Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.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 0.001044/0.001044, allocations: 84.53 kB / 19.93 MB, free: 4.609 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 0.0009603/0.0009603, allocations: 173.9 kB / 23.21 MB, free: 1.328 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 0.9711/0.9711, allocations: 177.1 MB / 203.5 MB, free: 5.742 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 1.614/1.614, allocations: 273.5 MB / 0.5209 GB, free: 14.96 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.PKTwoCompartmentModel,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel")
translateModel(Pharmacolibrary.Examples.PKTwoCompartmentModel,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel") [Timeout 660]
"Notification: Performance of FrontEnd - loaded program: time 1.904e-06/1.904e-06, allocations: 0 / 0.7558 GB, free: 10.71 MB / 0.5887 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 2.681e-05/2.872e-05, allocations: 2.281 kB / 0.7558 GB, free: 10.71 MB / 0.5887 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKTwoCompartmentModel): time 0.002868/0.002897, allocations: 2.237 MB / 0.7579 GB, free: 8.484 MB / 0.5887 GB
Notification: Performance of NFInst.instExpressions: time 0.001014/0.003911, allocations: 0.5921 MB / 0.7585 GB, free: 7.895 MB / 0.5887 GB
Notification: Performance of NFInst.updateImplicitVariability: time 9.895e-05/0.00401, allocations: 0 / 0.7585 GB, free: 7.895 MB / 0.5887 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001206/0.00413, allocations: 33.03 kB / 0.7586 GB, free: 7.863 MB / 0.5887 GB
Notification: Performance of NFTyping.typeBindings: time 0.000176/0.004306, allocations: 72.11 kB / 0.7586 GB, free: 7.816 MB / 0.5887 GB
Notification: Performance of NFTyping.typeClassSections: time 0.000203/0.004509, allocations: 63.84 kB / 0.7587 GB, free: 7.754 MB / 0.5887 GB
Notification: Performance of NFFlatten.flatten: time 0.0002755/0.004785, allocations: 286.2 kB / 0.759 GB, free: 7.488 MB / 0.5887 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001405/0.004925, allocations: 44.55 kB / 0.759 GB, free: 7.445 MB / 0.5887 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001584/0.005084, allocations: 143.8 kB / 0.7591 GB, free: 7.305 MB / 0.5887 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001113/0.005195, allocations: 91.7 kB / 0.7592 GB, free: 7.215 MB / 0.5887 GB
Notification: Performance of NFPackage.collectConstants: time 3.138e-05/0.005226, allocations: 20 kB / 0.7592 GB, free: 7.195 MB / 0.5887 GB
Notification: Performance of NFFlatten.collectFunctions: time 2.66e-05/0.005253, allocations: 20 kB / 0.7593 GB, free: 7.176 MB / 0.5887 GB
Notification: Performance of NFScalarize.scalarize: time 3.918e-05/0.005292, allocations: 43.84 kB / 0.7593 GB, free: 7.133 MB / 0.5887 GB
Notification: Performance of NFVerifyModel.verify: time 8.514e-05/0.005377, allocations: 91.8 kB / 0.7594 GB, free: 7.043 MB / 0.5887 GB
Notification: Performance of NFConvertDAE.convert: time 0.0002225/0.0056, allocations: 235.3 kB / 0.7596 GB, free: 6.812 MB / 0.5887 GB
Notification: Performance of FrontEnd - DAE generated: time 3.036e-06/0.005603, allocations: 0 / 0.7596 GB, free: 6.812 MB / 0.5887 GB
Notification: Performance of FrontEnd: time 1.333e-06/0.005604, allocations: 3.938 kB / 0.7596 GB, free: 6.809 MB / 0.5887 GB
Notification: Performance of Transformations before backend: time 5.089e-06/0.005609, allocations: 0 / 0.7596 GB, free: 6.809 MB / 0.5887 GB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 42
 * Number of variables: 42
Notification: Performance of Generate backend data structure: time 0.0007014/0.006311, allocations: 0.519 MB / 0.7601 GB, free: 6.238 MB / 0.5887 GB
