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 0.001116/0.001116, allocations: 81.17 kB / 19.87 MB, free: 4.621 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 0.001047/0.001047, allocations: 169 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 0.9674/0.9674, allocations: 177.2 MB / 203.7 MB, free: 5.512 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 1.674/1.674, allocations: 273.5 MB / 0.5212 GB, free: 14.7 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 1.223e-06/1.223e-06, allocations: 0 / 0.6474 GB, free: 38.42 MB / 0.5262 GB Notification: Performance of FrontEnd - Absyn->SCode: time 8.325e-06/9.548e-06, allocations: 3.625 kB / 0.6474 GB, free: 38.41 MB / 0.5262 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.PKTwoCompartmentModel): time 0.001871/0.00188, allocations: 2.377 MB / 0.6497 GB, free: 36.87 MB / 0.5262 GB Notification: Performance of NFInst.instExpressions: time 0.0005887/0.002469, allocations: 0.6131 MB / 0.6503 GB, free: 36.46 MB / 0.5262 GB Notification: Performance of NFInst.updateImplicitVariability: time 6.436e-05/0.002533, allocations: 3.656 kB / 0.6503 GB, free: 36.46 MB / 0.5262 GB Notification: Performance of NFTyping.typeComponents: time 4.557e-05/0.002579, allocations: 31.08 kB / 0.6504 GB, free: 36.44 MB / 0.5262 GB Notification: Performance of NFTyping.typeBindings: time 0.0001488/0.002728, allocations: 79.94 kB / 0.6504 GB, free: 36.41 MB / 0.5262 GB Notification: Performance of NFTyping.typeClassSections: time 0.0001327/0.002861, allocations: 59.11 kB / 0.6505 GB, free: 36.38 MB / 0.5262 GB Notification: Performance of NFFlatten.flatten: time 0.0001921/0.003053, allocations: 302.6 kB / 0.6508 GB, free: 36.25 MB / 0.5262 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001008/0.003153, allocations: 48.5 kB / 0.6508 GB, free: 36.22 MB / 0.5262 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0001371/0.003291, allocations: 160.7 kB / 0.651 GB, free: 36.16 MB / 0.5262 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001014/0.003392, allocations: 82.42 kB / 0.6511 GB, free: 36.13 MB / 0.5262 GB Notification: Performance of NFPackage.collectConstants: time 2.888e-05/0.003421, allocations: 23.44 kB / 0.6511 GB, free: 36.13 MB / 0.5262 GB Notification: Performance of NFFlatten.collectFunctions: time 2.508e-05/0.003446, allocations: 21.22 kB / 0.6511 GB, free: 36.13 MB / 0.5262 GB Notification: Performance of NFScalarize.scalarize: time 2.853e-05/0.003474, allocations: 51.77 kB / 0.6511 GB, free: 36.1 MB / 0.5262 GB Notification: Performance of NFVerifyModel.verify: time 5.967e-05/0.003534, allocations: 92.83 kB / 0.6512 GB, free: 36.06 MB / 0.5262 GB Notification: Performance of NFConvertDAE.convert: time 0.000145/0.003679, allocations: 178.5 kB / 0.6514 GB, free: 35.98 MB / 0.5262 GB Notification: Performance of FrontEnd - DAE generated: time 1.563e-06/0.003681, allocations: 0 / 0.6514 GB, free: 35.98 MB / 0.5262 GB Notification: Performance of FrontEnd: time 3.61e-07/0.003681, allocations: 1.312 kB / 0.6514 GB, free: 35.98 MB / 0.5262 GB Notification: Performance of Transformations before backend: time 3.136e-06/0.003684, allocations: 0 / 0.6514 GB, free: 35.98 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 0.0004691/0.004153, allocations: 0.6233 MB / 0.652 GB, free: 35.41 MB / 0.5262 GB Notification: Performance of prepare preOptimizeDAE: time 3.017e-05/0.004183, allocations: 9.938 kB / 0.652 GB, free: 35.41 MB / 0.5262 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 4.466e-05/0.004228, allocations: 36.33 kB / 0.6521 GB, free: 35.39 MB / 0.5262 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001151/0.004343, allocations: 175.8 kB / 0.6522 GB, free: 35.23 MB / 0.5262 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.691e-05/0.00436, allocations: 15.19 kB / 0.6522 GB, free: 35.22 MB / 0.5262 GB Notification: Performance of preOpt expandDerOperator (simulation): time 2.534e-05/0.004385, allocations: 28.61 kB / 0.6523 GB, free: 35.21 MB / 0.5262 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0001683/0.004554, allocations: 202.4 kB / 0.6525 GB, free: 35.08 MB / 0.5262 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.115e-05/0.004565, allocations: 3.984 