Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver.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 0.0009482/0.0009482, 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 0.0009825/0.0009825, allocations: 181 kB / 23.36 MB, free: 1.129 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 0.9489/0.9489, allocations: 177.1 MB / 203.8 MB, free: 5.438 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 1.657/1.657, allocations: 273.5 MB / 0.5212 GB, free: 14.64 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.SingleDoseVeinsGutSpleenPortalVeinLiver,tolerance=1e-06,outputFormat="empty",numberOfIntervals=495,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver") translateModel(Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver,tolerance=1e-06,outputFormat="empty",numberOfIntervals=495,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver") [Timeout 660] "Notification: Performance of FrontEnd - loaded program: time 1.513e-06/1.513e-06, allocations: 0 / 0.5954 GB, free: 2.719 MB / 0.5105 GB Notification: Performance of FrontEnd - Absyn->SCode: time 2.734e-05/2.886e-05, allocations: 5.688 kB / 0.5954 GB, free: 2.715 MB / 0.5105 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver): time 0.004412/0.004441, allocations: 4.071 MB / 0.5994 GB, free: 14.68 MB / 0.5261 GB Notification: Performance of NFInst.instExpressions: time 0.00175/0.00619, allocations: 0.9903 MB / 0.6003 GB, free: 13.7 MB / 0.5261 GB Notification: Performance of NFInst.updateImplicitVariability: time 0.0001758/0.006366, allocations: 8 kB / 0.6003 GB, free: 13.69 MB / 0.5261 GB Notification: Performance of NFTyping.typeComponents: time 0.0001665/0.006533, allocations: 76.58 kB / 0.6004 GB, free: 13.62 MB / 0.5261 GB Notification: Performance of NFTyping.typeBindings: time 0.0004375/0.00697, allocations: 213.6 kB / 0.6006 GB, free: 13.45 MB / 0.5261 GB Notification: Performance of NFTyping.typeClassSections: time 0.0002965/0.007267, allocations: 151.7 kB / 0.6008 GB, free: 13.3 MB / 0.5261 GB Notification: Performance of NFFlatten.flatten: time 0.0005534/0.00782, allocations: 0.7113 MB / 0.6015 GB, free: 12.59 MB / 0.5261 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0004885/0.008309, allocations: 0.5038 MB / 0.602 GB, free: 12.08 MB / 0.5261 GB Notification: Performance of NFEvalConstants.evaluate: time 0.00046/0.008769, allocations: 0.4913 MB / 0.6024 GB, free: 11.59 MB / 0.5261 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0004383/0.009207, allocations: 355.1 kB / 0.6028 GB, free: 11.24 MB / 0.5261 GB Notification: Performance of NFPackage.collectConstants: time 7.484e-05/0.009282, allocations: 72 kB / 0.6028 GB, free: 11.17 MB / 0.5261 GB Notification: Performance of NFFlatten.collectFunctions: time 7.936e-05/0.009361, allocations: 76 kB / 0.6029 GB, free: 11.09 MB / 0.5261 GB Notification: Performance of NFScalarize.scalarize: time 0.0001212/0.009482, allocations: 175.5 kB / 0.6031 GB, free: 10.92 MB / 0.5261 GB Notification: Performance of NFVerifyModel.verify: time 0.0001822/0.009665, allocations: 275.5 kB / 0.6033 GB, free: 10.65 MB / 0.5261 GB Notification: Performance of NFConvertDAE.convert: time 0.0007148/0.01038, allocations: 0.5178 MB / 0.6038 GB, free: 10.13 MB / 0.5261 GB Notification: Performance of FrontEnd - DAE generated: time 5.801e-06/0.01039, allocations: 4 kB / 0.6039 GB, free: 10.13 MB / 0.5261 GB Notification: Performance of FrontEnd: time 1.252e-06/0.01039, allocations: 4 kB / 0.6039 GB, free: 10.12 MB / 0.5261 GB Notification: Performance of Transformations before backend: time 7.895e-06/0.01039, allocations: 0 / 0.6039 GB, free: 10.12 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: 124 * Number of variables: 124 Notification: Performance of Generate backend data structure: time 0.0009602/0.01135, allocations: 0.7449 MB / 0.6046 GB, free: 9.344 