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 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo", uses=false)
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo", uses=false)
Using package BioChem with version 1.1.2 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo)
Using package Modelica with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo)
Using package Complex with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo)
Using package ModelicaServices with version 4.0.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo)
Running command: translateModel(BioChem.Examples.CaOscillations.Cytosol,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CaOscillations.Cytosol")
translateModel(BioChem.Examples.CaOscillations.Cytosol,tolerance=1e-06,outputFormat="empty",numberOfIntervals=-2,variableFilter="",fileNamePrefix="BioChem_BioChem.Examples.CaOscillations.Cytosol")
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.0.0+maint.om/package.mo): time 0.008519/0.008518, allocations: 101.1 kB / 15.88 MB, free: 5.863 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.0.0+maint.om/package.mo): time 0.001937/0.001937, allocations: 193 kB / 16.79 MB, free: 5.805 MB / 14.72 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.0.0+maint.om/package.mo): time 2.323/2.323, allocations: 222.9 MB / 240.5 MB, free: 4.605 MB / 190.1 MB
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/BioChem 1.1.2-master/package.mo): time 0.2748/0.2748, allocations: 12.27 MB / 302.9 MB, free: 1.402 MB / 238.1 MB
Warning: Ignoring unknown experiment annotation option: Algorithm = "dassl"
Notification: Performance of FrontEnd - loaded program: time 0.002201/0.002201, allocations: 55.91 kB / 365.7 MB, free: 10.25 MB / 302.1 MB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1613/0.1635, allocations: 52.09 MB / 417.8 MB, free: 6.051 MB / 350.1 MB
Notification: Performance of NFInst.instantiate(BioChem.Examples.CaOscillations.Cytosol): time 0.006659/0.1703, allocations: 2.857 MB / 420.7 MB, free: 3.176 MB / 350.1 MB
Notification: Performance of NFInst.instExpressions: time 0.0003734/0.1707, allocations: 187.2 kB / 420.9 MB, free: 2.992 MB / 350.1 MB
Notification: Performance of NFInst.updateImplicitVariability: time 0.0001083/0.1708, allocations: 8 kB / 420.9 MB, free: 2.984 MB / 350.1 MB
Notification: Performance of NFTyping.typeComponents: time 0.0001136/0.1709, allocations: 27.8 kB / 420.9 MB, free: 2.957 MB / 350.1 MB
Notification: Performance of NFTyping.typeBindings: time 0.0001976/0.1712, allocations: 31.7 kB / 420.9 MB, free: 2.926 MB / 350.1 MB
Notification: Performance of NFTyping.typeClassSections: time 0.0002663/0.1715, allocations: 43.95 kB / 421 MB, free: 2.883 MB / 350.1 MB
Notification: Performance of NFFlatten.flatten: time 0.0002868/0.1718, allocations: 175.2 kB / 421.1 MB, free: 2.711 MB / 350.1 MB
Notification: Performance of NFFlatten.resolveConnections: time 0.0003155/0.1721, allocations: 94.58 kB / 421.2 MB, free: 2.621 MB / 350.1 MB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001186/0.1722, allocations: 75.66 kB / 421.3 MB, free: 2.547 MB / 350.1 MB
Notification: Performance of NFSimplifyModel.simplify: time 0.000197/0.1724, allocations: 99.47 kB / 421.4 MB, free: 2.449 MB / 350.1 MB
Notification: Performance of NFPackage.collectConstants: time 4.675e-05/0.1725, allocations: 16 kB / 421.4 MB, free: 2.434 MB / 350.1 MB
Notification: Performance of NFFlatten.collectFunctions: time 4.429e-05/0.1725, allocations: 16 kB / 421.4 MB, free: 2.418 MB / 350.1 MB
Notification: Performance of NFScalarize.scalarize: time 6.481e-05/0.1726, allocations: 43.77 kB / 421.5 MB, free: 2.375 MB / 350.1 MB
