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 0.0009364/0.0009364, allocations: 80.94 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 0.001061/0.001061, allocations: 177 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 1.006/1.006, allocations: 177.1 MB / 203.8 MB, free: 5.48 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 1.693/1.693, allocations: 273.5 MB / 0.5213 GB, free: 14.66 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 2.104e-06/2.104e-06, allocations: 0 / 0.5954 GB, free: 2.715 MB / 0.5105 GB Notification: Performance of FrontEnd - Absyn->SCode: time 2.33e-05/2.541e-05, allocations: 2.312 kB / 0.5954 GB, free: 2.711 MB / 0.5105 GB Notification: Performance of NFInst.instantiate(Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver): time 0.003775/0.003801, allocations: 4.119 MB / 0.5995 GB, free: 14.63 MB / 0.5261 GB Notification: Performance of NFInst.instExpressions: time 0.001808/0.005609, allocations: 0.9821 MB / 0.6004 GB, free: 13.66 MB / 0.5261 GB Notification: Performance of NFInst.updateImplicitVariability: time 0.0001926/0.005802, allocations: 8 kB / 0.6004 GB, free: 13.65 MB / 0.5261 GB Notification: Performance of NFTyping.typeComponents: time 0.0001714/0.005973, allocations: 80.58 kB / 0.6005 GB, free: 13.57 MB / 0.5261 GB Notification: Performance of NFTyping.typeBindings: time 0.0004574/0.00643, allocations: 212.7 kB / 0.6007 GB, free: 13.4 MB / 0.5261 GB Notification: Performance of NFTyping.typeClassSections: time 0.0003267/0.006757, allocations: 159.6 kB / 0.6009 GB, free: 13.25 MB / 0.5261 GB Notification: Performance of NFFlatten.flatten: time 0.0006246/0.007382, allocations: 0.7113 MB / 0.6016 GB, free: 12.53 MB / 0.5261 GB Notification: Performance of NFFlatten.resolveConnections: time 0.0005454/0.007927, allocations: 0.5116 MB / 0.6021 GB, free: 12.02 MB / 0.5261 GB Notification: Performance of NFEvalConstants.evaluate: time 0.0005417/0.008469, allocations: 495.2 kB / 0.6025 GB, free: 11.53 MB / 0.5261 GB Notification: Performance of NFSimplifyModel.simplify: time 0.0005044/0.008973, allocations: 347.2 kB / 0.6029 GB, free: 11.19 MB / 0.5261 GB Notification: Performance of NFPackage.collectConstants: time 9.367e-05/0.009067, allocations: 80 kB / 0.6029 GB, free: 11.11 MB / 0.5261 GB Notification: Performance of NFFlatten.collectFunctions: time 9.362e-05/0.00916, allocations: 76 kB / 0.603 GB, free: 11.04 MB / 0.5261 GB Notification: Performance of NFScalarize.scalarize: time 0.0001161/0.009276, allocations: 179.5 kB / 0.6032 GB, free: 10.86 MB / 0.5261 GB Notification: Performance of NFVerifyModel.verify: time 0.000199/0.009476, allocations: 267.4 kB / 0.6034 GB, free: 10.6 MB / 0.5261 GB Notification: Performance of NFConvertDAE.convert: time 0.000504/0.009979, allocations: 0.5256 MB / 0.6039 GB, free: 10.07 MB / 0.5261 GB Notification: Performance of FrontEnd - DAE generated: time 3.557e-06/0.009983, allocations: 0 / 0.6039 GB, free: 10.07 MB / 0.5261 GB Notification: Performance of FrontEnd: time 1.563e-06/0.009985, allocations: 0 / 0.6039 GB, free: 10.07 MB / 0.5261 GB Notification: Performance of Transformations before backend: time 1.029e-05/0.009995, allocations: 0 / 0.6039 GB, free: 10.07 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 0.0009798/0.01097, allocations: 0.7372 MB / 0.6047 GB, free: 9.301 MB / 0.5261 GB Notification: Performance of prepare preOptimizeDAE: time 3.127e-05/0.01101, allocations: 8.031 kB / 0.6047 GB, free: 9.293 MB / 0.5261 GB Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001099/0.01112, allocations: 80.86 kB / 0.6047 GB, free: 9.215 MB / 0.5261 GB Notification: Performance of preOpt evaluateParameters (simulation): time 0.000286/0.0114, allocations: 222.1 kB / 0.605 GB, free: 8.973 MB / 0.5261 GB Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.195e-05/0.01143, allocations: 33.38 kB / 0.605 GB, free: 8.941 MB / 0.5261 GB Notification: Performance of preOpt expandDerOperator (simulation): time 6.63e-05/0.0115, allocations: 60.31 kB / 0.605 GB, free: 8.883 MB / 0.5261 GB Notification: Performance of preOpt clockPartitioning (simulation): time 0.000544/0.01204, allocations: 0.5787 MB / 0.6056 GB, free: 8.262 MB / 0.5261 GB Notification: Performance of preOpt findStateOrder (simulation): time 2.082e-05/0.01206, allocations: 7.938 kB / 0.6056 GB, free: 8.254 MB / 0.5261 GB Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.541e-05/0.0121, allocations: 