Ragnar {Groot Koerkamp} 🦋

PhD on high troughput bioinformatics @ ETH Zurich;
IMO, ICPC, Xoogler, Rust, road-cycling, hiking, wild camping, photography

[Ragnar {Groot Koerkamp} 🦋 @curious_coding]

@heufd4 ❤️

Basically "fuzzy grep for fasta files": search fasta/fastq files for short DNA patterns to verify that they are present/absent in the data in the right places, and what kind of errors there are.

[Ragnar {Groot Koerkamp} 🦋 @curious_coding]

To all folks dealing with biological data:
do you ever need to check if your reads contain barcodes/adapters/primers/...? Or off-target matches?

Sassy is the tool to use! A super fast implementation of "approximate string matching" with a grep-like CLI.

https://t.co/WWdcuh82Fb

[Ragnar {Groot Koerkamp} 🦋 @curious_coding]

https://t.co/9XwyNVhpIs

[Ragnar {Groot Koerkamp} 🦋 @curious_coding]

New preprint!
The SimdQuickHeap is the fastest priority queue, by far.
2x faster than a radix heap, and up to 10x faster than binary heaps.

Coauthored with Johannes Breitling and Marvin Williams.

[Data Structures and Algorithms Papers @AlgorithmPapers]

SimdQuickHeap: The QuickHeap Reconsidered

Johannes Breitling, Ragnar Groot Koerkamp, Marvin Williams
https://t.co/FMY7iqpEce [𝚌𝚜.𝙳𝚂]

[Ragnar {Groot Koerkamp} 🦋 @curious_coding]

As often: the SimdQuickHeap is a conceptually very simple data structure that thus can be easily optimized using SIMD, leading to pretty big speed gains.

[Ragnar {Groot Koerkamp} 🦋 @curious_coding]

https://t.co/ftWJFOqxEa

[Ragnar {Groot Koerkamp} 🦋 @curious_coding]

New preprint!
The SimdQuickHeap is the fastest priority queue, by far.
2x faster than a radix heap, and up to 10x faster than binary heaps.

Coauthored with Johannes Breitling and Marvin Williams.

[Ragnar {Groot Koerkamp} 🦋 @curious_coding]

OMG! By popular demand (🤗) I'm going to speak at P99 again!
This time about the SimdQuickHeap preprint that just came out: the fastest priority queue by 2x (or 10x comparing to a binary heap).

[P99CONF @P99CONF]

We've been working hard behind the scenes to bring you an unforgettable P99CONF 2026. Registration is now open, so take a look at who is coming back and the new speakers we have on board > https://t.co/HMlcvQNjFs

#ScyllaDB #P99CONF

[Data Structures and Algorithms Papers @AlgorithmPapers]

SimdQuickHeap: The QuickHeap Reconsidered

Johannes Breitling, Ragnar Groot Koerkamp, Marvin Williams
https://t.co/FMY7iqpEce [𝚌𝚜.𝙳𝚂]

[Geoff Langdale @geofflangdale]

@valigo Getting good at GPU programming will make you a better coder on modern CPUs. A throughput-oriented mentality, while critical on GPUs, is also a way better way of coaxing better performance out of the wide, deeply-pipelined, SIMD-enabled monstrosities that are modern CPUs.

[Ragnar {Groot Koerkamp} 🦋 @curious_coding]

@slimjimmy @sasuke___420 5s with avx2

https://t.co/0xrMEcqWfd

[Jennifer Doleac @jenniferdoleac]

Me 15 years ago, as a PhD student: “It seems like all the interesting questions have been answered & there are no useful studies left to do.”

Me now, as a funder focused on evidence-based criminal justice policy: “The biggest constraint we face is finding researchers with time to engage in important new projects.”

Truly, this is the most pressing problem I have. I need an army of scholars who understand causal methods & who would jump at an opportunity to study a program or policy. Would you like to help? Email me. 🙏

[The Lunduke Journal @LundukeJournal]

Microsoft has set a goal to “eliminate every line of C and C++ from Microsoft by 2030.”

What are they going to try to replace that C & C++ code with?

You guessed it. Rust.

And they’re going to use AI to do the “Rust re-write” at an insane speed.

“Our strategy is to combine AI *and* Algorithms to rewrite Microsoft’s largest codebases. Our North Star is “1 engineer, 1 month, 1 million lines of code”.

You read that right.

One million lines of code, per engineer, per month.

Pure insanity. This kind of decision making is common among those with a deeply held, delusional faith in the Cult of Rust.

Take battle tested code, and re-write it (without a clear benefit to the end user) at a recklessly rapid rate. Then force others to adopt that rewritten code before it is ready or properly tested.

All while holding a delusional belief that your new Rust code is superior in all ways, and is inherently bug free thanks to the divine nature of Rust.

We learned this from a post by Galen Hunt, Distinguished Engineer at Microsoft Research.

https://t.co/UQFk76ncXf

[Geoff Langdale @geofflangdale]

The experience of having some muddy mess of a hundred line function with goofy "do things one way here, then do almost the same thing somewhere else, then ..." become clear and turn into a 20-line clean "computer science" type function with nice clean data structures is bliss.

[𝕐 @nomad421]

If you really want to search quickly, use @curious_coding’s approach https://t.co/owTSeNXYyb!

[Geoff Langdale @geofflangdale]

@lemire I think we should have a new runtime option where stack, heap, bss, and tls are all in zones where it is guaranteed that any load of any legally addressable byte is guaranteed not to be <64 bytes from a page boundary or anything that will cause a disaster if loaded. ...

[Geoff Langdale @geofflangdale]

Contemplating a type system where the bit sizes required are 1, 2, 4, 8, 9, 16, 17, 32, 33, 64, 65, 128, 256, 512. Disgusting stuff, I should be ashamed of myself.

[lucy 🐧 @uneventual]

Having to pattern match Optional::None and Optional::Some(Optional::None) separately is exactly like that joke about Sartre ordering a coffee with no cream, only to be told “I’m sorry monsieur, we don’t have any cream, would you like it with no milk instead?”