Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.DevModels.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 0.0009734/0.0009734, 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 0.001146/0.001146, 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 0.9504/0.9504, allocations: 177.1 MB / 203.8 MB, free: 5.473 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: 14.65 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.PKTwoCompartmentModel,tolerance=1e-06,outputFormat="empty",numberOfIntervals=500,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel") translateModel(Pharmacolibrary.DevModels.PKTwoCompartmentModel,tolerance=1e-06,outputFormat="empty",numberOfIntervals=500,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel") [Timeout 660] "Notification: Performance of FrontEnd - loaded program: time 1.513e-06/1.513e-06, allocations: 0 / 0.5954 GB, free: 2.742 MB / 0.5105 GB Notification: Performance of FrontEnd - Absyn->SCode: time 2.456e-05/2.607e-05, allocations: 5.547 kB / 0.5954 GB, free: 2.738 MB / 0.5105 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.PKTwoCompartmentModel): time 0.00268/0.002706, allocations: 2.396 MB / 0.5977 GB, free: 364 kB / 0.5105 GB Notification: Performance of NFInst.instExpressions: time 0.0009486/0.003655, allocations: 0.616 MB / 0.5983 GB, free: 15.75 MB / 0.5261 GB Notification: Performance of NFInst.updateImplicitVariability: time 7.745e-05/0.003732, allocations: 4 kB / 0.5983 GB, free: 15.74 MB / 0.5261 GB Notification: Performance of NFTyping.typeComponents: time 5.691e-05/0.003789, allocations: 27.72 kB / 0.5984 GB, free: 15.71 MB / 0.5261 GB Notification: Performance of NFTyping.typeBindings: time 0.0002033/0.003992, allocations: 77.41 kB / 0.5984 GB, free: 15.66 MB / 0.5261 GB Notification: Performance of NFTyping.typeClassSections: time 0.0001964/0.004189, allocations: 71.78 kB / 0.5985 GB, free: 15.59 MB / 0.5261 GB Notification: Performance of NFFlatten.flatten: time 0.0002732/0.004462, allocations: 299.2 kB / 0.5988 GB, free: 15.35 MB / 0.5261 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001366/0.004598, allocations: 62.69 kB / 0.5989 GB, free: 15.29 MB / 0.5261 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0001885/0.004787, allocations: 147.7 kB / 0.599 GB, free: 15.14 MB / 0.5261 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001375/0.004924, allocations: 87.77 kB / 0.5991 GB, free: 15.06 MB / 0.5261 GB Notification: Performance of NFPackage.collectConstants: time 3.85e-05/0.004963, allocations: 24 kB / 0.5991 GB, free: 15.04 MB / 0.5261 GB Notification: Performance of NFFlatten.collectFunctions: time 2.634e-05/0.004989, allocations: 20 kB / 0.5991 GB, free: 15.02 MB / 0.5261 GB Notification: Performance of NFScalarize.scalarize: time 4.754e-05/0.005037, allocations: 43.83 kB / 0.5992 GB, free: 14.97 MB / 0.5261 GB Notification: Performance of NFVerifyModel.verify: time 8.365e-05/0.00512, allocations: 91.81 kB / 0.5992 GB, free: 14.88 MB / 0.5261 GB Notification: Performance of NFConvertDAE.convert: time 0.0001968/0.005317, allocations: 175.4 kB / 0.5994 GB, free: 14.71 MB / 0.5261 GB Notification: Performance of FrontEnd - DAE generated: time 1.994e-06/0.005319, allocations: 0 / 0.5994 GB, free: 14.71 MB / 0.5261 GB Notification: Performance of FrontEnd: time 8.41e-07/0.00532, allocations: 4 kB / 0.5994 GB, free: 14.71 MB / 0.5261 GB Notification: Performance of Transformations before backend: time 4.188e-06/0.005324, allocations: 0 / 0.5994 GB, free: 14.71 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: 45 * Number of variables: 45 Notification: Performance of Generate backend data structure: time 0.0005688/0.005893, allocations: 0.4937 MB / 0.5999 GB, free: 14.17 MB / 0.5261 GB Notification: Performance