Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PK_2C_Ibuprofen.conf.json loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo", uses=false) [Timeout 180] "[:1:22-1:33:writable] Warning: Modelica only supports 32-bit signed integers! Transforming: 13743895347 into a real Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo): time 0.0002097/0.0002097, allocations: 0 / 0, free: 0 / 0 " [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 0.0001736/0.0001736, allocations: 0 / 0, free: 0 / 0 " [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 0.09513/0.09513, allocations: 0 / 0, free: 0 / 0 " [Timeout remaining time 180] 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/Drugs/ATC/B/B02BD15.mo:9:22-9:32:writable] Warning: Modelica only supports 32-bit signed integers! Transforming: 6000000000 into a real [/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 0.5946/0.5946, allocations: 0 / 0, free: 0 / 0 " [Timeout remaining time 179] 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: simulate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PK_2C_Ibuprofen,startTime=0,stopTime=86400,tolerance=1e-06,numberOfIntervals=86400,outputFormat="empty",variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PK_2C_Ibuprofen",simflags="-abortSlowSimulation -alarm=240 -lv LOG_STATS") simulate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PK_2C_Ibuprofen,startTime=0,stopTime=86400,tolerance=1e-06,numberOfIntervals=86400,outputFormat="empty",variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.Pharmacogenomics.Patient_PK_2C_Ibuprofen",simflags="-abortSlowSimulation -alarm=240 -lv LOG_STATS") [Timeout 900] "Notification: Performance of FrontEnd - loaded program: time 1.573e-06/1.573e-06, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd - Absyn->SCode: time 2.461e-05/2.618e-05, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.Pharmacogenomics.Patient_PK_2C_Ibuprofen): time 0.005294/0.00532, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.instExpressions: time 0.001729/0.007049, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.updateImplicitVariability: time 0.0001564/0.007206, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeComponents: time 0.0001713/0.007377, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeBindings: time 0.00043/0.007807, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeClassSections: time 0.0003318/0.008139, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.flatten: time 0.0004081/0.008547, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.resolveConnections: time 0.0001805/0.008727, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFEvalConstants.evaluate: time 0.000345/0.009072, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFSimplifyModel.simplify: time 0.0002631/0.009335, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFPackage.collectConstants: time 4.174e-05/0.009377, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.collectFunctions: time 4.412e-05/0.009421, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFScalarize.scalarize: time 7.7e-05/0.009498, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFVerifyModel.verify: time 0.0001613/0.00966, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFConvertDAE.convert: time 0.0003816/0.01004, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd - DAE generated: time 5.319e-05/0.01009, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd: time 2.455e-06/0.0101, allocations: 0 / 0, free: 0 / 0 Notification: Performance of Transformations before backend: time 6.763e-06/0.0101, allocations: 0 / 0, free: 0 / 0 Notification: Model statistics after passing the front-end and creating the data structures used by the back-end: * Number of equations: 67 * Number of variables: 67 Notification: Performance of Generate backend data structure: time 0.0009344/0.01104, allocations: 0 / 0, free: 0 / 0 Notification: Performance of prepare preOptimizeDAE: time 0.00014/0.01118, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001294/0.01131, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002591/0.01157, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt simplifyIfEquations (simulation): time 4.964e-05/0.01162, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt expandDerOperator (simulation): time 6.158e-05/0.01168, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003852/0.01206, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt findStateOrder (simulation): time 1.774e-05/0.01208, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.798e-05/0.01212, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt inlineArrayEqn (simulation): time 8.005e-06/0.01213, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0002279/0.01235, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.00111/0.01346, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt comSubExp (simulation): time 0.0003054/0.01377, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt resolveLoops (simulation): time 8.703e-05/0.01386, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt evalFunc (simulation): time 1.914e-05/0.01388, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.0002983/0.01417, allocations: 0 / 0, free: 0 / 0 Notification: Performance of pre-optimization done (n=46): time 5.1e-06/0.01418, allocations: 0 / 0, free: 0 / 0 Notification: Performance of matching and sorting (n=49): time 0.001441/0.01562, allocations: 0 / 0, free: 0 / 0 Notification: Performance of inlineWhenForInitialization (initialization): time 5.961e-05/0.01568, allocations: 0 / 0, free: 0 / 0 Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001464/0.01583, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectPreVariables (initialization): time 5.169e-05/0.01588, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectInitialEqns (initialization): time 9.659e-05/0.01598, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectInitialBindings (initialization): time 0.0001322/0.01611, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001502/0.01626, allocations: 0 / 0, free: 0 / 0 Notification: Performance of setup shared object (initialization): time 3.98e-05/0.0163, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preBalanceInitialSystem (initialization): time 9.683e-05/0.01639, allocations: 0 / 0, free: 0 / 0 Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001257/0.01652, allocations: 0 / 0, free: 0 / 0 Notification: Performance of analyzeInitialSystem (initialization): time 0.0003505/0.01687, allocations: 0 / 0, free: 0 / 0 Notification: Performance of solveInitialSystemEqSystem (initialization): time 6.032e-06/0.01688, allocations: 0 / 0, free: 0 / 0 Notification: Performance of matching and sorting (n=73) (initialization): time 0.0003913/0.01727, allocations: 0 / 0, free: 0 / 0 Notification: Performance of prepare postOptimizeDAE: time 3.781e-05/0.01731, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyComplexFunction (initialization): time 8.817e-06/0.01731, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt tearingSystem (initialization): time 2.114e-05/0.01734, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003666/0.0177, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 2.007e-05/0.01772, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001955/0.01792, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt collapseArrayExpressions (initialization): time 3.484e-05/0.01795, allocations: 0 / 0, free: 0 / 0 Warning: Assuming fixed start value for the following 14 variables: central.