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 0.001154/0.001154, allocations: 80.88 kB / 19.94 MB, free: 4.547 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 0.00134/0.00134, allocations: 181 kB / 23.36 MB, free: 1.133 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 0.9341/0.9341, 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 1.677/1.677, allocations: 273.5 MB / 0.5213 GB, free: 14.71 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 1.413e-06/1.413e-06, allocations: 0 / 0.5954 GB, free: 2.77 MB / 0.5105 GB Notification: Performance of FrontEnd - Absyn->SCode: time 1.343e-05/1.484e-05, allocations: 2.312 kB / 0.5954 GB, free: 2.766 MB / 0.5105 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PKTwoCompartmentModel): time 0.002396/0.002411, allocations: 2.42 MB / 0.5978 GB, free: 368 kB / 0.5105 GB Notification: Performance of NFInst.instExpressions: time 0.0009231/0.003334, allocations: 0.6166 MB / 0.5984 GB, free: 15.75 MB / 0.5261 GB Notification: Performance of NFInst.updateImplicitVariability: time 8.49e-05/0.003419, allocations: 0 / 0.5984 GB, free: 15.75 MB / 0.5261 GB Notification: Performance of NFTyping.typeComponents: time 0.0001155/0.003534, allocations: 27.72 kB / 0.5984 GB, free: 15.72 MB / 0.5261 GB Notification: Performance of NFTyping.typeBindings: time 0.0001671/0.003702, allocations: 77.41 kB / 0.5985 GB, free: 15.67 MB / 0.5261 GB Notification: Performance of NFTyping.typeClassSections: time 0.0001905/0.003892, allocations: 55.92 kB / 0.5986 GB, free: 15.61 MB / 0.5261 GB Notification: Performance of NFFlatten.flatten: time 0.0002805/0.004173, allocations: 292.6 kB / 0.5988 GB, free: 15.38 MB / 0.5261 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0001209/0.004293, allocations: 54.44 kB / 0.5989 GB, free: 15.32 MB / 0.5261 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0001752/0.004469, allocations: 147.7 kB / 0.599 GB, free: 15.18 MB / 0.5261 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0001318/0.0046, allocations: 87.75 kB / 0.5991 GB, free: 15.09 MB / 0.5261 GB Notification: Performance of NFPackage.collectConstants: time 2.975e-05/0.00463, allocations: 24 kB / 0.5991 GB, free: 15.07 MB / 0.5261 GB Notification: Performance of NFFlatten.collectFunctions: time 2.342e-05/0.004653, allocations: 20 kB / 0.5992 GB, free: 15.05 MB / 0.5261 GB Notification: Performance of NFScalarize.scalarize: time 3.528e-05/0.004689, allocations: 39.84 kB / 0.5992 GB, free: 15.01 MB / 0.5261 GB Notification: Performance of NFVerifyModel.verify: time 7.13e-05/0.00476, allocations: 91.81 kB / 0.5993 GB, free: 14.92 MB / 0.5261 GB Notification: Performance of NFConvertDAE.convert: time 0.0001798/0.00494, allocations: 171.4 kB / 0.5994 GB, free: 14.75 MB / 0.5261 GB Notification: Performance of FrontEnd - DAE generated: time 2.044e-06/0.004942, allocations: 0 / 0.5994 GB, free: 14.75 MB / 0.5261 GB Notification: Performance of FrontEnd: time 6.51e-07/0.004943, allocations: 4 kB / 0.5994 GB, free: 14.75 MB / 0.5261 GB Notification: Performance of Transformations before backend: time 3.266e-06/0.004946, allocations: 0 / 0.5994 GB, free: 14.75 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 0.0005062/0.005452, allocations: 498 kB / 0.5999 GB, free: 14.22 MB / 0.5261 GB Notification: Performance of prepare preOptimizeDAE: time 2.839e-05/0.00548, allocations: 8.031 kB / 0.5999 GB, free: 14.21 MB / 0.5261 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 4.471e-05/0.005525, allocations: 28.92 kB / 0.6 GB, free: 14.18 MB / 0.5261 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001547/0.00568, allocations: 151 kB / 0.6001 GB, free: 14.01 MB / 0.5261 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.786e-05/0.005698, allocations: 12.7 kB / 0.6001 GB, free: 14 MB / 0.5261 GB Notification: Performance of preOpt expandDerOperator (simulation): time 3.282e-05/0.00573, allocations: 43.48 kB / 0.6002 GB, free: 13.96 MB / 0.5261 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0001913/0.005922, allocations: 203.8 kB / 0.6003 GB, free: 13.74 MB / 0.5261 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.442e-05/0.005936, allocations: 7.438 kB / 0.6004 GB, free: 13.74 MB / 0.5261 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.315e-05/0.005949, allocations: 