of prepare preOptimizeDAE: time 3.689e-05/0.00593, allocations: 16.02 kB / 0.5999 GB, free: 14.16 MB / 0.5261 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 5.235e-05/0.005982, allocations: 28.92 kB / 0.5999 GB, free: 14.13 MB / 0.5261 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001607/0.006143, allocations: 153.4 kB / 0.6001 GB, free: 13.95 MB / 0.5261 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.302e-05/0.006166, allocations: 12.38 kB / 0.6001 GB, free: 13.94 MB / 0.5261 GB Notification: Performance of preOpt expandDerOperator (simulation): time 3.073e-05/0.006197, allocations: 16.38 kB / 0.6001 GB, free: 13.93 MB / 0.5261 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002205/0.006417, allocations: 215.1 kB / 0.6003 GB, free: 13.69 MB / 0.5261 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.452e-05/0.006432, allocations: 7.938 kB / 0.6003 GB, free: 13.68 MB / 0.5261 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.304e-05/0.006445, allocations: 8 kB / 0.6003 GB, free: 13.68 MB / 0.5261 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.605e-06/0.006452, allocations: 4 kB / 0.6003 GB, free: 13.67 MB / 0.5261 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001225/0.006575, allocations: 133.1 kB / 0.6005 GB, free: 13.53 MB / 0.5261 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0004696/0.007045, allocations: 344.5 kB / 0.6008 GB, free: 13.18 MB / 0.5261 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0001607/0.007205, allocations: 156.2 kB / 0.6009 GB, free: 13.01 MB / 0.5261 GB Notification: Performance of preOpt resolveLoops (simulation): time 6.273e-05/0.007268, allocations: 107.5 kB / 0.601 GB, free: 12.89 MB / 0.5261 GB Notification: Performance of preOpt evalFunc (simulation): time 1.079e-05/0.007279, allocations: 7.047 kB / 0.6011 GB, free: 12.89 MB / 0.5261 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002089/0.007488, allocations: 301.5 kB / 0.6013 GB, free: 12.54 MB / 0.5261 GB Notification: Performance of pre-optimization done (n=31): time 2.104e-06/0.00749, allocations: 0 / 0.6013 GB, free: 12.54 MB / 0.5261 GB Notification: Performance of matching and sorting (n=33): time 0.0008312/0.008321, allocations: 0.7793 MB / 0.6021 GB, free: 11.67 MB / 0.5261 GB Notification: Performance of inlineWhenForInitialization (initialization): time 7.713e-05/0.008398, allocations: 221.6 kB / 0.6023 GB, free: 11.4 MB / 0.5261 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 9.755e-05/0.008496, allocations: 168.7 kB / 0.6025 GB, free: 11.23 MB / 0.5261 GB Notification: Performance of collectPreVariables (initialization): time 2.2e-05/0.008518, allocations: 37.7 kB / 0.6025 GB, free: 11.18 MB / 0.5261 GB Notification: Performance of collectInitialEqns (initialization): time 4.578e-05/0.008564, allocations: 112.9 kB / 0.6026 GB, free: 11.07 MB / 0.5261 GB Notification: Performance of collectInitialBindings (initialization): time 5.815e-05/0.008622, allocations: 115.1 kB / 0.6027 GB, free: 10.96 MB / 0.5261 GB Notification: Performance of simplifyInitialFunctions (initialization): time 5.986e-05/0.008682, allocations: 61.66 kB / 0.6028 GB, free: 10.89 MB / 0.5261 GB Notification: Performance of setup shared object (initialization): time 7.753e-05/0.008759, allocations: 334.8 kB / 0.6031 GB, free: 10.55 MB / 0.5261 GB Notification: Performance of preBalanceInitialSystem (initialization): time 8.075e-05/0.00884, allocations: 139 kB / 0.6032 GB, free: 10.4 MB / 0.5261 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001093/0.008949, allocations: 219 kB / 0.6035 GB, free: 10.13 MB / 0.5261 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0002469/0.009196, allocations: 435.9 kB / 0.6039 GB, free: 9.629 MB / 0.5261 