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 0.002059/0.002059, allocations: 93.47 kB / 19.44 MB, free: 336 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 0.002536/0.002536, allocations: 169.2 kB / 22.76 MB, free: 1.664 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 1.84/1.84, allocations: 177.1 MB / 203.1 MB, free: 5.543 MB / 186.7 MB " [Timeout remaining time 178] 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 7.497/7.497, allocations: 274.5 MB / 0.5215 GB, free: 14.2 MB / 458.7 MB " [Timeout remaining time 172] 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 3.186e-06/3.186e-06, allocations: 0 / 0.6472 GB, free: 39.14 MB / 0.5262 GB Notification: Performance of FrontEnd - Absyn->SCode: time 5.618e-05/5.936e-05, allocations: 5.922 kB / 0.6472 GB, free: 39.14 MB / 0.5262 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKTwoCompartmentModel): time 0.005648/0.005707, allocations: 2.337 MB / 0.6495 GB, free: 37.6 MB / 0.5262 GB Notification: Performance of NFInst.instExpressions: time 0.001711/0.007418, allocations: 0.6067 MB / 0.6501 GB, free: 37.2 MB / 0.5262 GB Notification: Performance of NFInst.updateImplicitVariability: time 0.0001673/0.007585, allocations: 5.219 kB / 0.6501 GB, free: 37.19 MB / 0.5262 GB Notification: Performance of NFTyping.typeComponents: time 0.0001674/0.007753, allocations: 29.88 kB / 0.6501 GB, free: 37.18 MB / 0.5262 GB Notification: Performance of NFTyping.typeBindings: time 0.0002836/0.008036, allocations: 69.5 kB / 0.6502 GB, free: 37.15 MB / 0.5262 GB Notification: Performance of NFTyping.typeClassSections: time 0.0002998/0.008336, allocations: 68.22 kB / 0.6503 GB, free: 37.11 MB / 0.5262 GB Notification: Performance of NFFlatten.flatten: time 0.0004433/0.00878, allocations: 289.3 kB / 0.6505 GB, free: 36.99 MB / 0.5262 GB Notification: Performance of NFFlatten.resolveConnections: time 0.000182/0.008962, allocations: 49.09 kB / 0.6506 GB, free: 36.96 MB / 0.5262 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0002266/0.009188, allocations: 145.9 kB / 0.6507 GB, free: 36.9 MB / 0.5262 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0002212/0.009409, allocations: 86.05 kB / 0.6508 GB, free: 36.88 MB / 0.5262 GB Notification: Performance of NFPackage.collectConstants: time 5.327e-05/0.009463, allocations: 20.94 kB / 0.6508 GB, free: 36.88 MB / 0.5262 GB Notification: Performance of NFFlatten.collectFunctions: time 5.529e-05/0.009518, allocations: 23 kB / 0.6508 GB, free: 36.88 MB / 0.5262 GB Notification: Performance of NFScalarize.scalarize: time 5.721e-05/0.009575, allocations: 48.17 kB / 0.6509 GB, free: 36.84 MB / 0.5262 GB Notification: Performance of NFVerifyModel.verify: time 0.0001515/0.009727, allocations: 85.03 kB / 0.651 GB, free: 36.81 MB / 0.5262 GB Notification: Performance of NFConvertDAE.convert: time 0.0003935/0.01012, allocations: 235.2 kB / 0.6512 GB, free: 36.71 MB / 0.5262 GB Notification: Performance of FrontEnd - DAE generated: time 8.586e-06/0.01013, allocations: 7.938 kB / 0.6512 GB, free: 36.71 MB / 0.5262 GB Notification: Performance of FrontEnd: time 2.875e-06/0.01013, allocations: 1.438 kB / 0.6512 GB, free: 36.71 MB / 0.5262 GB Notification: Performance of Transformations before backend: time 8.526e-06/0.01014, allocations: 0 / 0.6512 GB, free: 36.71 MB / 0.5262 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 0.001009/0.01115, allocations: 0.6228 MB / 0.6518 GB, free: 36.14 MB / 0.5262 GB Notification: Performance of prepare preOptimizeDAE: time 5.318e-05/0.0112, allocations: 9.156 kB / 0.6518 GB, free: 36.14 MB / 0.5262 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001266/0.01133, allocations: 41.42 kB / 0.6519 GB, free: 36.12 MB / 0.5262 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002428/0.01157, allocations: 176.4 kB / 0.652 GB, free: 35.96 MB / 0.5262 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.606e-05/0.0116, allocations: 16.83 kB / 0.652 GB, free: 35.95 MB / 0.5262 GB Notification: Performance of preOpt expandDerOperator (simulation): time 5.202e-05/0.01165, allocations: 22.14 kB / 0.6521 GB, free: 35.95 MB / 0.5262 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0004246/0.01207, allocations: 232.9 kB / 0.6523 GB, free: 35.81 MB / 