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Just another Genome hacker,

Jeroen Van Goey BioGeek

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Just another Genome hacker,
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@3outeille
3outeille / pipeline_parallel.py
Last active July 9, 2025 11:35
Self contained example of how pipeline parallel works (AFAB and 1F1B) in 200 LOC
#VERBOSE=0 torchrun --nproc_per_node 3 self_contained_pp_LOC.py
import os, random, numpy as np, torch, torch.nn as nn, torch.distributed as dist, torch.nn.functional as F
from torch.optim import AdamW
from torch.utils.data import DataLoader, DistributedSampler
from datasets import load_dataset
from transformers import AutoConfig, AutoModelForCausalLM, AutoTokenizer
STEP, local_rank, world_size, verbose = 0, int(os.environ["LOCAL_RANK"]), int(os.environ["WORLD_SIZE"]), os.environ.get("VERBOSE", "0") == "1"
def set_all_seed(seed):
@veekaybee
veekaybee / normcore-llm.md
Last active July 18, 2025 17:00
Normcore LLM Reads

Anti-hype LLM reading list

Goals: Add links that are reasonable and good explanations of how stuff works. No hype and no vendor content if possible. Practical first-hand accounts of models in prod eagerly sought.

Foundational Concepts

Screenshot 2023-12-18 at 10 40 27 PM

Pre-Transformer Models

@abishekmuthian
abishekmuthian / cudf_ARM64_jetson.md
Last active June 16, 2023 15:07
Installing cudf on ARM(aarch64)[Jetson Nano]

My setup

I'm using Nvidia Jetson nano.

Quad-core ARM® Cortex®-A57 MPCore processor

NVIDIA Maxwell™ architecture with 128 NVIDIA CUDA® cores

4 GB 64-bit LPDDR4 1600MHz - 25.6 GB/s

Ubuntu 18.04 LTS

#!/bin/sh
set -x
# == Swarm training (alpha release) ==
# Setup:
#
# git clone https://github.com/shawwn/gpt-2
# cd gpt-2
# git checkout dev-shard
@ines
ines / .zshrc
Last active February 28, 2021 19:42
Command to activate / create Python virtual environmment
function venv {
default_envdir=".env"
envdir=${1:-$default_envdir}
if [ ! -d $envdir ]; then
python -m venv $envdir
pip install ipython black flake8
echo -e "\x1b[38;5;2m✔ Created virtualenv $envdir\x1b[0m"
fi
source $envdir/bin/activate
@andy-thomason
andy-thomason / Genomics_A_Programmers_Guide.md
Created May 14, 2019 13:32
Genomics a programmers introduction

Genomics - A programmer's guide.

Andy Thomason is a Senior Programmer at Genomics PLC. He has been witing graphics systems, games and compilers since the '70s and specialises in code performance.

https://www.genomicsplc.com

1) Read an image from file
2) Display an image that you read from file
3) Capture Video using your webcam and display the feed
4) Display back and white live stream from your webcam.
5) Have a slider to change brightness of the webcam live stream. Display.
6) Have a slider to change contrast of the webcam live stream. Display.
7) Capture a snapshot from your webcam. Then display difference between live video stream and this snapshot. (Background subtraction)
8) Display Canny edge image from your live webcam stream
9) Have a slider to change smoothness / sharpness of image from live webcam stream.
10) Display histogram of colors (RGB) from your live webcam stream
@arfon
arfon / big_query_examples.md
Last active September 19, 2022 13:00
BigQuery Examples for blog post

How many times shouldn't it happen...

-- https://news.ycombinator.com/item?id=11396045

SELECT count(*)
FROM (SELECT id, repo_name, path
        FROM [bigquery-public-data:github_repos.sample_files]
 ) AS F
@pakt
pakt / rdwr.py
Created August 15, 2015 10:59
Direct read/write access to Python's memory
#
# read/write access to python's memory, using a custom bytearray.
# some code taken from: http://tinyurl.com/q7duzxj
#
# tested on:
# Python 2.7.10, ubuntu 32bit
# Python 2.7.8, win32
#
# example of correct output:
# inspecting int=0x41424344, at 0x0228f898