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[GH-ISSUE #6933] Chromadb warns that my database needs to be vacuumed #14539

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opened 2026-04-19 20:52:35 -05:00 by GiteaMirror · 0 comments
GiteaMirror commented 2026-04-19 20:52:35 -05:00
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Originally created by @ivy on GitHub (Nov 13, 2024).
Original GitHub issue: https://github.com/open-webui/open-webui/issues/6933

Bug Report

Thanks for making Open WebUI! 🙌💜 I'm not sure if this classifies as a bug or a feature request. Details to follow…

Installation Method

Docker image (details within) 
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Environment

  • Open WebUI Version: v0.3.35
  • Ollama (if applicable): n/a
  • Operating System: macOS Sonoma 14.6.1 (23G93)
  • Browser (if applicable): n/a

Confirmation:

  • I have read and followed all the instructions provided in the README.md.
  • I am on the latest version of both Open WebUI and Ollama.
  • I have included the browser console logs.
  • I have included the Docker container logs.
  • I have provided the exact steps to reproduce the bug in the "Steps to Reproduce" section below.

Expected Behavior:

I think Open WebUI should either:

  • Package executable utilities like chromadb with its Docker image so users can perform maintenance tasks; or
  • Open WebUI should perform database maintenance on its own when required (maybe there's a config setting in chromadb to support this?).

Actual Behavior:

Chromadb logs a message:

WARNI [chromadb.db.impl.sqlite] ⚠️ It looks like you upgraded from a version below 0.6 and could benefit from vacuuming your database. Run chromadb utils vacuum --help for more information.

I'm not sure what changes were made in chromadb to prompt this and unfortunately, chromadb isn't an executable on my $PATH within the distributed Docker image:

docker exec <open-webui container ID> /bin/bash
root@cf06ca28c6a1:/app/backend# chromadb utils vacuum --help
bash: chromadb: command not found
root@cf06ca28c6a1:/app/backend# find / -type f -name chromadb -executable
[no output -- nothing found]

Description

Bug Summary: Changes to chromadb are recommending running chromadb utils vacuum but this utility isn't available in the Docker image. Additionally, I'm wondering if Open WebUI should do this on its own (through a config setting or calling applicable methods).

Reproduction Details

Steps to Reproduce: I believe the steps to reproduce are to run a copy of Open WebUI with an earlier release of chromadb (create some data) then upgrade to the latest version (and dependencies). Subsequent startups will result in this log message.

Logs and Screenshots

Browser Console Logs: n/a

Docker Container Logs (expand to view) 
Loading WEBUI_SECRET_KEY from file, not provided as an environment variable.
Generating WEBUI_SECRET_KEY
Loading WEBUI_SECRET_KEY from .webui_secret_key
/app/backend/open_webui
/app/backend
/app
Running migrations
INFO  [alembic.runtime.migration] Context impl SQLiteImpl.
INFO  [alembic.runtime.migration] Will assume non-transactional DDL.
WARNI [open_webui.env] 

WARNING: CORS_ALLOW_ORIGIN IS SET TO '*' - NOT RECOMMENDED FOR PRODUCTION DEPLOYMENTS.

