Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.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 0.001015/0.001015, allocations: 92.2 kB / 20.19 MB, free: 4.363 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 0.001059/0.001059, allocations: 177.3 kB / 23.49 MB, free: 1.059 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 0.9938/0.9938, allocations: 177.1 MB / 203.8 MB, free: 5.637 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 1.701/1.701, allocations: 273.5 MB / 0.5213 GB, free: 14.77 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.SingleDoseDiffusion,tolerance=1e-06,outputFormat="empty",numberOfIntervals=500,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion") translateModel(Pharmacolibrary.DevModels.SingleDoseDiffusion,tolerance=1e-06,outputFormat="empty",numberOfIntervals=500,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion") [Timeout 660] "Notification: Performance of FrontEnd - loaded program: time 2.194e-06/2.194e-06, allocations: 3.938 kB / 0.647 GB, free: 38.59 MB / 0.5262 GB Notification: Performance of FrontEnd - Absyn->SCode: time 1.676e-05/1.896e-05, allocations: 5.406 kB / 0.647 GB, free: 38.58 MB / 0.5262 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.SingleDoseDiffusion): time 0.002681/0.0027, allocations: 2.904 MB / 0.6498 GB, free: 36.7 MB / 0.5262 GB Notification: Performance of NFInst.instExpressions: time 0.00109/0.00379, allocations: 0.7277 MB / 0.6505 GB, free: 36.21 MB / 0.5262 GB Notification: Performance of NFInst.updateImplicitVariability: time 0.0001115/0.003901, allocations: 5.156 kB / 0.6505 GB, free: 36.21 MB / 0.5262 GB Notification: Performance of NFTyping.typeComponents: time 7.2e-05/0.003973, allocations: 45.8 kB / 0.6506 GB, free: 36.19 MB / 0.5262 GB Notification: Performance of NFTyping.typeBindings: time 0.0002662/0.00424, allocations: 115.5 kB / 0.6507 GB, free: 36.14 MB / 0.5262 GB Notification: Performance of NFTyping.typeClassSections: time 0.0002515/0.004491, allocations: 93.53 kB / 0.6508 GB, free: 36.09 MB / 0.5262 GB Notification: Performance of NFFlatten.flatten: time 0.0003228/0.004814, allocations: 414.3 kB / 0.6512 GB, free: 35.88 MB / 0.5262 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0003077/0.005122, allocations: 213.2 kB / 0.6514 GB, free: 35.76 MB / 0.5262 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0002336/0.005355, allocations: 243.2 kB / 0.6516 GB, free: 35.66 MB / 0.5262 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001983/0.005553, allocations: 158.4 kB / 0.6518 GB, free: 35.61 MB / 0.5262 GB Notification: Performance of NFPackage.collectConstants: time 4.895e-05/0.005602, allocations: 38.38 kB / 0.6518 GB, free: 35.61 MB / 0.5262 GB Notification: Performance of NFFlatten.collectFunctions: time 4.128e-05/0.005644, allocations: 36.28 kB / 0.6518 GB, free: 35.61 MB / 0.5262 GB Notification: Performance of NFScalarize.scalarize: time 4.504e-05/0.005689, allocations: 72.23 kB / 0.6519 GB, free: 35.56 MB / 0.5262 GB Notification: Performance of NFVerifyModel.verify: time 0.000106/0.005795, allocations: 140.7 kB / 0.652 GB, free: 35.5 MB / 0.5262 GB Notification: Performance of NFConvertDAE.convert: time 0.0002498/0.006045, allocations: 261.5 kB / 0.6523 GB, free: 35.38 MB / 0.5262 GB Notification: Performance of FrontEnd - DAE generated: time 1.844e-06/0.006046, allocations: 0 / 0.6523 GB, free: 35.38 MB / 0.5262 GB Notification: Performance of FrontEnd: time 8.62e-07/0.006047, allocations: 3.344 kB / 0.6523 GB, free: 35.38 MB / 0.5262 GB Notification: Performance of Transformations before backend: time 5.511e-06/0.006053, allocations: 0 / 0.6523 GB, free: 35.38 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: 65 * Number of variables: 65 Notification: Performance of Generate backend data structure: time 0.0006927/0.006745, allocations: 0.6725 MB / 0.6529 GB, free: 34.81 