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 0.001095/0.001095, allocations: 80.94 kB / 19.94 MB, free: 4.543 MB / 18.57 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 0.001009/0.001009, allocations: 177 kB / 23.36 MB, free: 1.129 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 0.9727/0.9727, allocations: 177.2 MB / 203.8 MB, free: 5.484 MB / 186.7 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 1.68/1.68, allocations: 273.5 MB / 0.5213 GB, free: 14.7 MB / 458.7 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: Performance of FrontEnd - loaded program: time 1.983e-06/1.983e-06, allocations: 0 / 0.5954 GB, free: 2.762 MB / 0.5105 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.684e-05/2.882e-05, allocations: 2.312 kB / 0.5954 GB, free: 2.758 MB / 0.5105 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue): time 0.004918/0.004947, allocations: 3.008 MB / 0.5984 GB, free: 15.77 MB / 0.5261 GB
Notification: Performance of NFInst.instExpressions: time 0.002039/0.006986, allocations: 0.7737 MB / 0.5991 GB, free: 15 MB / 0.5261 GB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0002607/0.007246, allocations: 4 kB / 0.5991 GB, free: 15 MB / 0.5261 GB
Notification: Performance of NFTyping.typeComponents: time 0.0002076/0.007454, allocations: 47.56 kB / 0.5992 GB, free: 14.95 MB / 0.5261 GB
Notification: Performance of NFTyping.typeBindings: time 0.0004302/0.007884, allocations: 118.6 kB / 0.5993 GB, free: 14.88 MB / 0.5261 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0004469/0.008331, allocations: 99.75 kB / 0.5994 GB, free: 14.78 MB / 0.5261 GB
Notification: Performance of NFFlatten.flatten: time 0.0006358/0.008967, allocations: 434.7 kB / 0.5998 GB, free: 14.38 MB / 0.5261 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0004925/0.009459, allocations: 226.8 kB / 0.6 GB, free: 14.15 MB / 0.5261 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0004632/0.009923, allocations: 255.5 kB / 0.6003 GB, free: 13.9 MB / 0.5261 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.000334/0.01026, allocations: 163.5 kB / 0.6004 GB, free: 13.74 MB / 0.5261 GB
Notification: Performance of NFPackage.collectConstants: time 7.054e-05/0.01033, allocations: 36 kB / 0.6005 GB, free: 13.71 MB / 0.5261 GB
Notification: Performance of NFFlatten.collectFunctions: time 6.682e-05/0.01039, allocations: 39.94 kB / 0.6005 GB, free: 13.67 MB / 0.5261 GB
Notification: Performance of NFScalarize.scalarize: time 8.213e-05/0.01048, allocations: 83.72 kB / 0.6006 GB, free: 13.59 MB / 0.5261 GB
Notification: Performance of NFVerifyModel.verify: time 0.0001676/0.01064, allocations: 143.7 kB / 0.6007 GB, free: 13.45 MB / 0.5261 GB
Notification: Performance of NFConvertDAE.convert: time 0.0004246/0.01107, allocations: 259.1 kB / 0.601 GB, free: 13.19 MB / 0.5261 GB
Notification: Performance of FrontEnd - DAE generated: time 5.139e-06/0.01107, allocations: 0 / 0.601 GB, free: 13.19 MB / 0.5261 GB
Notification: Performance of FrontEnd: time 1.833e-06/0.01108, allocations: 0 / 0.601 GB, free: 13.19 MB / 0.5261 GB
Notification: Performance of Transformations before backend: time 6.823e-06/0.01108, allocations: 4 kB / 0.601 GB, free: 13.19 MB / 0.5261 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 0.0009796/0.01206, allocations: 0.529 MB / 0.6015 GB, free: 12.63 MB / 0.5261 GB
Notification: Performance of prepare preOptimizeDAE: time 4.983e-05/0.01211, allocations: 8.031 kB / 0.6015 GB, free: 12.62 MB / 0.5261 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 9.998e-05/0.01221, allocations: 44.91 kB / 0.6015 GB, free: 12.58 MB / 0.5261 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0003067/0.01252, allocations: 177.2 kB / 0.6017 GB, free: 12.38 MB / 0.5261 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.873e-05/0.01256, allocations: 28.91 kB / 0.6017 GB, free: 12.36 MB / 0.5261 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 5.961e-05/0.01262, allocations: 32.31 kB / 0.6018 GB, free: 12.32 MB / 0.5261 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004914/0.01311, allocations: 313.3 kB / 0.6021 GB, free: 11.99 MB / 0.5261 GB
