A look at the Mojo language for bioinformatics • Hacker News Board

Re: A look at the Mojo language for bioinformatics

#121

Post by bhansconnect » Mon, Feb 12, 2024, 10:10 PM UTC

mcqueenjordan wrote: post #9

Another point of clarification that is of great importance to the results, and is a common Rust newcomer error: The benchmarks for the Rust implementation (in the original post that got all the traction) were run with a /debug/ build of rust, i.e. not an optimized binary compiled with --release. So it was comparing something that a) didn't do meaningful parsing against b) the full parsing rust implementation in a non…

This is not accurate. The blog post used `--release` for it's Rust numbers. The confusion comes from the 50% performance win being specific to running on an M2 mac. On an x86_64 Linux machine, the results are more or less equivalent.

Re: A look at the Mojo language for bioinformatics

#122

Post by MohamedMabrouk » Mon, Feb 12, 2024, 11:28 PM UTC

fwip wrote: post #118

MohamedMabrouk wrote: post #113

Earlier quoted context omitted.

Hey, the Mojo parser author here. the test folder is just for the unit tests. All the benchmarking code is located in the /benchmark folder. It would be great if you can give it another go on your machine. https://github.com/MoSafi2/MojoFastTrim/tree/restructed/benc...

Thanks for the pointer, I had only checked the 'main' branch, which doesn't have the benchmarking code present. When running on the commit & code you point to here, here are my new results: $ hyperfine -N --warmup 5 './benchmark/fast_parser data/fastq_test.fastq' './benchmark/needletail_benchmark/target/release/rust_parser data/fastq_test.fastq ' Benchmark 1: ./benchmark/fast_parser data/fastq_test.fastq Time (mean ±…

That's great to see, thanks a ton. care to share your system information? I am trying to understand where the difference is coming from and that would really helpful.

Re: A look at the Mojo language for bioinformatics

#123

Post by fwip » Tue, Feb 13, 2024, 2:56 PM UTC

MohamedMabrouk wrote: post #122

fwip wrote: post #118

Earlier quoted context omitted.

Thanks for the pointer, I had only checked the 'main' branch, which doesn't have the benchmarking code present. When running on the commit & code you point to here, here are my new results: $ hyperfine -N --warmup 5 './benchmark/fast_parser data/fastq_test.fastq' './benchmark/needletail_benchmark/target/release/rust_parser data/fastq_test.fastq ' Benchmark 1: ./benchmark/fast_parser data/fastq_test.fastq Time (mean ±…

That's great to see, thanks a ton. care to share your system information? I am trying to understand where the difference is coming from and that would really helpful.

Sure, it's the 14-inch 2021 Macbook Pro (Apple M1 Pro chip), 16GB. Connected to power, other programs running, but nothing actively working. Timings were pretty stable when running a few times.

Re: A look at the Mojo language for bioinformatics

#124

Post by MohamedMabrouk » Tue, Feb 13, 2024, 7:15 PM UTC

fwip wrote: post #123

MohamedMabrouk wrote: post #122

Earlier quoted context omitted.

That's great to see, thanks a ton. care to share your system information? I am trying to understand where the difference is coming from and that would really helpful.

Sure, it's the 14-inch 2021 Macbook Pro (Apple M1 Pro chip), 16GB. Connected to power, other programs running, but nothing actively working. Timings were pretty stable when running a few times.

Thanks a lot!