Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral.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 0.001058/0.001058, 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 0.0009987/0.0009987, allocations: 173 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 0.9455/0.9455, allocations: 177.1 MB / 203.8 MB, free: 5.621 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 1.613/1.613, 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.PKTwoCompartmentModelOral,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral") translateModel(Pharmacolibrary.DevModels.PKTwoCompartmentModelOral,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral") [Timeout 660] "Notification: Performance of FrontEnd - loaded program: time 1.723e-06/1.723e-06, allocations: 0 / 0.6462 GB, free: 39.04 MB / 0.5262 GB Notification: Performance of FrontEnd - Absyn->SCode: time 2.511e-05/2.683e-05, allocations: 5.141 kB / 0.6462 GB, free: 39.03 MB / 0.5262 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.PKTwoCompartmentModelOral): time 0.003553/0.003579, allocations: 2.385 MB / 0.6485 GB, free: 37.48 MB / 0.5262 GB Notification: Performance of NFInst.instExpressions: time 0.00123/0.00481, allocations: 0.6107 MB / 0.6491 GB, free: 37.08 MB / 0.5262 GB Notification: Performance of NFInst.updateImplicitVariability: time 0.0001362/0.004946, allocations: 2.094 kB / 0.6491 GB, free: 37.08 MB / 0.5262 GB Notification: Performance of NFTyping.typeComponents: time 8.279e-05/0.005029, allocations: 25.28 kB / 0.6491 GB, free: 37.06 MB / 0.5262 GB Notification: Performance of NFTyping.typeBindings: time 0.0002954/0.005324, allocations: 88.97 kB / 0.6492 GB, free: 37.02 MB / 0.5262 GB Notification: Performance of NFTyping.typeClassSections: time 0.000248/0.005572, allocations: 68.22 kB / 0.6493 GB, free: 36.98 MB / 0.5262 GB Notification: Performance of NFFlatten.flatten: time 0.0003453/0.005917, allocations: 294.4 kB / 0.6496 GB, free: 36.86 MB / 0.5262 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001669/0.006084, allocations: 53.08 kB / 0.6496 GB, free: 36.83 MB / 0.5262 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0002735/0.006358, allocations: 156.1 kB / 0.6498 GB, free: 36.77 MB / 0.5262 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001721/0.00653, allocations: 84.44 kB / 0.6499 GB, free: 36.74 MB / 0.5262 GB Notification: Performance of NFPackage.collectConstants: time 5.121e-05/0.006581, allocations: 23.91 kB / 0.6499 GB, free: 36.74 MB / 0.5262 GB Notification: Performance of NFFlatten.collectFunctions: time 4.463e-05/0.006626, allocations: 20.41 kB / 0.6499 GB, free: 36.74 MB / 0.5262 GB Notification: Performance of NFScalarize.scalarize: time 5.056e-05/0.006676, allocations: 48.58 kB / 0.6499 GB, free: 36.71 MB / 0.5262 GB Notification: Performance of NFVerifyModel.verify: time 0.0001318/0.006808, allocations: 95.77 kB / 0.65 GB, free: 36.67 MB / 0.5262 GB Notification: Performance of NFConvertDAE.convert: time 0.0002778/0.007086, allocations: 175.4 kB / 0.6502 GB, free: 36.59 MB / 0.5262 GB Notification: Performance of FrontEnd - DAE generated: time 2.625e-06/0.007088, allocations: 3.938 kB / 0.6502 GB, free: 36.58 MB / 0.5262 GB Notification: Performance of FrontEnd: time 8.91e-07/0.007089, allocations: 1.656 kB / 0.6502 GB, free: 36.58 MB / 0.5262 GB Notification: Performance of Transformations before backend: time 7.615e-06/0.007097, allocations: 1.469 kB / 0.6502 GB, free: 36.58 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 0.0007549/0.007852, allocations: 0.6162 MB / 0.6508 GB, free: 36.02 MB / 0.5262 GB Notification: Performance of prepare preOptimizeDAE: time 4.011e-05/0.007892, allocations: 10.94 kB / 0.6508 GB, free: 36.02 MB / 0.5262 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 9.245e-05/0.007984, allocations: 38.77 kB / 0.6509 GB, free: 36.01 MB / 0.5262 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001364/0.008121, allocations: 149.7 kB / 0.651 GB, free: 35.85 MB / 0.5262 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.308e-05/0.008144, allocations: 17.59 kB / 0.651 GB, free: 35.84 MB / 0.5262 GB Notification: Performance of preOpt expandDerOperator (simulation): time 4.883e-05/0.008193, allocations: 25.08 kB / 0.651 GB, free: 35.84 MB / 0.5262 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003508/0.008544, allocations: 217.6 kB / 0.6513 GB, free: 35.7 MB / 0.5262 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.828e-05/0.008562, allocations: 3.188 kB / 0.6513 GB, free: 35.7 MB / 0.5262 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.326e-05/0.008585, allocations: 10.03 kB / 0.6513 GB, free: 35.69 MB / 0.5262 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.709e-06/0.008595, allocations: 4.75 kB / 0.6513 GB, free: 35.69 MB / 0.5262 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002047/0.0088, allocations: 148 kB / 0.6514 GB, free: 35.61 MB / 0.5262 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.000751/0.009551, allocations: 