8 kB / 0.6004 GB, free: 13.73 MB / 0.5261 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.284e-06/0.005957, allocations: 4 kB / 0.6004 GB, free: 13.73 MB / 0.5261 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001195/0.006076, allocations: 125.6 kB / 0.6005 GB, free: 13.59 MB / 0.5261 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0004681/0.006544, allocations: 332.5 kB / 0.6008 GB, free: 13.25 MB / 0.5261 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0001441/0.006688, allocations: 153.9 kB / 0.601 GB, free: 13.08 MB / 0.5261 GB Notification: Performance of preOpt resolveLoops (simulation): time 6.058e-05/0.006749, allocations: 92.25 kB / 0.601 GB, free: 12.98 MB / 0.5261 GB Notification: Performance of preOpt evalFunc (simulation): time 1.079e-05/0.00676, allocations: 4 kB / 0.601 GB, free: 12.97 MB / 0.5261 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002187/0.006978, allocations: 309.4 kB / 0.6013 GB, free: 12.62 MB / 0.5261 GB Notification: Performance of pre-optimization done (n=31): time 1.293e-06/0.00698, allocations: 0 / 0.6013 GB, free: 12.62 MB / 0.5261 GB Notification: Performance of matching and sorting (n=33): time 0.0007615/0.007741, allocations: 0.7755 MB / 0.6021 GB, free: 11.75 MB / 0.5261 GB Notification: Performance of inlineWhenForInitialization (initialization): time 7.284e-05/0.007814, allocations: 217.6 kB / 0.6023 GB, free: 11.49 MB / 0.5261 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 9.477e-05/0.007909, allocations: 170.2 kB / 0.6025 GB, free: 11.31 MB / 0.5261 GB Notification: Performance of collectPreVariables (initialization): time 1.844e-05/0.007927, allocations: 33.7 kB / 0.6025 GB, free: 11.27 MB / 0.5261 GB Notification: Performance of collectInitialEqns (initialization): time 4.64e-05/0.007974, allocations: 120.9 kB / 0.6026 GB, free: 11.15 MB / 0.5261 GB Notification: Performance of collectInitialBindings (initialization): time 5.269e-05/0.008026, allocations: 107.1 kB / 0.6027 GB, free: 11.05 MB / 0.5261 GB Notification: Performance of simplifyInitialFunctions (initialization): time 6.425e-05/0.00809, allocations: 65.66 kB / 0.6028 GB, free: 10.98 MB / 0.5261 GB Notification: Performance of setup shared object (initialization): time 7.424e-05/0.008165, allocations: 334.8 kB / 0.6031 GB, free: 10.64 MB / 0.5261 GB Notification: Performance of preBalanceInitialSystem (initialization): time 7.859e-05/0.008243, allocations: 142.9 kB / 0.6032 GB, free: 10.48 MB / 0.5261 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001145/0.008358, allocations: 231.1 kB / 0.6035 GB, free: 10.2 MB / 0.5261 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0002526/0.00861, allocations: 452.8 kB / 0.6039 GB, free: 9.68 MB / 0.5261 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.974e-06/0.008612, allocations: 4 kB / 0.6039 GB, free: 9.676 MB / 0.5261 GB Notification: Performance of matching and sorting (n=49) (initialization): time 0.0002468/0.008859, allocations: 365.8 kB / 0.6042 GB, free: 9.277 MB / 0.5261 GB Notification: Performance of prepare postOptimizeDAE: time 3.851e-05/0.008898, allocations: 85.11 kB / 0.6043 GB, free: 9.176 MB / 0.5261 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.031e-06/0.008904, allocations: 3.984 kB / 0.6043 GB, free: 9.172 MB / 0.5261 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.399e-05/0.008918, allocations: 7.938 kB / 0.6043 GB, free: 9.164 MB / 0.5261 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.000209/0.009127, allocations: 96.17 kB / 0.6044 GB, free: 9.07 MB / 0.5261 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 5.53e-06/0.009132, allocations: 7.984 kB / 0.6044 GB, free: 9.062 MB / 0.5261 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 8.297e-05/0.009215, allocations: 16 kB / 0.6044 GB, free: 9.047 MB / 0.5261 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.412e-05/0.009229, allocations: 8 kB / 0.6045 GB, free: 9.039 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 0.0001648/0.009394, allocations: 240.6 kB / 0.6047 GB, free: 8.785 MB / 0.5261 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 2.437e-05/0.009419, allocations: 19.98 kB / 0.6047 GB, free: 8.766 MB / 0.5261 