Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.DevModels.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 0.0009625/0.0009625, allocations: 93.06 kB / 19.65 MB, free: 280 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 0.0009589/0.0009589, allocations: 165 kB / 23.02 MB, free: 1.551 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 0.9421/0.9421, allocations: 177.1 MB / 203.4 MB, free: 5.629 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 1.636/1.636, 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.DevModels.PKTwoCompartmentModel,tolerance=1e-06,outputFormat="empty",numberOfIntervals=500,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel") translateModel(Pharmacolibrary.DevModels.PKTwoCompartmentModel,tolerance=1e-06,outputFormat="empty",numberOfIntervals=500,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel") [Timeout 660] "Notification: Performance of FrontEnd - loaded program: time 1.593e-06/1.593e-06, allocations: 0 / 0.6469 GB, free: 38.61 MB / 0.5262 GB Notification: Performance of FrontEnd - Absyn->SCode: time 2.151e-05/2.31e-05, allocations: 2.312 kB / 0.6469 GB, free: 38.61 MB / 0.5262 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.PKTwoCompartmentModel): time 0.003303/0.003326, allocations: 2.408 MB / 0.6493 GB, free: 37.05 MB / 0.5262 GB Notification: Performance of NFInst.instExpressions: time 0.0009461/0.004272, allocations: 0.6149 MB / 0.6499 GB, free: 36.64 MB / 0.5262 GB Notification: Performance of NFInst.updateImplicitVariability: time 8.039e-05/0.004352, allocations: 2.125 kB / 0.6499 GB, free: 36.64 MB / 0.5262 GB Notification: Performance of NFTyping.typeComponents: time 5.805e-05/0.00441, allocations: 31.16 kB / 0.6499 GB, free: 36.63 MB / 0.5262 GB Notification: Performance of NFTyping.typeBindings: time 0.0001869/0.004597, allocations: 79.73 kB / 0.65 GB, free: 36.59 MB / 0.5262 GB Notification: Performance of NFTyping.typeClassSections: time 0.0001767/0.004774, allocations: 62.88 kB / 0.6501 GB, free: 36.56 MB / 0.5262 GB Notification: Performance of NFFlatten.flatten: time 0.0002459/0.00502, allocations: 298.6 kB / 0.6503 GB, free: 36.43 MB / 0.5262 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001338/0.005154, allocations: 52.86 kB / 0.6504 GB, free: 36.4 MB / 0.5262 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0001769/0.005331, allocations: 153.6 kB / 0.6505 GB, free: 36.34 MB / 0.5262 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001307/0.005461, allocations: 89.89 kB / 0.6506 GB, free: 36.31 MB / 0.5262 GB Notification: Performance of NFPackage.collectConstants: time 3.471e-05/0.005496, allocations: 23 kB / 0.6506 GB, free: 36.31 MB / 0.5262 GB Notification: Performance of NFFlatten.collectFunctions: time 3.183e-05/0.005528, allocations: 22.03 kB / 0.6507 GB, free: 36.31 MB / 0.5262 GB Notification: Performance of NFScalarize.scalarize: time 3.701e-05/0.005565, allocations: 45.31 kB / 0.6507 GB, free: 36.28 MB / 0.5262 GB Notification: Performance of NFVerifyModel.verify: time 8.253e-05/0.005647, allocations: 90.75 kB / 0.6508 GB, free: 36.25 MB / 0.5262 GB Notification: Performance of NFConvertDAE.convert: time 0.0002015/0.005849, allocations: 182.5 kB / 0.651 GB, free: 36.16 MB / 0.5262 GB Notification: Performance of FrontEnd - DAE generated: time 2.014e-06/0.005851, allocations: 2.875 kB / 0.651 GB, free: 36.16 MB / 0.5262 GB Notification: Performance of FrontEnd: time 1.072e-06/0.005852, allocations: 0 / 0.651 GB, free: 36.16 MB / 0.5262 GB Notification: Performance of Transformations before backend: time 5.27e-06/0.005857, allocations: 0 / 0.651 GB, free: 36.16 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: 45 * Number of variables: 45 Notification: Performance of Generate backend data structure: time 0.0005843/0.006442, allocations: 0.6177 MB / 0.6516 GB, free: 35.59 MB / 0.5262 GB Notification: Performance of prepare preOptimizeDAE: time 3.337e-05/0.006475, allocations: 9.781 kB / 0.6516 GB, free: 35.59 MB / 0.5262 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 6.82e-05/0.006543, allocations: 42.5 kB / 0.6516 GB, free: 35.58 MB / 0.5262 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001188/0.006662, allocations: 140.9 kB / 0.6518 GB, free: 35.43 MB / 0.5262 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.452e-05/0.006687, allocations: 17.66 kB / 0.6518 GB, free: 35.42 MB / 0.5262 GB Notification: Performance of preOpt expandDerOperator (simulation): time 5.698e-05/0.006744, allocations: 22.7 kB / 0.6518 GB, free: 35.41 MB / 0.5262 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003333/0.007077, allocations: 220.8 kB / 0.652 GB, free: 35.27 MB / 0.5262 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.622e-05/0.007093, allocations: 2.781 kB / 0.652 GB, free: 35.27 MB / 0.5262 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.18e-05/0.007115, allocations: 13.78 kB / 0.652 GB, free: 35.26 MB / 0.5262 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.088e-05/0.007126, allocations: 4.031 kB / 0.652 GB, free: 