CoryKornowicz

Hello, Rust community!

My name is Hadrien and I am a software performance engineer in a particle physics lab. My daily job is to figure out ways to make scientific software use hardware more efficiently without sacrificing its correctness, primarily by adapting old-ish codebases to the changes that occured in the software and computing landscape since the days where they were designed:

CPU clock rates and instruction-level parallelism stopped going up, so optimizing code is now more important.
Multi-core CPUs went from an exotic niche to a cheap commodity, so parallelism is not optional anymore.
Core counts grow faster than RAM prices go down, so multi-processing is not enough anymore.
SIMD vectors become wider and wider, so vectorization is not a gimmick anymore.

Achieving warp speed with Rust

This gist contains some scripts for Amber.

anteligand.sh: Use antechamber to prepare a ligand for Amber
complex_tleap.sh: Use tleap to prepare a ligand-protein complex input parameter file (Amber14)
checkPDBID_MDprep.sh: After running many preparation jobs for PDB ligand-protein complexes, you should check whether the preparation is done.
rename_water.py: rename water to HOH O,H1,H2 for PDB/PQR

Maybe need some other tools installed, such as pdb2pqr and g09 and so on.

	import mlx.core as mx
	import mlx.nn as nn
	import mlx.optimizers as optim
	from mlx.data.datasets import load_mnist

	@mx.compile
	def matrix_exp(M):
	"""
	Compute matrix exponential using scaling and squaring with Padé approximation.
	This implements a simplified version suitable for small matrices.

	// Responsive Chips Selection
	// See Also: https://youtu.be/T82izB2XBMA?si=Cnf6rGdyisG8ZWoX

	import SwiftUI

	struct Tag: Hashable {
	var name: String
	var color: Color
	}

	kernel void add_arrays(device const float* inA [[buffer(0)]],
	device const float* inB [[buffer(1)]],
	device float* result [[buffer(2)]],
	uint index [[thread_position_in_grid]])
	{
	result[index] = inA[index] + inB[index];
	}

	"""Hello world, with a genetic algorithm.

	https://twitter.com/matthen2/status/1769368467067621791
	"""

	import random
	import time
	from dataclasses import dataclass
	from itertools import chain
	from typing import Iterable, List

	// Lines
	float hash( float n ) {
	return fract(sin(n)*753.5453123);
	}

	// Slight modification of iq's noise function.
	float noise(vector_float2 x )
	{
	vector_float2 p = floor(x);
	vector_float2 f = fract(x);

	#!/usr/bin/env python

	import sys
	from prody import *
	from rdkit import Chem
	from rdkit.Chem import AllChem
	from io import StringIO
	import pypdb

	import math
	import pybel


	def squared_distance(coordsA, coordsB):
	"""Find the squared distance between two 3-tuples"""
	sqrdist = sum((a - b)**2 for a, b in zip(coordsA, coordsB))
	return sqrdist

CoryKornowicz

Achieving warp speed with Rust

Contents:

This gist contains some scripts for Amber.