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 0.0009764/0.0009764, allocations: 92.22 kB / 19.65 MB, free: 276 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 0.0009819/0.0009819, allocations: 169 kB / 23.02 MB, free: 1.547 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 0.9766/0.9766, allocations: 177.1 MB / 203.4 MB, free: 5.641 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 1.558/1.558, allocations: 273.5 MB / 0.5209 GB, free: 14.79 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 1.442e-06/1.442e-06, allocations: 0 / 0.6469 GB, free: 38.78 MB / 0.5262 GB Notification: Performance of FrontEnd - Absyn->SCode: time 1.822e-05/1.967e-05, allocations: 6.219 kB / 0.647 GB, free: 38.78 MB / 0.5262 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKTwoCompartmentModel): time 0.002198/0.002218, allocations: 2.366 MB / 0.6493 GB, free: 37.25 MB / 0.5262 GB Notification: Performance of NFInst.instExpressions: time 0.0007244/0.002942, allocations: 0.6119 MB / 0.6499 GB, free: 36.84 MB / 0.5262 GB Notification: Performance of NFInst.updateImplicitVariability: time 8.027e-05/0.003022, allocations: 2.062 kB / 0.6499 GB, free: 36.84 MB / 0.5262 GB Notification: Performance of NFTyping.typeComponents: time 0.0001144/0.003137, allocations: 29 kB / 0.6499 GB, free: 36.82 MB / 0.5262 GB Notification: Performance of NFTyping.typeBindings: time 0.0001455/0.003282, allocations: 72.05 kB / 0.65 GB, free: 36.8 MB / 0.5262 GB Notification: Performance of NFTyping.typeClassSections: time 0.0001675/0.00345, allocations: 63.41 kB / 0.65 GB, free: 36.76 MB / 0.5262 GB Notification: Performance of NFFlatten.flatten: time 0.0002442/0.003694, allocations: 296.6 kB / 0.6503 GB, free: 36.64 MB / 0.5262 GB Notification: Performance of NFFlatten.resolveConnections: time 0.000134/0.003828, allocations: 49.23 kB / 0.6503 GB, free: 36.61 MB / 0.5262 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0001341/0.003962, allocations: 148.2 kB / 0.6505 GB, free: 36.55 MB / 0.5262 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001195/0.004082, allocations: 91.47 kB / 0.6506 GB, free: 36.52 MB / 0.5262 GB Notification: Performance of NFPackage.collectConstants: time 3.143e-05/0.004113, allocations: 20 kB / 0.6506 GB, free: 36.52 MB / 0.5262 GB Notification: Performance of NFFlatten.collectFunctions: time 2.777e-05/0.004141, allocations: 20.88 kB / 0.6506 GB, free: 36.52 MB / 0.5262 GB Notification: Performance of NFScalarize.scalarize: time 3.646e-05/0.004177, allocations: 43.97 kB / 0.6507 GB, free: 36.5 MB / 0.5262 GB Notification: Performance of NFVerifyModel.verify: time 7.584e-05/0.004253, allocations: 85.95 kB / 0.6507 GB, free: 36.46 MB / 0.5262 GB Notification: Performance of NFConvertDAE.convert: time 0.0001843/0.004437, allocations: 173.9 kB / 0.6509 GB, free: 36.38 MB / 0.5262 GB Notification: Performance of FrontEnd - DAE generated: time 1.703e-06/0.004439, allocations: 2.688 kB / 0.6509 GB, free: 36.38 MB / 0.5262 GB Notification: Performance of FrontEnd: time 1.182e-06/0.00444, allocations: 0 / 0.6509 GB, free: 36.38 MB / 0.5262 GB Notification: Performance of Transformations before backend: time 4.528e-06/0.004445, allocations: 3.328 kB / 0.6509 GB, free: 36.38 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 0.0005813/0.005026, allocations: 0.6097 MB / 0.6515 GB, free: 35.82 MB / 0.5262 GB Notification: Performance of prepare preOptimizeDAE: time 3.438e-05/0.00506, allocations: 9.281 kB / 0.6515 GB, free: 35.82 MB / 0.5262 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 6.174e-05/0.005122, allocations: 37.95 kB / 0.6516 GB, free: 35.8 MB / 0.5262 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001529/0.005275, allocations: 171.8 kB / 0.6517 GB, free: 35.64 MB / 0.5262 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.596e-05/0.005291, allocations: 20 kB / 0.6517 GB, free: 35.63 MB / 0.5262 GB Notification: Performance of preOpt expandDerOperator (simulation): time 4.647e-05/0.005338, allocations: 23.23 kB / 0.6518 GB, free: 35.62 MB / 0.5262 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002481/0.005586, allocations: 205.6 kB / 0.652 GB, free: 35.49 MB / 0.5262 