Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.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 0.0009465/0.0009465, allocations: 100.4 kB / 19.7 MB, free: 444 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 0.001093/0.001093, allocations: 216.9 kB / 23 MB, free: 2.973 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 1.053/1.053, allocations: 230.6 MB / 256.8 MB, free: 9.594 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 1.697/1.697, allocations: 334.2 MB / 0.6323 GB, free: 7.988 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.SingleDoseDiffusion,tolerance=1e-06,outputFormat="empty",numberOfIntervals=499,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion")
translateModel(Pharmacolibrary.DevModels.SingleDoseDiffusion,tolerance=1e-06,outputFormat="empty",numberOfIntervals=499,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion") [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 0.001406/0.001406, allocations: 68.98 kB / 0.867 GB, free: 8.18 MB / 0.573 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.2012/0.2026, allocations: 112.8 MB / 0.9772 GB, free: 7.102 MB / 0.6824 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.SingleDoseDiffusion): time 0.003992/0.2066, allocations: 2.69 MB / 0.9798 GB, free: 4.398 MB / 0.6824 GB
Notification: Performance of NFInst.instExpressions: time 0.00132/0.2079, allocations: 0.7051 MB / 0.9805 GB, free: 3.691 MB / 0.6824 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001304/0.2081, allocations: 4 kB / 0.9805 GB, free: 3.688 MB / 0.6824 GB
Notification: Performance of NFTyping.typeComponents: time 9.601e-05/0.2082, allocations: 39.56 kB / 0.9805 GB, free: 3.648 MB / 0.6824 GB
Notification: Performance of NFTyping.typeBindings: time 0.000324/0.2085, allocations: 111.1 kB / 0.9807 GB, free: 3.539 MB / 0.6824 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0003044/0.2088, allocations: 95.81 kB / 0.9807 GB, free: 3.445 MB / 0.6824 GB
Notification: Performance of NFFlatten.flatten: time 0.0003937/0.2092, allocations: 394.2 kB / 0.9811 GB, free: 3.059 MB / 0.6824 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0003569/0.2095, allocations: 198.2 kB / 0.9813 GB, free: 2.867 MB / 0.6824 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0002243/0.2098, allocations: 167.5 kB / 0.9815 GB, free: 2.703 MB / 0.6824 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0002808/0.2101, allocations: 171.4 kB / 0.9816 GB, free: 2.535 MB / 0.6824 GB
Notification: Performance of NFPackage.collectConstants: time 5.799e-05/0.2101, allocations: 36 kB / 0.9817 GB, free: 2.5 MB / 0.6824 GB
Notification: Performance of NFFlatten.collectFunctions: time 5.972e-05/0.2102, allocations: 36 kB / 0.9817 GB, free: 2.465 MB / 0.6824 GB
Notification: Performance of NFScalarize.scalarize: time 6.82e-05/0.2102, allocations: 75.69 kB / 0.9818 GB, free: 2.391 MB / 0.6824 GB
Notification: Performance of NFVerifyModel.verify: time 0.0001605/0.2104, allocations: 155.4 kB / 0.9819 GB, free: 2.238 MB / 0.6824 GB
Notification: Performance of NFConvertDAE.convert: time 0.0004078/0.2108, allocations: 362.7 kB / 0.9823 GB, free: 1.883 MB / 0.6824 GB
Notification: Performance of FrontEnd - DAE generated: time 5.981e-06/0.2108, allocations: 0 / 0.9823 GB, free: 1.883 MB / 0.6824 GB
Notification: Performance of FrontEnd: time 2.444e-06/0.2108, allocations: 0 / 0.9823 GB, free: 1.883 MB / 0.6824 GB
Notification: Performance of Transformations before backend: time 8.435e-06/0.2108, allocations: 0 / 0.9823 GB, free: 1.883 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: 65
 * Number of variables: 65
Notification: Performance of Generate backend data structure: time 0.0009992/0.2118, allocations: 0.5803 MB / 0.9828 GB, free: 1.262 MB / 0.6824 GB
Notification: Performance of prepare preOptimizeDAE: time 5.059e-05/0.2119, allocations: 8.031 kB / 0.9828 GB, free: 1.254 MB / 0.6824 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 6.687e-05/0.2119, allocations: 32.75 kB / 0.9829 GB, free: 1.223 MB / 0.6824 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002963/0.2122, allocations: 226.6 kB / 0.9831 GB, free: 0.9727 MB / 0.6824 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.707e-05/0.2123, allocations: 21.03 kB / 0.9831 GB, free: 0.9531 MB / 0.6824 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.827e-05/0.2123, allocations: 40.12 kB / 0.9831 GB, free: 0.9141 MB / 0.6824 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004194/0.2127, allocations: 405.7 kB / 0.9835 GB, free: 0.4922 MB / 0.6824 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.464e-05/0.2127, allocations: 0 / 0.9835 GB, free: 0.4922 MB / 0.6824 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.476e-05/0.2128, allocations: 19.97 kB / 0.9836 GB, free: 484 kB / 0.6824 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.123e-06/0.2128, allocations: 4 kB / 0.9836 GB, free: 480 kB / 0.6824 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0004985/0.2133, allocations: 263.5 kB / 0.9838 GB, free: 212 kB / 0.6824 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0009653/0.2142, allocations: 0.7921 MB / 0.9846 GB, free: 15.38 MB / 0.698 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0004187/0.2147, allocations: 230 kB / 0.9848 GB, free: 15.13 MB / 0.698 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001496/0.2148, allocations: 126.7 kB / 0.9849 GB, free: 15 MB / 0.698 GB
