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 0.0002036/0.0002036, 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 0.0001808/0.0001808, 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 0.09667/0.09667, 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 0.04916/0.04916, 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 1.152e-06/1.152e-06, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd - Absyn->SCode: time 1.366e-05/1.481e-05, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.instantiate(BioChem.Examples.GMO.cell): time 0.006556/0.006571, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.instExpressions: time 0.0006796/0.007251, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.updateImplicitVariability: time 9.752e-05/0.007348, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeComponents: time 0.000125/0.007473, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeBindings: time 0.0002034/0.007677, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeClassSections: time 0.0001756/0.007852, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.flatten: time 0.0002619/0.008114, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.resolveConnections: time 0.0002288/0.008343, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFEvalConstants.evaluate: time 0.0002586/0.008601, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFSimplifyModel.simplify: time 0.0001636/0.008765, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFPackage.collectConstants: time 4.014e-05/0.008805, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.collectFunctions: time 3.608e-05/0.008841, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFScalarize.scalarize: time 8.344e-05/0.008925, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFVerifyModel.verify: time 0.0001157/0.00904, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFConvertDAE.convert: time 0.0002893/0.00933, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd - DAE generated: time 3.977e-05/0.00937, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd: time 1.363e-06/0.009371, allocations: 0 / 0, free: 0 / 0 Notification: Performance of Transformations before backend: time 6.983e-06/0.009378, 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 0.0007011/0.01008, allocations: 0 / 0, free: 0 / 0 Notification: Performance of prepare preOptimizeDAE: time 6.874e-05/0.01015, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001016/0.01025, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001426/0.01039, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt simplifyIfEquations (simulation): time 4.524e-05/0.01044, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt expandDerOperator (simulation): time 5.999e-05/0.0105, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003535/0.01085, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt findStateOrder (simulation): time 2.003e-05/0.01087, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt replaceEdgeChange (simulation): time 4.212e-05/0.01091, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.027e-05/0.01092, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001912/0.01111, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001334/0.01245, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt comSubExp (simulation): time 0.0002116/0.01266, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt resolveLoops (simulation): time 0.0001057/0.01277, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt evalFunc (simulation): time 8.596e-06/0.01277, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.762e-05/0.01279, allocations: 0 / 0, free: 0 / 0 Notification: Performance of pre-optimization done (n=22): time 4.198e-06/0.0128, allocations: 0 / 0, free: 0 / 0 Notification: Performance of matching and sorting (n=26): time 0.001336/0.01413, allocations: 0 / 0, free: 0 / 0 Notification: Performance of inlineWhenForInitialization (initialization): time 2.707e-05/0.01416, allocations: 0 / 0, free: 0 / 0 Notification: Performance of selectInitializationVariablesDAE (initialization): time 7.316e-05/0.01423, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectPreVariables (initialization): time 2.926e-05/0.01426, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectInitialEqns (initialization): time 8.922e-05/0.01435, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectInitialBindings (initialization): time 7.292e-05/0.01442, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simplifyInitialFunctions (initialization): time 8.189e-05/0.01451, allocations: 0 / 0, free: 0 / 0 Notification: Performance of setup shared object (initialization): time 1.824e-05/0.01452, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preBalanceInitialSystem (initialization): time 4.794e-05/0.01457, allocations: 0 / 0, free: 0 / 0 Notification: Performance of partitionIndependentBlocks (initialization): time 7.531e-05/0.01465, allocations: 0 / 0, free: 0 / 0 Notification: Performance of analyzeInitialSystem (initialization): time 0.0002337/0.01488, allocations: 0 / 0, free: 0 / 0 Notification: Performance of solveInitialSystemEqSystem (initialization): time 4.638e-06/0.01489, allocations: 0 / 0, free: 0 / 0 Notification: Performance of matching and sorting (n=46) (initialization): time 0.0002628/0.01515, allocations: 0 / 0, free: 0 / 0 Notification: Performance of prepare postOptimizeDAE: time 1.667e-05/0.01517, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.642e-06/0.01517, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt tearingSystem (initialization): time 1.514e-05/0.01519, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0002015/0.01539, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.389e-05/0.0154, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001121/0.01551, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.997e-05/0.01553, 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 0.0001222/0.01566, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt lateInlineFunction (simulation): time 3.308e-05/0.01569, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt wrapFunctionCalls (simulation): time 5.315e-05/0.01574, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.707e-06/0.01575, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt constantLinearSystem (simulation): time 3.747e-06/0.01575, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifysemiLinear (simulation): time 4.038e-06/0.01575, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0003582/0.01611, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.454e-06/0.01612, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001401/0.01626, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt tearingSystem (simulation): time 3.166e-06/0.01626, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.236e-05/0.01628, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 3.757e-06/0.01628, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.503e-06/0.01629, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0002492/0.01654, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt removeConstants (simulation): time 2.536e-05/0.01656, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.259e-05/0.01662, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyAllExpressions (simulation): time 9.346e-05/0.01672, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt findZeroCrossings (simulation): time 3.989e-05/0.01676, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.322e-05/0.01677, allocations: 0 / 0, free: 0 / 0 Notification: Performance of sorting global known variables: time 2.606e-05/0.0168, allocations: 0 / 0, free: 0 / 0 Notification: Performance of sort global known variables: time 3.176e-06/0.0168, allocations: 0 / 0, free: 0 / 0 Notification: Performance of remove unused functions: time 0.0004668/0.01727, 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 9.029e-05/0.01736, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created initialization part: time 0.0002046/0.01756, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created event and clocks part: time 8.937e-06/0.01757, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created simulation system equations: time 7.391e-05/0.01764, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0003541/0.018, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0006881/0.01869, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: some other stuff during SimCode phase: time 6.062e-05/0.01875, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: alias equations: time 7.383e-05/0.01882, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001377/0.01896, allocations: 0 / 0, free: 0 / 0 Notification: Performance of SimCode: time 2.224e-05/0.01898, allocations: 0 / 0, free: 0 / 0 Notification: Performance of Templates: time 0.000781/0.01976, allocations: 0 / 0, free: 0 / 0 " [Timeout remaining time 900] [Calling sys.exit(0), Time elapsed: 0.6959017957560718]