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.733e-06/0.009198, allocations: 0 / 0.6039 GB, free: 9.629 MB / 0.5261 GB Notification: Performance of matching and sorting (n=48) (initialization): time 0.0002472/0.009445, allocations: 365.8 kB / 0.6042 GB, free: 9.23 MB / 0.5261 GB Notification: Performance of prepare postOptimizeDAE: time 4.058e-05/0.009486, allocations: 89.09 kB / 0.6043 GB, free: 9.125 MB / 0.5261 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.502e-06/0.009492, allocations: 4 kB / 0.6043 GB, free: 9.121 MB / 0.5261 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.402e-05/0.009506, allocations: 4 kB / 0.6043 GB, free: 9.117 MB / 0.5261 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001588/0.009665, allocations: 71.91 kB / 0.6044 GB, free: 9.047 MB / 0.5261 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 5.06e-06/0.00967, allocations: 7.938 kB / 0.6044 GB, free: 9.039 MB / 0.5261 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 8.382e-05/0.009754, allocations: 23.98 kB / 0.6044 GB, free: 9.016 MB / 0.5261 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.291e-05/0.009767, allocations: 8 kB / 0.6044 GB, free: 9.008 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 intestine.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real blood.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real intestine.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real intestine.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real blood.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real blood.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real blood.rising:DISCRETE(fixed = true protected = true ) type: Boolean intestine.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 ($PRE.intestine.Cmin,intestine.Cmin,$PRE.intestine.Cmax,intestine.Cmax,$PRE.blood.Cmin,blood.Cmin,$PRE.blood.Cmax,blood.Cmax,$PRE.blood.rising,$PRE.intestine.rising,$PRE.periodicDose.pulse.count,$PRE.periodicDose.pulse.T_start,blood.rising,intestine.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 (45): * Single equations (assignments): 42 * 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 0.0001743/0.009941, allocations: 229.3 kB / 0.6046 GB, free: 8.762 MB / 0.5261 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 3.046e-05/0.009971, allocations: 34.86 kB / 0.6047 GB, free: 8.73 MB / 0.5261 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.588e-05/0.01001, allocations: 25.97 kB / 0.6047 GB, free: 8.703 MB / 0.5261 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.154e-06/0.01001, allocations: 0 / 0.6047 GB, free: 8.703 MB / 0.5261 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 3.938e-06/0.01001, allocations: 3.984 kB / 0.6047 GB, free: 8.699 MB / 0.5261 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.058e-06/0.01002, allocations: 0 / 0.6047 GB, free: 8.699 MB / 0.5261 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004227/0.01044, allocations: 0.4909 MB / 0.6052 GB, free: 8.16 MB / 0.5261 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.074e-06/0.01044, allocations: 0 / 0.6052 GB, free: 8.16 MB / 0.5261 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001451/0.01059, allocations: 59.91 kB / 0.6052 GB, free: 8.102 MB / 0.5261 GB Notification: Performance of postOpt tearingSystem (simulation): time 2.485e-06/0.01059, allocations: 0 / 0.6052 GB, free: 8.102 MB / 0.5261 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.585e-05/0.01061, allocations: 11.94 kB / 0.6052 GB, free: 8.09 MB / 0.5261 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.649e-06/0.01061, allocations: 3.984 kB / 0.6052 GB, free: 8.086 MB / 0.5261 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.643e-06/0.01061, allocations: 0 / 0.6052 GB, free: 8.086 MB / 0.5261 