MB / 0.5262 GB Notification: Performance of prepare preOptimizeDAE: time 3.345e-05/0.006779, allocations: 7.719 kB / 0.6529 GB, free: 34.81 MB / 0.5262 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 8.478e-05/0.006864, allocations: 61.88 kB / 0.653 GB, free: 34.79 MB / 0.5262 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002503/0.007114, allocations: 220.9 kB / 0.6532 GB, free: 34.6 MB / 0.5262 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.765e-05/0.007132, allocations: 20.84 kB / 0.6532 GB, free: 34.59 MB / 0.5262 GB Notification: Performance of preOpt expandDerOperator (simulation): time 4.315e-05/0.007175, allocations: 32.48 kB / 0.6533 GB, free: 34.58 MB / 0.5262 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003523/0.007527, allocations: 358 kB / 0.6536 GB, free: 34.36 MB / 0.5262 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.565e-05/0.007543, allocations: 8.719 kB / 0.6536 GB, free: 34.36 MB / 0.5262 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.311e-05/0.007566, allocations: 12.38 kB / 0.6536 GB, free: 34.35 MB / 0.5262 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.067e-06/0.007575, allocations: 7.375 kB / 0.6536 GB, free: 34.35 MB / 0.5262 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002062/0.007781, allocations: 161.6 kB / 0.6538 GB, free: 34.3 MB / 0.5262 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0009115/0.008693, allocations: 0.8327 MB / 0.6546 GB, free: 33.7 MB / 0.5262 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0003021/0.008995, allocations: 169.9 kB / 0.6548 GB, free: 33.61 MB / 0.5262 GB Notification: Performance of preOpt resolveLoops (simulation): time 9.74e-05/0.009092, allocations: 92.42 kB / 0.6548 GB, free: 33.56 MB / 0.5262 GB Notification: Performance of preOpt evalFunc (simulation): time 2.048e-05/0.009113, allocations: 5.469 kB / 0.6549 GB, free: 33.56 MB / 0.5262 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002187/0.009331, allocations: 238.3 kB / 0.6551 GB, free: 33.39 MB / 0.5262 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.000122/0.009453, allocations: 38.55 kB / 0.6551 GB, free: 33.37 MB / 0.5262 GB Notification: Performance of pre-optimization done (n=30): time 1.563e-06/0.009455, allocations: 4.094 kB / 0.6551 GB, free: 33.37 MB / 0.5262 GB Notification: Performance of matching and sorting (n=31): time 0.0009681/0.01042, allocations: 0.7309 MB / 0.6558 GB, free: 32.91 MB / 0.5262 GB Notification: Performance of inlineWhenForInitialization (initialization): time 5.079e-05/0.01047, allocations: 141.5 kB / 0.656 GB, free: 32.75 MB / 0.5262 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001347/0.01061, allocations: 235.7 kB / 0.6562 GB, free: 32.55 MB / 0.5262 GB Notification: Performance of collectPreVariables (initialization): time 1.955e-05/0.01063, allocations: 40.11 kB / 0.6562 GB, free: 32.52 MB / 0.5262 GB Notification: Performance of collectInitialEqns (initialization): time 6.889e-05/0.0107, allocations: 210.5 kB / 0.6564 GB, free: 32.32 MB / 0.5262 GB Notification: Performance of collectInitialBindings (initialization): time 6.101e-05/0.01076, allocations: 111.2 kB / 0.6565 GB, free: 32.23 MB / 0.5262 GB Notification: Performance of simplifyInitialFunctions (initialization): time 9.982e-05/0.01086, allocations: 73.7 kB / 0.6566 GB, free: 32.19 MB / 0.5262 GB Notification: Performance of setup shared object (initialization): time 6.347e-05/0.01092, allocations: 0.5083 MB / 0.6571 GB, free: 31.68 MB / 0.5262 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001413/0.01106, allocations: 130 kB / 0.6572 GB, free: 31.59 MB / 0.5262 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.000179/0.01124, allocations: 265.2 kB / 0.6575 GB, free: 31.33 MB / 0.5262 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0004237/0.01167, allocations: 457.1 kB / 0.6579 GB, free: 30.95 