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 0.0001951/0.0001951, 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 0.0001879/0.0001879, 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 0.141/0.141, 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 0.02397/0.02397, 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 1.182e-06/1.182e-06, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd - Absyn->SCode: time 1.39e-05/1.508e-05, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.004004/0.00402, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.instExpressions: time 0.0005293/0.004549, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFInst.updateImplicitVariability: time 9.677e-05/0.004646, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeComponents: time 0.0001022/0.004748, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeBindings: time 0.0002122/0.00496, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFTyping.typeClassSections: time 0.0001891/0.005149, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.flatten: time 0.000195/0.005344, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.resolveConnections: time 0.0001624/0.005506, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFEvalConstants.evaluate: time 0.0001809/0.005687, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFSimplifyModel.simplify: time 0.0001099/0.005797, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFPackage.collectConstants: time 3.226e-05/0.005829, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFFlatten.collectFunctions: time 2.077e-05/0.00585, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFScalarize.scalarize: time 5.024e-05/0.005901, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFVerifyModel.verify: time 6.467e-05/0.005965, allocations: 0 / 0, free: 0 / 0 Notification: Performance of NFConvertDAE.convert: time 0.0002209/0.006186, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd - DAE generated: time 2.604e-05/0.006212, allocations: 0 / 0, free: 0 / 0 Notification: Performance of FrontEnd: time 1.723e-06/0.006214, allocations: 0 / 0, free: 0 / 0 Notification: Performance of Transformations before backend: time 5.51e-06/0.006219, 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 0.0005333/0.006753, allocations: 0 / 0, free: 0 / 0 Notification: Performance of prepare preOptimizeDAE: time 6.28e-05/0.006816, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt normalInlineFunction (simulation): time 8.074e-05/0.006896, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt evaluateParameters (simulation): time 8.89e-05/0.006985, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.287e-05/0.007018, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt expandDerOperator (simulation): time 5.086e-05/0.007069, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt clockPartitioning (simulation): time 0.0003217/0.007391, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt findStateOrder (simulation): time 1.523e-05/0.007406, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.452e-05/0.00744, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt inlineArrayEqn (simulation): time 7.343e-06/0.007448, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001256/0.007573, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0009608/0.008534, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt comSubExp (simulation): time 0.0001306/0.008665, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt resolveLoops (simulation): time 0.0001655/0.00883, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt evalFunc (simulation): time 1.517e-05/0.008845, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 1.954e-05/0.008865, allocations: 0 / 0, free: 0 / 0 Notification: Performance of pre-optimization done (n=15): time 4.208e-06/0.008869, allocations: 0 / 0, free: 0 / 0 Notification: Performance of matching and sorting (n=17): time 0.0009201/0.009789, allocations: 0 / 0, free: 0 / 0 Notification: Performance of inlineWhenForInitialization (initialization): time 2.157e-05/0.009811, allocations: 0 / 0, free: 0 / 0 Notification: Performance of selectInitializationVariablesDAE (initialization): time 5.567e-05/0.009866, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectPreVariables (initialization): time 2.405e-05/0.00989, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectInitialEqns (initialization): time 5.62e-05/0.009947, allocations: 0 / 0, free: 0 / 0 Notification: Performance of collectInitialBindings (initialization): time 5.25e-05/0.009999, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simplifyInitialFunctions (initialization): time 6.486e-05/0.01006, allocations: 0 / 0, free: 0 / 0 Notification: Performance of setup shared object (initialization): time 2.173e-05/0.01009, allocations: 0 / 0, free: 0 / 0 Notification: Performance of preBalanceInitialSystem (initialization): time 3.506e-05/0.01012, allocations: 0 / 0, free: 0 / 0 Notification: Performance of partitionIndependentBlocks (initialization): time 5.994e-05/0.01018, allocations: 0 / 0, free: 0 / 0 Notification: Performance of analyzeInitialSystem (initialization): time 0.0001916/0.01037, allocations: 0 / 0, free: 0 / 0 Notification: Performance of solveInitialSystemEqSystem (initialization): time 5.09e-06/0.01038, allocations: 0 / 0, free: 0 / 0 Notification: Performance of matching and sorting (n=28) (initialization): time 0.0002488/0.01063, allocations: 0 / 0, free: 0 / 0 Notification: Performance of prepare postOptimizeDAE: time 1.524e-05/0.01064, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.712e-06/0.01065, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt tearingSystem (initialization): time 1.125e-05/0.01066, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001634/0.01082, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.084e-05/0.01083, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyAllExpressions (initialization): time 7.58e-05/0.01091, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.013e-05/0.01093, 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 0.0001139/0.01104, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt lateInlineFunction (simulation): time 4.091e-05/0.01108, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0002097/0.01129, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.938e-06/0.0113, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt constantLinearSystem (simulation): time 4.689e-06/0.0113, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifysemiLinear (simulation): time 5.821e-06/0.01131, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0007517/0.01206, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.396e-06/0.01206, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001275/0.01219, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt tearingSystem (simulation): time 4.058e-06/0.0122, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.298e-05/0.01222, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.369e-06/0.01222, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.264e-06/0.01222, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0002625/0.01249, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt removeConstants (simulation): time 2.092e-05/0.01251, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 6.111e-05/0.01257, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001285/0.0127, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt findZeroCrossings (simulation): time 4.445e-05/0.01274, allocations: 0 / 0, free: 0 / 0 Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.333e-05/0.01276, allocations: 0 / 0, free: 0 / 0 Notification: Performance of sorting global known variables: time 2.598e-05/0.01278, allocations: 0 / 0, free: 0 / 0 Notification: Performance of sort global known variables: time 2.916e-06/0.01278, allocations: 0 / 0, free: 0 / 0 Notification: Performance of remove unused functions: time 0.0005515/0.01334, 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 9.575e-05/0.01343, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created initialization part: time 0.0001675/0.0136, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created event and clocks part: time 2.665e-06/0.0136, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created simulation system equations: time 6.075e-05/0.01366, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0007126/0.01438, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0006222/0.015, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: some other stuff during SimCode phase: time 5.562e-05/0.01505, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: alias equations: time 5.652e-05/0.01511, allocations: 0 / 0, free: 0 / 0 Notification: Performance of simCode: all other stuff during SimCode phase: time 0.0001079/0.01522, allocations: 0 / 0, free: 0 / 0 Notification: Performance of SimCode: time 2.061e-05/0.01524, allocations: 0 / 0, free: 0 / 0 Notification: Performance of Templates: time 0.0005873/0.01583, allocations: 0 / 0, free: 0 / 0 " [Timeout remaining time 900] [Calling sys.exit(0), Time elapsed: 0.7262491420842707]