Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr BioChem_BioChem.Examples.CircadianOscillator.Container.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 0.0005508/0.0005508, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInstanceAPI.mkTop(): time 0.007185/0.007735, 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 0.0005333/0.0005333, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInstanceAPI.mkTop(): time 0.0009453/0.001479, 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 0.2471/0.2471, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInstanceAPI.mkTop(): time 0.05087/0.298, 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 0.02805/0.02805, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInstanceAPI.mkTop(): time 0.003775/0.03182, 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.CircadianOscillator.Container,startTime=0,stopTime=150,tolerance=1e-06,numberOfIntervals=2500,outputFormat="empty",variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CircadianOscillator.Container",simflags="-abortSlowSimulation -alarm=240 -lv LOG_STATS") simulate(BioChem.Examples.CircadianOscillator.Container,startTime=0,stopTime=150,tolerance=1e-06,numberOfIntervals=2500,outputFormat="empty",variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CircadianOscillator.Container",simflags="-abortSlowSimulation -alarm=240 -lv LOG_STATS") [Timeout 900] "Notification: Performance of FrontEnd - loaded program: time 9.72e-07/9.72e-07, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd - Absyn->SCode: time 2.026e-05/2.123e-05, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.008766/0.008787, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.instExpressions: time 0.001755/0.01054, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.updateImplicitVariability: time 0.0002494/0.01079, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeComponents: time 0.0003594/0.01115, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeBindings: time 0.000642/0.01179, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeClassSections: time 0.0004426/0.01224, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.flatten: time 0.0006738/0.01291, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.resolveConnections: time 0.0005673/0.01348, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFEvalConstants.evaluate: time 0.0007227/0.0142, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFSimplifyModel.simplify: time 0.0003648/0.01456, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFPackage.collectConstants: time 0.0001056/0.01467, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.collectFunctions: time 0.0001001/0.01477, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFScalarize.scalarize: time 0.0001986/0.01497, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFVerifyModel.verify: time 0.0003286/0.0153, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFConvertDAE.convert: time 0.0008744/0.01617, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd - DAE generated: time 0.0001159/0.01629, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd: time 1.423e-06/0.01629, allocations: 0 / 0, free: 0 / 0 Notification: Performance of Transformations before backend: time 1.915e-05/0.01631, 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: 252 * Number of variables: 252 Notification: Performance of Generate backend data structure: time 0.001657/0.01796, allocations: 0 / 0, free: 0 / 0 Notification: Performance of prepare preOptimizeDAE: time 9.118e-05/0.01806, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001893/0.01825, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002409/0.01849, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt simplifyIfEquations (simulation): time 7.609e-05/0.01856, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt expandDerOperator (simulation): time 0.0001148/0.01868, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt clockPartitioning (simulation): time 0.0009755/0.01965, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt findStateOrder (simulation): time 3.472e-05/0.01969, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt replaceEdgeChange (simulation): time 0.0001003/0.01979, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.111e-05/0.01981, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt removeEqualRHS (simulation): time 0.000458/0.02027, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.003056/0.02332, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt comSubExp (simulation): time 0.000619/0.02394, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt resolveLoops (simulation): time 0.0002421/0.02418, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt evalFunc (simulation): time 1.733e-05/0.0242, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 2.982e-05/0.02423, allocations: 0 / 0, free: 0 / 0 Notification: Performance of pre-optimization done (n=50): time 5.52e-06/0.02424, allocations: 0 / 0, free: 0 / 0 Notification: Performance of matching and sorting (n=59): time 0.002653/0.02689, allocations: 0 / 0, free: 0 / 0 Notification: Performance of inlineWhenForInitialization (initialization): time 3.973e-05/0.02693, allocations: 0 / 0, free: 0 / 0 Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002256/0.02715, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectPreVariables (initialization): time 4.906e-05/0.0272, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectInitialEqns (initialization): time 0.0001689/0.02737, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectInitialBindings (initialization): time 0.0001294/0.0275, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001767/0.02768, allocations: 0 / 0, free: 0 / 0 Notification: Performance of setup shared object (initialization): time 