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Releases: CliMA/Oceananigans.jl

🍞 Oceananigans v0.42.0

15 Oct 01:22
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🍞 Oceananigans v0.42.0

Oceananigans v0.42.0

Diff since v0.41.0

Added support for time averaging to NetCDFOutputWriter and revamped how field slicing is done.

Breaking changes:

  • NetCDFOutputWriter constructor: The filename keyword argument is now filepath.
  • NetCDFOutputWriter constructor: To specify slices, pass a FieldSlicer(i, j, k; with_halos) instead of using the xC, xF, yC, yF, zC, and zF keyword arguments.

Closed issues:

  • Computation has result at wrong location (#876)
  • Split up TEST_GROUP=model? (#1048)
  • Initializing environment on Buildkite can be a testing bottleneck (#1056)

Merged pull requests:

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🎑 Oceananigans v0.41.0

14 Oct 14:02
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🎑 Oceananigans v0.41.0

Oceananigans v0.41.0

Diff since v0.40.0

Oceananigans.jl fully supports Julia 1.5 now!

Major changes:

Closed issues:

  • Obscure GPU error when time stepping a model with Julia 1.5 and Oceananigans v0.33.0 (#828)
  • Background tracer distributions and advecting velocity fields (#960)
  • FieldSlicer does not convert to parent indices for integer indices (#1028)
  • Run on GPU without network access (#1035)
  • Stop testing on GitLab CI (#1049)

Merged pull requests:

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🪔 Oceananigans v0.40.0

02 Oct 02:02
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🪔 Oceananigans v0.40.0

Oceananigans v0.40.0

Diff since v0.39.0

  • Support for Flat dimensions. See the grid section of the model setup documentation for more details and examples.
  • New advection schemes: UpwindBiasedThirdOrder and UpwindBiasedFifthOrder.
  • Grid halos are automatically adjusted on model construction depending on advection scheme and turbulence closure used.
  • Improved two-dimensional turbulence example.
  • Fixed Langmuir turbulence example.
  • Numerous bug fixes.

Closed issues:

  • Only perform operations as needed depending on model dimension. (#35)
  • Float32 tracer conservation test not actually Float32 (#487)
  • Utilities for calculating buoyancy and density offline (#516)
  • Floating point equality checking in 2D Leith (#535)
  • Model not enforcing zero vertical shear at top and bottom (do we expect this?) (#540)
  • Deepening mixed layer verification experiment (#547)
  • NetCDFOutputWriter output does not include global attributes (#576)
  • Incompressibility and pressure projection step test (#673)
  • ERROR: LoadError: UndefVarError: SolutionBoundaryConditions not defined (#686)
  • Cubic lattice grid with missing nodes (#743)
  • An example with stable mixed layer depth? (#749)
  • questions relating to Oceananigans.jl (#770)
  • Possible bug in checkpointing? (#778)
  • test Oceananigans returns CUDA error depsite being able to run examples on CPU and GPU (#788)
  • Is any way to simulate the hydrodynamic behaviour of a bioreactor with Oceananigans.jl? (#830)
  • Test failing on GPU (#882)
  • Eliding differences, interpolation, and fill_halo_regions for Flat dimensions (#902)
  • Stop simulation when output is NaN (#938)
  • Model immediately turns to NaN after 1 time step when grid length is zero along Flat dimensions (#940)
  • Model constructor should check that halos are big enough for chosen advection scheme and turbulence closure (#941)
  • Bug(s) somewhere in UpwindBiasedThirdOrder left-biased interpolation functions (#986)
  • Requiring Lz and Nz for two-dimensional grids is a bit counterintuitive (#1001)
  • Langmuir example broken (#1004)
  • Passing a Clock to restore_from_checkpoint gets overwritten by clock from checkpoint file (#1008)
  • Cannot use Forcings with field_dependencies on GPU with Oceananigans v0.39.0 (#1010)

Merged pull requests:

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🥊 Oceananigans v0.39.0

29 Sep 22:02
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v0.39.0
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🥊 Oceananigans v0.39.0

Oceananigans v0.39.0

Diff since v0.38.0

  • Overhauled interface for forcing functions. Instead of calling ModelForcing to set up model forcing functions, you should pass a named tuple of Forcing objects to the model constructor.

