Strange crash after upgrade 0.93 → 0.94.1

[fuzzykiller]

I have a server installation (Linux amd64 Docker). After upgrading from 0.93 to 0.94.1, the application crashed exactly once after upgrading, with an out-of-memory error.

This is the log I got from Docker:

trilium-1  | No USER_UID specified, leaving 1000
trilium-1  | No USER_GID specified, leaving 1000
trilium-1  | VectorSearchTool initialized using consolidated VectorSearchService
trilium-1  | App db version is 231, while db version is 229. Migration needed.
trilium-1  | DB size: 17641 KB
trilium-1  | Creating backup...
trilium-1  | Initializing embedding system...
trilium-1  | ERROR: Error resetting stuck embedding queue: no such table: embedding_queue
trilium-1  | ERROR: Error initializing embedding system: Option 'aiEnabled' doesn't exist
trilium-1  | Failed to initialize index service: Error: Option 'embeddingAutoUpdateEnabled' doesn't exist
trilium-1  |     at Lrt (/usr/src/app/main.cjs:715:1762)
trilium-1  |     at Object.KNi [as getOptionBool] (/usr/src/app/main.cjs:715:1997)
trilium-1  |     at P9e.initialize (/usr/src/app/main.cjs:2708:2112)
trilium-1  |     at tSt (/usr/src/app/main.cjs:3017:8428)
trilium-1  |     at async nwn (/usr/src/app/main.cjs:3018:179)
trilium-1  |     at async nio (/usr/src/app/main.cjs:3018:2854)
trilium-1  | {
trilium-1  |   "appVersion": "0.94.1",
trilium-1  |   "dbVersion": 231,
trilium-1  |   "nodeVersion": "v22.16.0",
trilium-1  |   "syncVersion": 35,
trilium-1  |   "buildDate": "2025-06-07T09:45:40Z",
trilium-1  |   "buildRevision": "7cbff47078012e32279c110c49b904bd24dcecb3",
trilium-1  |   "dataDirectory": "/home/node/trilium-data",
trilium-1  |   "clipperProtocolVersion": "1.0",
trilium-1  |   "utcDateTime": "2025-06-07T15:00:42.159Z"
trilium-1  | }
trilium-1  | CPU model: AMD Ryzen 7 7700 8-Core Processor, logical cores: 16, freq: 3000 Mhz
trilium-1  | Trusted reverse proxy: uniquelocal
trilium-1  | App HTTP server starting up at port 8080
trilium-1  | Listening on port 8080
trilium-1  | Created backup at /home/node/trilium-data/backup/backup-before-migration.db
trilium-1  | Attempting migration to version 230
trilium-1  | Migration with SQL script:             -- Store embeddings for notes
trilium-1  |             CREATE TABLE IF NOT EXISTS "note_embeddings" (
trilium-1  |                 "embedId" TEXT NOT NULL PRIMARY KEY,
trilium-1  |                 "noteId" TEXT NOT NULL,
trilium-1  |                 "providerId" TEXT NOT NULL,
trilium-1  |                 "modelId" TEXT NOT NULL,
trilium-1  |                 "dimension" INTEGER NOT NULL,
trilium-1  |                 "embedding" BLOB NOT NULL,
trilium-1  |                 "version" INTEGER NOT NULL DEFAULT 1,
trilium-1  |                 "dateCreated" TEXT NOT NULL,
trilium-1  |                 "utcDateCreated" TEXT NOT NULL,
trilium-1  |                 "dateModified" TEXT NOT NULL,
trilium-1  |                 "utcDateModified" TEXT NOT NULL
trilium-1  |             );
trilium-1  |
trilium-1  |             CREATE INDEX "IDX_note_embeddings_noteId" ON "note_embeddings" ("noteId");
trilium-1  |             CREATE INDEX "IDX_note_embeddings_providerId_modelId" ON "note_embeddings" ("providerId", "modelId");
trilium-1  |
trilium-1  |             -- Table to track which notes need embedding updates
trilium-1  |             CREATE TABLE IF NOT EXISTS "embedding_queue" (
trilium-1  |                 "noteId" TEXT NOT NULL PRIMARY KEY,
trilium-1  |                 "operation" TEXT NOT NULL, -- CREATE, UPDATE, DELETE
trilium-1  |                 "dateQueued" TEXT NOT NULL,
trilium-1  |                 "utcDateQueued" TEXT NOT NULL,
trilium-1  |                 "priority" INTEGER NOT NULL DEFAULT 0,
trilium-1  |                 "attempts" INTEGER NOT NULL DEFAULT 0,
trilium-1  |                 "lastAttempt" TEXT NULL,
trilium-1  |                 "error" TEXT NULL,
trilium-1  |                 "failed" INTEGER NOT NULL DEFAULT 0,
trilium-1  |                 "isProcessing" INTEGER NOT NULL DEFAULT 0