0.4997 MB / 0.6519 GB, free: 35.24 MB / 0.5262 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0002435/0.009794, allocations: 167.7 kB / 0.6521 GB, free: 35.12 MB / 0.5262 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.0001131/0.009907, allocations: 104.5 kB / 0.6522 GB, free: 35.04 MB / 0.5262 GB Notification: Performance of preOpt evalFunc (simulation): time 1.503e-05/0.009922, allocations: 7.156 kB / 0.6522 GB, free: 35.04 MB / 0.5262 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002891/0.01021, allocations: 310.7 kB / 0.6525 GB, free: 34.78 MB / 0.5262 GB Notification: Performance of pre-optimization done (n=30): time 2.194e-06/0.01021, allocations: 2.25 kB / 0.6525 GB, free: 34.78 MB / 0.5262 GB Notification: Performance of matching and sorting (n=32): time 0.001337/0.01155, allocations: 0.9068 MB / 0.6533 GB, free: 34.13 MB / 0.5262 GB Notification: Performance of inlineWhenForInitialization (initialization): time 5.694e-05/0.01161, allocations: 221.1 kB / 0.6536 GB, free: 33.88 MB / 0.5262 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001375/0.01175, allocations: 216.5 kB / 0.6538 GB, free: 33.7 MB / 0.5262 GB Notification: Performance of collectPreVariables (initialization): time 2.531e-05/0.01177, allocations: 33.42 kB / 0.6538 GB, free: 33.66 MB / 0.5262 GB Notification: Performance of collectInitialEqns (initialization): time 6.118e-05/0.01183, allocations: 170.1 kB / 0.654 GB, free: 33.51 MB / 0.5262 GB Notification: Performance of collectInitialBindings (initialization): time 8.107e-05/0.01191, allocations: 110.4 kB / 0.6541 GB, free: 33.42 MB / 0.5262 GB Notification: Performance of simplifyInitialFunctions (initialization): time 9.853e-05/0.01201, allocations: 69 kB / 0.6541 GB, free: 33.38 MB / 0.5262 GB Notification: Performance of setup shared object (initialization): time 6.26e-05/0.01207, allocations: 0.509 MB / 0.6546 GB, free: 32.87 MB / 0.5262 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001663/0.01224, allocations: 149.3 kB / 0.6548 GB, free: 32.75 MB / 0.5262 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001887/0.01243, allocations: 265.5 kB / 0.655 GB, free: 32.48 MB / 0.5262 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0004165/0.01285, allocations: 469.2 kB / 0.6555 GB, free: 32.06 MB / 0.5262 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.306e-06/0.01285, allocations: 1.281 kB / 0.6555 GB, free: 32.06 MB / 0.5262 GB Notification: Performance of matching and sorting (n=47) (initialization): time 0.0005012/0.01335, allocations: 442.6 kB / 0.6559 GB, free: 31.77 MB / 0.5262 GB Notification: Performance of prepare postOptimizeDAE: time 4.105e-05/0.01339, allocations: 93.62 kB / 0.656 GB, free: 31.67 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.544e-06/0.0134, allocations: 3.156 kB / 0.656 GB, free: 31.67 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.798e-05/0.01342, allocations: 6.938 kB / 0.656 GB, free: 31.67 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002858/0.0137, allocations: 73.59 kB / 0.6561 GB, free: 31.66 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.163e-05/0.01371, allocations: 8.594 kB / 0.6561 GB, free: 31.66 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001619/0.01388, allocations: 17.78 kB / 0.6561 GB, free: 31.66 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.724e-05/0.0139, allocations: 14.47 kB / 0.6561 GB, free: 31.65 MB / 0.5262 GB Warning: Assuming fixed start value for the following 10 variables: central.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real peripheral.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real periodicDose1.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true ) \"Total dose adminitrated by this source\" type: Real periodicDose1.variableDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true ) \"Total dose adminitrated by this source\" 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 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 peripheral.rising:DISCRETE(fixed = true protected = true ) type: Boolean central.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 ($PRE.central.Cmin,central.Cmin,$PRE.central.Cmax,central.Cmax,$PRE.peripheral.Cmin,peripheral.Cmin,$PRE.peripheral.Cmax,peripheral.Cmax,$PRE.periodicDose1.pulse.count,$PRE.periodicDose1.pulse.T_start,$PRE.peripheral.rising,$PRE.central.rising,periodicDose1.pulse.count,periodicDose1.pulse.T_start,peripheral.rising,central.rising,$whenCondition5,$whenCondition4,$whenCondition3,$whenCondition2,$whenCondition1) * Number of discrete states: 0 () * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for initialization (44): * Single equations (assignments): 41 * 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 0.0002077/0.01411, allocations: 292.3 kB / 0.6564 GB, free: 31.39 MB / 0.5262 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 5.25e-05/0.01416, allocations: 30.84 kB / 0.6564 GB, free: 31.38 MB / 0.5262 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 