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.716e-05/0.009456, allocations: 33.89 kB / 0.6047 GB, free: 8.73 MB / 0.5261 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.895e-06/0.009459, allocations: 4 kB / 0.6047 GB, free: 8.727 MB / 0.5261 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 3.126e-06/0.009462, allocations: 4 kB / 0.6047 GB, free: 8.723 MB / 0.5261 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.867e-06/0.009466, allocations: 0 / 0.6047 GB, free: 8.723 MB / 0.5261 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003942/0.00986, allocations: 0.4909 MB / 0.6052 GB, free: 8.184 MB / 0.5261 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 1.844e-06/0.009862, allocations: 0 / 0.6052 GB, free: 8.184 MB / 0.5261 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001678/0.01003, allocations: 67.88 kB / 0.6053 GB, free: 8.117 MB / 0.5261 GB Notification: Performance of postOpt tearingSystem (simulation): time 3.296e-06/0.01003, allocations: 4 kB / 0.6053 GB, free: 8.113 MB / 0.5261 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.491e-05/0.01005, allocations: 8 kB / 0.6053 GB, free: 8.105 MB / 0.5261 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.825e-06/0.01005, allocations: 3.938 kB / 0.6053 GB, free: 8.102 MB / 0.5261 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.243e-06/0.01005, allocations: 0 / 0.6053 GB, free: 8.102 MB / 0.5261 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0002987/0.01035, allocations: 0.4998 MB / 0.6058 GB, free: 7.551 MB / 0.5261 GB Notification: Performance of postOpt removeConstants (simulation): time 1.841e-05/0.01037, allocations: 19.86 kB / 0.6058 GB, free: 7.531 MB / 0.5261 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.545e-05/0.01039, allocations: 8 kB / 0.6058 GB, free: 7.523 MB / 0.5261 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 8.265e-05/0.01048, allocations: 15.98 kB / 0.6058 GB, free: 7.508 MB / 0.5261 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 5.314e-05/0.01053, allocations: 28.19 kB / 0.6059 GB, free: 7.48 MB / 0.5261 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.119e-05/0.01054, allocations: 8 kB / 0.6059 GB, free: 7.473 MB / 0.5261 GB Notification: Performance of sorting global known variables: time 3.117e-05/0.01057, allocations: 43.88 kB / 0.6059 GB, free: 7.43 MB / 0.5261 GB Notification: Performance of sort global known variables: time 5e-08/0.01057, allocations: 0 / 0.6059 GB, free: 7.43 MB / 0.5261 GB Notification: Performance of remove unused functions: time 0.0001855/0.01076, allocations: 68 kB / 0.606 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 8.12e-05/0.01084, allocations: 110.3 kB / 0.6061 GB, free: 7.254 MB / 0.5261 GB Notification: Performance of simCode: created initialization part: time 0.0002909/0.01113, allocations: 480.4 kB / 0.6065 GB, free: 6.715 MB / 0.5261 GB Notification: Performance of simCode: created event and clocks part: time 3.978e-06/0.01113, allocations: 0 / 0.6065 GB, free: 6.715 MB / 0.5261 GB Notification: Performance of simCode: created simulation system equations: time 0.0001299/0.01126, allocations: 258 kB / 0.6068 GB, free: 6.426 MB / 0.5261 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002256/0.01149, allocations: 80.3 kB / 0.6069 GB, free: 6.352 MB / 0.5261 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001139/0.01263, allocations: 0.644 MB / 0.6075 GB, free: 5.672 MB / 0.5261 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 5.108e-05/0.01268, allocations: 84.83 kB / 0.6076 GB, free: 5.566 MB / 0.5261 GB Notification: Performance of simCode: alias equations: time 7.599e-05/0.01276, allocations: 26.28 kB / 0.6076 GB, free: 5.539 MB / 0.5261 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001509/0.01291, allocations: 135.2 kB / 0.6077 GB, free: 5.406 MB / 0.5261 GB Notification: Performance of SimCode: time 1.042e-06/0.01291, allocations: 0 / 0.6077 GB, free: 5.406 MB / 0.5261 GB Notification: Performance of Templates: time 0.005453/0.01836, allocations: 3.815 MB / 0.6114 GB, free: 1.801 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 -s gbode -gbm=radauIIA3 -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.Examples.PKTwoCompartmentModel.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 4.681009883992374]