Closed issues:

  • getindex and setindex! much slower than just accessing array contents directly. (#13)
  • Can we inline source term calculation to save memory? (#98)
  • Unified forcing function interface (#896)
  • fourth-order advection tested? (#925)
  • Not sure why Oceananigans instantly kills a constant velocity field in a box (#951)
  • Flatten state in boundary condition functions and forcing functions to single tuple? (#985)
  • Remove SymPy dependency in next release of Oceananigans (#990)
  • MethodError when using Oceananigans with Julia 1.5 and OffsetArrays v1.3.0 (#991)

Merged pull requests:

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⚖️ Oceananigans v0.38.0

26 Sep 23:02
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v0.38.0
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⚖️ Oceananigans v0.38.0

Oceananigans v0.38.0

Diff since v0.37.0

  • New experimental WENO-5 advection scheme for momentum and tracers. Use by passing advection=WENO5() when creating a model. See #592 for convergence tests, comparisons, and benchmarks.
  • Very experimental automatically generated WENO{N} advection schemes.
  • New framework for high-order advection schemes abstracting centered and upwind schemes.
  • Lid-driven cavity verification experiment against data by Ghia et al. (1982). See the docs for movies.
  • New lazily-computed PressureField.
  • Avoiding unnecessary recomputation of fields in output evaluation.
  • Bug fixes for WindowedTimeAverage and AveragedField.
  • BREAKING: Internal functions run_diagnostic(model, diag) and write_output(model, output_writer) are now run_diagnostic!(diag, model) and write_output!(output_writer, model).

Closed issues:

  • Sugary syntax for boundary conditions (#637)
  • Don't require simulation.progress to subtype Function (#642)
  • Checkpointing docs are stale (#660)
  • Incorporate performance benchmarks into tests and CI (#684)
  • Doc strings for some kernel functions are out of date (#763)
  • Introduce "location" notation :u, :v, :w, :c ? (#766)
  • Incomplete docstring for SeawaterBuoyancy? (#768)
  • Proper bangs (#861)
  • Typo in docs, should be Non-traditional (#912)
  • Advection scheme benchmarks (#934)
  • halo points behaving differently in master branch compared with 0.36.0 (#949)
  • Identifier conflict warnings when using Oceananigans (#950)
  • Avoiding repeated computations in the evaluation of AbstractOperations (#955)
  • Docstring for RungeKutta3TimeStepper is incorrect (#957)
  • Bug due to "initialization" of WindowedTimeAverage diagnostic (#962)
  • Bugs in fourth order advection in bounded directions (#965)
  • Typo in docstring for AveragedField(op::AbstractOperation) (#967)

Merged pull requests:

  • Lid-driven cavity verification experiment (#572) (@ali-ramadhan)
  • WENO advection schemes and advection verification experiments (#592) (@ali-ramadhan)
  • Fixes bug in adapt_structure for ComputedField (#953) (@glwagner)
  • More specific imports from KernelAbstractions in Fields module to solve identifier conflict warnings (#954) (@glwagner)
  • PressureField and tests for AveragedFields and ComputedFields in operations (#956) (@glwagner)
  • Fixes initialization and finalization bugs in WindowedTimeAverage (#964) (@glwagner)
  • Updating Julia DOI (#966) (@arfon)
  • Avoiding unnecessary recomputation of fields in output evaluation (#968) (@glwagner)
  • Do not zero out halo regions in directions that arent averaged (#970) (@glwagner)
  • New framework for high-order advection schemes (#972) (@glwagner)
  • Add JOSS badge (#976) (@ali-ramadhan)
  • Fixes timestepper docstrings and simplifies constructor (#977) (@glwagner)
  • Fixes typo in docs for non-traditional beta plane and simplifies language (#978) (@glwagner)
  • Docs comply with julia = "^1.4" compat entry (#979) (@navidcy)
  • Adds bangs and conventionalizes signatures of run_diagnostic! and write_output! (#980) (@glwagner)
  • Completes docstring for SeawaterBuoyancy constructor (#981) (@glwagner)
  • Cleans up docstrings for tendency kernels (#982) (@glwagner)
  • Changes default progress from nothing to an innocuous function (#983) (@glwagner)
  • Moves boundary condition aliases to FieldBoundaryConditions (#984) (@glwagner)
  • Bump v0.38.0 (#988) (@ali-ramadhan)
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🌾 Oceananigans v0.37.0

