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 0.001152/0.001152, allocations: 81.95 kB / 19.87 MB, free: 4.617 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 0.001144/0.001144, allocations: 169.7 kB / 23.27 MB, free: 1.223 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 0.9676/0.9676, allocations: 177.2 MB / 203.7 MB, free: 5.508 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 1.634/1.634, allocations: 273.5 MB / 0.5212 GB, free: 14.75 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 1.834e-06/1.834e-06, allocations: 0 / 0.6474 GB, free: 38.43 MB / 0.5262 GB Notification: Performance of FrontEnd - Absyn->SCode: time 2.602e-05/2.785e-05, allocations: 5.625 kB / 0.6474 GB, free: 38.42 MB / 0.5262 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKTwoCompartmentModel): time 0.003251/0.003278, allocations: 2.361 MB / 0.6497 GB, free: 36.88 MB / 0.5262 GB Notification: Performance of NFInst.instExpressions: time 0.001133/0.004411, allocations: 0.6091 MB / 0.6503 GB, free: 36.48 MB / 0.5262 GB Notification: Performance of NFInst.updateImplicitVariability: time 0.0001344/0.004546, allocations: 7.656 kB / 0.6503 GB, free: 36.47 MB / 0.5262 GB Notification: Performance of NFTyping.typeComponents: time 0.0001308/0.004676, allocations: 25.92 kB / 0.6503 GB, free: 36.46 MB / 0.5262 GB Notification: Performance of NFTyping.typeBindings: time 0.0002196/0.004896, allocations: 71.64 kB / 0.6504 GB, free: 36.43 MB / 0.5262 GB Notification: Performance of NFTyping.typeClassSections: time 0.0002411/0.005137, allocations: 65.58 kB / 0.6504 GB, free: 36.39 MB / 0.5262 GB Notification: Performance of NFFlatten.flatten: time 0.0003405/0.005477, allocations: 293.2 kB / 0.6507 GB, free: 36.28 MB / 0.5262 GB Notification: Performance of NFFlatten.resolveConnections: time 0.000136/0.005613, allocations: 43.36 kB / 0.6508 GB, free: 36.25 MB / 0.5262 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0001761/0.005789, allocations: 150.5 kB / 0.6509 GB, free: 36.2 MB / 0.5262 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001223/0.005912, allocations: 85.45 kB / 0.651 GB, free: 36.16 MB / 0.5262 GB Notification: Performance of NFPackage.collectConstants: time 3.19e-05/0.005944, allocations: 24.47 kB / 0.651 GB, free: 36.16 MB / 0.5262 GB Notification: Performance of NFFlatten.collectFunctions: time 2.751e-05/0.005971, allocations: 19.28 kB / 0.651 GB, free: 36.16 MB / 0.5262 GB Notification: Performance of NFScalarize.scalarize: time 3.364e-05/0.006005, allocations: 42.86 kB / 0.6511 GB, free: 36.14 MB / 0.5262 GB Notification: Performance of NFVerifyModel.verify: time 6.706e-05/0.006072, allocations: 87.67 kB / 0.6512 GB, free: 36.1 MB / 0.5262 GB Notification: Performance of NFConvertDAE.convert: time 0.0001756/0.006248, allocations: 173.1 kB / 0.6513 GB, free: 36.02 MB / 0.5262 GB Notification: Performance of FrontEnd - DAE generated: time 2.545e-06/0.00625, allocations: 0 / 0.6513 GB, free: 36.02 MB / 0.5262 GB Notification: Performance of FrontEnd: time 8.01e-07/0.006251, allocations: 2.219 kB / 0.6513 GB, free: 36.02 MB / 0.5262 GB Notification: Performance of Transformations before backend: time 3.807e-06/0.006255, allocations: 1.406 kB / 0.6513 GB, free: 36.02 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 0.0005126/0.006767, allocations: 0.6154 MB / 0.6519 GB, free: 35.45 MB / 0.5262 GB Notification: Performance of prepare preOptimizeDAE: time 3.374e-05/0.006801, allocations: 8.875 kB / 0.6519 GB, free: 35.45 MB / 0.5262 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 5.227e-05/0.006853, allocations: 38.36 kB / 0.652 GB, free: 35.44 MB / 0.5262 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001326/0.006986, allocations: 179.2 kB / 0.6521 GB, free: 35.27 MB / 0.5262 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.791e-05/0.007004, allocations: 12.83 kB / 0.6522 GB, free: 35.27 MB / 0.5262 GB Notification: Performance of preOpt expandDerOperator (simulation): time 2.928e-05/0.007033, allocations: 25.44 kB / 0.6522 GB, free: 35.26 MB / 0.5262 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0001858/0.007219, allocations: 195.3 kB / 0.6524 GB, free: 35.13 MB / 0.5262 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.182e-05/0.007231, allocations: 