Zarr version

2.18.2

Numcodecs version

0.13.0

Python Version

3.12.4

Operating System

Linux

Installation

pip install zarr

Description

I've converted some ome.tiff files to .zarr and have had issues with the reading time of the zarr files.
For this example I'm using an image of shape [ 4, 16484, 11620 ], and I have stored it with chunk size (1,1024, 1024) as well as unchunked.
All files are stored in a RAID0 nvme ssd and have the same compression.

I've compared the reading times using 1, 10, and 50 logical threads (with taskset) and noticed the performance can vary greatly depending on the settings. If unchunked, additional threads significantly improves reading time, just like when reading ome.tiffs. In fact, reading unchunked files is significantly faster than ome.tiffs. However, chunked files do not seem to benefit from additional threads, even resulting in slower times. Reading with the dask library also seems to have inconsistent performance, although in a different way.

Additionally, considering the hardware (RAID0 nvme ssd, dual 56 core CPU Intel Xeon Platinum 8280) , I'd assume that reading chunked files with multiple workers would be much faster, as the processing is done in parallel. But here we see that not only does it not seem to benefit from more workers, but it's an order of magnitude slower than reading an unchunked file.

Is there something I could be missing here?

Steps to reproduce

This is the code I'm using:

start = time.time()z = zarr.open(path_zarr)[:]print(f"Zarr read time (chunked): {time.time() - start}")start = time.time()z_nochunk = zarr.open(path_zarr_nochunk)[:]print(f"Zarr read time (no chunks): {time.time() - start}")start = time.time()d = dask.array.from_zarr(path_zarr).compute()print(f"Dask read time (chunked): {time.time() - start}")start = time.time()d_nochunk = dask.array.from_zarr(path_zarr_nochunk).compute()print(f"Dask read time (no chunks): {time.time() - start}")start = time.time()t = tifffile.imread(path_tiff)print(f"Tiff read time: {time.time() - start}")

Results:

# 1 thread:Zarr read time (chunked): 2.8317720890045166Zarr read time (no chunks): 0.7048866748809814Dask read time (chunked): 3.4919939041137695Dask read time (no chunks): 0.7005000114440918Tiff read time: 1.094351053237915

# 10 threads:Zarr read time (chunked): 2.8606531620025635Zarr read time (no chunks): 0.32688140869140625Dask read time (chunked): 2.7447142601013184Dask read time (no chunks): 0.712876558303833Tiff read time: 0.4734377861022949

# 50 threads:Zarr read time (chunked): 2.8490779399871826Zarr read time (no chunks): 0.2691495418548584Dask read time (chunked): 2.9153594970703125Dask read time (no chunks): 0.716036319732666Tiff read time: 0.4784407615661621

Additional output

No response