Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver.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 0.001295/0.001295, allocations: 92.2 kB / 20.19 MB, free: 4.359 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 0.001587/0.001587, allocations: 173 kB / 23.49 MB, free: 1.055 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 0.9671/0.9671, allocations: 177.1 MB / 203.8 MB, free: 5.645 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 1.685/1.685, allocations: 273.5 MB / 0.5213 GB, free: 14.88 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.SingleDoseVeinsGutSpleenPortalVeinLiver,tolerance=1e-06,outputFormat="empty",numberOfIntervals=495,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver") translateModel(Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver,tolerance=1e-06,outputFormat="empty",numberOfIntervals=495,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver") [Timeout 660] "Notification: Performance of FrontEnd - loaded program: time 2.234e-06/2.234e-06, allocations: 0 / 0.647 GB, free: 38.7 MB / 0.5262 GB Notification: Performance of FrontEnd - Absyn->SCode: time 2.944e-05/3.167e-05, allocations: 5.266 kB / 0.647 GB, free: 38.69 MB / 0.5262 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver): time 0.005306/0.005338, allocations: 4.09 MB / 0.651 GB, free: 36.04 MB / 0.5262 GB Notification: Performance of NFInst.instExpressions: time 0.002126/0.007464, allocations: 0.968 MB / 0.6519 GB, free: 35.39 MB / 0.5262 GB Notification: Performance of NFInst.updateImplicitVariability: time 0.0002695/0.007733, allocations: 3.75 kB / 0.6519 GB, free: 35.39 MB / 0.5262 GB Notification: Performance of NFTyping.typeComponents: time 0.0002257/0.007959, allocations: 80.31 kB / 0.652 GB, free: 35.35 MB / 0.5262 GB Notification: Performance of NFTyping.typeBindings: time 0.0006078/0.008566, allocations: 210.8 kB / 0.6522 GB, free: 35.22 MB / 0.5262 GB Notification: Performance of NFTyping.typeClassSections: time 0.0004337/0.009, allocations: 158.5 kB / 0.6523 GB, free: 35.13 MB / 0.5262 GB Notification: Performance of NFFlatten.flatten: time 0.0008138/0.009814, allocations: 0.713 MB / 0.653 GB, free: 34.75 MB / 0.5262 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0007365/0.01055, allocations: 500 kB / 0.6535 GB, free: 34.46 MB / 0.5262 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0008201/0.01137, allocations: 0.4915 MB / 0.654 GB, free: 34.25 MB / 0.5262 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0007618/0.01213, allocations: 353.7 kB / 0.6543 GB, free: 34.16 MB / 0.5262 GB Notification: Performance of NFPackage.collectConstants: time 0.0001994/0.01233, allocations: 76.09 kB / 0.6544 GB, free: 34.16 MB / 0.5262 GB Notification: Performance of NFFlatten.collectFunctions: time 0.0001876/0.01252, allocations: 76.38 kB / 0.6545 GB, free: 34.16 MB / 0.5262 GB Notification: Performance of NFScalarize.scalarize: time 0.0001975/0.01272, allocations: 183.1 kB / 0.6547 GB, free: 34.04 MB / 0.5262 GB Notification: Performance of NFVerifyModel.verify: time 0.000417/0.01313, allocations: 268.7 kB / 0.6549 GB, free: 33.93 MB / 0.5262 GB Notification: Performance of NFConvertDAE.convert: time 0.0007345/0.01387, allocations: 0.5391 MB / 0.6554 GB, free: 33.66 MB / 0.5262 GB Notification: Performance of FrontEnd - DAE generated: time 5.15e-06/0.01387, allocations: 1.281 kB / 0.6554 GB, free: 33.66 MB / 0.5262 GB Notification: Performance of FrontEnd: time 1.733e-06/0.01388, allocations: 0 / 0.6554 GB, free: 33.66 MB / 0.5262 GB Notification: Performance of Transformations before backend: time 1.737e-05/0.01389, allocations: 0 / 0.6554 GB, free: 33.66 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: 124 * Number of variables: 124 Notification: Performance of Generate backend data structure: time 0.001933/0.01583, allocations: 0.8725 MB / 0.6563 GB, free: 33.02 MB / 0.5262 GB Notification: Performance of prepare preOptimizeDAE: time 5.769e-05/0.01588, allocations: 10.78 kB / 0.6563 GB, free: 33.02 MB / 0.5262 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0003121/0.0162, allocations: 97.97 kB / 0.6564 GB, free: 32.97 MB / 0.5262 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0006447/0.01684, allocations: 316.2 kB / 0.6567 GB, free: 32.73 MB / 0.5262 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 5.756e-05/0.0169, allocations: 40.2 kB / 0.6567 GB, free: 32.71 MB / 0.5262 GB Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001414/0.01704, allocations: 54.39 kB / 0.6568 GB, free: 32.7 MB / 0.5262 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.001124/0.01816, allocations: 0.6229 MB / 0.6574 GB, free: 32.41 MB / 0.5262 GB Notification: Performance of preOpt findStateOrder (simulation): time 3.222e-05/0.0182, allocations: 9.266 kB / 0.6574 GB, free: 32.4 MB / 0.5262 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 6.314e-05/0.01826, allocations: 20.22 kB / 0.6574 GB, free: 32.38 MB / 0.5262 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 4.871e-05/0.01831, allocations: 19.34 kB / 0.6574 GB, free: 32.38 MB / 0.5262 