4.127e-05/0.0142, allocations: 27.12 kB / 0.6564 GB, free: 31.36 MB / 0.5262 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.779e-06/0.01421, allocations: 5.312 kB / 0.6564 GB, free: 31.36 MB / 0.5262 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 5.981e-06/0.01422, allocations: 0 / 0.6564 GB, free: 31.36 MB / 0.5262 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.759e-06/0.01422, allocations: 0 / 0.6564 GB, free: 31.36 MB / 0.5262 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0008709/0.01509, allocations: 0.7167 MB / 0.6571 GB, free: 30.83 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.504e-06/0.01509, allocations: 0 / 0.6571 GB, free: 30.83 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002366/0.01533, allocations: 56.23 kB / 0.6572 GB, free: 30.82 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (simulation): time 6.031e-06/0.01534, allocations: 1.531 kB / 0.6572 GB, free: 30.82 MB / 0.5262 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.812e-05/0.01536, allocations: 12.03 kB / 0.6572 GB, free: 30.82 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.008e-06/0.01537, allocations: 5.078 kB / 0.6572 GB, free: 30.82 MB / 0.5262 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.333e-06/0.01537, allocations: 0 / 0.6572 GB, free: 30.82 MB / 0.5262 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0007881/0.01616, allocations: 0.6465 MB / 0.6578 GB, free: 30.36 MB / 0.5262 GB Notification: Performance of postOpt removeConstants (simulation): time 3.376e-05/0.01619, allocations: 13.41 kB / 0.6579 GB, free: 30.36 MB / 0.5262 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 5.676e-05/0.01625, allocations: 13.97 kB / 0.6579 GB, free: 30.35 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001625/0.01641, allocations: 10.78 kB / 0.6579 GB, free: 30.35 MB / 0.5262 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001031/0.01651, allocations: 31.5 kB / 0.6579 GB, free: 30.34 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.418e-05/0.01655, allocations: 12.39 kB / 0.6579 GB, free: 30.34 MB / 0.5262 GB Notification: Performance of sorting global known variables: time 0.0001141/0.01666, allocations: 162 kB / 0.6581 GB, free: 30.21 MB / 0.5262 GB Notification: Performance of sort global known variables: time 1e-07/0.01666, allocations: 0.5625 kB / 0.6581 GB, free: 30.21 MB / 0.5262 GB Notification: Performance of remove unused functions: time 0.0004738/0.01714, allocations: 70 kB / 0.6581 GB, free: 30.2 MB / 0.5262 GB Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 1 * Number of states: 6 (central.C,central.AUC,peripheral.C,peripheral.AUC,periodicDose1.TotalCumulativeMass,periodicDose1.variableDose.TotalCumulativeMass) * Number of discrete variables: 13 ($whenCondition1,$whenCondition2,$whenCondition3,$whenCondition4,$whenCondition5,central.Cmax,central.Cmin,central.rising,peripheral.Cmax,peripheral.Cmin,peripheral.rising,periodicDose1.pulse.T_start,periodicDose1.pulse.count) * Number of discrete states: 11 (periodicDose1.pulse.count,peripheral.Cmin,$whenCondition3,peripheral.Cmax,$whenCondition2,peripheral.rising,central.Cmin,$whenCondition5,central.Cmax,$whenCondition4,central.rising) * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for simulation (26): * Single equations (assignments): 22 * 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 0.0001448/0.01728, allocations: 124.9 kB / 0.6583 GB, free: 30.11 MB / 0.5262 GB Notification: Performance of simCode: created initialization part: time 0.0006194/0.0179, allocations: 0.49 MB / 0.6587 GB, free: 29.71 MB / 0.5262 GB Notification: Performance of simCode: created event and clocks part: time 1.983e-06/0.0179, allocations: 0 / 0.6587 GB, free: 29.71 MB / 0.5262 GB Notification: Performance of simCode: created simulation system equations: time 0.0002291/0.01813, allocations: 268.4 kB / 0.659 GB, free: 29.49 MB / 0.5262 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004605/0.01859, allocations: 60.36 kB / 0.6591 GB, free: 29.48 MB / 0.5262 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.002239/0.02083, allocations: 0.7711 MB / 0.6598 GB, free: 28.98 MB / 0.5262 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001194/0.02095, allocations: 137.1 kB / 0.6599 GB, free: 28.9 MB / 0.5262 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 8.921e-05/0.02104, allocations: 28.03 kB / 0.66 GB, free: 28.89 MB / 0.5262 GB Notification: Performance of SimCode: time 1.283e-06/0.02104, allocations: 0 / 0.66 GB, free: 28.89 MB / 0.5262 GB Notification: Performance of Templates: time 0.007554/0.02859, allocations: 3.135 MB / 0.663 GB, free: 28.63 MB / 0.5262 GB " [Timeout remaining time 660] make -j1 -f Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral.makefile [Timeout 660] (rm -f Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral.sim & ./Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral > Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 6.324468889972195]