fix: concat batches before writing to avoid small IO slow down #2384

chebbyChefNEQ · 2024-05-23T04:32:44Z

reduce number of IOs to improve shuffle performance.

eddyxu · 2024-05-23T04:37:03Z

rust/lance-index/src/vector/ivf/shuffler.rs

+ }
+ // concat to avoid slowdown due to small IOs
+ let batch = concat_batches(&batches[0].schema(), &batches)?;
+ file_writer.write(&[batch]).await?;


Is this still an issue for v2 ? @westonpace

huh I'm kind of shocked it's an issue for v1 in the first place. I thought our writer code was designed to efficiently handle &[ArrayRef].

codecov-commenter · 2024-05-23T04:48:22Z

Codecov Report

Attention: Patch coverage is 66.66667% with 2 lines in your changes are missing coverage. Please review.

Project coverage is 79.95%. Comparing base (3dd63b8) to head (efb1e16).

Files	Patch %	Lines
rust/lance-index/src/vector/ivf/shuffler.rs	66.66%	0 Missing and 2 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2384      +/-   ##
==========================================
- Coverage   79.97%   79.95%   -0.02%     
==========================================
  Files         200      200              
  Lines       54519    54524       +5     
  Branches    54519    54524       +5     
==========================================
- Hits        43599    43597       -2     
- Misses       8400     8403       +3     
- Partials     2520     2524       +4

Flag	Coverage Δ
unittests	`79.95% <66.66%> (-0.02%)`	⬇️

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#2384)" This reverts commit 571a70a.

#2384)" (#2387) This reverts commit 571a70a.