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0007838/0.01909, allocations: 320.9 kB / 0.6577 GB, free: 32.34 MB / 0.5262 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.002835/0.02193, allocations: 1.374 MB / 0.6591 GB, free: 31.49 MB / 0.5262 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0006558/0.02258, allocations: 243.7 kB / 0.6593 GB, free: 31.42 MB / 0.5262 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.0002936/0.02288, allocations: 120.8 kB / 0.6594 GB, free: 31.39 MB / 0.5262 GB Notification: Performance of preOpt evalFunc (simulation): time 3.915e-05/0.02292, allocations: 8.781 kB / 0.6594 GB, free: 31.39 MB / 0.5262 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0004802/0.0234, allocations: 257.7 kB / 0.6597 GB, free: 31.27 MB / 0.5262 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.0007496/0.02415, allocations: 159.9 kB / 0.6598 GB, free: 31.24 MB / 0.5262 GB Notification: Performance of pre-optimization done (n=46): time 5.79e-06/0.02415, allocations: 0 / 0.6598 GB, free: 31.24 MB / 0.5262 GB Notification: Performance of matching and sorting (n=46): time 0.001158/0.02531, allocations: 442.9 kB / 0.6603 GB, free: 31.12 MB / 0.5262 GB Notification: Performance of inlineWhenForInitialization (initialization): time 3.99e-05/0.02535, allocations: 57.06 kB / 0.6603 GB, free: 31.05 MB / 0.5262 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002575/0.02561, allocations: 298.1 kB / 0.6606 GB, free: 30.85 MB / 0.5262 GB Notification: Performance of collectPreVariables (initialization): time 4.795e-05/0.02565, allocations: 36.52 kB / 0.6606 GB, free: 30.81 MB / 0.5262 GB Notification: Performance of collectInitialEqns (initialization): time 0.0001339/0.02579, allocations: 292.6 kB / 0.6609 GB, free: 30.56 MB / 0.5262 GB Notification: Performance of collectInitialBindings (initialization): time 0.000136/0.02592, allocations: 175.1 kB / 0.6611 GB, free: 30.42 MB / 0.5262 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.0002134/0.02614, allocations: 128 kB / 0.6612 GB, free: 30.36 MB / 0.5262 GB Notification: Performance of setup shared object (initialization): time 9.272e-05/0.02623, allocations: 0.5103 MB / 0.6617 GB, free: 29.86 MB / 0.5262 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003727/0.0266, allocations: 180.1 kB / 0.6619 GB, free: 29.79 MB / 0.5262 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0004074/0.02701, allocations: 357.4 kB / 0.6622 GB, free: 29.49 MB / 0.5262 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0007198/0.02773, allocations: 466.1 kB / 0.6627 GB, free: 29.18 MB / 0.5262 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.621e-06/0.02774, allocations: 0 / 0.6627 GB, free: 29.18 MB / 0.5262 GB Notification: Performance of matching and sorting (n=72) (initialization): time 0.001085/0.02882, allocations: 0.576 MB / 0.6632 GB, free: 28.95 MB / 0.5262 GB Notification: Performance of prepare postOptimizeDAE: time 3.923e-05/0.02886, allocations: 36.77 kB / 0.6633 GB, free: 28.91 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.228e-05/0.02887, allocations: 5.156 kB / 0.6633 GB, free: 28.91 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (initialization): time 2.698e-05/0.0289, allocations: 7 kB / 0.6633 GB, free: 28.91 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0006743/0.02957, allocations: 172.2 kB / 0.6634 GB, free: 28.9 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.541e-05/0.02959, allocations: 9.297 kB / 0.6634 GB, free: 28.9 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0003739/0.02996, allocations: 20.3 kB / 0.6635 GB, free: 28.89 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 6.256e-05/0.03003, allocations: 31.56 kB / 0.6635 GB, free: 28.89 MB / 0.5262 GB Warning: Assuming fixed start value for the following 8 variables: singleDose1.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true ) \"Total dose adminitrated by this source\" type: Real singleDose1.variableDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true ) \"Total dose adminitrated by this source\" type: Real artery.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real gut.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real vein.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real spleen.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real liver.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real lungs.