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" type: Real periodicDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true ) \"Total dose adminitrated by this source\" type: Real periodicDose.absorptionLumen.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true ) \"area under curve\" 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 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 periodicDose.absorptionLumen.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true ) type: Real periodicDose.absorptionLumen.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 peripheral.rising:DISCRETE(fixed = true protected = true ) type: Boolean periodicDose.absorptionLumen.rising:DISCRETE(fixed = true protected = true ) type: Boolean central.rising:DISCRETE(fixed = true protected = true ) type: Boolean Notification: Model statistics after passing the back-end for initialization: * Number of independent subsystems: 16 * Number of states: 0 () * Number of discrete variables: 29 ($PRE.peripheral.Cmin,peripheral.Cmin,$PRE.peripheral.Cmax,peripheral.Cmax,$PRE.periodicDose.absorptionLumen.Cmin,periodicDose.absorptionLumen.Cmin,$PRE.periodicDose.absorptionLumen.Cmax,periodicDose.absorptionLumen.Cmax,$PRE.central.Cmin,central.Cmin,$PRE.central.Cmax,central.Cmax,$PRE.peripheral.rising,$PRE.periodicDose.pulse.count,$PRE.periodicDose.pulse.T_start,$PRE.periodicDose.absorptionLumen.rising,$PRE.central.rising,peripheral.rising,periodicDose.pulse.count,periodicDose.pulse.T_start,periodicDose.absorptionLumen.rising,central.rising,$whenCondition6,$whenCondition5,$whenCondition4,$whenCondition3,$whenCondition2,$whenCondition1,$whenCondition7) * Number of discrete states: 0 () * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for initialization (69): * Single equations (assignments): 65 * Array equations: 0 * Algorithm blocks: 4 * 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 0.0002368/0.01819, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt lateInlineFunction (simulation): time 6.619e-05/0.01826, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt wrapFunctionCalls (simulation): time 7.13e-05/0.01833, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.633e-06/0.01833, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt constantLinearSystem (simulation): time 9.227e-06/0.01834, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifysemiLinear (simulation): time 7.884e-06/0.01835, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0007607/0.01911, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.699e-06/0.01912, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0003046/0.01942, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt tearingSystem (simulation): time 6.111e-06/0.01943, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt inputDerivativesUsed (simulation): time 3.45e-05/0.01946, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 5.771e-06/0.01947, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.104e-06/0.01947, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005047/0.01997, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt removeConstants (simulation): time 0.0001312/0.02011, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001563/0.02026, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001697/0.02043, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001127/0.02054, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt collapseArrayExpressions (simulation): time 3.386e-05/0.02058, allocations: 0 / 0, free: 0 / 0 Notification: Performance of sorting global known variables: time 7.161e-05/0.02065, allocations: 0 / 0, free: 0 / 0 Notification: Performance of sort global known variables: time 6.782e-06/0.02066, allocations: 0 / 0, free: 0 / 0 Notification: Performance of remove unused functions: time 0.0005771/0.02123, allocations: 0 / 0, free: 0 / 0 Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 1 * Number of states: 9 (central.C,central.AUC,elim.MExc,periodicDose.TotalCumulativeMass,periodicDose.absorptionLumen.C,periodicDose.absorptionLumen.AUC,periodicDose.variableDose.TotalCumulativeMass,peripheral.C,peripheral.AUC) * Number of discrete variables: 18 ($whenCondition7,$whenCondition1,$whenCondition2,$whenCondition3,$whenCondition4,$whenCondition5,$whenCondition6,central.Cmax,central.Cmin,central.rising,periodicDose.absorptionLumen.Cmax,periodicDose.absorptionLumen.Cmin,periodicDose.absorptionLumen.rising,periodicDose.pulse.T_start,periodicDose.pulse.count,peripheral.Cmax,peripheral.Cmin,peripheral.rising) * Number of discrete states: 16 (periodicDose.pulse.count,peripheral.Cmin,$whenCondition6,peripheral.Cmax,$whenCondition5,peripheral.rising,periodicDose.absorptionLumen.Cmin,$whenCondition4,periodicDose.absorptionLumen.Cmax,$whenCondition3,periodicDose.absorptionLumen.rising,central.Cmin,$whenCondition2,central.Cmax,$whenCondition1,central.rising) * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for simulation (40): * Single equations (assignments): 35 * Array equations: 0 * Algorithm blocks: 3 * 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 0.0001843/0.02142, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created initialization part: time 0.0004591/0.02188, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created event and clocks part: time 7.274e-06/0.02188, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created simulation system equations: time 0.0001868/0.02207, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0006799/0.02275, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001476/0.02423, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: some other stuff during SimCode phase: time 8.545e-05/0.02431, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: alias equations: time 0.0001355/0.02445, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0003065/0.02475, allocations: 0 / 0, free: 0 / 0 Notification: Performance of SimCode: time 2.943e-05/0.02478, allocations: 0 / 0, free: 0 / 0 Notification: Performance of Templates: time 0.001573/0.02636, allocations: 0 / 0, free: 0 / 0 " [Timeout remaining time 900] [Calling sys.exit(0), Time elapsed: 1.380254038143903]