[![Mend Renovate](https://app.renovatebot.com/images/banner.svg)](https://renovatebot.com) This PR contains the following updates: | Package | Type | Update | Change | |---|---|---|---| | [lance](https://togithub.com/lancedb/lance) | dependencies | minor | `0.10.16` -> `0.12.0` | --- ### Release Notes <details> <summary>lancedb/lance (lance)</summary> ### [`v0.12.1`](https://togithub.com/lancedb/lance/releases/tag/v0.12.1) [Compare Source](https://togithub.com/lancedb/lance/compare/v0.12.0...v0.12.1)  #### What's Changed ##### Bug Fixes 🐛 - fix: incorrect chunking was making lance datasets use too much RAM by [@westonpace](https://togithub.com/westonpace) in [lancedb/lance#2438 **Full Changelog**: lancedb/lance@v0.12.0...v0.12.1 ### [`v0.12.0`](https://togithub.com/lancedb/lance/releases/tag/v0.12.0) [Compare Source](https://togithub.com/lancedb/lance/compare/v0.11.1...v0.12.0)  #### What's Changed ##### Breaking Changes 🛠 - feat: change dataset uri to return full qualified url instead of object store path by [@eddyxu](https://togithub.com/eddyxu) in [lancedb/lance#2416 ##### New Features 🎉 - feat: new shuffler by [@BubbleCal](https://togithub.com/BubbleCal) in [lancedb/lance#2404 - feat: new index builder by [@BubbleCal](https://togithub.com/BubbleCal) in [lancedb/lance#2401 - feat: stable row id manifest changes by [@wjones127](https://togithub.com/wjones127) in [lancedb/lance#2363 - feat: once a table has been created with v1 or v2 format then it should always use that format by [@westonpace](https://togithub.com/westonpace) in [lancedb/lance#2435 ##### Bug Fixes 🐛 - fix: fix file writer which was not writing page buffers in the correct order by [@westonpace](https://togithub.com/westonpace) in [lancedb/lance#2413 ##### Other Changes - refactor: refactor logical decoders into "field decoders" by [@westonpace](https://togithub.com/westonpace) in [lancedb/lance#2407 - refactor: rename use_experimental_writer to use_legacy_format by [@westonpace](https://togithub.com/westonpace) in [lancedb/lance#2433 - refactor: minor refactor to allow I/O scheduler to be cloned in page schedulers by [@westonpace](https://togithub.com/westonpace) in [lancedb/lance#2432 **Full Changelog**: lancedb/lance@v0.11.1...v0.12.0 ### [`v0.11.1`](https://togithub.com/lancedb/lance/releases/tag/v0.11.1) [Compare Source](https://togithub.com/lancedb/lance/compare/v0.11.0...v0.11.1)  #### What's Changed ##### New Features 🎉 - feat(java): support jdk8 by [@LuQQiu](https://togithub.com/LuQQiu) in [lancedb/lance#2362 - feat: support kmode with hamming distance by [@eddyxu](https://togithub.com/eddyxu) in [lancedb/lance#2366 - feat: row id index structures (experimental) by [@wjones127](https://togithub.com/wjones127) in [lancedb/lance#2303 - feat: update merge_insert to add statistics for inserted, updated, deleted rows by [@raunaks13](https://togithub.com/raunaks13) in [lancedb/lance#2357 - feat: define Flat index as a scan over VectorStorage by [@chebbyChefNEQ](https://togithub.com/chebbyChefNEQ) in [lancedb/lance#2380 - feat: add some schema utility methods to the v2 reader/writer by [@westonpace](https://togithub.com/westonpace) in [lancedb/lance#2389 - feat: general compression for value page buffer by [@niyue](https://togithub.com/niyue) in [lancedb/lance#2368 - feat: make the index cache size (in bytes) available by [@westonpace](https://togithub.com/westonpace) in [lancedb/lance#2381 - feat: add special uri scheme to use CloudFileReader for local fs by [@chebbyChefNEQ](https://togithub.com/chebbyChefNEQ) in [lancedb/lance#2402 - feat: add encoder utilities for pushdown by [@westonpace](https://togithub.com/westonpace) in [lancedb/lance#2388 ##### Bug Fixes 🐛 - fix: concat batches before writing to avoid small IO slow down by [@chebbyChefNEQ](https://togithub.com/chebbyChefNEQ) in [lancedb/lance#2384 - fix: low recall if the num partitions is more than num rows by [@BubbleCal](https://togithub.com/BubbleCal) in [lancedb/lance#2386 - fix: f32 reduce_min for x86 by [@heiher](https://togithub.com/heiher) in [lancedb/lance#2385 - fix: fix incorrect validation logic in updater by [@westonpace](https://togithub.com/westonpace) in [lancedb/lance#2408 ##### Performance Improvements 🚀 - perf: make VectorStorage and DistCalculator static to generate better code by [@BubbleCal](https://togithub.com/BubbleCal) in [lancedb/lance#2355 - perf: optimize IO path for reading manifest by [@wjones127](https://togithub.com/wjones127) in [lancedb/lance#2396 ##### Other Changes - refactor: make proto conversion fallible and not copy by [@wjones127](https://togithub.com/wjones127) in [lancedb/lance#2371 - refactor: separate take and schema evolution impls to own files by [@wjones127](https://togithub.com/wjones127) in [lancedb/lance#2372 - Revert "fix: concat batches before writing to avoid small IO slow down ([#2384](https://togithub.com/lancedb/lance/issues/2384))" by [@chebbyChefNEQ](https://togithub.com/chebbyChefNEQ) in [lancedb/lance#2387 - refactor: shuffle around v2 metadata sections to allow read-on-demand statistics by [@westonpace](https://togithub.com/westonpace) in [lancedb/lance#2400 #### New Contributors - [@niyue](https://togithub.com/niyue) made their first contribution in [lancedb/lance#2368 - [@heiher](https://togithub.com/heiher) made their first contribution in [lancedb/lance#2385 **Full Changelog**: lancedb/lance@v0.11.0...v0.11.1 ### [`v0.11.0`](https://togithub.com/lancedb/lance/releases/tag/v0.11.0) [Compare Source](https://togithub.com/lancedb/lance/compare/v0.10.18...v0.11.0)  #### What's Changed ##### Breaking Changes 🛠 - feat(rust)!: use BoxedError in Error::IO by [@broccoliSpicy](https://togithub.com/broccoliSpicy) in [lancedb/lance#2329 ##### New Features 🎉 - feat: add v2 support to fragment merge / update paths by [@westonpace](https://togithub.com/westonpace) in [lancedb/lance#2311 - feat: add priority to I/O scheduler by [@westonpace](https://togithub.com/westonpace) in [lancedb/lance#2315 - feat: add take_rows operation to the v2 file reader's python bindings by [@westonpace](https://togithub.com/westonpace) in [lancedb/lance#2331 - feat: added example for reading and writing dataset in rust by [@raunaks13](https://togithub.com/raunaks13) in [lancedb/lance#2349 - feat: new HNSW implementation by [@BubbleCal](https://togithub.com/BubbleCal) in [lancedb/lance#2353 - feat: add fragment take / fixed-size-binary support to v2 format by [@westonpace](https://togithub.com/westonpace) in [lancedb/lance#2354 ##### Bug Fixes 🐛 - fix: recognize a simple expression like 'is_foo' as a scalar index query by [@westonpace](https://togithub.com/westonpace) in [lancedb/lance#2356 - fix: rework list encoder to handle list-struct by [@westonpace](https://togithub.com/westonpace) in [lancedb/lance#2344 - fix: minor bug fixes for v2 by [@westonpace](https://togithub.com/westonpace) in [lancedb/lance#2361 ##### Documentation 📚 - docs: clearify comments in table.proto -> message DataFragment -> physical_rows by [@broccoliSpicy](https://togithub.com/broccoliSpicy) in [lancedb/lance#2346 ##### Performance Improvements 🚀 - perf: use the file metadata cache in scalar indices by [@westonpace](https://togithub.com/westonpace) in [lancedb/lance#2330 ##### Other Changes - chore: remove `m_max` and `use_heuristic` params from HNSW builder by [@BubbleCal](https://togithub.com/BubbleCal) in [lancedb/lance#2336 - fix(java): fix JNI jar loader issue by [@LuQQiu](https://togithub.com/LuQQiu) in [lancedb/lance#2340 - ci: fix labeler permissions by [@wjones127](https://togithub.com/wjones127) in [lancedb/lance#2348 - fix: rework decoding to fix bugs in nested struct decoding by [@westonpace](https://togithub.com/westonpace) in [lancedb/lance#2337 #### New Contributors - [@broccoliSpicy](https://togithub.com/broccoliSpicy) made their first contribution in [lancedb/lance#2346 - [@raunaks13](https://togithub.com/raunaks13) made their first contribution in [lancedb/lance#2349 **Full Changelog**: lancedb/lance@v0.10.18...v0.11.0 </details> --- ### Configuration 📅 **Schedule**: Branch creation - At any time (no schedule defined), Automerge - At any time (no schedule defined). 🚦 **Automerge**: Enabled. ♻ **Rebasing**: Whenever PR becomes conflicted, or you tick the rebase/retry checkbox. 🔕 **Ignore**: Close this PR and you won't be reminded about this update again. --- - [ ] If you want to rebase/retry this PR, check this box --- This PR has been generated by [Mend Renovate](https://www.mend.io/free-developer-tools/renovate/). 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fix: concat batches before writing to avoid small IO slow down