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real Notification: Model statistics after passing the back-end for initialization: * Number of independent subsystems: 16 * Number of states: 0 () * Number of discrete variables: 5 (singleDose1.pulse.count,$PRE.singleDose1.pulse.count,singleDose1.pulse.T_start,$PRE.singleDose1.pulse.T_start,$whenCondition1) * Number of discrete states: 0 () * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for initialization (71): * Single equations (assignments): 70 * Array equations: 0 * Algorithm blocks: 1 * 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 0.0002894/0.03032, allocations: 226.3 kB / 0.6637 GB, free: 28.7 MB / 0.5262 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 0.0001115/0.03043, allocations: 57.06 kB / 0.6638 GB, free: 28.66 MB / 0.5262 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0008758/0.0313, allocations: 404.8 kB / 0.6641 GB, free: 28.52 MB / 0.5262 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 7.524e-06/0.03131, allocations: 4.219 kB / 0.6642 GB, free: 28.52 MB / 0.5262 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 6.492e-06/0.03132, allocations: 1.375 kB / 0.6642 GB, free: 28.52 MB / 0.5262 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 8.686e-06/0.03133, allocations: 6.844 kB / 0.6642 GB, free: 28.52 MB / 0.5262 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001101/0.03243, allocations: 0.7295 MB / 0.6649 GB, free: 28.07 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.857e-06/0.03243, allocations: 0 / 0.6649 GB, free: 28.07 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.000473/0.0329, allocations: 79.91 kB / 0.6649 GB, free: 28.07 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (simulation): time 7.114e-06/0.03291, allocations: 1.406 kB / 0.6649 GB, free: 28.07 MB / 0.5262 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 4.621e-05/0.03296, allocations: 16.91 kB / 0.665 GB, free: 28.06 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 5.31e-06/0.03296, allocations: 4.844 kB / 0.665 GB, free: 28.06 MB / 0.5262 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.124e-06/0.03296, allocations: 1.344 kB / 0.665 GB, free: 28.06 MB / 0.5262 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.001005/0.03397, allocations: 0.5957 MB / 0.6656 GB, free: 27.74 MB / 0.5262 GB Notification: Performance of postOpt removeConstants (simulation): time 6.385e-05/0.03403, allocations: 31.61 kB / 0.6656 GB, free: 27.72 MB / 0.5262 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 7.829e-05/0.03411, allocations: 16.28 kB / 0.6656 GB, free: 27.71 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.000286/0.0344, allocations: 14.48 kB / 0.6656 GB, free: 27.71 MB / 0.5262 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 9.38e-05/0.03449, allocations: 36.08 kB / 0.6656 GB, free: 27.7 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 4.001e-05/0.03453, allocations: 13.3 kB / 0.6657 GB, free: 27.7 MB / 0.5262 GB Notification: Performance of sorting global known variables: time 0.0001838/0.03472, allocations: 226.9 kB / 0.6659 GB, free: 27.56 MB / 0.5262 GB Notification: Performance of sort global known variables: time 1e-07/0.03472, allocations: 0 / 0.6659 GB, free: 27.56 MB / 0.5262 GB Notification: Performance of remove unused functions: time 0.0006877/0.0354, allocations: 171 kB / 0.666 GB, free: 27.52 MB / 0.5262 GB Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 2 * Number of states: 14 (singleDose1.TotalCumulativeMass,singleDose1.variableDose.TotalCumulativeMass,artery.M,artery.AUC,gut.M,gut.AUC,vein.M,vein.AUC,spleen.M,spleen.AUC,liver.M,liver.AUC,lungs.M,lungs.AUC) * Number of discrete variables: 3 ($whenCondition1,singleDose1.pulse.T_start,singleDose1.pulse.count) * Number of discrete states: 1 (singleDose1.pulse.count) * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for simulation (46): * Single equations (assignments): 44 * Array equations: 0 * Algorithm blocks: 0 * 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 0.0001497/0.03555, allocations: 110.9 kB / 0.6661 GB, free: 27.42 MB / 0.5262 GB Notification: Performance of simCode: created initialization part: time 0.0008147/0.03637, allocations: 428 kB / 0.6666 GB, free: 27.26 MB / 0.5262 GB Notification: Performance of simCode: created event and clocks part: time 3.066e-06/0.03637, allocations: 1.75 kB / 0.6666 GB, free: 27.26 MB / 0.5262 GB Notification: Performance of simCode: created simulation system equations: time 0.0003057/0.03668, allocations: 156.7 kB / 0.6667 GB, free: 27.21 MB / 0.5262 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0007765/0.03745, allocations: 140.5 kB / 0.6668 GB, free: 27.16 MB / 0.5262 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.003293/0.04075, allocations: 1.328 MB / 0.6681 GB, free: 26.33 MB / 0.5262 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001049/0.04085, allocations: 119 kB / 0.6682 GB, free: 26.26 MB / 0.5262 GB Notification: Performance of simCode: alias equations: time 0.000378/0.04123, allocations: 71.75 kB / 0.6683 GB, free: 26.25 MB / 0.5262 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0002439/0.04147, allocations: 60.95 kB / 0.6684 GB, free: 26.24 MB / 0.5262 GB Notification: Performance of SimCode: time 1.573e-06/0.04147, allocations: 1.656 kB / 0.6684 GB, free: 26.24 MB / 0.5262 GB Notification: Performance of Templates: time 0.01591/0.05739, allocations: 7.908 MB / 0.6761 GB, free: 24.43 MB / 0.5262 GB " [Timeout remaining time 660] make -j1 -f Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver.makefile [Timeout 660] (rm -f Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver.sim & ./Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver -abortSlowSimulation -alarm=240 -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 6.309331763070077]