kB / 0.6525 GB, free: 35.07 MB / 0.5262 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.17e-05/0.004577, allocations: 7.469 kB / 0.6525 GB, free: 35.07 MB / 0.5262 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.122e-06/0.004583, allocations: 3.875 kB / 0.6525 GB, free: 35.07 MB / 0.5262 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 9.652e-05/0.004679, allocations: 139.1 kB / 0.6526 GB, free: 35 MB / 0.5262 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0004129/0.005092, allocations: 484.7 kB / 0.6531 GB, free: 34.65 MB / 0.5262 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0001288/0.005221, allocations: 173.5 kB / 0.6532 GB, free: 34.54 MB / 0.5262 GB Notification: Performance of preOpt resolveLoops (simulation): time 5.089e-05/0.005272, allocations: 102.5 kB / 0.6533 GB, free: 34.45 MB / 0.5262 GB Notification: Performance of preOpt evalFunc (simulation): time 9.498e-06/0.005281, allocations: 7.125 kB / 0.6533 GB, free: 34.45 MB / 0.5262 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0001602/0.005442, allocations: 310.9 kB / 0.6536 GB, free: 34.19 MB / 0.5262 GB Notification: Performance of pre-optimization done (n=31): time 1.563e-06/0.005443, allocations: 1.375 kB / 0.6536 GB, free: 34.19 MB / 0.5262 GB Notification: Performance of matching and sorting (n=33): time 0.0007129/0.006156, allocations: 0.8442 MB / 0.6545 GB, free: 33.59 MB / 0.5262 GB Notification: Performance of inlineWhenForInitialization (initialization): time 4.044e-05/0.006197, allocations: 223.9 kB / 0.6547 GB, free: 33.33 MB / 0.5262 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 8.043e-05/0.006277, allocations: 219.5 kB / 0.6549 GB, free: 33.14 MB / 0.5262 GB Notification: Performance of collectPreVariables (initialization): time 1.474e-05/0.006292, allocations: 38.36 kB / 0.6549 GB, free: 33.11 MB / 0.5262 GB Notification: Performance of collectInitialEqns (initialization): time 3.936e-05/0.006331, allocations: 166.1 kB / 0.6551 GB, free: 32.95 MB / 0.5262 GB Notification: Performance of collectInitialBindings (initialization): time 4.164e-05/0.006373, allocations: 109.1 kB / 0.6552 GB, free: 32.87 MB / 0.5262 GB Notification: Performance of simplifyInitialFunctions (initialization): time 5.68e-05/0.00643, allocations: 71.78 kB / 0.6553 GB, free: 32.82 MB / 0.5262 GB Notification: Performance of setup shared object (initialization): time 4.669e-05/0.006476, allocations: 0.5094 MB / 0.6557 GB, free: 32.32 MB / 0.5262 GB Notification: Performance of preBalanceInitialSystem (initialization): time 6.454e-05/0.006541, allocations: 142.7 kB / 0.6559 GB, free: 32.2 MB / 0.5262 GB Notification: Performance of partitionIndependentBlocks (initialization): time 9.033e-05/0.006631, allocations: 255 kB / 0.6561 GB, free: 31.94 MB / 0.5262 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0002114/0.006842, allocations: 464.3 kB / 0.6566 GB, free: 31.52 MB / 0.5262 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.903e-06/0.006844, allocations: 2.188 kB / 0.6566 GB, free: 31.52 MB / 0.5262 GB Notification: Performance of matching and sorting (n=48) (initialization): time 0.0003359/0.00718, allocations: 429.8 kB / 0.657 GB, free: 31.23 MB / 0.5262 GB Notification: Performance of prepare postOptimizeDAE: time 3.362e-05/0.007214, allocations: 92.77 kB / 0.6571 GB, free: 31.13 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.474e-06/0.007221, allocations: 2.188 kB / 0.6571 GB, free: 31.13 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.601e-05/0.007237, allocations: 5.062 kB / 0.6571 GB, free: 31.13 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001925/0.00743, allocations: 68.56 kB / 0.6571 GB, free: 31.13 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 7.785e-06/0.007438, allocations: 11.12 kB / 0.6572 GB, free: 31.12 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 8.87e-05/0.007526, allocations: 19.5 kB / 0.6572 GB, free: 31.12 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.914e-05/0.007545, allocations: 16.25 kB / 0.6572 GB, free: 31.11 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 0.0001536/0.007699, allocations: 272.6 kB / 0.6574 GB, free: 30.86 MB / 0.5262 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 