Notification: Performance of prepare preOptimizeDAE: time 4.016e-05/0.006351, allocations: 8.031 kB / 0.7601 GB, free: 6.23 MB / 0.5887 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 5.783e-05/0.006409, allocations: 24.8 kB / 0.7602 GB, free: 6.207 MB / 0.5887 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001867/0.006595, allocations: 178.1 kB / 0.7603 GB, free: 6.008 MB / 0.5887 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.652e-05/0.006612, allocations: 16.22 kB / 0.7603 GB, free: 5.996 MB / 0.5887 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 4.139e-05/0.006653, allocations: 28.33 kB / 0.7604 GB, free: 5.969 MB / 0.5887 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002976/0.006951, allocations: 242.9 kB / 0.7606 GB, free: 5.715 MB / 0.5887 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.651e-05/0.006967, allocations: 7.938 kB / 0.7606 GB, free: 5.707 MB / 0.5887 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.6e-05/0.006983, allocations: 4 kB / 0.7606 GB, free: 5.703 MB / 0.5887 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.002e-06/0.006989, allocations: 4 kB / 0.7606 GB, free: 5.699 MB / 0.5887 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002454/0.007235, allocations: 219.9 kB / 0.7608 GB, free: 5.473 MB / 0.5887 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0006441/0.007879, allocations: 456.9 kB / 0.7613 GB, free: 4.996 MB / 0.5887 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002969/0.008176, allocations: 229.9 kB / 0.7615 GB, free: 4.75 MB / 0.5887 GB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0001344/0.00831, allocations: 140.2 kB / 0.7616 GB, free: 4.598 MB / 0.5887 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.28e-05/0.008323, allocations: 4 kB / 0.7616 GB, free: 4.594 MB / 0.5887 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0003233/0.008646, allocations: 364.4 kB / 0.762 GB, free: 4.191 MB / 0.5887 GB
Notification: Performance of pre-optimization done (n=31): time 3.226e-06/0.008649, allocations: 0 / 0.762 GB, free: 4.191 MB / 0.5887 GB
Notification: Performance of matching and sorting (n=33): time 0.0013/0.009949, allocations: 1.051 MB / 0.763 GB, free: 3.047 MB / 0.5887 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 8.694e-05/0.01004, allocations: 217.6 kB / 0.7632 GB, free: 2.785 MB / 0.5887 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.00013/0.01017, allocations: 170.3 kB / 0.7634 GB, free: 2.609 MB / 0.5887 GB
Notification: Performance of collectPreVariables (initialization): time 2.286e-05/0.01019, allocations: 33.7 kB / 0.7634 GB, free: 2.57 MB / 0.5887 GB
Notification: Performance of collectInitialEqns (initialization): time 6.77e-05/0.01026, allocations: 128.9 kB / 0.7635 GB, free: 2.441 MB / 0.5887 GB
Notification: Performance of collectInitialBindings (initialization): time 5.895e-05/0.01032, allocations: 103.2 kB / 0.7636 GB, free: 2.34 MB / 0.5887 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 7.032e-05/0.01039, allocations: 65.69 kB / 0.7637 GB, free: 2.27 MB / 0.5887 GB
Notification: Performance of setup shared object (initialization): time 9.396e-05/0.01048, allocations: 330.8 kB / 0.764 GB, free: 1.938 MB / 0.5887 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001922/0.01067, allocations: 203 kB / 0.7642 GB, free: 1.719 MB / 0.5887 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002941/0.01097, allocations: 291.7 kB / 0.7645 GB, free: 1.379 MB / 0.5887 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0007475/0.01171, allocations: 0.7451 MB / 0.7652 GB, free: 0.5391 MB / 0.5887 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.318e-06/0.01172, allocations: 4 kB / 0.7652 GB, free: 0.5352 MB / 0.5887 GB
Notification: Performance of matching and sorting (n=49) (initialization): time 0.0005188/0.01224, allocations: 0.5278 MB / 0.7657 GB, free: 15.96 MB / 0.6043 GB