MB / 0.5261 GB Notification: Performance of prepare preOptimizeDAE: time 3.68e-05/0.01139, allocations: 8.031 kB / 0.6046 GB, free: 9.336 MB / 0.5261 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 9.866e-05/0.01149, allocations: 68.89 kB / 0.6047 GB, free: 9.27 MB / 0.5261 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002727/0.01176, allocations: 230.1 kB / 0.6049 GB, free: 9.016 MB / 0.5261 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 4.016e-05/0.0118, allocations: 37.38 kB / 0.6049 GB, free: 8.98 MB / 0.5261 GB Notification: Performance of preOpt expandDerOperator (simulation): time 6.423e-05/0.01187, allocations: 56.33 kB / 0.605 GB, free: 8.926 MB / 0.5261 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.0005188/0.01239, allocations: 0.5709 MB / 0.6055 GB, free: 8.312 MB / 0.5261 GB Notification: Performance of preOpt findStateOrder (simulation): time 1.94e-05/0.01241, allocations: 7.875 kB / 0.6055 GB, free: 8.305 MB / 0.5261 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.514e-05/0.01244, allocations: 28 kB / 0.6056 GB, free: 8.277 MB / 0.5261 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 3.365e-05/0.01247, allocations: 17 kB / 0.6056 GB, free: 8.262 MB / 0.5261 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002672/0.01274, allocations: 219.3 kB / 0.6058 GB, free: 8.047 MB / 0.5261 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001501/0.01424, allocations: 1.032 MB / 0.6068 GB, free: 6.996 MB / 0.5261 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0003025/0.01454, allocations: 180.8 kB / 0.607 GB, free: 6.812 MB / 0.5261 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.0001125/0.01466, allocations: 89.53 kB / 0.607 GB, free: 6.723 MB / 0.5261 GB Notification: Performance of preOpt evalFunc (simulation): time 2.873e-05/0.01469, allocations: 15.8 kB / 0.6071 GB, free: 6.711 MB / 0.5261 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002628/0.01495, allocations: 232.3 kB / 0.6073 GB, free: 6.469 MB / 0.5261 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.0003827/0.01533, allocations: 159.6 kB / 0.6074 GB, free: 6.312 MB / 0.5261 GB Notification: Performance of pre-optimization done (n=46): time 3.607e-06/0.01533, allocations: 0 / 0.6074 GB, free: 6.312 MB / 0.5261 GB Notification: Performance of matching and sorting (n=46): time 0.0004458/0.01578, allocations: 283.2 kB / 0.6077 GB, free: 6.031 MB / 0.5261 GB Notification: Performance of inlineWhenForInitialization (initialization): time 4.328e-05/0.01582, allocations: 59.41 kB / 0.6078 GB, free: 5.961 MB / 0.5261 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.000154/0.01598, allocations: 240.9 kB / 0.608 GB, free: 5.719 MB / 0.5261 GB Notification: Performance of collectPreVariables (initialization): time 3.926e-05/0.01602, allocations: 33.7 kB / 0.608 GB, free: 5.68 MB / 0.5261 GB Notification: Performance of collectInitialEqns (initialization): time 0.0001052/0.01612, allocations: 229.5 kB / 0.6082 GB, free: 5.449 MB / 0.5261 GB Notification: Performance of collectInitialBindings (initialization): time 9.757e-05/0.01622, allocations: 178.5 kB / 0.6084 GB, free: 5.273 MB / 0.5261 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001152/0.01634, allocations: 110.2 kB / 0.6085 GB, free: 5.16 MB / 0.5261 GB Notification: Performance of setup shared object (initialization): time 0.0001013/0.01644, allocations: 346.7 kB / 0.6089 GB, free: 4.812 MB / 0.5261 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001513/0.01659, allocations: 152.6 kB / 0.609 GB, free: 4.656 MB / 0.5261 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0002067/0.01679, allocations: 265 kB / 0.6092 GB, free: 4.336 MB / 0.5261 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0003246/0.01712, allocations: 375 kB / 0.6096 GB, free: 3.918 MB / 0.5261 