Seth sstadick

Rust, Mojo, Bioinformatics.

sstadick / refresh

Last active January 2, 2026 15:03

	#!/usr/bin/env bash

	# Kill all open things except iTerm2
	osascript \
	-e 'tell application "System Events" to set quitapps to name of every application process whose background only is false and name is not "iTerm2"' \
	-e 'repeat with appName in quitapps' \
	-e 'try' \
	-e 'quit application appName' \
	-e 'end try' \
	-e 'end repeat'; \

sstadick / rusty_iterator.mojo

Created September 19, 2025 15:18

Rust flavored iteration

	trait RustyIterator(Copyable, Movable):
	alias Element: Copyable & Movable

	fn next(mut self) -> Optional[Self.Element]:
	...


	@fieldwise_init
	struct OwningIterator(RustyIterator):
	alias Element = Int

sstadick / ish_parasail_timings.txt

Last active July 21, 2025 23:33

ish and parasail timings

	# Parasail commit: 600fb261 (v2.6.2)
	# Ish commit: 5090c3e (v1.3.0)
	# Capping parasail threads to 16, to match ish which can only use physical cores (mojo bug), so both use 16 threads

	# SSE
	time ./apps/parasail_aligner -a sg_striped_sse41_128_16 -X 2 -x -M 2 -o 3 -e 1 -d -t 1 -q ./patterns.fa -f /srv/refdata/chm13v2.0.fa -v -V
	--> 1m21.371s
	time ./apps/parasail_aligner -a sg_dx_striped_sse41_128_16 -X 2 -x -M 2 -o 3 -e 1 -d -t 1 -q ./patterns.fa -f /srv/refdata/chm13v2.0.fa -v -V
	--> 1m20.438s
	time ./apps/parasail_aligner -a sg_dx_striped_sse41_128_16 -X 2 -x -M 2 -o 3 -e 1 -d -t 16 -q ./patterns.fa -f /srv/refdata/chm13v2.0.fa -v -V

sstadick / read_delim.mojo

Last active July 3, 2025 10:43

Example reading a simple delimited file in Mojo.

	"""Example usage of DelimReader on World Cities Pop.

	Deps:
	- pixi add extramojo (this example uses v0.15.0)
	- mojo 25.4

	Data:
	- https://github.com/BurntSushi/rust-csv/blob/master/examples/data/bench/worldcitiespop.csv
	- cat worldcitiespop.csv \| cut -f6,7 -d, \| tail -n +2 > lat_long.csv

sstadick / load_simd.mojo

Created May 9, 2025 17:47

UnsafePointer.load vs @parameter setting

sstadick / bench_bitset.mojo

Created May 7, 2025 14:42

	import math

	from algorithm import vectorize
	from benchmark import (
	Bench,
	Bencher,
	BenchId,
	BenchMetric,
	ThroughputMeasure,
	keep,

sstadick / count_nucleotide.mojo

Last active May 6, 2025 19:17

	import math

	from algorithm import vectorize
	from bit import pop_count
	from memory import pack_bits
	from sys import simdwidthof

	alias U8_SIMD_WIDTH = simdwidthof[DType.uint8]()
	"""Get the HW SIMD register size for uint8"""

sstadick / tree.mojo

Created January 28, 2025 11:57

	from memory import UnsafePointer
	from os import abort


	@value
	struct TreeNode:
	var data: String
	var key: String
	var hash: Int
	var left: UnsafePointer[Self]

sstadick / monitor.sh

Created January 22, 2025 22:13

Monitor a Process Memory Usage

	#!/bin/bash
	set -eo pipefail

	# redirect all stdout and stderr to a logfile AND display it on the terminal
	exec &> >(tee -a monitor.log)


	# pid: Process ID number
	# x_pmem: Memory usage as percentage of total system memory (multiplied by 10 (unit conversion between rss and mem_tot))
	# x_vsz: Virtual memory size in KB (allocated memory)

sstadick / splitmix64.rs

Created January 21, 2025 22:23

SplitMix64 Hasher for Rust u64

	use std::hash::{BuildHasher, Hasher};

	#[derive(Clone, Copy, Default)]
	pub struct SplitMix64Hasher(u64);

	impl Hasher for SplitMix64Hasher {
	#[inline]
	fn finish(&self) -> u64 {
	self.0
	}