 4 kB / 0.9884 GB, free: 11.29 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.965e-06/0.2167, allocations: 8 kB / 0.9884 GB, free: 11.28 MB / 0.698 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.173e-06/0.2167, allocations: 0 / 0.9884 GB, free: 11.28 MB / 0.698 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005176/0.2172, allocations: 373.8 kB / 0.9887 GB, free: 10.9 MB / 0.698 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.746e-05/0.2172, allocations: 19.84 kB / 0.9887 GB, free: 10.88 MB / 0.698 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.077e-05/0.2172, allocations: 12 kB / 0.9887 GB, free: 10.87 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 8.396e-05/0.2173, allocations: 16.08 kB / 0.9888 GB, free: 10.85 MB / 0.698 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.425e-05/0.2174, allocations: 19.91 kB / 0.9888 GB, free: 10.83 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.423e-05/0.2174, allocations: 11.98 kB / 0.9888 GB, free: 10.82 MB / 0.698 GB
Notification: Performance of sorting global known variables: time 8.514e-05/0.2175, allocations: 143.2 kB / 0.9889 GB, free: 10.68 MB / 0.698 GB
Notification: Performance of sort global known variables: time 7e-08/0.2175, allocations: 0 / 0.9889 GB, free: 10.68 MB / 0.698 GB
Notification: Performance of remove unused functions: time 0.0002222/0.2177, allocations: 91.84 kB / 0.989 GB, free: 10.59 MB / 0.698 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 8.744e-05/0.2178, allocations: 106.1 kB / 0.9891 GB, free: 10.48 MB / 0.698 GB
Notification: Performance of simCode: created initialization part: time 0.000418/0.2182, allocations: 320.4 kB / 0.9894 GB, free: 10.15 MB / 0.698 GB
Notification: Performance of simCode: created event and clocks part: time 1.803e-06/0.2182, allocations: 4.062 kB / 0.9894 GB, free: 10.14 MB / 0.698 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001469/0.2184, allocations: 95.88 kB / 0.9895 GB, free: 10.05 MB / 0.698 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002797/0.2186, allocations: 68.08 kB / 0.9896 GB, free: 9.984 MB / 0.698 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.3984/0.617, allocations: 1.008 MB / 0.9906 GB, free: 26.87 MB / 0.698 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001166/0.6171, allocations: 159.1 kB / 0.9907 GB, free: 26.79 MB / 0.698 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001283/0.6172, allocations: 32.8 kB / 0.9908 GB, free: 26.78 MB / 0.698 GB
Notification: Performance of SimCode: time 1.112e-06/0.6172, allocations: 0 / 0.9908 GB, free: 26.78 MB / 0.698 GB
Notification: Performance of Templates: time 0.004806/0.622, allocations: 3.62 MB / 0.9943 GB, free: 26.63 MB / 0.698 GB
"
[Timeout remaining time 659]
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 > Pharmacolibrary_Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 7.658899200847372]