MB / 0.5262 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.665e-06/0.01167, allocations: 2.625 kB / 0.6579 GB, free: 30.95 MB / 0.5262 GB Notification: Performance of matching and sorting (n=49) (initialization): time 0.000451/0.01212, allocations: 420 kB / 0.6583 GB, free: 30.71 MB / 0.5262 GB Notification: Performance of prepare postOptimizeDAE: time 2.923e-05/0.01215, allocations: 63.97 kB / 0.6584 GB, free: 30.64 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.692e-06/0.01215, allocations: 6 kB / 0.6584 GB, free: 30.64 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.358e-05/0.01217, allocations: 8.219 kB / 0.6584 GB, free: 30.64 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002045/0.01237, allocations: 91.72 kB / 0.6585 GB, free: 30.63 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 7.785e-06/0.01238, allocations: 4.25 kB / 0.6585 GB, free: 30.63 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001044/0.01249, allocations: 20.12 kB / 0.6585 GB, free: 30.62 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.995e-05/0.01251, allocations: 20.25 kB / 0.6585 GB, free: 30.62 MB / 0.5262 GB Warning: Assuming fixed start value for the following 8 variables: singleDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true ) \"Total dose adminitrated by this source\" type: Real singleDose.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 tissueCompartment.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real RBC.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real RBC.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real RBC.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real RBC.rising:DISCRETE(fixed = true protected = true ) type: Boolean Notification: Model statistics after passing the back-end for initialization: * Number of independent subsystems: 12 * Number of states: 0 () * Number of discrete variables: 13 ($PRE.RBC.Cmin,RBC.Cmin,$PRE.RBC.Cmax,RBC.Cmax,$PRE.RBC.rising,$PRE.singleDose.pulse.count,$PRE.singleDose.pulse.T_start,RBC.rising,singleDose.pulse.count,singleDose.pulse.T_start,$whenCondition2,$whenCondition1,$whenCondition3) * Number of discrete states: 0 () * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for initialization (47): * Single equations (assignments): 45 * Array equations: 0 * Algorithm blocks: 2 * 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 0.0001548/0.01266, allocations: 240.6 kB / 0.6588 GB, free: 30.4 MB / 0.5262 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 3.703e-05/0.0127, allocations: 37 kB / 0.6588 GB, free: 30.38 MB / 0.5262 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.000333/0.01303, allocations: 307.2 kB / 0.6591 GB, free: 30.23 MB / 0.5262 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.838e-06/0.01303, allocations: 2.875 kB / 0.6591 GB, free: 30.23 MB / 0.5262 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 3.446e-06/0.01304, allocations: 1.375 kB / 0.6591 GB, free: 30.23 MB / 0.5262 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.368e-06/0.01304, allocations: 0 / 0.6591 GB, free: 30.23 MB / 0.5262 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.000502/0.01354, allocations: 0.6381 MB / 0.6597 GB, free: 29.77 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.444e-06/0.01355, allocations: 3.906 kB / 0.6597 GB, free: 29.77 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001697/0.01372, allocations: 49.11 kB / 0.6598 GB, free: 29.77 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (simulation): time 3.166e-06/0.01372, allocations: 2.812 kB / 0.6598 GB, free: 29.77 MB / 0.5262 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.746e-05/0.01374, allocations: 6.781 kB / 0.6598 GB, free: 29.77 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.673e-06/0.01374, allocations: 1.469 kB / 0.6598 GB, free: 29.77 MB / 0.5262 