Notification: Performance of preOpt evalFunc (simulation): time 2.454e-05/0.2148, allocations: 4 kB / 0.9849 GB, free: 15 MB / 0.698 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002892/0.2151, allocations: 276.5 kB / 0.9852 GB, free: 14.7 MB / 0.698 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.000113/0.2152, allocations: 35.86 kB / 0.9852 GB, free: 14.66 MB / 0.698 GB
Notification: Performance of pre-optimization done (n=30): time 1.793e-06/0.2152, allocations: 3.938 kB / 0.9852 GB, free: 14.66 MB / 0.698 GB
Notification: Performance of matching and sorting (n=31): time 0.001192/0.2164, allocations: 0.8842 MB / 0.9861 GB, free: 13.72 MB / 0.698 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.585e-05/0.2165, allocations: 136.5 kB / 0.9862 GB, free: 13.56 MB / 0.698 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001297/0.2166, allocations: 194.9 kB / 0.9864 GB, free: 13.36 MB / 0.698 GB
Notification: Performance of collectPreVariables (initialization): time 2.197e-05/0.2166, allocations: 33.7 kB / 0.9864 GB, free: 13.32 MB / 0.698 GB
Notification: Performance of collectInitialEqns (initialization): time 7.552e-05/0.2167, allocations: 160.6 kB / 0.9866 GB, free: 13.16 MB / 0.698 GB
Notification: Performance of collectInitialBindings (initialization): time 6.304e-05/0.2168, allocations: 115.2 kB / 0.9867 GB, free: 13.04 MB / 0.698 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 8.147e-05/0.2168, allocations: 73.97 kB / 0.9868 GB, free: 12.96 MB / 0.698 GB
Notification: Performance of setup shared object (initialization): time 8.085e-05/0.2169, allocations: 330.8 kB / 0.9871 GB, free: 12.63 MB / 0.698 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001813/0.2171, allocations: 177.5 kB / 0.9873 GB, free: 12.44 MB / 0.698 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002223/0.2173, allocations: 289.7 kB / 0.9875 GB, free: 12.09 MB / 0.698 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0009146/0.2182, allocations: 0.7261 MB / 0.9882 GB, free: 11.29 MB / 0.698 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.044e-06/0.2183, allocations: 4 kB / 0.9882 GB, free: 11.29 MB / 0.698 GB
Notification: Performance of matching and sorting (n=49) (initialization): time 0.0004952/0.2187, allocations: 0.4972 MB / 0.9887 GB, free: 10.76 MB / 0.698 GB
Notification: Performance of prepare postOptimizeDAE: time 4.363e-05/0.2188, allocations: 59.41 kB / 0.9888 GB, free: 10.69 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 5.931e-06/0.2188, allocations: 0 / 0.9888 GB, free: 10.69 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.604e-05/0.2188, allocations: 8 kB / 0.9888 GB, free: 10.68 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001913/0.219, allocations: 91.81 kB / 0.9889 GB, free: 10.59 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 7.655e-06/0.219, allocations: 4 kB / 0.9889 GB, free: 10.59 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001075/0.2191, allocations: 19.98 kB / 0.9889 GB, free: 10.57 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.076e-05/0.2191, allocations: 24.27 kB / 0.9889 GB, free: 10.54 MB / 0.698 GB
Warning: Assuming fixed start value for the following 8 variables:
         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
         artery.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         tissueCompartment.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         RBC.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         RBC.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         RBC.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         RBC.rising:DISCRETE(fixed = true protected = true )  type: Boolean
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 12
 * Number of states: 0 ()
 * Number of discrete variables: 13 ($PRE.RBC.Cmin,RBC.Cmin,$PRE.RBC.Cmax,RBC.Cmax,$PRE.RBC.rising,$PRE.singleDose.pulse.count,$PRE.singleDose.pulse.T_start,RBC.rising,singleDose.pulse.count,singleDose.pulse.T_start,$whenCondition2,$whenCondition1,$whenCondition3)
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (47):
 * Single equations (assignments): 45
 * Array equations: 0
 * Algorithm blocks: 2