Notification: Performance of prepare postOptimizeDAE: time 5.875e-05/0.0123, allocations: 97.03 kB / 0.7658 GB, free: 15.85 MB / 0.6043 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.544e-06/0.0123, allocations: 4 kB / 0.7658 GB, free: 15.85 MB / 0.6043 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.8e-05/0.01232, allocations: 4 kB / 0.7658 GB, free: 15.84 MB / 0.6043 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001771/0.0125, allocations: 76.17 kB / 0.7659 GB, free: 15.77 MB / 0.6043 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 9.948e-06/0.01251, allocations: 7.938 kB / 0.7659 GB, free: 15.76 MB / 0.6043 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.00012/0.01263, allocations: 19.98 kB / 0.7659 GB, free: 15.74 MB / 0.6043 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.914e-05/0.01265, allocations: 16 kB / 0.7659 GB, free: 15.73 MB / 0.6043 GB
Warning: Assuming fixed start value for the following 10 variables:
         periodicDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         periodicDose.variableDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         peripheral.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         central.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         peripheral.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         peripheral.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         central.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         central.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         central.rising:DISCRETE(fixed = true protected = true )  type: Boolean
         peripheral.rising:DISCRETE(fixed = true protected = true )  type: Boolean
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 10
 * Number of states: 0 ()
 * Number of discrete variables: 21 ($PRE.peripheral.Cmin,peripheral.Cmin,$PRE.peripheral.Cmax,peripheral.Cmax,$PRE.central.Cmin,central.Cmin,$PRE.central.Cmax,central.Cmax,$PRE.central.rising,$PRE.peripheral.rising,$PRE.periodicDose.pulse.count,$PRE.periodicDose.pulse.T_start,central.rising,peripheral.rising,periodicDose.pulse.count,periodicDose.pulse.T_start,$whenCondition5,$whenCondition4,$whenCondition3,$whenCondition2,$whenCondition1)
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (46):
 * Single equations (assignments): 43
 * Array equations: 0
 * Algorithm blocks: 3
 * 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 0.000226/0.01287, allocations: 243.2 kB / 0.7662 GB, free: 15.47 MB / 0.6043 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 2.449e-05/0.0129, allocations: 23.84 kB / 0.7662 GB, free: 15.45 MB / 0.6043 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 4.369e-05/0.01294, allocations: 33.89 kB / 0.7662 GB, free: 15.41 MB / 0.6043 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.597e-06/0.01295, allocations: 4 kB / 0.7662 GB, free: 15.41 MB / 0.6043 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 7.734e-06/0.01295, allocations: 8 kB / 0.7662 GB, free: 15.4 MB / 0.6043 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.499e-06/0.01296, allocations: 0 / 0.7662 GB, free: 15.4 MB / 0.6043 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0006979/0.01366, allocations: 0.7367 MB / 0.7669 GB, free: 14.61 MB / 0.6043 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.465e-06/0.01366, allocations: 0 / 0.7669 GB, free: 14.61 MB / 0.6043 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001505/0.01381, allocations: 51.95 kB / 0.767 GB, free: 14.55 MB / 0.6043 GB