19.66 kB / 0.6056 GB, free: 8.238 MB / 0.5261 GB Notification: Performance of preOpt inlineArrayEqn (simulation): time 3.008e-05/0.01213, allocations: 21 kB / 0.6057 GB, free: 8.219 MB / 0.5261 GB Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002774/0.01241, allocations: 218.8 kB / 0.6059 GB, free: 8.004 MB / 0.5261 GB Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001434/0.01384, allocations: 1.032 MB / 0.6069 GB, free: 6.949 MB / 0.5261 GB Notification: Performance of preOpt comSubExp (simulation): time 0.0002907/0.01413, allocations: 184.8 kB / 0.6071 GB, free: 6.762 MB / 0.5261 GB Notification: Performance of preOpt resolveLoops (simulation): time 0.0001132/0.01425, allocations: 85.55 kB / 0.6071 GB, free: 6.676 MB / 0.5261 GB Notification: Performance of preOpt evalFunc (simulation): time 2.528e-05/0.01427, allocations: 12.38 kB / 0.6071 GB, free: 6.664 MB / 0.5261 GB Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002452/0.01452, allocations: 235.4 kB / 0.6074 GB, free: 6.418 MB / 0.5261 GB Notification: Performance of preOpt simplifyInStream (simulation): time 0.0003915/0.01491, allocations: 151.6 kB / 0.6075 GB, free: 6.27 MB / 0.5261 GB Notification: Performance of pre-optimization done (n=46): time 2.424e-06/0.01491, allocations: 4 kB / 0.6075 GB, free: 6.266 MB / 0.5261 GB Notification: Performance of matching and sorting (n=46): time 0.0004271/0.01534, allocations: 291 kB / 0.6078 GB, free: 5.977 MB / 0.5261 GB Notification: Performance of inlineWhenForInitialization (initialization): time 3.169e-05/0.01537, allocations: 55.41 kB / 0.6078 GB, free: 5.91 MB / 0.5261 GB Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001426/0.01551, allocations: 240.9 kB / 0.6081 GB, free: 5.668 MB / 0.5261 GB Notification: Performance of collectPreVariables (initialization): time 3.367e-05/0.01555, allocations: 37.7 kB / 0.6081 GB, free: 5.625 MB / 0.5261 GB Notification: Performance of collectInitialEqns (initialization): time 8.957e-05/0.01564, allocations: 225.5 kB / 0.6083 GB, free: 5.398 MB / 0.5261 GB Notification: Performance of collectInitialBindings (initialization): time 9.386e-05/0.01573, allocations: 178.5 kB / 0.6085 GB, free: 5.223 MB / 0.5261 GB Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001166/0.01585, allocations: 114.2 kB / 0.6086 GB, free: 5.105 MB / 0.5261 GB Notification: Performance of setup shared object (initialization): time 9.492e-05/0.01594, allocations: 358.7 kB / 0.609 GB, free: 4.746 MB / 0.5261 GB Notification: Performance of preBalanceInitialSystem (initialization): time 0.0003864/0.01633, allocations: 132.7 kB / 0.6091 GB, free: 4.609 MB / 0.5261 GB Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001842/0.01651, allocations: 264.9 kB / 0.6093 GB, free: 4.289 MB / 0.5261 GB Notification: Performance of analyzeInitialSystem (initialization): time 0.0003494/0.01686, allocations: 375 kB / 0.6097 GB, free: 3.871 MB / 0.5261 GB Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.186e-06/0.01686, allocations: 0 / 0.6097 GB, free: 3.871 MB / 0.5261 GB Notification: Performance of matching and sorting (n=72) (initialization): time 0.0003955/0.01726, allocations: 401.5 kB / 0.6101 GB, free: 3.461 MB / 0.5261 GB Notification: Performance of prepare postOptimizeDAE: time 3.096e-05/0.01729, allocations: 38.17 kB / 0.6101 GB, free: 3.418 MB / 0.5261 GB Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.456e-06/0.0173, allocations: 11.94 kB / 0.6101 GB, free: 3.406 MB / 0.5261 GB Notification: Performance of postOpt tearingSystem (initialization): time 1.579e-05/0.01731, allocations: 8 kB / 0.6101 GB, free: 3.398 MB / 0.5261 GB Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0005666/0.01788, allocations: 204.3 kB / 0.6103 GB, free: 3.199 MB / 0.5261 GB Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 7.043e-06/0.01789, allocations: 8 kB / 0.6103 GB, free: 3.191 MB / 0.5261 GB Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001669/0.01805, allocations: 19.98 kB / 0.6103 GB, free: 3.172 MB / 0.5261 GB Notification: Performance of postOpt collapseArrayExpressions (initialization): time 3.124e-05/0.01809, allocations: 27.97 kB / 0.6104 GB, free: 3.145 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 0.0001795/0.01827, allocations: 173.7 kB / 0.6105 GB, free: 2.969 MB / 0.5261 GB Notification: Performance of postOpt lateInlineFunction (simulation): time 5.185e-05/0.01832, allocations: 43.91 