Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.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 0.0009954/0.0009954, allocations: 80.88 kB / 19.94 MB, free: 4.551 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 0.0009868/0.0009868, allocations: 177 kB / 23.36 MB, free: 1.137 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 0.9719/0.9719, allocations: 177.1 MB / 203.8 MB, free: 5.457 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 1.621/1.621, allocations: 273.5 MB / 0.5213 GB, free: 14.59 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.Examples.PKTwoCompartmentModel,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel") translateModel(Pharmacolibrary.Examples.PKTwoCompartmentModel,tolerance=1e-08,outputFormat="empty",numberOfIntervals=5000,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel") [Timeout 660] "Notification: Performance of FrontEnd - loaded program: time 7.82e-07/7.82e-07, allocations: 1.312 kB / 0.5954 GB, free: 2.695 MB / 0.5105 GB Notification: Performance of FrontEnd - Absyn->SCode: time 8.056e-06/8.838e-06, allocations: 2.312 kB / 0.5954 GB, free: 2.691 MB / 0.5105 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKTwoCompartmentModel): time 0.00214/0.002149, allocations: 2.372 MB / 0.5977 GB, free: 340 kB / 0.5105 GB Notification: Performance of NFInst.instExpressions: time 0.0006625/0.002811, allocations: 0.6118 MB / 0.5983 GB, free: 15.72 MB / 0.5261 GB Notification: Performance of NFInst.updateImplicitVariability: time 5.784e-05/0.002869, allocations: 4 kB / 0.5983 GB, free: 15.72 MB / 0.5261 GB Notification: Performance of NFTyping.typeComponents: time 8.191e-05/0.002951, allocations: 29.02 kB / 0.5983 GB, free: 15.69 MB / 0.5261 GB Notification: Performance of NFTyping.typeBindings: time 0.0001184/0.00307, allocations: 75.69 kB / 0.5984 GB, free: 15.64 MB / 0.5261 GB Notification: Performance of NFTyping.typeClassSections: time 0.000123/0.003193, allocations: 65.53 kB / 0.5985 GB, free: 15.58 MB / 0.5261 GB Notification: Performance of NFFlatten.flatten: time 0.0002193/0.003412, allocations: 284.6 kB / 0.5987 GB, free: 15.36 MB / 0.5261 GB Notification: Performance of NFFlatten.resolveConnections: time 9.128e-05/0.003503, allocations: 54.39 kB / 0.5988 GB, free: 15.3 MB / 0.5261 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0001239/0.003627, allocations: 147.7 kB / 0.5989 GB, free: 15.16 MB / 0.5261 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001005/0.003728, allocations: 83.72 kB / 0.599 GB, free: 15.07 MB / 0.5261 GB Notification: Performance of NFPackage.collectConstants: time 2.533e-05/0.003753, allocations: 20 kB / 0.599 GB, free: 15.05 MB / 0.5261 GB Notification: Performance of NFFlatten.collectFunctions: time 2.125e-05/0.003774, allocations: 24 kB / 0.5991 GB, free: 15.03 MB / 0.5261 GB Notification: Performance of NFScalarize.scalarize: time 3.416e-05/0.003808, allocations: 47.81 kB / 0.5991 GB, free: 14.98 MB / 0.5261 GB Notification: Performance of NFVerifyModel.verify: time 6.395e-05/0.003872, allocations: 91.83 kB / 0.5992 GB, free: 14.89 MB / 0.5261 GB Notification: Performance of NFConvertDAE.convert: time 0.0001451/0.004017, allocations: 163.5 kB / 0.5993 GB, free: 14.73 MB / 0.5261 GB Notification: Performance of FrontEnd - DAE generated: time 1.603e-06/0.004019, allocations: 0 / 0.5993 GB, free: 14.73 MB / 0.5261 GB Notification: Performance of FrontEnd: time 4.61e-07/0.004019, allocations: 0 / 0.5993 GB, free: 14.73 MB / 0.5261 GB Notification: Performance of Transformations before backend: time 2.996e-06/0.004022, allocations: 4 kB / 0.5993 GB, free: 14.73 MB / 0.5261 GB Notification: Model statistics after passing the front-end and creating the data structures used by the back-end: * Number of equations: 42 * Number of variables: 42 Notification: Performance of Generate backend data structure: time 0.0005821/0.004605, allocations: 0.4902 MB / 0.5998 GB, free: 14.2 MB / 0.5261 GB Notification: Performance of prepare preOptimizeDAE: time 2.541e-05/0.00463, allocations: 12.03 kB / 0.5998 GB, free: 14.18 MB / 0.5261 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 4.217e-05/0.004672, allocations: 28.91 kB / 0.5999 GB, free: 14.16 MB / 0.5261 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001318/0.004804, allocations: 159 kB / 0.6 GB, free: 13.98 MB / 0.5261 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.647e-05/0.00482, allocations: 12.7 kB / 0.6 GB, free: 13.96 MB / 0.5261 GB Notification: Performance of preOpt expandDerOperator (simulation): time 2.981e-05/0.00485, allocations: 24.33 kB / 0.6001 GB, free: 13.94 MB / 0.5261 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0001659/0.005016, allocations: 199.9 kB / 0.6002 GB, free: 13.73 MB / 0.5261 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.219e-05/0.005028, allocations: 3.938 kB / 0.6002 GB, free: 13.72 MB / 0.5261 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.209e-05/0.00504, allocations: 8 kB / 0.6003 GB, free: 13.71 MB / 0.5261 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 6.272e-06/0.005047, allocations: 4 kB / 0.6003 GB, free: 13.71 MB / 0.5261 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.000107/0.005154, allocations: 129.4 kB / 0.6004 GB, free: 13.57 MB / 0.5261 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0003754/0.005529, allocations: 336.7 kB / 0.6007 GB, free: 13.23 MB / 0.5261 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0001264/0.005655, allocations: 153.4 kB / 0.6008 GB, free: 13.06 MB / 0.5261 GB Notification: Performance of preOpt resolveLoops (simulation): time 5.272e-05/0.005708, allocations: 95.86 kB / 0.6009 GB, free: 12.96 MB / 0.5261 GB Notification: Performance of preOpt evalFunc (simulation): time 8.566e-06/0.005717, allocations: 4 kB / 0.6009 GB, free: 12.95 MB / 0.5261 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.000179/0.005896, allocations: 313.3 kB / 0.6012 GB, free: 12.6 MB / 0.5261 GB Notification: Performance of pre-optimization done (n=31): time 1.393e-06/0.005897, allocations: 0 / 0.6012 GB, free: 12.6 MB / 0.5261 GB Notification: Performance of matching and sorting (n=33): time 0.0006909/0.006588, allocations: 0.7762 MB / 0.602 GB, free: 11.73 MB / 0.5261 GB Notification: Performance of inlineWhenForInitialization (initialization): time 6.255e-05/0.00665, allocations: 213.6 kB / 0.6022 GB, free: 11.47 MB / 0.5261 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 8.19e-05/0.006732, allocations: 173.5 kB / 0.6024 GB, free: 11.29 MB / 0.5261 GB Notification: Performance of collectPreVariables (initialization): time 1.777e-05/0.00675, allocations: 33.7 kB / 0.6024 GB, free: 11.25 MB / 0.5261 GB Notification: Performance of collectInitialEqns (initialization): time 3.954e-05/0.00679, allocations: 116.9 kB / 0.6025 GB, free: 11.13 MB / 0.5261 GB Notification: Performance of collectInitialBindings (initialization): time 4.912e-05/0.006839, allocations: 107.1 kB / 0.6026 GB, free: 11.03 MB / 0.5261 GB Notification: Performance of simplifyInitialFunctions (initialization): time 5.692e-05/0.006896, allocations: 65.66 kB / 0.6027 GB, free: 10.96 MB / 0.5261 GB Notification: Performance of setup shared object (initialization): time 0.0003207/0.007216, allocations: 338.8 kB / 0.603 GB, free: 10.62 MB / 0.5261 GB Notification: Performance of preBalanceInitialSystem (initialization): time 7.327e-05/0.00729, allocations: 146.9 kB / 0.6031 GB, free: 10.45 MB / 0.5261 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001024/0.007392, allocations: 227.1 kB / 0.6034 GB, free: 10.18 MB / 0.5261 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0002233/0.007615, allocations: 