MOLE.jl Software Development Plan

[valeriabarra]

Goal

Produce a native, well-tested, high-performance Julia package MOLE.jl that matches the functionality and numerical correctness of the MATLAB/Octave reference in src/matlab_octave, offers idiomatic Julia APIs (multiple dispatch, sparse arrays, types), integrates with Julia ecosystem tooling (Documenter, BenchmarkTools, Test, etc), and provides parity tests and examples.

We will use the MATLAB/Octave code in src/matlab_octave as the canonical reference to port from

Architecture & directory layout

MOLE.jl/
├── Project.toml
├── src/
│   ├── MOLE.jl                # top-level module (re-exports)
│   ├── Grid/                  # grid types & helpers
│   │   ├── types.jl
│   │   ├── uniform.jl
│   │   └── curvilinear.jl
│   ├── Operators/             # core operators; each source file will contain the 1D, 2D and 3D implementation
│   │   ├── interpolation.jl
│   │   ├── gradient.jl
│   │   ├── divergence.jl
│   │   ├── curl.jl
│   │   └── laplacian.jl
│   ├── BCs/                   # boundary condition helpers
│   ├── Utils/                 # numerical utilities (staggering, indexing)
│   └── IO/                    # load/save, sample meshes
├── test/
│   ├── runtests.jl
│   ├── Grid/ 
│   |    ├── grid_tests.jl
|   ├── Operators/
│   |    ├── operator_tests.jl
│   ├── BCs/
│   |    ├── bc_tests.jl
│   ├── Utils/
│   |    ├── util_tests.jl 
│   └── IO/
│   |    ├── io_tests.jl 
├── docs/                      # Documenter.jl docs source
└── examples/

• Precision: default Float64, accept T<:AbstractFloat

Interoperability and compatibility

• Consider compatibility with DifferentialEquations.jl time integrators.

Performance considerations

• Julia has an interactive REPL, is Just-In-Time (JIT) compiled (triggered by first evaluation of function). It allows polymorphism via multiple dispatch (at compile or run time). We definitely want to take advantage of this.
• Can support CPUs and GPUs programming using a common open-source (single-source) code base
• We can write generic code and the compiler will specialize on types of calling arguments, e.g., f(x::AbstractArray) where AbstractArray can be Array of Float32, Float64 or a CuArray.
• We want to use Julia broadcasting:
  • apply a vectorized function point-wise to an array. Scalar values are "broadcast" over arrays; Fusion of multiple operations.

• Support user-extensible API: can be specialized for custom functions or argument types (e.g., CuArray compiles and applies a custom CUDA kernel).
• The current MATLAB/Octave implementation relies on sparse storage, but
  • Do we want MOLE Operators (grad, div, interpol) as "pseudo-functions"? In that case, they need to act like functions when broadcasted over an array of values, but can’t be called on a single value; can be composed and fused w/ function calls. (Very much like performant methods such as matrix-free methods, i.e., no assembly required; they specify the action of the operator.)

• Use @inbounds for bounds-checking and @view/@views for slices

Milestones and plan

Here is a tentative inventory for the porting

MOLE_Inventory__MATLAB-_Julia__Preview.csv

Subtasks

• Refactor existing MOLE.jl directory structure to match proposed directory layout #280
• Translate the addScalarBC1D Boundary Condition and add an example that shows its usage (elliptic1DaddScalarBC) #299

[Tony-Drummond]

@valeriabarra, I think your proposed code directory structure for Julia agrees with its functional modularity, which can be important for functional extensibility. It also sets a good software base model for other language implementations.

[gpagallo]

@valeriabarra +1 on Tony's comment above. I have a couple of questions/comments as I am not as familiar with Julia.

1. The names of the top directories are lower case, while the ones one level down are upper case. Is the difference in casing commonly done?
2. I think BC should be spelled out
   Thanks.

[valeriabarra]

@valeriabarra +1 on Tony's comment above. I have a couple of questions/comments as I am not as familiar with Julia.

1. The names of the top directories are lower case, while the ones one level down are upper case. Is the difference in casing commonly done?
2. I think BC should be spelled out
   Thanks.

Hi @gpagallo , thank you for your questions.

1. Yes, src/, test/, docs/, and examples/ are all standard names in Julia packages. The lower-level directories do not necessarily have to follow any convention. I went with capitalization to reflect Module naming conventions.
2. BCs is very standard in analytical/numerical PDEs communities to refer to Boundary Conditions, so I think we are ok leaving it like that :)

Thanks!

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This issue has had no activity for 21 days. It will be marked stale in 7 days if there is no further activity.

[valeriabarra]

Sub-Issues #305 and #354 are still pending.

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