Notification: Performance of NFVerifyModel.verify: time 0.0001428/0.1728, allocations: 99.47 kB / 421.6 MB, free: 2.277 MB / 350.1 MB
Notification: Performance of NFConvertDAE.convert: time 0.0002794/0.1731, allocations: 179.8 kB / 421.8 MB, free: 2.102 MB / 350.1 MB
Notification: Performance of FrontEnd - DAE generated: time 1.01e-05/0.1731, allocations: 4 kB / 421.8 MB, free: 2.098 MB / 350.1 MB
Notification: Performance of FrontEnd: time 1.633e-06/0.1731, allocations: 0 / 421.8 MB, free: 2.098 MB / 350.1 MB
Notification: Performance of Transformations before backend: time 6.352e-06/0.1731, allocations: 0 / 421.8 MB, free: 2.098 MB / 350.1 MB
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 0.00109/0.1742, allocations: 0.4916 MB / 422.3 MB, free: 1.555 MB / 350.1 MB
Notification: Performance of prepare preOptimizeDAE: time 5.489e-05/0.1743, allocations: 12.03 kB / 422.3 MB, free: 1.543 MB / 350.1 MB
Notification: Performance of preOpt normalInlineFunction (simulation): time 8.511e-05/0.1744, allocations: 28.64 kB / 422.3 MB, free: 1.516 MB / 350.1 MB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.000206/0.1746, allocations: 192 kB / 422.5 MB, free: 1.289 MB / 350.1 MB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 3.189e-05/0.1746, allocations: 16.94 kB / 422.5 MB, free: 1.273 MB / 350.1 MB
Notification: Performance of preOpt expandDerOperator (simulation): time 6.975e-05/0.1747, allocations: 24.38 kB / 422.5 MB, free: 1.25 MB / 350.1 MB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0005468/0.1753, allocations: 205.5 kB / 422.7 MB, free: 1.047 MB / 350.1 MB
Notification: Performance of preOpt findStateOrder (simulation): time 1.822e-05/0.1753, allocations: 192 / 422.7 MB, free: 1.047 MB / 350.1 MB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 3.984e-05/0.1753, allocations: 15.94 kB / 422.7 MB, free: 1.031 MB / 350.1 MB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 1.275e-05/0.1754, allocations: 7.984 kB / 422.7 MB, free: 1.023 MB / 350.1 MB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0003739/0.1757, allocations: 138.1 kB / 422.9 MB, free: 0.8906 MB / 350.1 MB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.001982/0.1777, allocations: 0.771 MB / 423.7 MB, free: 60 kB / 350.1 MB
Notification: Performance of preOpt comSubExp (simulation): time 0.2478/0.4256, allocations: 98.25 kB / 423.7 MB, free: 40.7 MB / 350.1 MB
Notification: Performance of preOpt resolveLoops (simulation): time 0.0005204/0.4262, allocations: 96.77 kB / 423.8 MB, free: 40.69 MB / 350.1 MB
Notification: Performance of preOpt evalFunc (simulation): time 4.106e-05/0.4263, allocations: 2.641 kB / 423.8 MB, free: 40.69 MB / 350.1 MB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 3.276e-05/0.4263, allocations: 33.31 kB / 423.9 MB, free: 40.65 MB / 350.1 MB
Notification: Performance of pre-optimization done (n=15): time 3.797e-06/0.4263, allocations: 4.781 kB / 423.9 MB, free: 40.65 MB / 350.1 MB
Notification: Performance of matching and sorting (n=17): time 0.002027/0.4283, allocations: 0.5715 MB / 424.5 MB, free: 40.41 MB / 350.1 MB
Notification: Performance of inlineWhenForInitialization (initialization): time 4.285e-05/0.4284, allocations: 54.78 kB / 424.5 MB, free: 40.34 MB / 350.1 MB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001807/0.4286, allocations: 153.2 kB / 424.7 MB, free: 40.24 MB / 350.1 MB
Notification: Performance of collectPreVariables (initialization): time 2.077e-05/0.4286, allocations: 32.42 kB / 424.7 MB, free: 40.21 MB / 350.1 MB
Notification: Performance of collectInitialEqns (initialization): time 9.307e-05/0.4287, allocations: 152.4 kB / 424.8 MB, free: 40.09 MB / 350.1 MB