0.5262 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.852e-05/0.01209, allocations: 5.688 kB / 0.6523 GB, free: 35.8 MB / 0.5262 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.67e-05/0.01212, allocations: 10 kB / 0.6523 GB, free: 35.8 MB / 0.5262 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.718e-06/0.01213, allocations: 4.688 kB / 0.6523 GB, free: 35.8 MB / 0.5262 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0004084/0.01254, allocations: 209 kB / 0.6525 GB, free: 35.7 MB / 0.5262 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0009386/0.01348, allocations: 0.5244 MB / 0.653 GB, free: 35.31 MB / 0.5262 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0004707/0.01395, allocations: 234.9 kB / 0.6532 GB, free: 35.17 MB / 0.5262 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.0002193/0.01417, allocations: 140.8 kB / 0.6534 GB, free: 35.07 MB / 0.5262 GB Notification: Performance of preOpt evalFunc (simulation): time 2.49e-05/0.01419, allocations: 2.719 kB / 0.6534 GB, free: 35.07 MB / 0.5262 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0004998/0.01469, allocations: 354.3 kB / 0.6537 GB, free: 34.8 MB / 0.5262 GB Notification: Performance of pre-optimization done (n=31): time 1.763e-06/0.01469, allocations: 0 / 0.6537 GB, free: 34.8 MB / 0.5262 GB Notification: Performance of matching and sorting (n=33): time 0.00221/0.0169, allocations: 1.045 MB / 0.6547 GB, free: 34.1 MB / 0.5262 GB Notification: Performance of inlineWhenForInitialization (initialization): time 0.0001386/0.01704, allocations: 224.9 kB / 0.6549 GB, free: 33.84 MB / 0.5262 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0003186/0.01736, allocations: 246.2 kB / 0.6552 GB, free: 33.64 MB / 0.5262 GB Notification: Performance of collectPreVariables (initialization): time 4.293e-05/0.0174, allocations: 37.66 kB / 0.6552 GB, free: 33.61 MB / 0.5262 GB Notification: Performance of collectInitialEqns (initialization): time 0.0001221/0.01752, allocations: 170 kB / 0.6554 GB, free: 33.45 MB / 0.5262 GB Notification: Performance of collectInitialBindings (initialization): time 0.000133/0.01766, allocations: 119.7 kB / 0.6555 GB, free: 33.36 MB / 0.5262 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001801/0.01784, allocations: 84.67 kB / 0.6556 GB, free: 33.31 MB / 0.5262 GB Notification: Performance of setup shared object (initialization): time 0.0002484/0.01809, allocations: 0.5161 MB / 0.6561 GB, free: 32.8 MB / 0.5262 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003988/0.01849, allocations: 204.7 kB / 0.6563 GB, free: 32.66 MB / 0.5262 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0005019/0.01899, allocations: 326.6 kB / 0.6566 GB, free: 32.36 MB / 0.5262 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.001041/0.02003, allocations: 0.5969 MB / 0.6572 GB, free: 31.86 MB / 0.5262 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.347e-06/0.02003, allocations: 1.5 kB / 0.6572 GB, free: 31.86 MB / 0.5262 GB Notification: Performance of matching and sorting (n=49) (initialization): time 0.0009848/0.02102, allocations: 0.5393 MB / 0.6577 GB, free: 31.52 MB / 0.5262 GB Notification: Performance of prepare postOptimizeDAE: time 0.0001218/0.02114, allocations: 96.91 kB / 0.6578 GB, free: 31.42 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 9.097e-06/0.02115, allocations: 4.719 kB / 0.6578 GB, free: 31.42 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (initialization): time 2.549e-05/0.02117, allocations: 4.188 kB / 0.6578 GB, free: 31.42 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.000337/0.02151, allocations: 73.3 kB / 0.6579 GB, free: 31.41 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.659e-05/0.02153, allocations: 7.594 kB / 0.6579 GB, free: 31.41 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001802/0.02171, allocations: 17.94 kB / 0.6579 GB, free: 31.41 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 3.502e-05/0.02174, allocations: 11.28 kB / 0.6579 GB, free: 31.41 MB / 0.5262 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 0.0003684/0.02211, allocations: 307.9 kB / 0.6582 GB, free: 31.14 MB / 0.5262 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 7.319e-05/0.02218, allocations: 37.03 kB / 0.6582 