INFO  [open_webui.env] 'CONTENT_EXTRACTION_ENGINE' loaded from the latest database entry
INFO  [open_webui.env] 'TIKA_SERVER_URL' loaded from the latest database entry
INFO  [open_webui.env] 'RAG_TOP_K' loaded from the latest database entry
INFO  [open_webui.env] 'RAG_RELEVANCE_THRESHOLD' loaded from the latest database entry
INFO  [open_webui.env] 'ENABLE_RAG_HYBRID_SEARCH' loaded from the latest database entry
INFO  [open_webui.env] 'RAG_EMBEDDING_ENGINE' loaded from the latest database entry
INFO  [open_webui.env] 'PDF_EXTRACT_IMAGES' loaded from the latest database entry
INFO  [open_webui.env] 'RAG_EMBEDDING_MODEL' loaded from the latest database entry
INFO  [open_webui.env] Embedding model set: sentence-transformers/all-MiniLM-L6-v2
INFO  [open_webui.env] 'CHUNK_SIZE' loaded from the latest database entry
INFO  [open_webui.env] 'CHUNK_OVERLAP' loaded from the latest database entry
INFO  [open_webui.env] 'RAG_TEMPLATE' loaded from the latest database entry
INFO  [open_webui.env] 'YOUTUBE_LOADER_LANGUAGE' loaded from the latest database entry
INFO  [open_webui.env] 'ENABLE_RAG_WEB_SEARCH' loaded from the latest database entry
INFO  [open_webui.env] 'RAG_WEB_SEARCH_ENGINE' loaded from the latest database entry
INFO  [open_webui.env] 'SEARXNG_QUERY_URL' loaded from the latest database entry
INFO  [open_webui.env] 'GOOGLE_PSE_API_KEY' loaded from the latest database entry
INFO  [open_webui.env] 'GOOGLE_PSE_ENGINE_ID' loaded from the latest database entry
INFO  [open_webui.env] 'BRAVE_SEARCH_API_KEY' loaded from the latest database entry
INFO  [open_webui.env] 'SERPSTACK_API_KEY' loaded from the latest database entry
INFO  [open_webui.env] 'SERPSTACK_HTTPS' loaded from the latest database entry
INFO  [open_webui.env] 'SERPER_API_KEY' loaded from the latest database entry
INFO  [open_webui.env] 'SERPLY_API_KEY' loaded from the latest database entry
INFO  [open_webui.env] 'TAVILY_API_KEY' loaded from the latest database entry
INFO  [open_webui.env] 'RAG_WEB_SEARCH_RESULT_COUNT' loaded from the latest database entry
INFO  [open_webui.env] 'RAG_WEB_SEARCH_CONCURRENT_REQUESTS' loaded from the latest database entry
INFO  [open_webui.env] 'IMAGE_GENERATION_ENGINE' loaded from the latest database entry
INFO  [open_webui.env] 'ENABLE_IMAGE_GENERATION' loaded from the latest database entry
INFO  [open_webui.env] 'IMAGES_OPENAI_API_BASE_URL' loaded from the latest database entry
INFO  [open_webui.env] 'IMAGES_OPENAI_API_KEY' loaded from the latest database entry
INFO  [open_webui.env] 'IMAGE_SIZE' loaded from the latest database entry
INFO  [open_webui.env] 'IMAGE_STEPS' loaded from the latest database entry
INFO  [open_webui.env] 'IMAGE_GENERATION_MODEL' loaded from the latest database entry
INFO  [open_webui.apps.audio.main] whisper_device_type: cpu
WARNI [chromadb.db.impl.sqlite] ⚠️ It looks like you upgraded from a version below 0.6 and could benefit from vacuuming your database. Run chromadb utils vacuum --help for more information.
WARNI [langchain_community.utils.user_agent] USER_AGENT environment variable not set, consider setting it to identify your requests.
INFO:     Started server process [1]
INFO:     Waiting for application startup.
INFO:     Application startup complete.
INFO:     Uvicorn running on http://0.0.0.0:8080 (Press CTRL+C to quit)
INFO  [open_webui.apps.openai.main] get_all_models()
INFO  [open_webui.apps.ollama.main] get_all_models()
ERROR [open_webui.apps.ollama.main] Connection error: Cannot connect to host host.docker.internal:11434 ssl:default [Connect call failed ('192.168.5.2', 11434)]

  ___                    __        __   _     _   _ ___
 / _ \ _ __   ___ _ __   \ \      / /__| |__ | | | |_ _|
| | | | '_ \ / _ \ '_ \   \ \ /\ / / _ \ '_ \| | | || |
| |_| | |_) |  __/ | | |   \ V  V /  __/ |_) | |_| || |
 \___/| .__/ \___|_| |_|    \_/\_/ \___|_.__/ \___/|___|
      |_|


v0.3.35 - building the best open-source AI user interface.

https://github.com/open-webui/open-webui

Screenshots/Screen Recordings (if applicable): n/a

Additional Information

It looks like chromadb's provided utility just performs a VACUUM (see this changeset).