35.26 MB / 0.5262 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002071/0.007333, allocations: 155.7 kB / 0.6522 GB, free: 35.18 MB / 0.5262 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0007392/0.008072, allocations: 0.4903 MB / 0.6527 GB, free: 34.81 MB / 0.5262 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0002456/0.008318, allocations: 184.2 kB / 0.6528 GB, free: 34.69 MB / 0.5262 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.0001066/0.008424, allocations: 113 kB / 0.6529 GB, free: 34.61 MB / 0.5262 GB Notification: Performance of preOpt evalFunc (simulation): time 1.403e-05/0.008438, allocations: 5.75 kB / 0.6529 GB, free: 34.61 MB / 0.5262 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002545/0.008693, allocations: 317.2 kB / 0.6532 GB, free: 34.34 MB / 0.5262 GB Notification: Performance of pre-optimization done (n=31): time 1.623e-06/0.008694, allocations: 1.438 kB / 0.6532 GB, free: 34.34 MB / 0.5262 GB Notification: Performance of matching and sorting (n=33): time 0.001218/0.009913, allocations: 0.9123 MB / 0.6541 GB, free: 33.7 MB / 0.5262 GB Notification: Performance of inlineWhenForInitialization (initialization): time 5.273e-05/0.009966, allocations: 221.6 kB / 0.6544 GB, free: 33.44 MB / 0.5262 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001224/0.01009, allocations: 217.5 kB / 0.6546 GB, free: 33.26 MB / 0.5262 GB Notification: Performance of collectPreVariables (initialization): time 2.384e-05/0.01011, allocations: 32.61 kB / 0.6546 GB, free: 33.23 MB / 0.5262 GB Notification: Performance of collectInitialEqns (initialization): time 6.733e-05/0.01018, allocations: 174.7 kB / 0.6548 GB, free: 33.07 MB / 0.5262 GB Notification: Performance of collectInitialBindings (initialization): time 7.553e-05/0.01025, allocations: 103.8 kB / 0.6549 GB, free: 32.98 MB / 0.5262 GB Notification: Performance of simplifyInitialFunctions (initialization): time 9.284e-05/0.01035, allocations: 69.16 kB / 0.6549 GB, free: 32.94 MB / 0.5262 GB Notification: Performance of setup shared object (initialization): time 6.489e-05/0.01041, allocations: 0.5047 MB / 0.6554 GB, free: 32.44 MB / 0.5262 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001317/0.01054, allocations: 148.2 kB / 0.6556 GB, free: 32.32 MB / 0.5262 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001704/0.01071, allocations: 268.5 kB / 0.6558 GB, free: 32.05 MB / 0.5262 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0003754/0.01109, allocations: 498.6 kB / 0.6563 GB, free: 31.61 MB / 0.5262 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.454e-06/0.01109, allocations: 0 / 0.6563 GB, free: 31.61 MB / 0.5262 GB Notification: Performance of matching and sorting (n=48) (initialization): time 0.0005826/0.01167, allocations: 447.7 kB / 0.6567 GB, free: 31.32 MB / 0.5262 GB Notification: Performance of prepare postOptimizeDAE: time 4.629e-05/0.01172, allocations: 93.2 kB / 0.6568 GB, free: 31.22 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.826e-06/0.01173, allocations: 2.188 kB / 0.6568 GB, free: 31.22 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (initialization): time 2.377e-05/0.01175, allocations: 5.25 kB / 0.6568 GB, free: 31.22 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002804/0.01203, allocations: 76.73 kB / 0.6569 GB, free: 31.21 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.248e-05/0.01205, allocations: 3.875 kB / 0.6569 GB, free: 31.21 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001446/0.01219, allocations: 22.81 kB / 0.6569 GB, free: 31.2 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 3.647e-05/0.01223, allocations: 10.91 kB / 0.6569 GB, free: 31.2 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 intestine.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real blood.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real intestine.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real intestine.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real blood.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real blood.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real blood.rising:DISCRETE(fixed = true protected = true ) type: Boolean intestine.rising:DISCRETE(fixed = true protected = true ) type: Boolean Notification: Model statistics after passing the back-end for initialization: * Number of independent subsystems: 9 * Number of states: 0 () * Number of discrete variables: 21 ($PRE.intestine.Cmin,intestine.Cmin,$PRE.intestine.Cmax,intestine.Cmax,$PRE.blood.Cmin,blood.Cmin,$PRE.blood.Cmax,blood.Cmax,$PRE.blood.rising,$PRE.intestine.rising,$PRE.periodicDose.pulse.count,$PRE.periodicDose.pulse.T_start,blood.rising,intestine.