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 0.0002216/0.0002216, 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 0.0002774/0.0002774, 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 0.131/0.131, 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 0.01276/0.01276, 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 1.343e-06/1.343e-06, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd - Absyn->SCode: time 2.135e-05/2.269e-05, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.instantiate(BioChem.Examples.CircadianOscillator.Container): time 0.01001/0.01003, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.instExpressions: time 0.001798/0.01183, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.updateImplicitVariability: time 0.0002492/0.01208, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeComponents: time 0.0003165/0.0124, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeBindings: time 0.0005319/0.01293, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeClassSections: time 0.0003649/0.01329, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.flatten: time 0.000612/0.01391, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.resolveConnections: time 0.0005767/0.01448, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFEvalConstants.evaluate: time 0.0006955/0.01518, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFSimplifyModel.simplify: time 0.0003853/0.01556, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFPackage.collectConstants: time 0.000103/0.01567, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.collectFunctions: time 9.039e-05/0.01576, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFScalarize.scalarize: time 0.0002072/0.01596, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFVerifyModel.verify: time 0.0002795/0.01624, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFConvertDAE.convert: time 0.0007398/0.01698, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd - DAE generated: time 0.0001002/0.01708, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd: time 3.136e-06/0.01709, allocations: 0 / 0, free: 0 / 0 Notification: Performance of Transformations before backend: time 8.225e-06/0.01709, 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 0.001259/0.01835, allocations: 0 / 0, free: 0 / 0 Notification: Performance of prepare preOptimizeDAE: time 8.184e-05/0.01844, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt normalInlineFunction (simulation): time 0.0001692/0.0186, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002408/0.01885, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt simplifyIfEquations (simulation): time 8.257e-05/0.01893, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt expandDerOperator (simulation): time 9.871e-05/0.01903, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt clockPartitioning (simulation): time 0.0007577/0.01978, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt findStateOrder (simulation): time 2.807e-05/0.01981, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt replaceEdgeChange (simulation): time 6.643e-05/0.01988, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt inlineArrayEqn (simulation): time 2.218e-05/0.0199, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003381/0.02024, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.002737/0.02298, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt comSubExp (simulation): time 0.0005159/0.02349, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt resolveLoops (simulation): time 0.0002337/0.02373, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt evalFunc (simulation): time 1.569e-05/0.02374, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.87e-05/0.02378, allocations: 0 / 0, free: 0 / 0 Notification: Performance of pre-optimization done (n=50): time 7.975e-06/0.02379, allocations: 0 / 0, free: 0 / 0 Notification: Performance of matching and sorting (n=59): time 0.00237/0.02616, allocations: 0 / 0, free: 0 / 0 Notification: Performance of inlineWhenForInitialization (initialization): time 3.117e-05/0.02619, allocations: 0 / 0, free: 0 / 0 Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0002018/0.02639, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectPreVariables (initialization): time 4.614e-05/0.02644, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectInitialEqns (initialization): time 0.0002088/0.02665, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectInitialBindings (initialization): time 0.0001392/0.02679, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simplifyInitialFunctions (initialization): time 0.0001391/0.02692, allocations: 0 / 0, free: 0 / 0 Notification: Performance of setup shared object (initialization): time 4.131e-05/0.02697, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001157/0.02708, allocations: 0 / 0, free: 0 / 0 Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001764/0.02726, allocations: 0 / 0, free: 0 / 0 Notification: Performance of analyzeInitialSystem (initialization): time 0.0004967/0.02775, allocations: 0 / 0, free: 0 / 0 Notification: Performance of solveInitialSystemEqSystem (initialization): time 9.528e-06/0.02776, allocations: 0 / 0, free: 0 / 0 Notification: Performance of matching and sorting (n=107) (initialization): time 0.0006391/0.0284, allocations: 0 / 0, free: 0 / 0 Notification: Performance of prepare postOptimizeDAE: time 3.535e-05/0.02844, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.598e-05/0.02845, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt tearingSystem (initialization): time 2.88e-05/0.02848, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0004302/0.02891, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 2.834e-05/0.02894, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0002466/0.02919, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt collapseArrayExpressions (initialization): time 4.156e-05/0.02923, allocations: 0 / 0, free: 0 / 0 Warning: Assuming fixed start value for the following 12 variables: V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer ) \"Compartment volume\" type: Real nucleus.V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer ) \"Compartment volume\" type: Real cytoplasm.V:VARIABLE(start = 1.0 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 0.000318/0.02955, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt lateInlineFunction (simulation): time 7.347e-05/0.02962, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001062/0.02973, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.743e-06/0.02973, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt constantLinearSystem (simulation): time 8.356e-06/0.02974, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifysemiLinear (simulation): time 7.875e-06/0.02975, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0008463/0.0306, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyComplexFunction (simulation): time 4.869e-06/0.0306, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.000302/0.0309, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt tearingSystem (simulation): time 7.374e-06/0.03091, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt inputDerivativesUsed (simulation): time 4.075e-05/0.03095, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 7.784e-06/0.03096, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 3.016e-06/0.03096, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0005413/0.0315, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt removeConstants (simulation): time 7.302e-05/0.03158, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 0.000136/0.03171, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.000188/0.0319, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt findZeroCrossings (simulation): time 7.661e-05/0.03198, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt collapseArrayExpressions (simulation): time 2.832e-05/0.03201, allocations: 0 / 0, free: 0 / 0 Notification: Performance of sorting global known variables: time 9.273e-05/0.0321, allocations: 0 / 0, free: 0 / 0 Notification: Performance of sort global known variables: time 8.967e-06/0.03211, allocations: 0 / 0, free: 0 / 0 Notification: Performance of remove unused functions: time 0.0008087/0.03292, 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 0.0002217/0.03314, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created initialization part: time 0.0004857/0.03362, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created event and clocks part: time 2.284e-06/0.03363, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created simulation system equations: time 0.0001647/0.03379, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0007178/0.03451, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001696/0.0362, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001526/0.03636, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: alias equations: time 0.0002089/0.03657, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0002558/0.03682, allocations: 0 / 0, free: 0 / 0 Notification: Performance of SimCode: time 3.223e-05/0.03685, allocations: 0 / 0, free: 0 / 0 Notification: Performance of Templates: time 0.001838/0.03869, allocations: 0 / 0, free: 0 / 0 " [Timeout remaining time 900] [Calling sys.exit(0), Time elapsed: 0.7486891592852771]