Lux.jl VS OffsetArrays.jl

There is also the less known Lux.jl package: https://github.com/avik-pal/Lux.jl

Can you point to a concrete example of one that someone would run into when using the differential equation solvers with the default and recommended Enzyme AD for vector-Jacobian products? I'd be happy to look into it, but there do not currently seem to be any correctness issues in the Enzyme issue tracker that are current (3 issues are open but they all seem to be fixed, other than https://github.com/EnzymeAD/Enzyme.jl/issues/278 which is actually an activity analysis bug in LLVM). So please be more specific. The issue with Enzyme right now seems to moreso be about finding functional forms that compile, and it throws compile-time errors in the event that it cannot fully analyze the program and if it has too much dynamic behavior (example: https://github.com/EnzymeAD/Enzyme.jl/issues/368).

Additional note, we recently did a overhaul of SciMLSensitivity (https://sensitivity.sciml.ai/dev/) and setup a system which amounts to 15 hours of direct unit tests doing a combinatoric check of arguments with 4 hours of downstream testing (https://github.com/SciML/SciMLSensitivity.jl/actions/runs/25...). What that identified is that any remaining issues that can arise are due to the implicit parameters mechanism in Zygote (Zygote.params). To counteract this upstream issue, we (a) try to default to never default to Zygote VJPs whenever we can avoid it (hence defaulting to Enzyme and ReverseDiff first as previously mentioned), and (b) put in a mechanism for early error throwing if Zygote hits any not implemented derivative case with an explicit error message (https://github.com/SciML/SciMLSensitivity.jl/blob/v7.0.1/src...). We have alerted the devs of the machine learning libraries, and from this there has been a lot of movement. In particular, a globals-free machine learning library, Lux.jl, was created with fully explicit parameters https://lux.csail.mit.edu/dev/, and thus by design it cannot have this issue. In addition, the Flux.jl library itself is looking to do a redesign that eliminates implicit parameters (https://github.com/FluxML/Flux.jl/issues/1986). Which design will be the one in the end, that's uncertain right now, but it's clear that no matter what the future designs of the deep learning libraries will fully cut out that part of Zygote.jl. And additionally, the other AD libraries (Enzyme and Diffractor for example) do not have this "feature", so it's an issue that can only arise from a specific (not recommended) way of using Zygote (which now throws explicit error messages early and often if used anywhere near SciML because I don't tolerate it).

So from this, SciML should be rather safe and if not, please share some details and I'd be happy to dig in.

Lots of things are being rewritten. Remember we just released a new neural network library the other day, SimpleChains.jl, and showed that it gave about a 10x speed improvement on modern CPUs with multithreading enabled vs Jax Equinox (and 22x when AVX-512 is enabled) for smaller neural network and matrix-vector types of cases (https://julialang.org/blog/2022/04/simple-chains/). Then there's Lux.jl fixing some major issues of Flux.jl (https://github.com/avik-pal/Lux.jl). Pretty much everything is switching to Enzyme which improves performance quite a bit over Zygote and allows for full mutation support (https://github.com/EnzymeAD/Enzyme.jl). So an entire machine learning stack is already seeing parts release.

Right now we're in a bit of an uncomfortable spot where we have to use Zygote for a few things and then Enzyme for everything else, but the custom rules system is rather close and that's the piece that's needed to make the full transition.

Well, there is OffsetArrays in Julia, but it has acquired a reputation as a poison pill because most code assumes the 1-based indexing and it's easy to forget to convert the indexing and screw up the code.

Similar correctness issues are a big part of the reason that, several years ago, I submitted a series of pull requests to Julia so that its entire test suite would run without memory errors under Valgrind, save for a few that either (i) we understood and wrote suppressions for, or (ii) we did not understand and had open issues for. Unfortunately, no one ever integrated Valgrind into the CI system, so the test suite no longer fully runs under it, last time I checked. (The test suite took nearly a day to run under Valgrind on a fast desktop machine when it worked, so is infeasible for every pull request, but could be done periodically, e.g. once every few days.)

Even a revived effort on getting core Julia tests to pass under Valgrind would not do much to help catch correctness bugs due to composing different packages in the ecosystem. For that, running in testing with `--check-bounds=yes` is probably a better solution, and much quicker to execute as well. (see e.g. https://github.com/JuliaArrays/OffsetArrays.jl/issues/282)

You might be interested in OffsetArrays.jl.

Counting starts at one, as do most vector/matrix/tensor indices. If it bothers you too much, see OffsetArrays.jl and Arrays with custom indices.

No need for another version, Julia supports custom indices by default. Check out https://docs.julialang.org/en/v1/devdocs/offset-arrays/ and https://github.com/JuliaArrays/OffsetArrays.jl