4.531e-05/0.007744, allocations: 37.47 kB / 0.6575 GB, free: 30.85 MB / 0.5262 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.264e-05/0.007777, allocations: 23.7 kB / 0.6575 GB, free: 30.83 MB / 0.5262 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.929e-06/0.007782, allocations: 4.781 kB / 0.6575 GB, free: 30.83 MB / 0.5262 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 1.563e-06/0.007784, allocations: 0.5625 kB / 0.6575 GB, free: 30.83 MB / 0.5262 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.589e-06/0.007788, allocations: 4.219 kB / 0.6575 GB, free: 30.83 MB / 0.5262 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004649/0.008253, allocations: 0.6799 MB / 0.6582 GB, free: 30.33 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.623e-06/0.008255, allocations: 0 / 0.6582 GB, free: 30.33 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001295/0.008384, allocations: 55.48 kB / 0.6582 GB, free: 30.32 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (simulation): time 2.265e-06/0.008386, allocations: 1.344 kB / 0.6582 GB, free: 30.32 MB / 0.5262 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.403e-05/0.0084, allocations: 11.97 kB / 0.6582 GB, free: 30.32 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.433e-06/0.008402, allocations: 1.375 kB / 0.6582 GB, free: 30.32 MB / 0.5262 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.102e-06/0.008403, allocations: 2.875 kB / 0.6582 GB, free: 30.32 MB / 0.5262 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003372/0.00874, allocations: 0.6329 MB / 0.6589 GB, free: 29.87 MB / 0.5262 GB Notification: Performance of postOpt removeConstants (simulation): time 1.642e-05/0.008757, allocations: 24.95 kB / 0.6589 GB, free: 29.86 MB / 0.5262 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.575e-05/0.008782, allocations: 9.531 kB / 0.6589 GB, free: 29.86 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.656e-05/0.008859, allocations: 12.5 kB / 0.6589 GB, free: 29.85 MB / 0.5262 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 4.452e-05/0.008903, allocations: 26.77 kB / 0.6589 GB, free: 29.85 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.138e-05/0.008915, allocations: 13.62 kB / 0.659 GB, free: 29.84 MB / 0.5262 GB Notification: Performance of sorting global known variables: time 3.633e-05/0.008951, allocations: 152.2 kB / 0.6591 GB, free: 29.72 MB / 0.5262 GB Notification: Performance of sort global known variables: time 5e-08/0.008951, allocations: 0 / 0.6591 GB, free: 29.72 MB / 0.5262 GB Notification: Performance of remove unused functions: time 0.0001982/0.009149, allocations: 71 kB / 0.6592 GB, free: 29.71 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 6.72e-05/0.009217, allocations: 114 kB / 0.6593 GB, free: 29.62 MB / 0.5262 GB Notification: Performance of simCode: created initialization part: time 0.0002265/0.009443, allocations: 477.1 kB / 0.6597 GB, free: 29.23 MB / 0.5262 GB Notification: Performance of simCode: created event and clocks part: time 9.82e-07/0.009444, allocations: 0 / 0.6597 GB, free: 29.23 MB / 0.5262 GB Notification: Performance of simCode: created simulation system equations: time 0.0001065/0.009551, allocations: 268.1 kB / 0.66 GB, free: 29.02 MB / 0.5262 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002551/0.009806, allocations: 66.03 kB / 0.66 GB, free: 29 MB / 0.5262 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001168/0.01097, allocations: 0.7388 MB / 0.6608 GB, free: 28.52 MB / 0.5262 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 3.795e-05/0.01101, allocations: 86.19 kB / 0.6609 GB, free: 28.45 MB / 0.5262 GB Notification: Performance of simCode: alias equations: time 6.139e-05/0.01107, allocations: 29.45 kB / 0.6609 GB, free: 28.44 MB / 0.5262 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001382/0.01121, allocations: 147.6 kB / 0.661 GB, free: 28.37 MB / 0.5262 GB Notification: Performance of SimCode: time 6.32e-07/0.01121, allocations: 0 / 0.661 GB, free: 28.37 MB / 0.5262 GB Notification: Performance of Templates: time 0.005499/0.01671, allocations: 3.768 MB / 0.6647 GB, free: 28.01 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: 4.7258722791448236]