Notification: Performance of preOpt findStateOrder (simulation): time 2.494e-05/0.01313, allocations: 7.922 kB / 0.6021 GB, free: 11.98 MB / 0.5261 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.299e-05/0.01317, allocations: 16 kB / 0.6021 GB, free: 11.97 MB / 0.5261 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.226e-05/0.01318, allocations: 8 kB / 0.6021 GB, free: 11.96 MB / 0.5261 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002206/0.0134, allocations: 93.38 kB / 0.6022 GB, free: 11.87 MB / 0.5261 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001319/0.01472, allocations: 0.6133 MB / 0.6028 GB, free: 11.24 MB / 0.5261 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0003107/0.01503, allocations: 102.5 kB / 0.6029 GB, free: 11.13 MB / 0.5261 GB
Notification: Performance of preOpt resolveLoops (simulation): time 7.914e-05/0.01511, allocations: 36.84 kB / 0.6029 GB, free: 11.09 MB / 0.5261 GB
Notification: Performance of preOpt evalFunc (simulation): time 3.176e-05/0.01514, allocations: 11.28 kB / 0.6029 GB, free: 11.08 MB / 0.5261 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002376/0.01538, allocations: 128.8 kB / 0.603 GB, free: 10.95 MB / 0.5261 GB
Notification: Performance of preOpt simplifyInStream (simulation): time 0.000175/0.01555, allocations: 35.88 kB / 0.6031 GB, free: 10.91 MB / 0.5261 GB
Notification: Performance of pre-optimization done (n=25): time 2.965e-06/0.01556, allocations: 4 kB / 0.6031 GB, free: 10.91 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=25): time 0.0003419/0.0159, allocations: 149.3 kB / 0.6032 GB, free: 10.76 MB / 0.5261 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.674e-05/0.01594, allocations: 55.41 kB / 0.6033 GB, free: 10.69 MB / 0.5261 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001631/0.01611, allocations: 188 kB / 0.6034 GB, free: 10.5 MB / 0.5261 GB
Notification: Performance of collectPreVariables (initialization): time 2.816e-05/0.01613, allocations: 29.7 kB / 0.6035 GB, free: 10.46 MB / 0.5261 GB
Notification: Performance of collectInitialEqns (initialization): time 9.243e-05/0.01623, allocations: 156.6 kB / 0.6036 GB, free: 10.3 MB / 0.5261 GB
Notification: Performance of collectInitialBindings (initialization): time 7.843e-05/0.01631, allocations: 99.14 kB / 0.6037 GB, free: 10.21 MB / 0.5261 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001025/0.01641, allocations: 69.59 kB / 0.6038 GB, free: 10.13 MB / 0.5261 GB
Notification: Performance of setup shared object (initialization): time 0.0001161/0.01652, allocations: 338.8 kB / 0.6041 GB, free: 9.793 MB / 0.5261 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001234/0.01665, allocations: 79.14 kB / 0.6042 GB, free: 9.707 MB / 0.5261 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.000159/0.01681, allocations: 175 kB / 0.6044 GB, free: 9.484 MB / 0.5261 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0002573/0.01706, allocations: 206.1 kB / 0.6045 GB, free: 9.246 MB / 0.5261 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.797e-06/0.01707, allocations: 0 / 0.6045 GB, free: 9.246 MB / 0.5261 GB
Notification: Performance of matching and sorting (n=41) (initialization): time 0.0003603/0.01743, allocations: 253 kB / 0.6048 GB, free: 8.98 MB / 0.5261 GB
Notification: Performance of prepare postOptimizeDAE: time 4.621e-05/0.01747, allocations: 33.64 kB / 0.6048 GB, free: 8.941 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.046e-05/0.01748, allocations: 4 kB / 0.6048 GB, free: 8.938 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (initialization): time 2.185e-05/0.01751, allocations: 7.984 kB / 0.6048 GB, free: 8.93 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0004112/0.01792, allocations: 103.8 kB / 0.6049 GB, free: 8.828 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.406e-06/0.01793, allocations: 4 kB / 0.6049 GB, free: 8.824 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001525/0.01808, allocations: 15.98 kB / 0.605 GB, free: 8.809 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.607e-05/0.01811, allocations: 15.98 kB / 0.605 GB, free: 8.793 MB / 0.5261 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 0.0002053/0.01831, allocations: 150.1 kB / 0.6051 GB, free: 8.641 MB / 0.5261 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 4.052e-05/0.01835, allocations: 23.97 kB / 0.6051 GB, free: 8.617 MB / 0.5261 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0002971/0.01865, allocations: 