Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr BioChem_BioChem.Examples.CaOscillations.Cytosol.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 0.000364/0.000364, 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 0.0002488/0.0002488, 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 0.2259/0.2259, 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 0.01896/0.01896, 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.CaOscillations.Cytosol,startTime=0,stopTime=120,tolerance=1e-06,numberOfIntervals=2400,outputFormat="empty",variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CaOscillations.Cytosol",simflags="-abortSlowSimulation -alarm=240 -lv LOG_STATS") simulate(BioChem.Examples.CaOscillations.Cytosol,startTime=0,stopTime=120,tolerance=1e-06,numberOfIntervals=2400,outputFormat="empty",variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CaOscillations.Cytosol",simflags="-abortSlowSimulation -alarm=240 -lv LOG_STATS") [Timeout 900] "Notification: Performance of FrontEnd - loaded program: time 1.142e-06/1.142e-06, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd - Absyn->SCode: time 2.222e-05/2.336e-05, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.005487/0.00551, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.instExpressions: time 0.0003474/0.005857, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.updateImplicitVariability: time 5.198e-05/0.005909, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeComponents: time 6.182e-05/0.005971, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeBindings: time 0.0001095/0.006081, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeClassSections: time 0.0002506/0.006331, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.flatten: time 0.0001362/0.006467, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.resolveConnections: time 0.0001037/0.006571, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFEvalConstants.evaluate: time 0.0001008/0.006672, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFSimplifyModel.simplify: time 8.061e-05/0.006753, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFPackage.collectConstants: time 2.032e-05/0.006773, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.collectFunctions: time 1.51e-05/0.006788, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFScalarize.scalarize: time 3.763e-05/0.006826, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFVerifyModel.verify: time 4.57e-05/0.006871, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFConvertDAE.convert: time 0.0001322/0.007004, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd - DAE generated: time 1.471e-05/0.007018, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd: time 1.102e-06/0.007019, allocations: 0 / 0, free: 0 / 0 Notification: Performance of Transformations before backend: time 9.598e-06/0.007029, 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: 60 * Number of variables: 60 Notification: Performance of Generate backend data structure: time 0.0004442/0.007473, allocations: 0 / 0, free: 0 / 0 Notification: Performance of prepare preOptimizeDAE: time 5.585e-05/0.007529, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt normalInlineFunction (simulation): time 6.75e-05/0.007597, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt evaluateParameters (simulation): time 0.0001192/0.007716, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt simplifyIfEquations (simulation): time 2.456e-05/0.00774, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt expandDerOperator (simulation): time 3.412e-05/0.007774, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002246/0.007999, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt findStateOrder (simulation): time 1.202e-05/0.008011, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt replaceEdgeChange (simulation): time 2.671e-05/0.008038, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt inlineArrayEqn (simulation): time 3.947e-06/0.008042, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001093/0.008151, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.003678/0.01183, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt comSubExp (simulation): time 9.956e-05/0.01193, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt resolveLoops (simulation): time 0.0001009/0.01203, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt evalFunc (simulation): time 1.476e-05/0.01204, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.416e-05/0.01206, allocations: 0 / 0, free: 0 / 0 Notification: Performance of pre-optimization done (n=15): time 2.956e-06/0.01206, allocations: 0 / 0, free: 0 / 0 Notification: Performance of matching and sorting (n=17): time 0.0007938/0.01286, allocations: 0 / 0, free: 0 / 0 Notification: Performance of inlineWhenForInitialization (initialization): time 2.502e-05/0.01288, allocations: 0 / 0, free: 0 / 0 Notification: Performance of selectInitializationVariablesDAE (initialization): time 3.826e-05/0.01292, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectPreVariables (initialization): time 1.533e-05/0.01293, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectInitialEqns (initialization): time 3.477e-05/0.01297, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectInitialBindings (initialization): time 3.01e-05/0.013, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simplifyInitialFunctions (initialization): time 4.393e-05/0.01304, allocations: 0 / 0, free: 0 / 0 Notification: Performance