17 Sep 14:02
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v0.37.0
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🌾 Oceananigans v0.37.0

Oceananigans v0.37.0

Diff since v0.36.0

  • More empowered Field abstraction:
    • AbstractReducedField and concrete ReducedField for representing fields that are reduced along one or more dimensions.
    • AveragedField <: AbstractReducedField representing a field that is averaged along one dimension. AveragedField will replace Average in the near future and can be inserted into AbstractOperations.
    • ComputedField representing fields whose data must be "computed". ComputedFields are intended to hold the results of AbstractOperations. They can also participate in AbstractOperations.
  • FieldSlicer abstraction representing a "slice" or sub-indexing operation applied to fields prior to output.
  • Functionality in JLD2OutputWriter for handling field output. This eliminates the need for the FieldOuputs constructor. FieldSlicer can be used with JLD2OutputWriter.
  • Bugfixes and improvements to WindowedTimeAverage and full integration with FieldSlicer and JLD2OutputWriter.
  • Support for closure = nothing so that models can be run with no diffusivity or turbulence closure.
  • A new, as-of-now non-default third-order Runge-Kutta time-stepper, along with dynamics tests and convergence tests.
  • Bugfix in the experimental fourth order advection scheme.
  • Bugfix that incorrectly created MultiaryOperations when they should have been BinaryOperations.

Breaking changes:

  • FieldOutputs no longer exists; named tuples of fields should be passed directly to JLD2OutputWriter instead (and halos are omitted by default when using this functionality)

Closed issues:

  • Explicitly time-step w instead of recomputing it from continuity? (#338)
  • Forward Euler + 3rd order Runge-Kutta time-stepping (or integration with DifferentialEquations.jl) (#506)
  • ReducedField type (#525)
  • zero_halo_regions needs to know about field and grid topology (#734)
  • Need to update ParameterizedForcing constructor (#785)
  • Setting up inflow condition in bounded domain with buoyancy as tracer (#789)
  • Why is w*T is a MultiaryOperation? (#892)
  • Docstring for IncompressibleModel is incorrect (#895)
  • Keyword array_type in JLD2OutputWriter (and perhaps NetCDFOutputWriter) (#901)
  • More meaningful notation for non-traditional beta plane (#918)
  • zero_halo_regions is incorrect for fields located on faces in bounded directions (#919)
  • The values of slices dictionary in NetCDFOutputWriter are identical for every field (#926)
  • Cannot create model with closure = nothing (#939)

Merged pull requests:

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🧻 Oceananigans v0.36.0

08 Sep 16:02
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v0.36.0
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🧻 Oceananigans v0.36.0

Oceananigans v0.36.0

Diff since v0.35.0

This release coincides with the publication of the Oceananigans.jl Journal of Open Source Software (JOSS) paper.

Changelog:

  • Simplified boundary condition interface, types, and constructors. See the "boundary conditions" section under "Model setup" in the documentation for updated examples.
  • Support for a NonTraditionalBetaPlane Coriolis force implementation.
  • The AnisotropicBiharmonicDiffusivity closure now works properly in closed domains with zero Flux boundary conditions, as higher-order boundary conditions are enforced.
  • Bug fix: Appending to NetCDF files with NetCDFOutputWriter works now.
  • Bug fix: Computations of abstract operations compute the right end point of face-centered fields along bounded dimensions.
  • Bug fix: Averages with_halos=false return results with the correct dimensions for face-centered results along bounded dimensions.
  • Small bug fixes for show methods.

Breaking changes:

  • When constructing a NetCDFOutputWriter, use mode="c" instead of clobber=true and mode="a" instead of clobber=false.

Closed issues:

  • More streamlined interface for boundary functions? (#769)
  • Return of the multiple of 16 bug (#780)
  • When printing an AbstractOperation, the tree should be indented for readability (and without newline separation) (#893)
  • Is the warning "This simulation will recalculate the time step every iteration which can be slow" correct? (#903)
  • Wrong size for averages with halos of face-centered fields along bounded dimensions (#906)
  • Computations do not compute the right end point faces of bounded dimensions (#908)
  • Cannot append to NetCDF file even with clobber=false (#913)
  • Docs for 0.35.0 seem to be missing (#917)

Merged pull requests:

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🧵 Oceananigans v0.35.0

02 Sep 15:02
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v0.35.0
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🧵 Oceananigans v0.35.0