3.938 kB / 0.6524 GB, free: 35.13 MB / 0.5262 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.396e-05/0.007245, allocations: 7.375 kB / 0.6524 GB, free: 35.12 MB / 0.5262 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.142e-06/0.007251, allocations: 8.219 kB / 0.6524 GB, free: 35.12 MB / 0.5262 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001036/0.007354, allocations: 141.5 kB / 0.6525 GB, free: 35.05 MB / 0.5262 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0004367/0.007791, allocations: 457.5 kB / 0.653 GB, free: 34.71 MB / 0.5262 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0001357/0.007927, allocations: 167.4 kB / 0.6531 GB, free: 34.6 MB / 0.5262 GB Notification: Performance of preOpt resolveLoops (simulation): time 5.791e-05/0.007985, allocations: 100.7 kB / 0.6532 GB, free: 34.52 MB / 0.5262 GB Notification: Performance of preOpt evalFunc (simulation): time 1.003e-05/0.007995, allocations: 3.5 kB / 0.6532 GB, free: 34.52 MB / 0.5262 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002043/0.008199, allocations: 307.6 kB / 0.6535 GB, free: 34.26 MB / 0.5262 GB Notification: Performance of pre-optimization done (n=31): time 1.653e-06/0.008201, allocations: 1.469 kB / 0.6535 GB, free: 34.26 MB / 0.5262 GB Notification: Performance of matching and sorting (n=33): time 0.0008094/0.00901, allocations: 0.851 MB / 0.6543 GB, free: 33.65 MB / 0.5262 GB Notification: Performance of inlineWhenForInitialization (initialization): time 5.043e-05/0.00906, allocations: 222.9 kB / 0.6546 GB, free: 33.39 MB / 0.5262 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001015/0.009162, allocations: 214 kB / 0.6548 GB, free: 33.22 MB / 0.5262 GB Notification: Performance of collectPreVariables (initialization): time 2.08e-05/0.009183, allocations: 36.52 kB / 0.6548 GB, free: 33.18 MB / 0.5262 GB Notification: Performance of collectInitialEqns (initialization): time 5.781e-05/0.009241, allocations: 174.2 kB / 0.655 GB, free: 33.02 MB / 0.5262 GB Notification: Performance of collectInitialBindings (initialization): time 6.16e-05/0.009302, allocations: 109.1 kB / 0.6551 GB, free: 32.93 MB / 0.5262 GB Notification: Performance of simplifyInitialFunctions (initialization): time 7.929e-05/0.009381, allocations: 74.75 kB / 0.6551 GB, free: 32.89 MB / 0.5262 GB Notification: Performance of setup shared object (initialization): time 6.274e-05/0.009444, allocations: 0.5056 MB / 0.6556 GB, free: 32.38 MB / 0.5262 GB Notification: Performance of preBalanceInitialSystem (initialization): time 7.221e-05/0.009516, allocations: 143.1 kB / 0.6558 GB, free: 32.27 MB / 0.5262 GB Notification: Performance of partitionIndependentBlocks (initialization): time 9.988e-05/0.009616, allocations: 268.5 kB / 0.656 GB, free: 31.99 MB / 0.5262 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0002351/0.009851, allocations: 469.2 kB / 0.6565 GB, free: 31.56 MB / 0.5262 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.006e-06/0.009854, allocations: 2.219 kB / 0.6565 GB, free: 31.56 MB / 0.5262 GB Notification: Performance of matching and sorting (n=49) (initialization): time 0.0003297/0.01018, allocations: 437 kB / 0.6569 GB, free: 31.27 MB / 0.5262 GB Notification: Performance of prepare postOptimizeDAE: time 4.449e-05/0.01023, allocations: 91.17 kB / 0.657 GB, free: 31.18 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 9.467e-06/0.01024, allocations: 6.688 kB / 0.657 GB, free: 31.18 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.692e-05/0.01025, allocations: 7.219 kB / 0.657 GB, free: 31.18 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002112/0.01047, allocations: 76.16 kB / 0.6571 GB, free: 31.17 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.596e-06/0.01047, allocations: 7.75 kB / 0.6571 GB, free: 31.16 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.872e-05/0.01057, allocations: 25.53 kB / 0.6571 GB, free: 31.16 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.102e-05/0.01059, allocations: 9.469 kB / 0.6571 GB, free: 31.16 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 0.0001894/0.01078, allocations: 280.9 kB / 0.6574 GB, free: 30.9 MB / 0.5262 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 