efb1e16

chebbyChefNEQ requested review from eddyxu, westonpace, wjones127 and BubbleCal May 23, 2024 04:32

github-actions bot added the bug Something isn't working label May 23, 2024

BubbleCal approved these changes May 23, 2024

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eddyxu reviewed May 23, 2024

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chebbyChefNEQ merged commit 571a70a into main May 23, 2024
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chebbyChefNEQ deleted the rmeng/fix-shuffler-perf branch May 23, 2024 15:59

chebbyChefNEQ added a commit that referenced this pull request May 23, 2024

Revert "fix: concat batches before writing to avoid small IO slow down (

f5b9618

#2384)" This reverts commit 571a70a.

chebbyChefNEQ added a commit that referenced this pull request May 23, 2024

Revert "fix: concat batches before writing to avoid small IO slow down (

8c1ee00

#2384)" (#2387) This reverts commit 571a70a.

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fix: concat batches before writing to avoid small IO slow down #2384

fix: concat batches before writing to avoid small IO slow down #2384

chebbyChefNEQ commented May 23, 2024

eddyxu May 23, 2024

wjones127 May 23, 2024 •

edited

codecov-commenter commented May 23, 2024

fix: concat batches before writing to avoid small IO slow down #2384

fix: concat batches before writing to avoid small IO slow down #2384

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wjones127 May 23, 2024 •

edited