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.803e-06/0.01374, allocations: 2.562 kB / 0.6598 GB, free: 29.77 MB / 0.5262 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004282/0.01417, allocations: 0.5427 MB / 0.6603 GB, free: 29.4 MB / 0.5262 GB Notification: Performance of postOpt removeConstants (simulation): time 2.03e-05/0.01419, allocations: 16.95 kB / 0.6603 GB, free: 29.39 MB / 0.5262 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.312e-05/0.01422, allocations: 18.53 kB / 0.6603 GB, free: 29.38 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 9.613e-05/0.01432, allocations: 8.984 kB / 0.6603 GB, free: 29.38 MB / 0.5262 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 6.319e-05/0.01438, allocations: 24.12 kB / 0.6604 GB, free: 29.38 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.691e-05/0.0144, allocations: 14.56 kB / 0.6604 GB, free: 29.37 MB / 0.5262 GB Notification: Performance of sorting global known variables: time 7.979e-05/0.01448, allocations: 178 kB / 0.6606 GB, free: 29.24 MB / 0.5262 GB Notification: Performance of sort global known variables: time 8e-08/0.01448, allocations: 1.094 kB / 0.6606 GB, free: 29.24 MB / 0.5262 GB Notification: Performance of remove unused functions: time 0.0002522/0.01473, allocations: 79.41 kB / 0.6606 GB, free: 29.23 MB / 0.5262 GB Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 1 * Number of states: 8 (singleDose.TotalCumulativeMass,singleDose.variableDose.TotalCumulativeMass,artery.M,artery.AUC,tissueCompartment.M,tissueCompartment.AUC,RBC.C,RBC.AUC) * Number of discrete variables: 8 ($whenCondition3,$whenCondition1,$whenCondition2,singleDose.pulse.T_start,singleDose.pulse.count,RBC.Cmax,RBC.Cmin,RBC.rising) * Number of discrete states: 6 (singleDose.pulse.count,RBC.Cmin,$whenCondition2,RBC.Cmax,$whenCondition1,RBC.rising) * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for simulation (28): * Single equations (assignments): 25 * Array equations: 0 * Algorithm blocks: 1 * 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 9.912e-05/0.01483, allocations: 109.3 kB / 0.6607 GB, free: 29.14 MB / 0.5262 GB Notification: Performance of simCode: created initialization part: time 0.0003468/0.01518, allocations: 397.5 kB / 0.6611 GB, free: 28.87 MB / 0.5262 GB Notification: Performance of simCode: created event and clocks part: time 2.014e-06/0.01518, allocations: 1.344 kB / 0.6611 GB, free: 28.87 MB / 0.5262 GB Notification: Performance of simCode: created simulation system equations: time 0.000137/0.01531, allocations: 178.7 kB / 0.6613 GB, free: 28.75 MB / 0.5262 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003236/0.01564, allocations: 86.36 kB / 0.6614 GB, free: 28.72 MB / 0.5262 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001552/0.01719, allocations: 0.8496 MB / 0.6622 GB, free: 28.16 MB / 0.5262 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 4.753e-05/0.01724, allocations: 98.48 kB / 0.6623 GB, free: 28.08 MB / 0.5262 GB Notification: Performance of simCode: alias equations: time 9.586e-05/0.01733, allocations: 33.12 kB / 0.6623 GB, free: 28.07 MB / 0.5262 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 6.755e-05/0.0174, allocations: 30.42 kB / 0.6624 GB, free: 28.06 MB / 0.5262 GB Notification: Performance of SimCode: time 8.41e-07/0.0174, allocations: 0 / 0.6624 GB, free: 28.06 MB / 0.5262 GB Notification: Performance of Templates: time 0.005805/0.02321, allocations: 4.035 MB / 0.6663 GB, free: 27.71 MB / 0.5262 GB " [Timeout remaining time 660] make -j1 -f Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.makefile [Timeout 660] (rm -f Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.sim & ./Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion -abortSlowSimulation -alarm=240 -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseDiffusion.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 5.85245394310914]