5.772e-05/0.01084, allocations: 32.95 kB / 0.6574 GB, free: 30.89 MB / 0.5262 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.813e-05/0.01088, allocations: 33.08 kB / 0.6574 GB, free: 30.86 MB / 0.5262 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.939e-06/0.01088, allocations: 2.719 kB / 0.6574 GB, free: 30.86 MB / 0.5262 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 2.274e-06/0.01089, allocations: 1.969 kB / 0.6574 GB, free: 30.86 MB / 0.5262 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.018e-06/0.01089, allocations: 0.5312 kB / 0.6574 GB, free: 30.86 MB / 0.5262 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.000643/0.01153, allocations: 0.6727 MB / 0.6581 GB, free: 30.38 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.645e-06/0.01154, allocations: 3.531 kB / 0.6581 GB, free: 30.38 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001502/0.01169, allocations: 49.67 kB / 0.6581 GB, free: 30.38 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (simulation): time 2.815e-06/0.01169, allocations: 3.938 kB / 0.6582 GB, free: 30.37 MB / 0.5262 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.49e-05/0.0117, allocations: 9.594 kB / 0.6582 GB, free: 30.37 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.372e-06/0.01171, allocations: 1.406 kB / 0.6582 GB, free: 30.37 MB / 0.5262 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.172e-06/0.01171, allocations: 0 / 0.6582 GB, free: 30.37 MB / 0.5262 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003621/0.01207, allocations: 0.6353 MB / 0.6588 GB, free: 29.92 MB / 0.5262 GB Notification: Performance of postOpt removeConstants (simulation): time 2.069e-05/0.01209, allocations: 21.45 kB / 0.6588 GB, free: 29.9 MB / 0.5262 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.955e-05/0.01212, allocations: 9.562 kB / 0.6588 GB, free: 29.9 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 8.163e-05/0.0122, allocations: 17.62 kB / 0.6588 GB, free: 29.89 MB / 0.5262 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 5.255e-05/0.01225, allocations: 23.12 kB / 0.6589 GB, free: 29.89 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.387e-05/0.01227, allocations: 16.7 kB / 0.6589 GB, free: 29.89 MB / 0.5262 GB Notification: Performance of sorting global known variables: time 4.355e-05/0.01231, allocations: 158.8 kB / 0.659 GB, free: 29.76 MB / 0.5262 GB Notification: Performance of sort global known variables: time 6e-08/0.01231, allocations: 1.5 kB / 0.659 GB, free: 29.76 MB / 0.5262 GB Notification: Performance of remove unused functions: time 0.0002219/0.01253, allocations: 73.91 kB / 0.6591 GB, free: 29.75 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 8.594e-05/0.01262, allocations: 115 kB / 0.6592 GB, free: 29.66 MB / 0.5262 GB Notification: Performance of simCode: created initialization part: time 0.0002625/0.01288, allocations: 480.2 kB / 0.6597 GB, free: 29.27 MB / 0.5262 GB Notification: Performance of simCode: created event and clocks part: time 2.455e-06/0.01288, allocations: 1.469 kB / 0.6597 GB, free: 29.27 MB / 0.5262 GB Notification: Performance of simCode: created simulation system equations: time 0.0001276/0.01301, allocations: 273.8 kB / 0.6599 GB, free: 29.05 MB / 0.5262 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002809/0.01329, allocations: 60.48 kB / 0.66 GB, free: 29.04 MB / 0.5262 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001289/0.01458, allocations: 0.7737 MB / 0.6607 GB, free: 28.52 MB / 0.5262 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 7.75e-05/0.01466, allocations: 85.38 kB / 0.6608 GB, free: 28.45 MB / 0.5262 GB Notification: Performance of simCode: alias equations: time 8.427e-05/0.01474, allocations: 28.89 kB / 0.6608 GB, free: 28.44 MB / 0.5262 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001499/0.01489, allocations: 147.3 kB / 0.661 GB, free: 28.37 MB / 0.5262 GB Notification: Performance of SimCode: time 7.21e-07/0.01489, allocations: 0 / 0.661 GB, free: 28.37 MB / 0.5262 GB Notification: Performance of Templates: time 0.005391/0.02029, allocations: 3.806 MB / 0.6647 GB, free: 28.02 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: 4.517156179994345]