448.8 kB / 0.6038 GB, free: 9.66 MB / 0.5261 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.405e-06/0.007618, allocations: 4 kB / 0.6038 GB, free: 9.656 MB / 0.5261 GB Notification: Performance of matching and sorting (n=49) (initialization): time 0.0002196/0.007837, allocations: 361.8 kB / 0.6041 GB, free: 9.262 MB / 0.5261 GB Notification: Performance of prepare postOptimizeDAE: time 3.671e-05/0.007874, allocations: 89.09 kB / 0.6042 GB, free: 9.156 MB / 0.5261 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 4.839e-06/0.007879, allocations: 4 kB / 0.6042 GB, free: 9.152 MB / 0.5261 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.301e-05/0.007892, allocations: 8.219 kB / 0.6042 GB, free: 9.145 MB / 0.5261 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001527/0.008045, allocations: 87.83 kB / 0.6043 GB, free: 9.059 MB / 0.5261 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 4.489e-06/0.008049, allocations: 4 kB / 0.6043 GB, free: 9.055 MB / 0.5261 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 7.991e-05/0.008129, allocations: 12 kB / 0.6043 GB, free: 9.043 MB / 0.5261 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.464e-05/0.008144, allocations: 15.98 kB / 0.6043 GB, free: 9.027 MB / 0.5261 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 peripheral.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real central.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" 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 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 central.rising:DISCRETE(fixed = true protected = true ) type: Boolean peripheral.rising:DISCRETE(fixed = true protected = true ) type: Boolean Notification: Model statistics after passing the back-end for initialization: * Number of independent subsystems: 10 * Number of states: 0 () * Number of discrete variables: 21 ($PRE.peripheral.Cmin,peripheral.Cmin,$PRE.peripheral.Cmax,peripheral.Cmax,$PRE.central.Cmin,central.Cmin,$PRE.central.Cmax,central.Cmax,$PRE.central.rising,$PRE.peripheral.rising,$PRE.periodicDose.pulse.count,$PRE.periodicDose.pulse.T_start,central.rising,peripheral.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 (46): * Single equations (assignments): 43 * 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 0.0001376/0.008281, allocations: 225.4 kB / 0.6046 GB, free: 8.781 MB / 0.5261 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 2.715e-05/0.008308, allocations: 31.27 kB / 0.6046 GB, free: 8.754 MB / 0.5261 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 2.781e-05/0.008336, allocations: 25.95 kB / 0.6046 GB, free: 8.727 MB / 0.5261 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.817e-06/0.00834, allocations: 11.94 kB / 0.6046 GB, free: 8.715 MB / 0.5261 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 1.483e-06/0.008342, allocations: 3.938 kB / 0.6046 GB, free: 8.711 MB / 0.5261 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.597e-06/0.008345, allocations: 0 / 0.6046 GB, free: 8.711 MB / 0.5261 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003526/0.008698, allocations: 0.4946 MB / 0.6051 GB, free: 8.172 MB / 0.5261 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.263e-06/0.008699, allocations: 0 / 0.6051 GB, free: 8.172 MB / 0.5261 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001231/0.008822, allocations: 51.91 kB / 0.6052 GB, free: 8.121 MB / 0.5261 GB Notification: Performance of postOpt tearingSystem (simulation): time 2.204e-06/0.008824, allocations: 7.938 kB / 0.6052 GB, free: 8.113 MB / 0.5261 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.252e-05/0.008837, allocations: 8 kB / 0.6052 GB, free: 8.105 MB / 0.5261 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 9.11e-07/0.008838, allocations: 0 / 0.6052 GB, free: 8.105 