 * 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 0.0001973/0.2193, allocations: 217.2 kB / 0.9891 GB, free: 10.31 MB / 0.698 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 2.615e-05/0.2194, allocations: 27.84 kB / 0.9892 GB, free: 10.29 MB / 0.698 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0004473/0.2198, allocations: 371 kB / 0.9895 GB, free: 9.91 MB / 0.698 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.817e-06/0.2198, allocations: 4 kB / 0.9895 GB, free: 9.906 MB / 0.698 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 4.078e-06/0.2198, allocations: 0 / 0.9895 GB, free: 9.906 MB / 0.698 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.861e-06/0.2198, allocations: 3.984 kB / 0.9895 GB, free: 9.902 MB / 0.698 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0006327/0.2205, allocations: 0.6579 MB / 0.9902 GB, free: 9.195 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.873e-06/0.2205, allocations: 4 kB / 0.9902 GB, free: 9.191 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001608/0.2206, allocations: 51.95 kB / 0.9902 GB, free: 9.141 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.925e-06/0.2206, allocations: 0 / 0.9902 GB, free: 9.141 MB / 0.698 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.709e-05/0.2206, allocations: 8 kB / 0.9902 GB, free: 9.133 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.096e-06/0.2206, allocations: 4 kB / 0.9902 GB, free: 9.129 MB / 0.698 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.937e-06/0.2206, allocations: 11.88 kB / 0.9902 GB, free: 9.117 MB / 0.698 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0007547/0.2214, allocations: 0.5916 MB / 0.9908 GB, free: 8.492 MB / 0.698 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.191e-05/0.2214, allocations: 23.86 kB / 0.9908 GB, free: 8.469 MB / 0.698 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.255e-05/0.2215, allocations: 11.98 kB / 0.9909 GB, free: 8.457 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 9.853e-05/0.2216, allocations: 19.92 kB / 0.9909 GB, free: 8.438 MB / 0.698 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 6.557e-05/0.2216, allocations: 19.97 kB / 0.9909 GB, free: 8.418 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.386e-05/0.2216, allocations: 11.98 kB / 0.9909 GB, free: 8.406 MB / 0.698 GB
Notification: Performance of sorting global known variables: time 8.957e-05/0.2217, allocations: 139.2 kB / 0.991 GB, free: 8.27 MB / 0.698 GB
Notification: Performance of sort global known variables: time 7e-08/0.2217, allocations: 0 / 0.991 GB, free: 8.27 MB / 0.698 GB
Notification: Performance of remove unused functions: time 0.0002317/0.222, allocations: 80 kB / 0.9911 GB, free: 8.191 MB / 0.698 GB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 8 (singleDose.TotalCumulativeMass,singleDose.variableDose.TotalCumulativeMass,artery.M,artery.AUC,tissueCompartment.M,tissueCompartment.AUC,RBC.C,RBC.AUC)
 * Number of discrete variables: 8 ($whenCondition3,$whenCondition1,$whenCondition2,singleDose.pulse.T_start,singleDose.pulse.count,RBC.Cmax,RBC.Cmin,RBC.rising)
 * Number of discrete states: 6 (singleDose.pulse.count,RBC.Cmin,$whenCondition2,RBC.Cmax,$whenCondition1,RBC.rising)
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (28):
 * Single equations (assignments): 25
 * Array equations: 0
 * Algorithm blocks: 1
 * 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 0.0001004/0.2221, allocations: 122.4 kB / 0.9912 GB, free: 8.062 MB / 0.698 GB
Notification: Performance of simCode: created initialization part: time 0.3714/0.5934, allocations: 450.4 kB / 0.9917 GB, free: 26.93 MB / 0.698 GB
Notification: Performance of simCode: created event and clocks part: time 5.139e-06/0.5934, allocations: 1.719 kB / 0.9917 GB, free: 26.93 MB / 0.698 GB
Notification: Performance of simCode: created simulation system equations: time 0.0002828/0.5937, allocations: 207.9 kB / 0.9919 GB, free: 26.83 MB / 0.698 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0005046/0.5942, allocations: 70.25 kB / 0.9919 GB, free: 26.83 MB / 0.698 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001357/0.5956, allocations: 1.015 MB / 0.9929 GB, free: 26.27 MB / 0.698 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001175/0.5957, allocations: 162.2 kB / 0.9931 GB, free: 26.19 MB / 0.698 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 8.584e-05/0.5958, allocations: 30.59 kB / 0.9931 GB, free: 26.18 MB / 0.698 GB
Notification: Performance of SimCode: time 9.42e-07/0.5958, allocations: 0 / 0.9931 GB, free: 26.18 MB / 0.698 GB
Notification: Performance of Templates: time 0.004984/0.6008, allocations: 3.745 MB / 0.9968 GB, free: 25.85 MB / 0.698 GB
"
[Timeout remaining time 659]
make -j1 -f Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.sim & ./Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion > Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 7.631156005896628]