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 0.001308/0.001308, allocations: 88.23 kB / 19.42 MB, free: 492 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 0.001448/0.001448, allocations: 169 kB / 22.72 MB, free: 1.824 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 1.041/1.041, allocations: 177.1 MB / 203.1 MB, free: 5.355 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 1.663/1.663, allocations: 273.5 MB / 0.5205 GB, free: 14.92 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 2.104e-06/2.104e-06, allocations: 1.422 kB / 0.6462 GB, free: 38.78 MB / 0.5262 GB Notification: Performance of FrontEnd - Absyn->SCode: time 2.918e-05/3.128e-05, allocations: 6.141 kB / 0.6462 GB, free: 38.77 MB / 0.5262 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.PKTwoCompartmentModelOral): time 0.003901/0.003932, allocations: 2.395 MB / 0.6486 GB, free: 37.22 MB / 0.5262 GB Notification: Performance of NFInst.instExpressions: time 0.001224/0.005156, allocations: 0.6135 MB / 0.6492 GB, free: 36.82 MB / 0.5262 GB Notification: Performance of NFInst.updateImplicitVariability: time 0.0001366/0.005293, allocations: 2.594 kB / 0.6492 GB, free: 36.82 MB / 0.5262 GB Notification: Performance of NFTyping.typeComponents: time 8.635e-05/0.005379, allocations: 28.19 kB / 0.6492 GB, free: 36.8 MB / 0.5262 GB Notification: Performance of NFTyping.typeBindings: time 0.0002786/0.005658, allocations: 77.62 kB / 0.6493 GB, free: 36.77 MB / 0.5262 GB Notification: Performance of NFTyping.typeClassSections: time 0.0002436/0.005901, allocations: 66.88 kB / 0.6493 GB, free: 36.73 MB / 0.5262 GB Notification: Performance of NFFlatten.flatten: time 0.0003703/0.006272, allocations: 296.6 kB / 0.6496 GB, free: 36.61 MB / 0.5262 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001693/0.006441, allocations: 59.64 kB / 0.6497 GB, free: 36.57 MB / 0.5262 GB Notification: Performance of NFEvalConstants.evaluate: time 0.000281/0.006722, allocations: 148.2 kB / 0.6498 GB, free: 36.52 MB / 0.5262 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001974/0.006919, allocations: 93.45 kB / 0.6499 GB, free: 36.49 MB / 0.5262 GB Notification: Performance of NFPackage.collectConstants: time 5.143e-05/0.006971, allocations: 22.28 kB / 0.6499 GB, free: 36.49 MB / 0.5262 GB Notification: Performance of NFFlatten.collectFunctions: time 4.989e-05/0.007021, allocations: 22.41 kB / 0.6499 GB, free: 36.49 MB / 0.5262 GB Notification: Performance of NFScalarize.scalarize: time 5.096e-05/0.007072, allocations: 47.81 kB / 0.65 GB, free: 36.46 MB / 0.5262 GB Notification: Performance of NFVerifyModel.verify: time 0.0001141/0.007186, allocations: 83.42 kB / 0.6501 GB, free: 36.42 MB / 0.5262 GB Notification: Performance of NFConvertDAE.convert: time 0.0002748/0.007461, allocations: 178.5 kB / 0.6502 GB, free: 36.34 MB / 0.5262 GB Notification: Performance of FrontEnd - DAE generated: time 3.417e-06/0.007464, allocations: 1.344 kB / 0.6502 GB, free: 36.34 MB / 0.5262 GB Notification: Performance of FrontEnd: time 1.122e-06/0.007465, allocations: 0 / 0.6502 GB, free: 36.34 MB / 0.5262 GB Notification: Performance of Transformations before backend: time 6.893e-06/0.007472, allocations: 0 / 0.6502 GB, free: 36.34 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 0.0007791/0.008251, allocations: 0.628 MB / 0.6508 GB, free: 35.77 MB / 0.5262 GB Notification: Performance of prepare preOptimizeDAE: time 4.366e-05/0.008295, allocations: 10.69 kB / 0.6509 GB, free: 35.77 MB / 0.5262 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 9.216e-05/0.008387, allocations: 37.48 kB / 0.6509 GB, free: 35.75 MB / 0.5262 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002248/0.008612, allocations: 172.4 kB / 0.6511 GB, free: 35.59 MB / 0.5262 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.052e-05/0.008642, allocations: 11.88 kB / 0.6511 GB, free: 35.59 MB / 0.5262 GB Notification: Performance of preOpt expandDerOperator (simulation): time 5.494e-05/0.008697, allocations: 32.36 kB / 0.6511 GB, free: 35.57 MB / 0.5262 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003466/0.009044, allocations: 217.3 kB / 0.6513 GB, free: 35.43 MB / 0.5262 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.915e-05/0.009063, allocations: 7.25 kB / 0.6513 GB, free: 35.43 MB / 0.5262 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.136e-05/0.009084, allocations: 6.156 kB / 0.6513 GB, free: 35.43 MB / 0.5262 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.082e-05/0.009095, allocations: 3.656 kB / 0.6513 GB, free: 35.43 MB / 0.5262 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002453/0.009341, allocations: 150.2 kB / 0.6515 GB, free: 35.35 MB / 0.5262 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0008166/0.01016, allocations: 0.4985 MB / 0.6519 GB, free: 34.98 MB / 0.5262 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0002545/0.01041, allocations: 170.9 kB / 0.6521 GB, free: 34.86 MB / 0.5262 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.0001191/0.01053, allocations: 103.7 kB / 0.6522 GB, free: 34.78 MB / 0.5262 GB Notification: Performance of preOpt evalFunc (simulation): time 1.52e-05/0.01055, allocations: 8.688 kB / 0.6522 GB, free: 34.77 MB / 0.5262 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0003093/0.01086, allocations: 315.5 kB / 0.6525 GB, free: 34.51 MB / 0.5262 GB Notification: Performance of pre-optimization done (n=30): time 2.164e-06/0.01086, allocations: 1.75 kB / 0.6525 GB, free: 34.51 MB / 0.5262 GB Notification: Performance of matching and sorting (n=32): time 0.001339/0.0122, allocations: 0.8952 MB / 0.6534 GB, free: 33.88 MB / 0.5262 GB Notification: Performance of inlineWhenForInitialization (initialization): time 5.88e-05/0.01226, allocations: 224.2 kB / 0.6536 GB, free: 33.62 MB / 0.5262 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001487/0.0124, allocations: 216.6 kB / 0.6538 GB, free: 33.44 MB / 0.5262 GB Notification: Performance of collectPreVariables (initialization): time 2.812e-05/0.01243, allocations: 37.11 kB / 0.6539 GB, free: 33.41 MB / 0.5262 GB Notification: Performance of collectInitialEqns (initialization): time 6.742e-05/0.0125, allocations: 177.4 kB / 0.654 GB, free: 33.24 MB / 0.5262 GB Notification: Performance of collectInitialBindings (initialization): time 7.783e-05/0.01258, allocations: 102.9 kB / 0.6541 GB, free: 33.16 MB / 0.5262 GB Notification: Performance of simplifyInitialFunctions (initialization): time 9.628e-05/0.01267, allocations: 67.31 kB / 0.6542 GB, free: 33.11 MB / 0.5262 GB Notification: Performance of setup shared object (initialization): time 7.39e-05/0.01275, allocations: 0.5062 MB / 0.6547 GB, free: 32.61 MB / 0.5262 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001863/0.01293, allocations: 151.3 kB / 0.6548 GB, free: 32.49 MB / 0.5262 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002178/0.01315, allocations: 262.9 kB / 0.6551 GB, free: 32.22 MB / 0.5262 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0004473/0.0136, allocations: 480.7 kB / 0.6555 GB, free: 31.79 MB / 0.5262 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.94e-06/0.0136, allocations: 5.922 kB / 0.6555 GB, free: 31.79 MB / 0.5262 GB Notification: Performance of matching and sorting (n=47) (initialization): time 0.0004991/0.0141, allocations: 441 kB / 0.656 GB, free: 31.5 MB / 0.5262 GB Notification: Performance of prepare postOptimizeDAE: time 4.617e-05/0.01415, allocations: 89.52 kB / 0.656 GB, free: 31.41 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 9.859e-06/0.01416, allocations: 2.25 kB / 0.656 GB, free: 31.41 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (initialization): time 2.805e-05/0.01419, allocations: 3.938 kB / 0.656 GB, free: 31.41 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002749/0.01446, allocations: 79.25 kB / 0.6561 GB, free: 31.4 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.29e-05/0.01447, allocations: 7.781 kB / 0.6561 GB, free: 31.39 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 9.952e-05/0.01457, allocations: 14.81 kB / 0.6561 GB, free: 31.39 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.297e-05/0.0146, allocations: 18.5 kB / 0.6562 GB, free: 31.39 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 0.0001981/0.0148, allocations: 284.3 kB / 0.6564 GB, free: 31.12 MB / 0.5262 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 5.259e-05/0.01485, allocations: 32.91 kB / 0.6565 GB, free: 31.11 MB / 0.5262 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 