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.738e-05/0.005603, allocations: 10.38 kB / 0.652 GB, free: 35.48 MB / 0.5262 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.878e-05/0.005622, allocations: 10 kB / 0.652 GB, free: 35.48 MB / 0.5262 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.266e-05/0.005635, allocations: 3.688 kB / 0.652 GB, free: 35.48 MB / 0.5262 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001705/0.005805, allocations: 148.8 kB / 0.6521 GB, free: 35.4 MB / 0.5262 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0006146/0.00642, allocations: 490.5 kB / 0.6526 GB, free: 35.04 MB / 0.5262 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0002146/0.006634, allocations: 180.6 kB / 0.6528 GB, free: 34.92 MB / 0.5262 GB Notification: Performance of preOpt resolveLoops (simulation): time 8.056e-05/0.006715, allocations: 108.8 kB / 0.6529 GB, free: 34.83 MB / 0.5262 GB Notification: Performance of preOpt evalFunc (simulation): time 1.265e-05/0.006727, allocations: 5.75 kB / 0.6529 GB, free: 34.83 MB / 0.5262 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002432/0.006971, allocations: 312.5 kB / 0.6532 GB, free: 34.57 MB / 0.5262 GB Notification: Performance of pre-optimization done (n=31): time 1.643e-06/0.006972, allocations: 0 / 0.6532 GB, free: 34.57 MB / 0.5262 GB Notification: Performance of matching and sorting (n=33): time 0.001013/0.007985, allocations: 0.9062 MB / 0.654 GB, free: 33.93 MB / 0.5262 GB Notification: Performance of inlineWhenForInitialization (initialization): time 4.333e-05/0.008029, allocations: 226.7 kB / 0.6543 GB, free: 33.68 MB / 0.5262 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001051/0.008134, allocations: 222 kB / 0.6545 GB, free: 33.49 MB / 0.5262 GB Notification: Performance of collectPreVariables (initialization): time 1.576e-05/0.008149, allocations: 33.48 kB / 0.6545 GB, free: 33.46 MB / 0.5262 GB Notification: Performance of collectInitialEqns (initialization): time 4.859e-05/0.008198, allocations: 170.5 kB / 0.6547 GB, free: 33.3 MB / 0.5262 GB Notification: Performance of collectInitialBindings (initialization): time 4.611e-05/0.008244, allocations: 108.8 kB / 0.6548 GB, free: 33.21 MB / 0.5262 GB Notification: Performance of simplifyInitialFunctions (initialization): time 6.543e-05/0.008309, allocations: 74.2 kB / 0.6548 GB, free: 33.17 MB / 0.5262 GB Notification: Performance of setup shared object (initialization): time 5.34e-05/0.008363, allocations: 0.5002 MB / 0.6553 GB, free: 32.67 MB / 0.5262 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001009/0.008464, allocations: 153.9 kB / 0.6555 GB, free: 32.55 MB / 0.5262 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001424/0.008606, allocations: 272.6 kB / 0.6557 GB, free: 32.27 MB / 0.5262 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0003791/0.008985, allocations: 494.6 kB / 0.6562 GB, free: 31.83 MB / 0.5262 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.515e-06/0.008988, allocations: 4.469 kB / 0.6562 GB, free: 31.83 MB / 0.5262 GB Notification: Performance of matching and sorting (n=49) (initialization): time 0.0004854/0.009473, allocations: 463.4 kB / 0.6567 GB, free: 31.53 MB / 0.5262 GB Notification: Performance of prepare postOptimizeDAE: time 3.85e-05/0.009512, allocations: 93.19 kB / 0.6567 GB, free: 31.43 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.034e-06/0.009519, allocations: 4.969 kB / 0.6568 GB, free: 31.43 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (initialization): time 2.257e-05/0.009541, allocations: 4.375 kB / 0.6568 GB, free: 31.43 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002221/0.009763, allocations: 77.5 kB / 0.6568 GB, free: 31.42 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 9.648e-06/0.009773, allocations: 4.562 kB / 0.6568 GB, free: 31.42 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.339e-05/0.009866, allocations: 22.45 kB / 0.6569 GB, free: 31.41 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.816e-05/0.009885, allocations: 12.06 kB / 0.6569 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 0.0001591/0.01004, allocations: 292 kB / 0.6571 GB, free: 31.15 MB / 0.5262 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 