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0003196/0.01093, allocations: 0.4933 MB / 0.6057 GB, free: 7.543 MB / 0.5261 GB Notification: Performance of postOpt removeConstants (simulation): time 1.932e-05/0.01095, allocations: 15.91 kB / 0.6057 GB, free: 7.527 MB / 0.5261 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.02e-05/0.01098, allocations: 8 kB / 0.6058 GB, free: 7.52 MB / 0.5261 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.677e-05/0.01106, allocations: 19.92 kB / 0.6058 GB, free: 7.5 MB / 0.5261 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 5.225e-05/0.01111, allocations: 24.19 kB / 0.6058 GB, free: 7.477 MB / 0.5261 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.381e-05/0.01112, allocations: 19.98 kB / 0.6058 GB, free: 7.457 MB / 0.5261 GB Notification: Performance of sorting global known variables: time 3.223e-05/0.01116, allocations: 36.55 kB / 0.6058 GB, free: 7.422 MB / 0.5261 GB Notification: Performance of sort global known variables: time 1e-07/0.01116, allocations: 0 / 0.6058 GB, free: 7.422 MB / 0.5261 GB Notification: Performance of remove unused functions: time 0.0001881/0.01134, allocations: 72 kB / 0.6059 GB, free: 7.352 MB / 0.5261 GB Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 1 * Number of states: 6 (periodicDose.TotalCumulativeMass,periodicDose.variableDose.TotalCumulativeMass,intestine.C,intestine.AUC,blood.C,blood.AUC) * Number of discrete variables: 13 ($whenCondition1,$whenCondition2,$whenCondition3,$whenCondition4,$whenCondition5,periodicDose.pulse.T_start,periodicDose.pulse.count,intestine.Cmax,intestine.Cmin,intestine.rising,blood.Cmax,blood.Cmin,blood.rising) * Number of discrete states: 11 (periodicDose.pulse.count,blood.Cmin,$whenCondition3,blood.Cmax,$whenCondition2,blood.rising,intestine.Cmin,$whenCondition5,intestine.Cmax,$whenCondition4,intestine.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 9.652e-05/0.01144, allocations: 92.41 kB / 0.606 GB, free: 7.254 MB / 0.5261 GB Notification: Performance of simCode: created initialization part: time 0.0002989/0.01174, allocations: 479.9 kB / 0.6065 GB, free: 6.719 MB / 0.5261 GB Notification: Performance of simCode: created event and clocks part: time 2.946e-06/0.01174, allocations: 4 kB / 0.6065 GB, free: 6.715 MB / 0.5261 GB Notification: Performance of simCode: created simulation system equations: time 0.0001341/0.01188, allocations: 259 kB / 0.6067 GB, free: 6.422 MB / 0.5261 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002317/0.01211, allocations: 63.77 kB / 0.6068 GB, free: 6.363 MB / 0.5261 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001226/0.01333, allocations: 0.6522 MB / 0.6074 GB, free: 5.676 MB / 0.5261 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 4.926e-05/0.01338, allocations: 84.83 kB / 0.6075 GB, free: 5.57 MB / 0.5261 GB Notification: Performance of simCode: alias equations: time 6.985e-05/0.01345, allocations: 29.64 kB / 0.6075 GB, free: 5.543 MB / 0.5261 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001427/0.0136, allocations: 123.3 kB / 0.6076 GB, free: 5.422 MB / 0.5261 GB Notification: Performance of SimCode: time 5.51e-07/0.0136, allocations: 0 / 0.6076 GB, free: 5.422 MB / 0.5261 GB Notification: Performance of Templates: time 0.005533/0.01913, allocations: 3.673 MB / 0.6112 GB, free: 1.938 MB / 0.5261 GB " [Timeout remaining time 660] make -j1 -f Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.makefile [Timeout 660] (rm -f Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.sim & ./Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel -abortSlowSimulation -alarm=240 -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.DevModels.PKTwoCompartmentModel.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 4.78709957189858]