kB / 0.6106 GB, free: 2.926 MB / 0.5261 GB Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0003939/0.01871, allocations: 310.4 kB / 0.6109 GB, free: 2.629 MB / 0.5261 GB Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.569e-06/0.01872, allocations: 8 kB / 0.6109 GB, free: 2.621 MB / 0.5261 GB Notification: Performance of postOpt constantLinearSystem (simulation): time 1.423e-06/0.01872, allocations: 0 / 0.6109 GB, free: 2.621 MB / 0.5261 GB Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.7e-06/0.01872, allocations: 3.984 kB / 0.6109 GB, free: 2.617 MB / 0.5261 GB Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0005103/0.01923, allocations: 0.503 MB / 0.6114 GB, free: 2.086 MB / 0.5261 GB Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.024e-06/0.01924, allocations: 0 / 0.6114 GB, free: 2.086 MB / 0.5261 GB Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0002697/0.0195, allocations: 87.88 kB / 0.6115 GB, free: 2 MB / 0.5261 GB Notification: Performance of postOpt tearingSystem (simulation): time 3.296e-06/0.01951, allocations: 0 / 0.6115 GB, free: 2 MB / 0.5261 GB Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.314e-05/0.01953, allocations: 11.98 kB / 0.6115 GB, free: 1.988 MB / 0.5261 GB Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.356e-06/0.01953, allocations: 4 kB / 0.6115 GB, free: 1.984 MB / 0.5261 GB Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.934e-06/0.01954, allocations: 0 / 0.6115 GB, free: 1.984 MB / 0.5261 GB Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004286/0.01997, allocations: 441.6 kB / 0.6119 GB, free: 1.535 MB / 0.5261 GB Notification: Performance of postOpt removeConstants (simulation): time 2.724e-05/0.01999, allocations: 23.81 kB / 0.6119 GB, free: 1.512 MB / 0.5261 GB Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.925e-05/0.02003, allocations: 15.95 kB / 0.6119 GB, free: 1.496 MB / 0.5261 GB Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001441/0.02018, allocations: 19.92 kB / 0.612 GB, free: 1.477 MB / 0.5261 GB Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001882/0.02036, allocations: 27.94 kB / 0.612 GB, free: 1.449 MB / 0.5261 GB Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.261e-05/0.02039, allocations: 19.92 kB / 0.612 GB, free: 1.43 MB / 0.5261 GB Notification: Performance of sorting global known variables: time 7.107e-05/0.02046, allocations: 92.62 kB / 0.6121 GB, free: 1.344 MB / 0.5261 GB Notification: Performance of sort global known variables: time 4e-08/0.02046, allocations: 0 / 0.6121 GB, free: 1.344 MB / 0.5261 GB Notification: Performance of remove unused functions: time 0.0003075/0.02077, allocations: 171.7 kB / 0.6123 GB, free: 1.176 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 0.0001048/0.02087, allocations: 96.36 kB / 0.6123 GB, free: 1.074 MB / 0.5261 GB Notification: Performance of simCode: created initialization part: time 0.0003673/0.02124, allocations: 354.4 kB / 0.6127 GB, free: 0.7109 MB / 0.5261 GB Notification: Performance of simCode: created event and clocks part: time 4.819e-06/0.02124, allocations: 0 / 0.6127 GB, free: 0.7109 MB / 0.5261 GB Notification: Performance of simCode: created simulation system equations: time 0.0001393/0.02138, allocations: 124.8 kB / 0.6128 GB, free: 0.5859 MB / 0.5261 GB Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003819/0.02176, allocations: 143.9 kB / 0.6129 GB, free: 460 kB / 0.5261 GB Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.3553/0.3771, allocations: 1.025 MB / 0.6139 GB, free: 52.91 MB / 0.5262 GB Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001048/0.3772, allocations: 123.8 kB / 0.6141 GB, free: 52.84 MB / 0.5262 GB Notification: Performance of simCode: alias equations: time 0.0003547/0.3775, allocations: 74.56 kB / 0.6141 GB, free: 52.84 MB / 0.5262 GB Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003859/0.3779, allocations: 181.7 kB / 0.6143 GB, free: 52.8 MB / 0.5262 GB Notification: Performance of SimCode: time 2.625e-06/0.3779, allocations: 2.094 kB / 0.6143 GB, free: 52.8 MB / 0.5262 GB Notification: Performance of Templates: time 0.01112/0.3891, allocations: 8.749 MB / 0.6229 GB, free: 50.54 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 -s gbode -gbm=radauIIA3 -lv LOG_STATS > Pharmacolibrary_Pharmacolibrary.DevModels.SingleDoseVeinsGutSpleenPortalVeinLiver.pipe 2>&1) [Timeout 240] [Calling sys.exit(0), Time elapsed: 5.305992326699197]