Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr BioChem_BioChem.Examples.GMO.cell.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 0.0002489/0.0002489, 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 0.0001815/0.0001815, 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 0.1076/0.1076, allocations: 0 / 0, free: 0 / 0 " [Timeout remaining time 180] loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.3/package.mo", uses=false) [Timeout 180] "Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.3/package.mo): time 0.07827/0.07827, allocations: 0 / 0, free: 0 / 0 " [Timeout remaining time 180] Using package BioChem with version 1.1.3 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.3/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(BioChem.Examples.GMO.cell,startTime=0,stopTime=100,tolerance=1e-06,numberOfIntervals=2500,outputFormat="empty",variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.GMO.cell",simflags="-abortSlowSimulation -alarm=240 -lv LOG_STATS") simulate(BioChem.Examples.GMO.cell,startTime=0,stopTime=100,tolerance=1e-06,numberOfIntervals=2500,outputFormat="empty",variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.GMO.cell",simflags="-abortSlowSimulation -alarm=240 -lv LOG_STATS") [Timeout 900] "Notification: Performance of FrontEnd - loaded program: time 3.807e-06/3.807e-06, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd - Absyn->SCode: time 2.15e-05/2.531e-05, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.007716/0.007741, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.instExpressions: time 0.0009282/0.008669, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.updateImplicitVariability: time 0.0001287/0.008798, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeComponents: time 0.000166/0.008964, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeBindings: time 0.0002178/0.009182, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeClassSections: time 0.0002048/0.009387, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.flatten: time 0.0002955/0.009682, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.resolveConnections: time 0.0002327/0.009915, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFEvalConstants.evaluate: time 0.0002467/0.01016, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFSimplifyModel.simplify: time 0.0001444/0.01031, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFPackage.collectConstants: time 4.521e-05/0.01035, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.collectFunctions: time 3.922e-05/0.01039, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFScalarize.scalarize: time 7.939e-05/0.01047, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFVerifyModel.verify: time 9.236e-05/0.01056, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFConvertDAE.convert: time 0.0002803/0.01084, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd - DAE generated: time 4.605e-05/0.01089, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd: time 4.608e-06/0.01089, allocations: 0 / 0, free: 0 / 0 Notification: Performance of Transformations before backend: time 1.08e-05/0.0109, 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: 96 * Number of variables: 96 Notification: Performance of Generate backend data structure: time 0.0008427/0.01175, allocations: 0 / 0, free: 0 / 0 Notification: Performance of prepare preOptimizeDAE: time 0.0001041/0.01185, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt normalInlineFunction (simulation): time 9.916e-05/0.01195, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt evaluateParameters (simulation): time 0.000125/0.01208, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt simplifyIfEquations (simulation): time 4.761e-05/0.01212, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt expandDerOperator (simulation): time 5.939e-05/0.01218, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003049/0.01249, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt findStateOrder (simulation): time 1.577e-05/0.0125, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.437e-05/0.01254, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt inlineArrayEqn (simulation): time 9.137e-06/0.01255, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001621/0.01271, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001271/0.01398, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt comSubExp (simulation): time 0.0002123/0.01419, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt resolveLoops (simulation): time 9.013e-05/0.01428, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt evalFunc (simulation): time 8.355e-06/0.01429, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.966e-05/0.01431, allocations: 0 / 0, free: 0 / 0 Notification: Performance of pre-optimization done (n=22): time 4.138e-06/0.01431, allocations: 0 / 0, free: 0 / 0 Notification: Performance of matching and sorting (n=26): time 0.001348/0.01566, allocations: 0 / 0, free: 0 / 0 Notification: Performance of inlineWhenForInitialization (initialization): time 3.792e-05/0.0157, allocations: 0 / 0, free: 0 / 0 Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001088/0.01581, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectPreVariables (initialization): time 3.355e-05/0.01584, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectInitialEqns (initialization): time 9.764e-05/0.01594, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectInitialBindings (initialization): time 6.561e-05/0.01601, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simplifyInitialFunctions (initialization): time 