Oceananigans v0.35.0

Diff since v0.34.1

  • Support for multithreaded CPU simulations! Set the number of threads via the JULIA_NUM_THREADS environment variable or via the -t flag in Julia 1.5+.
  • New OceananigansLogger for fancy log messages with time stamps.
  • New experimental diagnostic: the WindowedTimeAverage.
  • Average diagnostic can include or exclude halos via the with_halos keyword argument.
  • Improved testing infrastructure made possible by splitting tests into four groups, selectable with the TEST_GROUP environment variable.
  • Cleaned up convergence test scripts and plots. Convergence tests can now be fully run by running the tests with the TEST_GROUP=convergence environment variable.
  • Numerous bug fixes and documentation updates.

Closed issues:

  • We need to upgrade our testing infrastructure soon-ish. (#139)
  • Abstraction / Diagnostic for moving averages (#501)
  • Failed to precompile GPUArrays, CUDA, Oceananigans on macOS (#854)
  • Error when trying to diagnose Average of an abstract operation (#857)
  • Error with NetCDF output - Julia v1.5, Oceananigans v0.34.1 (#862)
  • scalar getindex is disallowed with topology = (Periodic, Bounded, Bounded) using Oceananigans v0.34.1 (#864)
  • {x,y,z}nodes function docstrings do not document the reshape keyword argument (#865)
  • Getting GPU name in versioninfo_with_gpu() fails with CUDA v1.3.0 (#866)
  • Use FFTW.set_num_threads (#867)
  • test/test_*.jl is a redundant naming scheme (#871)
  • Run convergence tests as part of the verification testset (#873)
  • Include all convergence test plots in documentation (#879)
  • total_size(grid::AbstractGrid) seems wrong (#883)

Merged pull requests:

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⏳ Oceananigans v0.34.1

12 Aug 17:01
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⏳ Oceananigans v0.34.1

Oceananigans v0.34.1

Diff since v0.34.0

This is a bugfix release that disables CuArray scalar operations by default (to avoid surprise scalar operations that can cause huge slowdowns) and fixes a related bug where writing GPU fields to NetCDF was very slow. Also includes small updates to the documentation.

Closed issues:

  • Dynamically disable CuArray scalar operations (#276)
  • Update performance benchmarks plot and discuss results (#607)
  • Fix citations and references in documentation (#609)
  • Link documentation of numerical methods with code and API (#610)

Merged pull requests:

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🏵️ Oceananigans v0.34.0

08 Aug 12:02
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🏵️ Oceananigans v0.34.0

Oceananigans v0.34.0

Diff since v0.33.0

This release adds some new features, fixes some bugs, and improves the API (so there are some breaking changes, listed below).

Major changes:

  • Triply periodic models are now available by passing the topology = (Periodic, Periodic, Periodic) keyword argument to grids.
  • All 1D, 2D, and 3D averages are now available through the Average diagnostic with the dims keyword argument.
  • Fixed some checkpointing bugs.
  • BREAKING: Use Average(..., dims=(1, 2)) instead of HorizontalAverage(...).
  • BREAKING: Use iteration_interval and time_interval instead of frequency and interval for diagnostics and output writers.
  • BREAKING: Use iteration_interval instead of progress_frequency for simulations.
  • BREAKING: Use IsotropicDiffusivity and AnisotropicDiffusivity instead of ConstantIsotropicDiffusivity and ConstantAnisotropicDiffusivity. Also, use νz instead of νv and κz instead of κv.
  • BREAKING: To restore_from_checkpoint, pass model constructor arguments as you would to a normal constructor, e.g. restore_from_checkpoint("my_checkpoint.jld2", boundary_conditions=custom_bcs). Previous behavior was to pass a dictionary which was less user friendly.

Closed issues:

  • Update README and fix broken links (#608)
  • Clearer names for frequency and interval for diagnostics (#672)
  • Misleading documentation for JLD2OutputWriter (#827)
  • Typo: no such thing as "tradient" (#831)
  • IsotropicDiffusivity and AnisotropicDiffusivity are not exported by Oceananigans.jl (#835)
  • Flux boundary condition docstring should mention the sign convention (#837)
  • versioninfo_with_gpu util fails on machine with CUDA but running CPU models (#840)
  • NetCDFOutputWriter should recast the type of global_attributes into Dict{String,Any} (#841)

Merged pull requests:

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