GB, free: 31.12 MB / 0.5262 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 6.76e-05/0.02225, allocations: 24.73 kB / 0.6583 GB, free: 31.1 MB / 0.5262 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.232e-06/0.02226, allocations: 2.75 kB / 0.6583 GB, free: 31.1 MB / 0.5262 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 9.688e-06/0.02227, allocations: 1.938 kB / 0.6583 GB, free: 31.1 MB / 0.5262 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.699e-06/0.02227, allocations: 0 / 0.6583 GB, free: 31.1 MB / 0.5262 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001273/0.02354, allocations: 0.8167 MB / 0.6591 GB, free: 30.53 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.324e-06/0.02355, allocations: 1.406 kB / 0.6591 GB, free: 30.53 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002576/0.0238, allocations: 44.77 kB / 0.6591 GB, free: 30.53 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (simulation): time 6.903e-06/0.02381, allocations: 1.438 kB / 0.6591 GB, free: 30.53 MB / 0.5262 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.954e-05/0.02384, allocations: 8.219 kB / 0.6591 GB, free: 30.53 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 5.951e-06/0.02385, allocations: 4.812 kB / 0.6591 GB, free: 30.53 MB / 0.5262 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.533e-06/0.02385, allocations: 0 / 0.6591 GB, free: 30.53 MB / 0.5262 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001167/0.02501, allocations: 0.7823 MB / 0.6599 GB, free: 30.01 MB / 0.5262 GB Notification: Performance of postOpt removeConstants (simulation): time 3.378e-05/0.02505, allocations: 13.47 kB / 0.6599 GB, free: 30 MB / 0.5262 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 4.928e-05/0.0251, allocations: 9.594 kB / 0.6599 GB, free: 30 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001601/0.02526, allocations: 15.69 kB / 0.6599 GB, free: 29.99 MB / 0.5262 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001028/0.02536, allocations: 31.66 kB / 0.6599 GB, free: 29.98 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.991e-05/0.02539, allocations: 12.97 kB / 0.66 GB, free: 29.98 MB / 0.5262 GB Notification: Performance of sorting global known variables: time 0.0001524/0.02554, allocations: 172.4 kB / 0.6601 GB, free: 29.85 MB / 0.5262 GB Notification: Performance of sort global known variables: time 5e-08/0.02554, allocations: 0.5312 kB / 0.6601 GB, free: 29.85 MB / 0.5262 GB Notification: Performance of remove unused functions: time 0.0004076/0.02595, allocations: 71.72 kB / 0.6602 GB, free: 29.84 MB / 0.5262 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 0.0001663/0.02612, allocations: 115.4 kB / 0.6603 GB, free: 29.75 MB / 0.5262 GB Notification: Performance of simCode: created initialization part: time 0.0008428/0.02696, allocations: 0.5843 MB / 0.6609 GB, free: 29.31 MB / 0.5262 GB Notification: Performance of simCode: created event and clocks part: time 1.513e-06/0.02696, allocations: 0 / 0.6609 GB, free: 29.31 MB / 0.5262 GB Notification: Performance of simCode: created simulation system equations: time 0.0004012/0.02736, allocations: 325.6 kB / 0.6612 GB, free: 29.07 MB / 0.5262 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004609/0.02782, allocations: 72.44 kB / 0.6613 GB, free: 29.05 MB / 0.5262 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001467/0.02929, allocations: 0.7536 MB / 0.662 GB, free: 28.54 MB / 0.5262 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001697/0.02946, allocations: 134.8 kB / 0.6621 GB, free: 28.46 MB / 0.5262 GB Notification: Performance of simCode: alias equations: time 0.0001029/0.02956, allocations: 29.81 kB / 0.6621 GB, free: 28.45 MB / 0.5262 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 7.059e-05/0.02963, allocations: 22.5 kB / 0.6622 GB, free: 28.45 MB / 0.5262 GB Notification: Performance of SimCode: time 1.142e-06/0.02963, allocations: 0 / 0.6622 GB, free: 28.45 MB / 0.5262 GB Notification: Performance of Templates: time 0.01518/0.04481, allocations: 3.481 MB / 0.6656 GB, free: 28.14 MB / 0.5262 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 -abortSlowSimulation -alarm=240 -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 13.621287744957954]