scverse / scverse/spatialdata

Benchmarks performance on HPC

Open
#741 1 comment 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Dominant language
Python
Stars
394
Forks
95
Avg merge
4d 3h
Merged PRs (30d)
7

Description

CC @melonora @berombau

Working with Zarr files on a HPC may create problems due to Zarr v2. One of the challenges for the hackathon will be to setup a set of benchmarks, which will help evaluate the transition to Zarr v3.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by locating the code paths that read and write Zarr v2 data and checking how Zarr v3 transition work is currently handled. Define benchmark cases that expose HPC-related performance or compatibility problems, then run them on representative HPC storage. Done means a documented benchmark set can compare the two Zarr versions.

Written by the indexing model from the issue text.

Assessment

Tech stack
hpc, python
Domain
hpc, performance
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.