Outperforming Rust DNA sequence parsing benchmarks by 50% with Mojo

Re:Outperforming Rust DNA sequence parsing benchmarks by 50%... by one-punch on Wednesday February 07, 2024 @08:54PM (#39296889)

Chris, how would you respond to the remark that the article is comparing a flawed Mojo implementation against a more correct Rust implementation? https://news.ycombinator.com/item?id=39296559

> Insightful Reddit comment https://old.reddit.com/r/rust/comments/1al8cuc/modular_commu...

> > The TL;DR is that the Mojo implementation is fast because it essentially memchrs four times per read to find a newline, without any kind of validation or further checking. The memchr is manually implemented by loading a SIMD vector, and comparing it to 0x0a, and continuing if the result is all zeros. This is not a serious FASTQ parser. It cuts so many corners that it doesn't really make it comparable to other parsers (although I'm not crazy about Needletails somewhat similar approach either).

> > I implemented the same algorithm in < 100 lines of Julia and were >60% faster than the provided needletail benchmark, beating Mojo. I'm confident it could be done in Rust, too.

[ Parent | on HN ]

Re:Outperforming Rust DNA sequence parsing benchmarks by 50%... by heuermh on Thursday February 08, 2024 @04:01PM (#39307629)

Here is a cache of valid and invalid FASTQ files for unit tests

https://github.com/biojava/biojava/tree/master/biojava-genom...

[ Parent | on HN ]

Re:Outperforming Rust DNA sequence parsing benchmarks by 50%... by chrislattner on Monday February 12, 2024 @12:59PM (#39348083)

As far as I know, the Mojo implementation is doing the same algorithm as the baseline rust implementation. The person commenting on that is complaining about the rust impl as well.

[ Parent | on HN ]