3.476e-05/0.01008, allocations: 37.09 kB / 0.6572 GB, free: 31.13 MB / 0.5262 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.233e-05/0.01011, allocations: 28.42 kB / 0.6572 GB, free: 31.11 MB / 0.5262 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.266e-06/0.01011, allocations: 2.875 kB / 0.6572 GB, free: 31.11 MB / 0.5262 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 3.777e-06/0.01012, allocations: 1.094 kB / 0.6572 GB, free: 31.11 MB / 0.5262 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.551e-06/0.01012, allocations: 5.062 kB / 0.6572 GB, free: 31.11 MB / 0.5262 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005419/0.01067, allocations: 0.7206 MB / 0.6579 GB, free: 30.58 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.665e-06/0.01067, allocations: 1.188 kB / 0.6579 GB, free: 30.58 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001523/0.01082, allocations: 45.08 kB / 0.658 GB, free: 30.58 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (simulation): time 2.545e-06/0.01082, allocations: 1.375 kB / 0.658 GB, free: 30.58 MB / 0.5262 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.766e-05/0.01084, allocations: 12.66 kB / 0.658 GB, free: 30.58 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.365e-06/0.01084, allocations: 1.375 kB / 0.658 GB, free: 30.58 MB / 0.5262 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.853e-06/0.01084, allocations: 2.125 kB / 0.658 GB, free: 30.58 MB / 0.5262 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004284/0.01127, allocations: 0.6622 MB / 0.6586 GB, free: 30.11 MB / 0.5262 GB Notification: Performance of postOpt removeConstants (simulation): time 1.92e-05/0.01129, allocations: 16.69 kB / 0.6586 GB, free: 30.11 MB / 0.5262 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.069e-05/0.01132, allocations: 13.5 kB / 0.6587 GB, free: 30.1 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 8.257e-05/0.01141, allocations: 16.03 kB / 0.6587 GB, free: 30.09 MB / 0.5262 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 6.468e-05/0.01147, allocations: 26.73 kB / 0.6587 GB, free: 30.09 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.536e-05/0.01149, allocations: 12.38 kB / 0.6587 GB, free: 30.09 MB / 0.5262 GB Notification: Performance of sorting global known variables: time 5.046e-05/0.01154, allocations: 158.5 kB / 0.6589 GB, free: 29.96 MB / 0.5262 GB Notification: Performance of sort global known variables: time 7e-08/0.01154, allocations: 0 / 0.6589 GB, free: 29.96 MB / 0.5262 GB Notification: Performance of remove unused functions: time 0.0002272/0.01176, allocations: 72.38 kB / 0.6589 GB, free: 29.95 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 8.146e-05/0.01184, allocations: 114.3 kB / 0.659 GB, free: 29.86 MB / 0.5262 GB Notification: Performance of simCode: created initialization part: time 0.000327/0.01217, allocations: 0.4912 MB / 0.6595 GB, free: 29.46 MB / 0.5262 GB Notification: Performance of simCode: created event and clocks part: time 1.273e-06/0.01217, allocations: 0.7188 kB / 0.6595 GB, free: 29.46 MB / 0.5262 GB Notification: Performance of simCode: created simulation system equations: time 0.0001428/0.01232, allocations: 279 kB / 0.6598 GB, free: 29.24 MB / 0.5262 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003015/0.01262, allocations: 64.67 kB / 0.6598 GB, free: 29.22 MB / 0.5262 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001431/0.01405, allocations: 0.776 MB / 0.6606 GB, free: 28.71 MB / 0.5262 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 6.514e-05/0.01411, allocations: 82.41 kB / 0.6607 GB, free: 28.64 MB / 0.5262 GB Notification: Performance of simCode: alias equations: time 6.703e-05/0.01418, allocations: 22.05 kB / 0.6607 GB, free: 28.63 MB / 0.5262 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 6.785e-05/0.01425, allocations: 27.88 kB / 0.6607 GB, free: 28.62 MB / 0.5262 GB Notification: Performance of SimCode: time 9.02e-07/0.01425, allocations: 0 / 0.6607 GB, free: 28.62 MB / 0.5262 GB Notification: Performance of Templates: time 0.005969/0.02022, allocations: 3.484 MB / 0.6641 GB, free: 28.32 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: 4.796038079075515]