Notification: Performance of collectInitialBindings (initialization): time 6.43e-05/0.4288, allocations: 69.3 kB / 424.9 MB, free: 40.04 MB / 350.1 MB
Notification: Performance of simplifyInitialFunctions (initialization): time 0.000102/0.4289, allocations: 41.17 kB / 424.9 MB, free: 40.03 MB / 350.1 MB
Notification: Performance of setup shared object (initialization): time 8.172e-05/0.429, allocations: 326.7 kB / 425.3 MB, free: 39.71 MB / 350.1 MB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001248/0.4292, allocations: 40.22 kB / 425.3 MB, free: 39.71 MB / 350.1 MB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001768/0.4293, allocations: 102.9 kB / 425.4 MB, free: 39.66 MB / 350.1 MB
Notification: Performance of analyzeInitialSystem (initialization): time 0.002015/0.4314, allocations: 393 kB / 425.8 MB, free: 39.6 MB / 350.1 MB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 3.486e-06/0.4314, allocations: 0.5 kB / 425.8 MB, free: 39.6 MB / 350.1 MB
Notification: Performance of matching and sorting (n=28) (initialization): time 0.0004883/0.4319, allocations: 210.2 kB / 426 MB, free: 39.56 MB / 350.1 MB
Notification: Performance of prepare postOptimizeDAE: time 3.409e-05/0.4319, allocations: 10.97 kB / 426 MB, free: 39.55 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 1.222e-05/0.432, allocations: 1.344 kB / 426 MB, free: 39.55 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (initialization): time 3.202e-05/0.432, allocations: 3.281 kB / 426 MB, free: 39.55 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0003349/0.4323, allocations: 52.62 kB / 426.1 MB, free: 39.55 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.568e-05/0.4324, allocations: 6.906 kB / 426.1 MB, free: 39.55 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 0.0001598/0.4325, allocations: 10.31 kB / 426.1 MB, free: 39.55 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 2.359e-05/0.4326, allocations: 7.984 kB / 426.1 MB, free: 39.55 MB / 350.1 MB
Warning: Assuming fixed start value for the following 5 variables:
         V:VARIABLE(start = 1.0 fixed = true stateSelect=StateSelect.prefer )  "Compartment volume" type: Real
         endoplasmicReticulum.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
         endoplasmicReticulum.CaER.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: 7
 * 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 0.000413/0.433, allocations: 147.2 kB / 426.2 MB, free: 39.44 MB / 350.1 MB
Notification: Performance of postOpt lateInlineFunction (simulation): time 6.489e-05/0.4331, allocations: 20.48 kB / 426.2 MB, free: 39.43 MB / 350.1 MB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 0.0004255/0.4335, allocations: 166.3 kB / 426.4 MB, free: 39.39 MB / 350.1 MB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 6.051e-06/0.4335, allocations: 3.969 kB / 426.4 MB, free: 39.39 MB / 350.1 MB
Notification: Performance of postOpt constantLinearSystem (simulation): time 8.737e-06/0.4335, allocations: 2 kB / 426.4 MB, free: 39.39 MB / 350.1 MB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 6.702e-06/0.4336, allocations: 2.906 kB / 426.4 MB, free: 39.39 MB / 350.1 MB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.001097/0.4347, allocations: 0.5188 MB / 426.9 MB, free: 39.09 MB / 350.1 MB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 3.346e-06/0.4347, allocations: 0.7031 kB / 426.9 MB, free: 39.09 MB / 350.1 MB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.00029/0.435, allocations: 38.73 kB / 427 MB, free: 39.09 MB / 350.1 MB