151.2 kB / 0.6053 GB, free: 8.465 MB / 0.5261 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.45e-06/0.01865, allocations: 8 kB / 0.6053 GB, free: 8.457 MB / 0.5261 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 2.625e-06/0.01866, allocations: 0 / 0.6053 GB, free: 8.457 MB / 0.5261 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 1.071e-05/0.01867, allocations: 3.984 kB / 0.6053 GB, free: 8.453 MB / 0.5261 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0002505/0.01892, allocations: 149.5 kB / 0.6054 GB, free: 8.293 MB / 0.5261 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.036e-06/0.01892, allocations: 0 / 0.6054 GB, free: 8.293 MB / 0.5261 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002228/0.01914, allocations: 51.84 kB / 0.6055 GB, free: 8.242 MB / 0.5261 GB
Notification: Performance of postOpt tearingSystem (simulation): time 4.108e-06/0.01915, allocations: 4 kB / 0.6055 GB, free: 8.238 MB / 0.5261 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.137e-05/0.01917, allocations: 4 kB / 0.6055 GB, free: 8.234 MB / 0.5261 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.769e-06/0.01917, allocations: 4 kB / 0.6055 GB, free: 8.23 MB / 0.5261 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.573e-06/0.01917, allocations: 0 / 0.6055 GB, free: 8.23 MB / 0.5261 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003695/0.01954, allocations: 205 kB / 0.6057 GB, free: 8.016 MB / 0.5261 GB
Notification: Performance of postOpt removeConstants (simulation): time 4.536e-05/0.01959, allocations: 23.8 kB / 0.6057 GB, free: 7.992 MB / 0.5261 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.934e-05/0.01963, allocations: 4 kB / 0.6057 GB, free: 7.988 MB / 0.5261 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.000121/0.01975, allocations: 15.98 kB / 0.6057 GB, free: 7.973 MB / 0.5261 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 7.059e-05/0.01982, allocations: 15.97 kB / 0.6057 GB, free: 7.957 MB / 0.5261 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.83e-05/0.01984, allocations: 7.984 kB / 0.6058 GB, free: 7.949 MB / 0.5261 GB
Notification: Performance of sorting global known variables: time 7.877e-05/0.01992, allocations: 52.88 kB / 0.6058 GB, free: 7.898 MB / 0.5261 GB
Notification: Performance of sort global known variables: time 3.2e-07/0.01992, allocations: 3.938 kB / 0.6058 GB, free: 7.895 MB / 0.5261 GB
Notification: Performance of remove unused functions: time 0.0003804/0.0203, allocations: 95.83 kB / 0.6059 GB, free: 7.801 MB / 0.5261 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 0.000179/0.02048, allocations: 86.64 kB / 0.606 GB, free: 7.711 MB / 0.5261 GB
Notification: Performance of simCode: created initialization part: time 0.0003939/0.02087, allocations: 222.3 kB / 0.6062 GB, free: 7.473 MB / 0.5261 GB
Notification: Performance of simCode: created event and clocks part: time 1.146e-05/0.02088, allocations: 0 / 0.6062 GB, free: 7.473 MB / 0.5261 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001336/0.02102, allocations: 65.38 kB / 0.6063 GB, free: 7.406 MB / 0.5261 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003529/0.02137, allocations: 79.42 kB / 0.6063 GB, free: 7.332 MB / 0.5261 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002006/0.02337, allocations: 0.6813 MB / 0.607 GB, free: 6.629 MB / 0.5261 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 7.638e-05/0.02345, allocations: 92.3 kB / 0.6071 GB, free: 6.516 MB / 0.5261 GB
Notification: Performance of simCode: alias equations: time 0.000159/0.02361, allocations: 37.75 kB / 0.6071 GB, free: 6.48 MB / 0.5261 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0002324/0.02384, allocations: 115.3 kB / 0.6072 GB, free: 6.367 MB / 0.5261 GB
Notification: Performance of SimCode: time 1.332e-06/0.02384, allocations: 3.938 kB / 0.6072 GB, free: 6.363 MB / 0.5261 GB
Notification: Performance of Templates: time 0.009195/0.03304, allocations: 4.061 MB / 0.6112 GB, free: 2.512 MB / 0.5261 GB
"
[Timeout remaining time 660]
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 -abortSlowSimulation -alarm=240 -s gbode -gbm=radauIIA3 -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PBPK_SingleDoseVenousArteryTissue.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 4.67764452798292]