4.965e-05/0.02773, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001548/0.02788, allocations: 0 / 0, free: 0 / 0 Notification: Performance of partitionIndependentBlocks (initialization): time 0.000233/0.02812, allocations: 0 / 0, free: 0 / 0 Notification: Performance of analyzeInitialSystem (initialization): time 0.0006182/0.02873, allocations: 0 / 0, free: 0 / 0 Notification: Performance of solveInitialSystemEqSystem (initialization): time 1.017e-05/0.02874, allocations: 0 / 0, free: 0 / 0 Notification: Performance of matching and sorting (n=107) (initialization): time 0.0007061/0.02945, allocations: 0 / 0, free: 0 / 0 Notification: Performance of prepare postOptimizeDAE: time 1.89e-05/0.02947, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.194e-05/0.02948, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt tearingSystem (initialization): time 2.931e-05/0.02951, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0005382/0.03005, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 2.07e-05/0.03007, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0002281/0.0303, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.265e-05/0.03034, allocations: 0 / 0, free: 0 / 0 Warning: Assuming fixed start value for the following 12 variables: V:VARIABLE(start = 1.0 unit = \"l\" fixed = true stateSelect=StateSelect.prefer ) \"Compartment volume\" type: Real nucleus.V:VARIABLE(start = 1.0 unit = \"l\" fixed = true stateSelect=StateSelect.prefer ) \"Compartment volume\" type: Real cytoplasm.V:VARIABLE(start = 1.0 unit = \"l\" fixed = true stateSelect=StateSelect.prefer ) \"Compartment volume\" type: Real cytoplasm.ambientSubstance.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real cytoplasm.y5.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real cytoplasm.y4.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real cytoplasm.y2.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real cytoplasm.y1.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real nucleus.ambientSubstance.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real nucleus.y7.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real nucleus.y6.n:VARIABLE(min = 0.0 unit = \"mol\" fixed = true stateSelect=StateSelect.prefer ) \"Number of moles of substance in pool (mol)\" type: Real nucleus.y3.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: 39 * 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 (107): * Single equations (assignments): 107 * 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 0.0002839/0.03062, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt lateInlineFunction (simulation): time 8.374e-05/0.03071, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001086/0.03082, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt inlineArrayEqn (simulation): time 5.691e-06/0.03082, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt constantLinearSystem (simulation): time 1.203e-05/0.03083, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.603e-06/0.03084, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0007605/0.0316, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.388e-06/0.03161, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0004225/0.03203, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt tearingSystem (simulation): time 6.091e-06/0.03203, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt inputDerivativesUsed (simulation): time 4.168e-05/0.03208, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 5.781e-06/0.03208, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.973e-06/0.03208, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0006361/0.03272, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt removeConstants (simulation): time 5.834e-05/0.03278, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.0001133/0.03289, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001901/0.03308, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt findZeroCrossings (simulation): time 0.0001056/0.03319, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.746e-05/0.03321, allocations: 0 / 0, free: 0 / 0 Notification: Performance of sorting global known variables: time 0.0001197/0.03333, allocations: 0 / 0, free: 0 / 0 Notification: Performance of sort global known variables: time 9.047e-06/0.03334, allocations: 0 / 0, free: 0 / 0 Notification: Performance of remove unused functions: time 0.0005017/0.03384, allocations: 0 / 0, free: 0 / 0 Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 2 * Number of states: 12 (nucleus.V,nucleus.y3.n,nucleus.y6.n,nucleus.y7.n,nucleus.ambientSubstance.n,cytoplasm.V,cytoplasm.y1.n,cytoplasm.y2.n,cytoplasm.y4.n,cytoplasm.y5.n,cytoplasm.ambientSubstance.n,V) * 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 (59): * Single equations (assignments): 59 * 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 0.0002018/0.03405, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created initialization part: time 0.0005474/0.03459, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created event and clocks part: time 1.89e-05/0.03461, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created simulation system equations: time 0.0002055/0.03482, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0006871/0.03551, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001976/0.03748, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001601/0.03764, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: alias equations: time 0.0002423/0.03788, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0002389/0.03812, allocations: 0 / 0, free: 0 / 0 Notification: Performance of SimCode: time 2.56e-05/0.03815, allocations: 0 / 0, free: 0 / 0 Notification: Performance of Templates: time 0.002445/0.04059, allocations: 0 / 0, free: 0 / 0 " [Timeout remaining time 900] [Calling sys.exit(0), Time elapsed: 0.839150178944692]