Notification: Performance of postOpt tearingSystem (simulation): time 6.862e-06/0.435, allocations: 3.625 kB / 427 MB, free: 39.09 MB / 350.1 MB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 2.272e-05/0.435, allocations: 0 / 427 MB, free: 39.09 MB / 350.1 MB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 4.388e-06/0.4351, allocations: 0 / 427 MB, free: 39.09 MB / 350.1 MB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 2.405e-06/0.4351, allocations: 2.625 kB / 427 MB, free: 39.09 MB / 350.1 MB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004979/0.4356, allocations: 309.6 kB / 427.3 MB, free: 38.95 MB / 350.1 MB
Notification: Performance of postOpt removeConstants (simulation): time 4.555e-05/0.4356, allocations: 91.25 kB / 427.4 MB, free: 38.85 MB / 350.1 MB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 3.696e-05/0.4357, allocations: 4.656 kB / 427.4 MB, free: 38.85 MB / 350.1 MB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 0.0001642/0.4358, allocations: 6.219 kB / 427.4 MB, free: 38.85 MB / 350.1 MB
Notification: Performance of postOpt findZeroCrossings (simulation): time 3.976e-05/0.4359, allocations: 14.05 kB / 427.4 MB, free: 38.85 MB / 350.1 MB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.801e-05/0.4359, allocations: 4.219 kB / 427.4 MB, free: 38.85 MB / 350.1 MB
Notification: Performance of sorting global known variables: time 9.125e-05/0.436, allocations: 112.8 kB / 427.5 MB, free: 38.77 MB / 350.1 MB
Notification: Performance of sort global known variables: time 2.2e-07/0.436, allocations: 0 / 427.5 MB, free: 38.77 MB / 350.1 MB
Notification: Performance of remove unused functions: time 0.0004573/0.4365, allocations: 40.38 kB / 427.6 MB, free: 38.77 MB / 350.1 MB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 5 (V,endoplasmicReticulum.V,endoplasmicReticulum.CaER.n,Ca_Cyt.n,p3_sbml)
 * 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 0.0001212/0.4366, allocations: 107.5 kB / 427.7 MB, free: 38.68 MB / 350.1 MB
Notification: Performance of simCode: created initialization part: time 0.0003563/0.437, allocations: 137.6 kB / 427.8 MB, free: 38.68 MB / 350.1 MB
Notification: Performance of simCode: created event and clocks part: time 2.805e-06/0.437, allocations: 0 / 427.8 MB, free: 38.68 MB / 350.1 MB
Notification: Performance of simCode: created simulation system equations: time 0.0001205/0.4371, allocations: 63.11 kB / 427.9 MB, free: 38.68 MB / 350.1 MB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0004328/0.4376, allocations: 18.16 kB / 427.9 MB, free: 38.68 MB / 350.1 MB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.001231/0.4388, allocations: 0.6275 MB / 428.5 MB, free: 38.32 MB / 350.1 MB
Notification: Performance of simCode: some other stuff during SimCode phase: time 0.0001912/0.439, allocations: 0.7386 MB / 429.2 MB, free: 37.62 MB / 350.1 MB
Notification: Performance of simCode: all other stuff during SimCode phase: time 9.162e-05/0.4391, allocations: 17.34 kB / 429.3 MB, free: 37.62 MB / 350.1 MB
Notification: Performance of SimCode: time 3.61e-07/0.4392, allocations: 4 kB / 429.3 MB, free: 37.62 MB / 350.1 MB
Notification: Performance of Templates: time 0.004247/0.4434, allocations: 2.004 MB / 431.3 MB, free: 37.52 MB / 350.1 MB
make -j1 -f BioChem_BioChem.Examples.CaOscillations.Cytosol.makefile
(rm -f BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe ; mkfifo BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe ; head -c 1048576 < BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe >> ../files/BioChem_BioChem.Examples.CaOscillations.Cytosol.sim & ./BioChem_BioChem.Examples.CaOscillations.Cytosol  -abortSlowSimulation -alarm=480 -lv LOG_STATS > BioChem_BioChem.Examples.CaOscillations.Cytosol.pipe 2>&1)