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.497e-06/0.01712, allocations: 0 / 0.6096 GB, free: 3.918 MB / 0.5261 GB Notification: Performance of matching and sorting (n=72) (initialization): time 0.0004057/0.01753, allocations: 401.6 kB / 0.61 GB, free: 3.508 MB / 0.5261 GB Notification: Performance of prepare postOptimizeDAE: time 3.844e-05/0.01757, allocations: 33.7 kB / 0.61 GB, free: 3.469 MB / 0.5261 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.004e-05/0.01758, allocations: 11.92 kB / 0.61 GB, free: 3.457 MB / 0.5261 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.742e-05/0.01759, allocations: 4 kB / 0.61 GB, free: 3.453 MB / 0.5261 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003472/0.01794, allocations: 160.2 kB / 0.6102 GB, free: 3.297 MB / 0.5261 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.867e-06/0.01795, allocations: 15.94 kB / 0.6102 GB, free: 3.281 MB / 0.5261 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.000159/0.01811, allocations: 19.98 kB / 0.6102 GB, free: 3.262 MB / 0.5261 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 3.106e-05/0.01814, allocations: 27.97 kB / 0.6103 GB, free: 3.234 MB / 0.5261 GB Warning: Assuming fixed start value for the following 8 variables: singleDose1.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true ) \"Total dose adminitrated by this source\" type: Real singleDose1.variableDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true ) \"Total dose adminitrated by this source\" type: Real artery.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real gut.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real vein.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real spleen.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real liver.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real lungs.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real Notification: Model statistics after passing the back-end for initialization: * Number of independent subsystems: 16 * Number of states: 0 () * Number of discrete variables: 5 (singleDose1.pulse.count,$PRE.singleDose1.pulse.count,singleDose1.pulse.T_start,$PRE.singleDose1.pulse.T_start,$whenCondition1) * Number of discrete states: 0 () * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for initialization (71): * Single equations (assignments): 70 * Array equations: 0 * Algorithm blocks: 1 * 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 0.0002048/0.01834, allocations: 169.3 kB / 0.6104 GB, free: 3.059 MB / 0.5261 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 4.811e-05/0.01839, allocations: 31.97 kB / 0.6104 GB, free: 3.027 MB / 0.5261 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0007185/0.01911, allocations: 313.9 kB / 0.6107 GB, free: 2.73 MB / 0.5261 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.97e-06/0.01912, allocations: 4 kB / 0.6107 GB, free: 2.727 MB / 0.5261 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 2.124e-06/0.01912, allocations: 3.938 kB / 0.6107 GB, free: 2.723 MB / 0.5261 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.021e-06/0.01912, allocations: 3.984 kB / 0.6108 GB, free: 2.719 MB / 0.5261 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005376/0.01966, allocations: 0.5021 MB / 0.6112 GB, free: 2.191 MB / 0.5261 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.344e-06/0.01966, allocations: 0 / 0.6112 GB, free: 2.191 MB / 0.5261 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002487/0.01991, allocations: 79.89 kB / 0.6113 GB, free: 2.113 MB / 0.5261 GB Notification: Performance of postOpt tearingSystem (simulation): time 5.139e-06/0.01992, allocations: 7.938 kB / 0.6113 GB, free: 2.105 MB / 0.5261 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.335e-05/0.01994, allocations: 11.98 kB / 0.6113 GB, free: 2.094 MB / 0.5261 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.258e-06/0.01995, allocations: 