MB / 0.5261 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 9.82e-07/0.008839, allocations: 0 / 0.6052 GB, free: 8.105 MB / 0.5261 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.000277/0.009116, allocations: 0.4999 MB / 0.6057 GB, free: 7.555 MB / 0.5261 GB Notification: Performance of postOpt removeConstants (simulation): time 1.523e-05/0.009131, allocations: 15.86 kB / 0.6057 GB, free: 7.539 MB / 0.5261 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.576e-05/0.009157, allocations: 11.94 kB / 0.6057 GB, free: 7.527 MB / 0.5261 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.32e-05/0.00923, allocations: 19.92 kB / 0.6057 GB, free: 7.508 MB / 0.5261 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 4.54e-05/0.009275, allocations: 24.19 kB / 0.6057 GB, free: 7.484 MB / 0.5261 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.206e-05/0.009287, allocations: 12 kB / 0.6057 GB, free: 7.473 MB / 0.5261 GB Notification: Performance of sorting global known variables: time 2.731e-05/0.009315, allocations: 39.88 kB / 0.6058 GB, free: 7.434 MB / 0.5261 GB Notification: Performance of sort global known variables: time 4e-08/0.009315, allocations: 0 / 0.6058 GB, free: 7.434 MB / 0.5261 GB Notification: Performance of remove unused functions: time 0.000172/0.009487, allocations: 72 kB / 0.6059 GB, free: 7.363 MB / 0.5261 GB Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 1 * Number of states: 7 (periodicDose.TotalCumulativeMass,periodicDose.variableDose.TotalCumulativeMass,peripheral.C,peripheral.AUC,central.C,central.AUC,elim.MExc) * Number of discrete variables: 13 ($whenCondition1,$whenCondition2,$whenCondition3,$whenCondition4,$whenCondition5,periodicDose.pulse.T_start,periodicDose.pulse.count,peripheral.Cmax,peripheral.Cmin,peripheral.rising,central.Cmax,central.Cmin,central.rising) * Number of discrete states: 11 (periodicDose.pulse.count,peripheral.Cmin,$whenCondition5,peripheral.Cmax,$whenCondition4,peripheral.rising,central.Cmin,$whenCondition3,central.Cmax,$whenCondition2,central.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 7.372e-05/0.00956, allocations: 102.2 kB / 0.606 GB, free: 7.258 MB / 0.5261 GB Notification: Performance of simCode: created initialization part: time 0.0002426/0.009803, allocations: 476.5 kB / 0.6064 GB, free: 6.723 MB / 0.5261 GB Notification: Performance of simCode: created event and clocks part: time 2.966e-06/0.009806, allocations: 4 kB / 0.6064 GB, free: 6.719 MB / 0.5261 GB Notification: Performance of simCode: created simulation system equations: time 0.0001187/0.009925, allocations: 258 kB / 0.6067 GB, free: 6.43 MB / 0.5261 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002029/0.01013, allocations: 75.19 kB / 0.6067 GB, free: 6.363 MB / 0.5261 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001026/0.01115, allocations: 0.6557 MB / 0.6074 GB, free: 5.672 MB / 0.5261 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 4.138e-05/0.01119, allocations: 84.83 kB / 0.6074 GB, free: 5.566 MB / 0.5261 GB Notification: Performance of simCode: alias equations: time 5.991e-05/0.01125, allocations: 29.88 kB / 0.6075 GB, free: 5.539 MB / 0.5261 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001287/0.01138, allocations: 119.3 kB / 0.6076 GB, free: 5.422 MB / 0.5261 GB Notification: Performance of SimCode: time 5.21e-07/0.01138, allocations: 0 / 0.6076 GB, free: 5.422 MB / 0.5261 GB Notification: Performance of Templates: time 0.004918/0.0163, allocations: 3.719 MB / 0.6112 GB, free: 1.891 MB / 0.5261 GB " [Timeout remaining time 660] make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.makefile [Timeout 660] (rm -f Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel -abortSlowSimulation -alarm=240 -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 4.791783266235143]