Notification: Performance of postOpt tearingSystem (simulation): time 3.767e-06/0.01381, allocations: 4 kB / 0.767 GB, free: 14.55 MB / 0.6043 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.841e-05/0.01383, allocations: 8 kB / 0.767 GB, free: 14.54 MB / 0.6043 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.925e-06/0.01383, allocations: 0 / 0.767 GB, free: 14.54 MB / 0.6043 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.483e-06/0.01384, allocations: 4 kB / 0.767 GB, free: 14.54 MB / 0.6043 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005983/0.01443, allocations: 0.7115 MB / 0.7677 GB, free: 13.77 MB / 0.6043 GB
Notification: Performance of postOpt removeConstants (simulation): time 2.408e-05/0.01446, allocations: 11.91 kB / 0.7677 GB, free: 13.76 MB / 0.6043 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.331e-05/0.01449, allocations: 15.98 kB / 0.7677 GB, free: 13.75 MB / 0.6043 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 8.964e-05/0.01458, allocations: 15.98 kB / 0.7677 GB, free: 13.73 MB / 0.6043 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 8.07e-05/0.01466, allocations: 31.95 kB / 0.7678 GB, free: 13.7 MB / 0.6043 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.346e-05/0.01467, allocations: 8 kB / 0.7678 GB, free: 13.69 MB / 0.6043 GB
Notification: Performance of sorting global known variables: time 6.515e-05/0.01474, allocations: 126.3 kB / 0.7679 GB, free: 13.57 MB / 0.6043 GB
Notification: Performance of sort global known variables: time 7e-08/0.01474, allocations: 4 kB / 0.7679 GB, free: 13.57 MB / 0.6043 GB
Notification: Performance of remove unused functions: time 0.0002216/0.01496, allocations: 71.94 kB / 0.768 GB, free: 13.5 MB / 0.6043 GB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 7 (periodicDose.TotalCumulativeMass,periodicDose.variableDose.TotalCumulativeMass,peripheral.C,peripheral.AUC,central.C,central.AUC,elim.MExc)
 * Number of discrete variables: 13 ($whenCondition1,$whenCondition2,$whenCondition3,$whenCondition4,$whenCondition5,periodicDose.pulse.T_start,periodicDose.pulse.count,peripheral.Cmax,peripheral.Cmin,peripheral.rising,central.Cmax,central.Cmin,central.rising)
 * Number of discrete states: 11 (periodicDose.pulse.count,peripheral.Cmin,$whenCondition5,peripheral.Cmax,$whenCondition4,peripheral.rising,central.Cmin,$whenCondition3,central.Cmax,$whenCondition2,central.rising)
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (27):
 * Single equations (assignments): 23
 * Array equations: 0
 * Algorithm blocks: 2
 * 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 0.0001132/0.01507, allocations: 122.6 kB / 0.7681 GB, free: 13.37 MB / 0.6043 GB
Notification: Performance of simCode: created initialization part: time 0.0004797/0.01555, allocations: 0.5497 MB / 0.7686 GB, free: 12.75 MB / 0.6043 GB
Notification: Performance of simCode: created event and clocks part: time 2.134e-06/0.01556, allocations: 0 / 0.7686 GB, free: 12.75 MB / 0.6043 GB
Notification: Performance of simCode: created simulation system equations: time 0.000207/0.01576, allocations: 306.1 kB / 0.7689 GB, free: 12.42 MB / 0.6043 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003039/0.01607, allocations: 62.53 kB / 0.769 GB, free: 12.36 MB / 0.6043 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0009509/0.01702, allocations: 0.7623 MB / 0.7697 GB, free: 11.57 MB / 0.6043 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 9.986e-05/0.01712, allocations: 138.1 kB / 0.7699 GB, free: 11.41 MB / 0.6043 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 5.726e-05/0.01718, allocations: 24.5 kB / 0.7699 GB, free: 11.39 MB / 0.6043 GB
Notification: Performance of SimCode: time 7.72e-07/0.01718, allocations: 0 / 0.7699 GB, free: 11.39 MB / 0.6043 GB
Notification: Performance of Templates: time 0.004082/0.02126, allocations: 3.156 MB / 0.773 GB, free: 8.297 MB / 0.6043 GB
"
[Timeout remaining time 660]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel > Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 6.548967342125252]