of setup shared object (initialization): time 1.579e-05/0.01306, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preBalanceInitialSystem (initialization): time 2.367e-05/0.01308, allocations: 0 / 0, free: 0 / 0 Notification: Performance of partitionIndependentBlocks (initialization): time 3.811e-05/0.01312, allocations: 0 / 0, free: 0 / 0 Notification: Performance of analyzeInitialSystem (initialization): time 0.0001199/0.01324, allocations: 0 / 0, free: 0 / 0 Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.264e-06/0.01324, allocations: 0 / 0, free: 0 / 0 Notification: Performance of matching and sorting (n=28) (initialization): time 0.0001388/0.01338, allocations: 0 / 0, free: 0 / 0 Notification: Performance of prepare postOptimizeDAE: time 9.798e-06/0.01339, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyComplexFunction (initialization): time 3.877e-06/0.0134, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt tearingSystem (initialization): time 1.357e-05/0.01341, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001058/0.01351, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 8.335e-06/0.01352, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyAllExpressions (initialization): time 4.387e-05/0.01357, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.155e-05/0.01358, allocations: 0 / 0, free: 0 / 0 Warning: Assuming fixed start value for the following 5 variables: endoplasmicReticulum.V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer ) \"Compartment volume\" type: Real endoplasmicReticulum.CaER.c:VARIABLE(min = 0.0 start = 0.0 unit = \"mol/l\" fixed = true stateSelect=StateSelect.prefer ) \"Current concentration of substance (mM)\" type: Real V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer ) \"Compartment volume\" type: Real p3_sbml:VARIABLE(start = 0.95 fixed = true ) type: Real Ca_Cyt.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: 8 * 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 (28): * Single equations (assignments): 28 * 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 0.0001033/0.01368, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt lateInlineFunction (simulation): time 3.848e-05/0.01372, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0001334/0.01385, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt inlineArrayEqn (simulation): time 2.565e-06/0.01386, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt constantLinearSystem (simulation): time 5.16e-06/0.01386, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.206e-06/0.01386, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.003481/0.01735, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.625e-06/0.01735, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001007/0.01745, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt tearingSystem (simulation): time 3.807e-06/0.01745, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.919e-05/0.01747, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 2.675e-06/0.01747, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.603e-06/0.01748, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0001686/0.01764, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt removeConstants (simulation): time 1.545e-05/0.01766, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.284e-05/0.01769, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyAllExpressions (simulation): time 6.984e-05/0.01776, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt findZeroCrossings (simulation): time 3.212e-05/0.01779, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt collapseArrayExpressions (simulation): time 7.614e-06/0.0178, allocations: 0 / 0, free: 0 / 0 Notification: Performance of sorting global known variables: time 1.704e-05/0.01782, allocations: 0 / 0, free: 0 / 0 Notification: Performance of sort global known variables: time 1.984e-06/0.01782, allocations: 0 / 0, free: 0 / 0 Notification: Performance of remove unused functions: time 0.0001999/0.01802, allocations: 0 / 0, free: 0 / 0 Notification: Model statistics after passing the back-end for simulation: * Number of independent subsystems: 3 * Number of states: 5 (V,Ca_Cyt.n,p3_sbml,endoplasmicReticulum.V,endoplasmicReticulum.CaER.c) * 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 (18): * Single equations (assignments): 18 * 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 9.207e-05/0.01811, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created initialization part: time 0.0001456/0.01826, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created event and clocks part: time 1.483e-06/0.01826, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created simulation system equations: time 4.022e-05/0.0183, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004126/0.01871, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0004748/0.01919, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: some other stuff during SimCode phase: time 3.901e-05/0.01923, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: alias equations: time 4.278e-05/0.01927, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: all other stuff during SimCode phase: time 8.83e-05/0.01936, allocations: 0 / 0, free: 0 / 0 Notification: Performance of SimCode: time 1.323e-05/0.01937, allocations: 0 / 0, free: 0 / 0 Notification: Performance of Templates: time 0.0006064/0.01998, allocations: 0 / 0, free: 0 / 0 " [Timeout remaining time 900] [Calling sys.exit(0), Time elapsed: 0.7432396356016397]