7.603e-05/0.01608, allocations: 0 / 0, free: 0 / 0 Notification: Performance of setup shared object (initialization): time 2.109e-05/0.0161, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preBalanceInitialSystem (initialization): time 4.527e-05/0.01615, allocations: 0 / 0, free: 0 / 0 Notification: Performance of partitionIndependentBlocks (initialization): time 8.77e-05/0.01624, allocations: 0 / 0, free: 0 / 0 Notification: Performance of analyzeInitialSystem (initialization): time 0.0002603/0.0165, allocations: 0 / 0, free: 0 / 0 Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.638e-06/0.0165, allocations: 0 / 0, free: 0 / 0 Notification: Performance of matching and sorting (n=46) (initialization): time 0.0002653/0.01677, allocations: 0 / 0, free: 0 / 0 Notification: Performance of prepare postOptimizeDAE: time 1.655e-05/0.01678, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyComplexFunction (initialization): time 7.364e-06/0.01679, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt tearingSystem (initialization): time 1.617e-05/0.01681, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002015/0.01701, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.323e-05/0.01702, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001105/0.01713, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.039e-05/0.01715, allocations: 0 / 0, free: 0 / 0 Warning: Assuming fixed start value for the following 5 variables: V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer ) \"Compartment volume\" type: Real ambientSubstance.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real X.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real M.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real C.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" 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: 0 () * Number of discrete states: 0 () * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for initialization (46): * Single equations (assignments): 46 * Array equations: 0 * Algorithm blocks: 0 * 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 0.0001729/0.01732, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt lateInlineFunction (simulation): time 3.649e-05/0.01736, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt wrapFunctionCalls (simulation): time 5.839e-05/0.01742, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt inlineArrayEqn (simulation): time 4.268e-06/0.01742, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt constantLinearSystem (simulation): time 4.549e-06/0.01743, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.168e-06/0.01743, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004112/0.01784, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.747e-06/0.01785, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001429/0.01799, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt tearingSystem (simulation): time 4.098e-06/0.01799, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.307e-05/0.01802, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.268e-06/0.01802, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.854e-06/0.01802, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0002933/0.01832, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt removeConstants (simulation): time 4.168e-05/0.01836, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 7.639e-05/0.01843, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyAllExpressions (simulation): time 9.786e-05/0.01853, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt findZeroCrossings (simulation): time 4.156e-05/0.01857, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.568e-05/0.01859, allocations: 0 / 0, free: 0 / 0 Notification: Performance of sorting global known variables: time 3.1e-05/0.01862, allocations: 0 / 0, free: 0 / 0 Notification: Performance of sort global known variables: time 3.066e-06/0.01862, allocations: 0 / 0, free: 0 / 0 Notification: Performance of remove unused functions: time 0.0004659/0.01909, allocations: 0 / 0, free: 0 / 0 Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 1 * Number of states: 5 (V,C.n,M.n,X.n,ambientSubstance.n) * Number of discrete variables: 0 () * Number of discrete states: 0 () * Number of clocked states: 0 () * Top-level inputs: 0 Notification: Strong component statistics for simulation (26): * Single equations (assignments): 26 * Array equations: 0 * Algorithm blocks: 0 * 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 Backend phase and start with SimCode phase: time 0.0001293/0.01922, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created initialization part: time 0.0003066/0.01953, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created event and clocks part: time 5.741e-06/0.01953, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created simulation system equations: time 7.916e-05/0.01961, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.000444/0.02005, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0008814/0.02094, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: some other stuff during SimCode phase: time 6.598e-05/0.021, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: alias equations: time 8.673e-05/0.02109, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001902/0.02128, allocations: 0 / 0, free: 0 / 0 Notification: Performance of SimCode: time 5.058e-05/0.02133, allocations: 0 / 0, free: 0 / 0 Notification: Performance of Templates: time 0.0008103/0.02214, allocations: 0 / 0, free: 0 / 0 " [Timeout remaining time 900] [Calling sys.exit(0), Time elapsed: 0.7396405842155218]