Originally created by @ivy on GitHub (Nov 13, 2024). Original GitHub issue: https://github.com/open-webui/open-webui/issues/6933 # Bug Report Thanks for making Open WebUI! 🙌💜 I'm not sure if this classifies as a bug or a feature request. 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"MergedDir": "/var/lib/docker/overlay2/8f442d502f8b8b9799383115e55c72ad045aeb7f2cd4e66af6a1b472a0ef2eb4/merged", "UpperDir": "/var/lib/docker/overlay2/8f442d502f8b8b9799383115e55c72ad045aeb7f2cd4e66af6a1b472a0ef2eb4/diff", "WorkDir": "/var/lib/docker/overlay2/8f442d502f8b8b9799383115e55c72ad045aeb7f2cd4e66af6a1b472a0ef2eb4/work" }, "Name": "overlay2" }, "RootFS": { "Type": "layers", "Layers": [ "sha256:f0f039847c0897e41273775d599cc761049c809342ff8362efb4caf561186ada", "sha256:c6fe574d28cee88986e7a83cd3aa90cf971e618ce75dc5ef30fbeaaf74ab10b8", "sha256:d37582ba90d59a93322a22baf56a21e074dcf0fdf641f12c7af4ba76e156b0c6", "sha256:069dda5e673b37b18c361c6b5938bfdd9cf1f979d3a87cbe4a7bd501ca570119", "sha256:10141a24bd842d8d97b7b355fe4527294c903dc0a3340d095c40765bf521dfd5", "sha256:5f70bf18a086007016e948b04aed3b82103a36bea41755b6cddfaf10ace3c6ef", "sha256:0b3f016125e32708ac9f979bf0e62db26b699bc5a7b76ef3e8ec7e53a8ec7aab", "sha256:2ee6958913ee79a8df0e1112adb8e999c2b85dfba3cb7bac00064124f77d3524", "sha256:5f70bf18a086007016e948b04aed3b82103a36bea41755b6cddfaf10ace3c6ef", "sha256:8605fab1816c120ee049c7b8dd1285a2603c07a3be15c72981149595fa707517", "sha256:fc593493f49a1ed57afbea55ddc426a992563acd2795654e7d04c7e6486668d0", "sha256:2dd286073ed4454f85a80ec9c152c07a8f2f16bc294be8692e8cf39f877721bf", "sha256:099c47ecbeef18b3b250dceb1265affd4a8d2dc16eb4254fa0a0d2cf7f3326cb", "sha256:33f89fed9395d2ce9c7f0ff93cdb5fb7948f6e18c213dc70799b7b5607fa8db8", "sha256:6c51df98b12fe430778dc4de32490cb24d882b338693c54c63c997a446a500bb", "sha256:a89350848ec8982fd2a7ef9e9c2a5c06bd8163dc22924d6489d54a13403e10d7" ] }, "Metadata": { "LastTagTime": "0001-01-01T00:00:00Z" } } ] ``` </details> ## Environment - **Open WebUI Version:** v0.3.35 - **Ollama (if applicable):** n/a - **Operating System:** macOS Sonoma 14.6.1 (23G93) - **Browser (if applicable):** n/a **Confirmation:** - [x] I have read and followed all the instructions provided in the README.md. - [x] I am on the latest version of both Open WebUI and Ollama. - [x] I have included the browser console logs. - [x] I have included the Docker container logs. - [x] I have provided the exact steps to reproduce the bug in the "Steps to Reproduce" section below. ## Expected Behavior: I think Open WebUI should either: - Package executable utilities like `chromadb` with its Docker image so users can perform maintenance tasks; or - Open WebUI should perform database maintenance on its own when required (maybe there's a config setting in chromadb to support this?). ## Actual Behavior: Chromadb logs a message: ``` WARNI [chromadb.db.impl.sqlite] ⚠️ It looks like you upgraded from a version below 0.6 and could benefit from vacuuming your database. Run chromadb utils vacuum --help for more information. ``` I'm not sure what changes were made in chromadb to prompt this and unfortunately, `chromadb` isn't an executable on my `$PATH` within the distributed Docker image: ``` docker exec <open-webui container ID> /bin/bash root@cf06ca28c6a1:/app/backend# chromadb utils vacuum --help bash: chromadb: command not found root@cf06ca28c6a1:/app/backend# find / -type f -name chromadb -executable [no output -- nothing found] ``` ## Description **Bug Summary:** Changes to chromadb are recommending running `chromadb utils vacuum` but this utility isn't available in the Docker image. Additionally, I'm wondering if Open WebUI should do this on its own (through a config setting or calling applicable methods). ## Reproduction Details **Steps to Reproduce:** I believe the steps to reproduce are to run a copy of Open WebUI with an earlier release of chromadb (create some data) then upgrade to the latest version (and dependencies). Subsequent startups will result in this log message. ## Logs and Screenshots **Browser Console Logs:** n/a <details><summary>Docker Container Logs (expand to view)</summary> ``` Loading WEBUI_SECRET_KEY from file, not provided as an environment variable. Generating WEBUI_SECRET_KEY Loading WEBUI_SECRET_KEY from .webui_secret_key /app/backend/open_webui /app/backend /app Running migrations INFO [alembic.runtime.migration] Context impl SQLiteImpl. INFO [alembic.runtime.migration] Will assume non-transactional DDL. WARNI [open_webui.env] WARNING: CORS_ALLOW_ORIGIN IS SET TO '*' - NOT RECOMMENDED FOR PRODUCTION DEPLOYMENTS. INFO [open_webui.env] 'CONTENT_EXTRACTION_ENGINE' loaded from the latest database entry INFO [open_webui.env] 'TIKA_SERVER_URL' loaded from the latest database entry INFO [open_webui.env] 'RAG_TOP_K' loaded from the latest database entry INFO [open_webui.env] 'RAG_RELEVANCE_THRESHOLD' loaded from the latest database entry INFO [open_webui.env] 'ENABLE_RAG_HYBRID_SEARCH' loaded from the latest database entry INFO [open_webui.env] 'RAG_EMBEDDING_ENGINE' loaded from the latest database entry INFO [open_webui.env] 'PDF_EXTRACT_IMAGES' loaded from the latest database entry INFO [open_webui.env] 'RAG_EMBEDDING_MODEL' loaded from the latest database entry INFO [open_webui.env] Embedding model set: sentence-transformers/all-MiniLM-L6-v2 INFO [open_webui.env] 'CHUNK_SIZE' loaded from the latest database entry INFO [open_webui.env] 'CHUNK_OVERLAP' loaded from the latest database entry INFO [open_webui.env] 'RAG_TEMPLATE' loaded from the latest database entry INFO [open_webui.env] 'YOUTUBE_LOADER_LANGUAGE' loaded from the latest database entry INFO [open_webui.env] 'ENABLE_RAG_WEB_SEARCH' loaded from the latest database entry INFO [open_webui.env] 'RAG_WEB_SEARCH_ENGINE' loaded from the latest database entry INFO [open_webui.env] 'SEARXNG_QUERY_URL' loaded from the latest database entry INFO [open_webui.env] 'GOOGLE_PSE_API_KEY' loaded from the latest database entry INFO [open_webui.env] 'GOOGLE_PSE_ENGINE_ID' loaded from the latest database entry INFO [open_webui.env] 'BRAVE_SEARCH_API_KEY' loaded from the latest database entry INFO [open_webui.env] 'SERPSTACK_API_KEY' loaded from the latest database entry INFO [open_webui.env] 'SERPSTACK_HTTPS' loaded from the latest database entry INFO [open_webui.env] 'SERPER_API_KEY' loaded from the latest database entry INFO [open_webui.env] 'SERPLY_API_KEY' loaded from the latest database entry INFO [open_webui.env] 'TAVILY_API_KEY' loaded from the latest database entry INFO [open_webui.env] 'RAG_WEB_SEARCH_RESULT_COUNT' loaded from the latest database entry INFO [open_webui.env] 'RAG_WEB_SEARCH_CONCURRENT_REQUESTS' loaded from the latest database entry INFO [open_webui.env] 'IMAGE_GENERATION_ENGINE' loaded from the latest database entry INFO [open_webui.env] 'ENABLE_IMAGE_GENERATION' loaded from the latest database entry INFO [open_webui.env] 'IMAGES_OPENAI_API_BASE_URL' loaded from the latest database entry INFO [open_webui.env] 'IMAGES_OPENAI_API_KEY' loaded from the latest database entry INFO [open_webui.env] 'IMAGE_SIZE' loaded from the latest database entry INFO [open_webui.env] 'IMAGE_STEPS' loaded from the latest database entry INFO [open_webui.env] 'IMAGE_GENERATION_MODEL' loaded from the latest database entry INFO [open_webui.apps.audio.main] whisper_device_type: cpu WARNI [chromadb.db.impl.sqlite] ⚠️ It looks like you upgraded from a version below 0.6 and could benefit from vacuuming your database. Run chromadb utils vacuum --help for more information. WARNI [langchain_community.utils.user_agent] USER_AGENT environment variable not set, consider setting it to identify your requests. INFO: Started server process [1] INFO: Waiting for application startup. INFO: Application startup complete. INFO: Uvicorn running on http://0.0.0.0:8080 (Press CTRL+C to quit) INFO [open_webui.apps.openai.main] get_all_models() INFO [open_webui.apps.ollama.main] get_all_models() ERROR [open_webui.apps.ollama.main] Connection error: Cannot connect to host host.docker.internal:11434 ssl:default [Connect call failed ('192.168.5.2', 11434)] ___ __ __ _ _ _ ___ / _ \ _ __ ___ _ __ \ \ / /__| |__ | | | |_ _| | | | | '_ \ / _ \ '_ \ \ \ /\ / / _ \ '_ \| | | || | | |_| | |_) | __/ | | | \ V V / __/ |_) | |_| || | \___/| .__/ \___|_| |_| \_/\_/ \___|_.__/ \___/|___| |_| v0.3.35 - building the best open-source AI user interface. https://github.com/open-webui/open-webui ``` </details> **Screenshots/Screen Recordings (if applicable):** n/a ## Additional Information It looks like chromadb's provided utility just performs a `VACUUM` (see [this changeset](https://github.com/chroma-core/chroma/commit/ea3ec083231621a919c94670730379e23abac4f8#diff-7750d4d797ef6cffa62cff21e9fce1ccd1706704665e93bdc10ced236d3ff249R263-R273)).
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GiteaMirror ninjasurge (Kaehlen Rog)
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Reference: github-starred/open-webui#14539