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 (45): * Single equations (assignments): 42 * 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 0.0002232/0.01245, allocations: 280.4 kB / 0.6572 GB, free: 30.95 MB / 0.5262 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 6.525e-05/0.01252, allocations: 37.8 kB / 0.6572 GB, free: 30.93 MB / 0.5262 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 4.178e-05/0.01256, allocations: 24.97 kB / 0.6572 GB, free: 30.91 MB / 0.5262 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.332e-06/0.01256, allocations: 6.5 kB / 0.6573 GB, free: 30.91 MB / 0.5262 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 7.474e-06/0.01257, allocations: 1.719 kB / 0.6573 GB, free: 30.91 MB / 0.5262 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.551e-06/0.01258, allocations: 0.5625 kB / 0.6573 GB, free: 30.91 MB / 0.5262 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0006955/0.01327, allocations: 0.7198 MB / 0.658 GB, free: 30.39 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.234e-06/0.01328, allocations: 1.938 kB / 0.658 GB, free: 30.39 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001907/0.01347, allocations: 52.86 kB / 0.658 GB, free: 30.38 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (simulation): time 3.106e-06/0.01347, allocations: 1.406 kB / 0.658 GB, free: 30.38 MB / 0.5262 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.269e-05/0.01349, allocations: 11.7 kB / 0.658 GB, free: 30.38 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.565e-06/0.01349, allocations: 1.375 kB / 0.658 GB, free: 30.38 MB / 0.5262 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.472e-06/0.0135, allocations: 3.938 kB / 0.658 GB, free: 30.38 MB / 0.5262 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005515/0.01405, allocations: 0.6626 MB / 0.6587 GB, free: 29.91 MB / 0.5262 GB Notification: Performance of postOpt removeConstants (simulation): time 2.482e-05/0.01407, allocations: 12.03 kB / 0.6587 GB, free: 29.9 MB / 0.5262 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 4.21e-05/0.01411, allocations: 15.09 kB / 0.6587 GB, free: 29.89 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001184/0.01423, allocations: 10.22 kB / 0.6587 GB, free: 29.89 MB / 0.5262 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 7.685e-05/0.01431, allocations: 30.67 kB / 0.6587 GB, free: 29.89 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.01e-05/0.01433, allocations: 10.97 kB / 0.6588 GB, free: 29.89 MB / 0.5262 GB Notification: Performance of sorting global known variables: time 6.863e-05/0.0144, allocations: 159 kB / 0.6589 GB, free: 29.76 MB / 0.5262 GB Notification: Performance of sort global known variables: time 9e-08/0.0144, allocations: 0 / 0.6589 GB, free: 29.76 MB / 0.5262 GB Notification: Performance of remove unused functions: time 0.0003364/0.01473, allocations: 74 kB / 0.659 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: 6 (periodicDose.TotalCumulativeMass,periodicDose.variableDose.TotalCumulativeMass,intestine.C,intestine.AUC,blood.C,blood.AUC) * Number of discrete variables: 13 ($whenCondition1,$whenCondition2,$whenCondition3,$whenCondition4,$whenCondition5,periodicDose.pulse.T_start,periodicDose.pulse.count,intestine.Cmax,intestine.Cmin,intestine.rising,blood.Cmax,blood.Cmin,blood.rising) * Number of discrete states: 11 (periodicDose.pulse.count,blood.Cmin,$whenCondition3,blood.Cmax,$whenCondition2,blood.rising,intestine.Cmin,$whenCondition5,intestine.Cmax,$whenCondition4,intestine.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 9.542e-05/0.01483, allocations: 119.6 kB / 0.6591 GB, free: 29.65 MB / 0.5262 GB Notification: Performance of simCode: created initialization part: time 0.0004114/0.01524, allocations: 493.8 kB / 0.6596 GB, free: 29.26 MB / 0.5262 GB Notification: Performance of simCode: created event and clocks part: time 1.623e-06/0.01524, allocations: 1.375 kB / 0.6596 GB, free: 29.26 MB / 0.5262 GB Notification: Performance of simCode: created simulation system equations: time 0.000184/0.01543, allocations: 276.3 kB / 0.6598 GB, free: 29.04 MB / 0.5262 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003913/0.01582, allocations: 70.95 kB / 0.6599 GB, free: 29.02 MB / 0.5262 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001919/0.01774, allocations: 0.7518 MB / 0.6606 GB, free: 28.54 MB / 0.5262 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 5.964e-05/0.0178, allocations: 84.91 kB / 0.6607 GB, free: 28.46 MB / 0.5262 GB Notification: Performance of simCode: alias equations: time 9.918e-05/0.0179, allocations: 24.77 kB / 0.6607 GB, free: 28.45 MB / 0.5262 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 6.913e-05/0.01797, allocations: 22.5 kB / 0.6608 GB, free: 28.45 MB / 0.5262 GB Notification: Performance of SimCode: time 9.02e-07/0.01797, allocations: 0 / 0.6608 GB, free: 28.45 MB / 0.5262 GB Notification: Performance of Templates: time 0.006875/0.02484, allocations: 3.435 MB / 0.6641 GB, free: 28.14 MB / 0.5262 GB " [Timeout remaining time 660] make -j1 -f Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.makefile [Timeout 660] (rm -f Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.sim & ./Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel -abortSlowSimulation -alarm=240 -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 4.958805727772415]