fpm VS SciPyDiffEq.jl

Make sure you have the latest fpm binary installed somewhere so that your $PATH can see it: curl -o ~/.local/bin/fpm -L https://github.com/fortran-lang/fpm/releases/download/v0.8.2/fpm-0.8.2-linux-x86_64 && chmod 0755 ~/.local/bin/fpm

Hopefully, the SciPy community can stay open-minded about modern Fortran libraries.

Modern Fortran is quite different from Fortran 77, while being as powerful, if not more.

In addition, there has been a significant community effort on improving and modernising the legacy packages, the ecosystem, and the language itself.

With projects like LFortran (https://lfortran.org/), fpm (https://github.com/fortran-lang/fpm), and stdlib (https://github.com/fortran-lang/stdlib), I believe that Fortran will enjoy prosperity again.

Anyway, first release of Fortran Package Manager was in November 2020: https://github.com/fortran-lang/fpm/releases/tag/v0.1.0 - more recently than I expected.

There is actually a Fortran Package Manager that will hopefully make things easier in the future. It's quite new, so it might not be entirely mature yet.

Author here, so I'm biased toward Fortran, though I've been enjoying learning Rust as well. I think there are a few reasons.

First, Rust's multidimensional arrays are either limited and/or difficult to use. Fast, flexible, and ergonomic multidimensional arrays and arithmetic are essential for HPC. They are possible with Rust, but my two favorite Rust books not mentioning them suggests to me that they're not the focus of the language. This may or may not change in the future.

Second, Rust may be too complex to learn for scientists who aren't paid to write software but to do research. Fortran is opposite--multidimensional whole-array arithmetic looks like you would write it as math on a whiteboard. While scientists can sure learn to program Rust effectively, I think most scientists don't think like Rust, but they do think like Fortran. For somebody not familiar with Fortran but familiar with Python, I'd say Fortran very much feels like NumPy.

Third, such ecosystem would be built in Rust from scratch. In Fortran, most of the value is already there, but needs to be made more accessible with better and more modern tooling. For example, Fortran's fpm (https://github.com/fortran-lang/fpm) is largely modeled after Rust's Cargo because we recognize the importance of good user experience when it comes to building and packaging software. With the recent Fortran-lang efforts, we study many programming language ecosystems and communities (e.g. Python, Julia, Rust, etc.) to find what could work best for modern Fortran tooling.

I recently started learning Fortran for a lark. It reminds me a lot of R, in some respects. It's clearly a very, very good language for doing the parts of one's job that are very math-centric. But it's equally underwhelming as a general purpose programming language.

Largely, I think, due to gaps in the library ecosystem. But there are other challenges. You can see from the install instructions on the linked page, for example, that Fortran still lacks a package manager.

What's interesting, though, is that that's changing. There are currently serious efforts to give it a "standard" library (https://github.com/fortran-lang/stdlib) and package manager (https://github.com/fortran-lang/fpm).

And I've been watching the new LFortran compiler (https://lfortran.org) with extreme interest.

FPM has entered the chat https://github.com/fortran-lang/fpm

Check out the SciML ecosystem. They are doing amazing work in that space. You might also want to integrate your methods with their libraries, as it will boost their potential audience massively. https://sciml.ai/

Interesting response. I develop the Julia SciML organization https://sciml.ai/ and we'd be more than happy to work with you to get wrappers for PRIMA into Optimization.jl's general interface (https://docs.sciml.ai/Optimization/stable/). Please get in touch and we can figure out how to set this all up. I personally would be curious to try this out and do some benchmarks against nlopt methods.

Overall, your analysis is very Python centric. It's not very clear to me why Julia should focus on convincing Python users or developers. There are many areas of numerical and scientific computing that are not well served by Python, and it's exactly those areas that Julia is pushing into. The whole SciML https://sciml.ai/ ecosystem is a great toolbox for writing models and optimizations that would have otherwise required FORTRAN, C, and MATLAB. Staying within Julia provides access to a consistent set of autodiff technologies to further accelerate those efforts.

What about the other benchmarks on the same site? https://docs.sciml.ai/SciMLBenchmarksOutput/stable/Bio/BCR/ BCR takes about a hundred seconds and is pretty indicative of systems biological models, coming from 1122 ODEs with 24388 terms that describe a stiff chemical reaction network modeling the BCR signaling network from Barua et al. Or the discrete diffusion models https://docs.sciml.ai/SciMLBenchmarksOutput/stable/Jumps/Dif... which are the justification behind the claims in https://www.biorxiv.org/content/10.1101/2022.07.30.502135v1 that the O(1) scaling methods scale better than O(log n) scaling for large enough models? I mean.

> If you use special routines (BLAS/LAPACK, ...), use them everywhere as the respective community does.

It tests with and with BLAS/LAPACK (which isn't always helpful, which of course you'd see from the benchmarks if you read them). One of the key differences of course though is that there are some pure Julia tools like https://github.com/JuliaLinearAlgebra/RecursiveFactorization... which outperform the respective OpenBLAS/MKL equivalent in many scenarios, and that's one noted factor for the performance boost (and is not trivial to wrap into the interface of the other solvers, so it's not done). There are other benchmarks showing that it's not apples to apples and is instead conservative in many cases, for example https://github.com/SciML/SciPyDiffEq.jl#measuring-overhead showing the SciPyDiffEq handling with the Julia JIT optimizations gives a lower overhead than direct SciPy+Numba, so we use the lower overhead numbers in https://docs.sciml.ai/SciMLBenchmarksOutput/stable/MultiLang....

> you must compile/write whole programs in each of the respective languages to enable full compiler/interpreter optimizations

You do realize that a .so has lower overhead to call from a JIT compiled language than from a static compiled language like C because you can optimize away some of the bindings at the runtime right? https://github.com/dyu/ffi-overhead is a measurement of that, and you see LuaJIT and Julia as faster than C and Fortran here. This shouldn't be surprising because it's pretty clear how that works?

I mean yes, someone can always ask for more benchmarks, but now we have a site that's auto updating tons and tons of ODE benchmarks with ODE systems ranging from size 2 to the thousands, with as many things as we can wrap in as many scenarios as we can wrap. And we don't even "win" all of our benchmarks because unlike for you, these benchmarks aren't for winning but for tracking development (somehow for Hacker News folks they ignore the utility part and go straight to language wars...).

If you have a concrete change you think can improve the benchmarks, then please share it at https://github.com/SciML/SciMLBenchmarks.jl. We'll be happy to make and maintain another.