4 kB / 0.6113 GB, free: 2.09 MB / 0.5261 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.333e-06/0.01995, allocations: 0 / 0.6113 GB, free: 2.09 MB / 0.5261 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004423/0.02039, allocations: 437.7 kB / 0.6118 GB, free: 1.645 MB / 0.5261 GB Notification: Performance of postOpt removeConstants (simulation): time 3.022e-05/0.02042, allocations: 23.81 kB / 0.6118 GB, free: 1.621 MB / 0.5261 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.883e-05/0.02046, allocations: 15.95 kB / 0.6118 GB, free: 1.605 MB / 0.5261 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001402/0.0206, allocations: 15.98 kB / 0.6118 GB, free: 1.59 MB / 0.5261 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 5.935e-05/0.02066, allocations: 31.94 kB / 0.6118 GB, free: 1.559 MB / 0.5261 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.934e-05/0.02068, allocations: 11.98 kB / 0.6119 GB, free: 1.547 MB / 0.5261 GB Notification: Performance of sorting global known variables: time 6.846e-05/0.02075, allocations: 96.62 kB / 0.6119 GB, free: 1.457 MB / 0.5261 GB Notification: Performance of sort global known variables: time 4e-08/0.02075, allocations: 0 / 0.6119 GB, free: 1.457 MB / 0.5261 GB Notification: Performance of remove unused functions: time 0.0003251/0.02107, allocations: 175.6 kB / 0.6121 GB, free: 1.285 MB / 0.5261 GB Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 2 * Number of states: 14 (singleDose1.TotalCumulativeMass,singleDose1.variableDose.TotalCumulativeMass,artery.M,artery.AUC,gut.M,gut.AUC,vein.M,vein.AUC,spleen.M,spleen.AUC,liver.M,liver.AUC,lungs.M,lungs.AUC) * Number of discrete variables: 3 ($whenCondition1,singleDose1.pulse.T_start,singleDose1.pulse.count) * Number of discrete states: 1 (singleDose1.pulse.count) * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for simulation (46): * Single equations (assignments): 44 * Array equations: 0 * Algorithm blocks: 0 * 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 0.0001254/0.0212, allocations: 95.2 kB / 0.6122 GB, free: 1.188 MB / 0.5261 GB Notification: Performance of simCode: created initialization part: time 0.0003622/0.02156, allocations: 358.3 kB / 0.6125 GB, free: 0.8203 MB / 0.5261 GB Notification: Performance of simCode: created event and clocks part: time 6.512e-06/0.02157, allocations: 7.938 kB / 0.6126 GB, free: 0.8125 MB / 0.5261 GB Notification: Performance of simCode: created simulation system equations: time 0.0001384/0.0217, allocations: 120.7 kB / 0.6127 GB, free: 0.6914 MB / 0.5261 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003837/0.02209, allocations: 150.6 kB / 0.6128 GB, free: 0.5469 MB / 0.5261 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.3538/0.3759, allocations: 1.024 MB / 0.6138 GB, free: 52.98 MB / 0.5262 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001126/0.376, allocations: 120.5 kB / 0.6139 GB, free: 52.91 MB / 0.5262 GB Notification: Performance of simCode: alias equations: time 0.0003724/0.3764, allocations: 71.23 kB / 0.614 GB, free: 52.91 MB / 0.5262 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.000404/0.3768, allocations: 178.4 kB / 0.6142 GB, free: 52.88 MB / 0.5262 GB Notification: Performance of SimCode: time 3.356e-06/0.3768, allocations: 1.125 kB / 0.6142 GB, free: 52.88 MB / 0.5262 GB Notification: Performance of Templates: time 0.01309/0.3899, allocations: 8.438 MB / 0.6224 GB, free: 50.73 MB / 0.5262 GB " [Timeout remaining time 660] make -j1 -f Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver.makefile [Timeout 660] (rm -f Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver.sim & ./Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver -abortSlowSimulation -alarm=240 -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 5.0164768868125975]