4.496e-05/0.01489, allocations: 25.88 kB / 0.6565 GB, free: 31.09 MB / 0.5262 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.152e-06/0.0149, allocations: 2.75 kB / 0.6565 GB, free: 31.09 MB / 0.5262 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 5.701e-06/0.0149, allocations: 0.5625 kB / 0.6565 GB, free: 31.09 MB / 0.5262 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.22e-06/0.01491, allocations: 3.656 kB / 0.6565 GB, free: 31.09 MB / 0.5262 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0006833/0.01559, allocations: 0.7178 MB / 0.6572 GB, free: 30.57 MB / 0.5262 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.585e-06/0.0156, allocations: 0.5 kB / 0.6572 GB, free: 30.57 MB / 0.5262 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001643/0.01576, allocations: 50.69 kB / 0.6572 GB, free: 30.56 MB / 0.5262 GB Notification: Performance of postOpt tearingSystem (simulation): time 3.176e-06/0.01576, allocations: 0 / 0.6572 GB, free: 30.56 MB / 0.5262 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.94e-05/0.01578, allocations: 6.781 kB / 0.6573 GB, free: 30.56 MB / 0.5262 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.294e-06/0.01578, allocations: 3 kB / 0.6573 GB, free: 30.56 MB / 0.5262 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.453e-06/0.01579, allocations: 0 / 0.6573 GB, free: 30.56 MB / 0.5262 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004514/0.01624, allocations: 0.6543 MB / 0.6579 GB, free: 30.1 MB / 0.5262 GB Notification: Performance of postOpt removeConstants (simulation): time 2.064e-05/0.01626, allocations: 17.62 kB / 0.6579 GB, free: 30.09 MB / 0.5262 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.123e-05/0.01629, allocations: 11.66 kB / 0.6579 GB, free: 30.09 MB / 0.5262 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 8.239e-05/0.01637, allocations: 14.47 kB / 0.6579 GB, free: 30.08 MB / 0.5262 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 6.542e-05/0.01644, allocations: 25.98 kB / 0.658 GB, free: 30.08 MB / 0.5262 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.681e-05/0.01645, allocations: 16.09 kB / 0.658 GB, free: 30.07 MB / 0.5262 GB Notification: Performance of sorting global known variables: time 5.27e-05/0.01651, allocations: 162.7 kB / 0.6581 GB, free: 29.95 MB / 0.5262 GB Notification: Performance of sort global known variables: time 8e-08/0.01651, allocations: 0.7188 kB / 0.6581 GB, free: 29.95 MB / 0.5262 GB Notification: Performance of remove unused functions: time 0.000224/0.01673, allocations: 70.06 kB / 0.6582 GB, free: 29.94 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 9.115e-05/0.01682, allocations: 124.7 kB / 0.6583 GB, free: 29.84 MB / 0.5262 GB Notification: Performance of simCode: created initialization part: time 0.0003245/0.01715, allocations: 0.4906 MB / 0.6588 GB, free: 29.44 MB / 0.5262 GB Notification: Performance of simCode: created event and clocks part: time 1.503e-06/0.01715, allocations: 0 / 0.6588 GB, free: 29.44 MB / 0.5262 GB Notification: Performance of simCode: created simulation system equations: time 0.0001473/0.0173, allocations: 269.6 kB / 0.6591 GB, free: 29.22 MB / 0.5262 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002961/0.01759, allocations: 58.98 kB / 0.6591 GB, free: 29.21 MB / 0.5262 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.00143/0.01902, allocations: 0.7451 MB / 0.6598 GB, free: 28.73 MB / 0.5262 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 4.822e-05/0.01907, allocations: 89.58 kB / 0.6599 GB, free: 28.66 MB / 0.5262 GB Notification: Performance of simCode: alias equations: time 7.026e-05/0.01914, allocations: 16.98 kB / 0.6599 GB, free: 28.66 MB / 0.5262 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 5.494e-05/0.0192, allocations: 26.02 kB / 0.66 GB, free: 28.65 MB / 0.5262 GB Notification: Performance of SimCode: time 5.71e-07/0.0192, allocations: 0 / 0.66 GB, free: 28.65 MB / 0.5262 GB Notification: Performance of Templates: time 0.006065/0.02526, allocations: 3.413 MB / 0.6633 GB, free: 28.35 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 -abortSlowSimulation -alarm=240 -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModelOral.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 5.149597093928605]