trilium-1  |             );
trilium-1  |
trilium-1  |             -- Table to store embedding provider configurations
trilium-1  |             CREATE TABLE IF NOT EXISTS "embedding_providers" (
trilium-1  |                 "providerId" TEXT NOT NULL PRIMARY KEY,
trilium-1  |                 "name" TEXT NOT NULL,
trilium-1  |                 "priority" INTEGER NOT NULL DEFAULT 0,
trilium-1  |                 "config" TEXT NOT NULL, -- JSON config object
trilium-1  |                 "dateCreated" TEXT NOT NULL,
trilium-1  |                 "utcDateCreated" TEXT NOT NULL,
trilium-1  |                 "dateModified" TEXT NOT NULL,
trilium-1  |                 "utcDateModified" TEXT NOT NULL
trilium-1  |             );
trilium-1  |
trilium-1  | Migration to version 230 has been successful.
trilium-1  | Attempting migration to version 231
trilium-1  | Migration with SQL script:             CREATE TABLE IF NOT EXISTS sessions (
trilium-1  |                 id TEXT PRIMARY KEY,
trilium-1  |                 data TEXT,
trilium-1  |                 expires INTEGER
trilium-1  |             );
trilium-1  |
trilium-1  | Migration to version 231 has been successful.
trilium-1  | Becca (note cache) load took 8ms
trilium-1  | Created option "codeNoteTheme" with default value "default:vs-code-light"
trilium-1  | AI settings changed, updating index service configuration
trilium-1  | ERROR: Error updating index service configuration: Option 'embeddingUpdateInterval' doesn't exist
trilium-1  | Created option "aiEnabled" with default value "false"
trilium-1  | Created option "openaiApiKey" with default value ""
trilium-1  | Created option "openaiDefaultModel" with default value ""
trilium-1  | Created option "openaiEmbeddingModel" with default value ""
trilium-1  | Created option "openaiBaseUrl" with default value "https://api.openai.com/v1"
trilium-1  | Created option "anthropicApiKey" with default value ""
trilium-1  | Created option "anthropicDefaultModel" with default value ""
trilium-1  | Created option "voyageEmbeddingModel" with default value ""
trilium-1  | Created option "voyageApiKey" with default value ""
trilium-1  | Created option "anthropicBaseUrl" with default value "https://api.anthropic.com/v1"
trilium-1  | Created option "ollamaEnabled" with default value "false"
trilium-1  | Created option "ollamaDefaultModel" with default value ""
trilium-1  | Created option "ollamaBaseUrl" with default value "http://localhost:11434"
trilium-1  | Created option "ollamaEmbeddingModel" with default value ""
trilium-1  | AI settings changed, updating index service configuration
trilium-1  | ERROR: Error updating index service configuration: Option 'embeddingUpdateInterval' doesn't exist
trilium-1  | Created option "embeddingAutoUpdateEnabled" with default value "true"
trilium-1  | Created option "openaiEmbeddingApiKey" with default value ""
trilium-1  | Created option "openaiEmbeddingBaseUrl" with default value "https://api.openai.com/v1"
trilium-1  | Created option "voyageEmbeddingBaseUrl" with default value "https://api.voyageai.com/v1"
trilium-1  | Created option "ollamaEmbeddingBaseUrl" with default value "http://localhost:11434"
trilium-1  | AI settings changed, updating index service configuration
trilium-1  | ERROR: Error updating index service configuration: Option 'embeddingUpdateInterval' doesn't exist
trilium-1  | Created option "aiTemperature" with default value "0.7"
trilium-1  | AI settings changed, updating index service configuration
trilium-1  | ERROR: Error updating index service configuration: Option 'embeddingUpdateInterval' doesn't exist
trilium-1  | Created option "aiSystemPrompt" with default value ""
trilium-1  | AI settings changed, updating index service configuration
trilium-1  | ERROR: Error updating index service configuration: Option 'embeddingUpdateInterval' doesn't exist
trilium-1  | Created option "aiSelectedProvider" with default value "openai"
trilium-1  | AI settings changed, updating index service configuration
trilium-1  | ERROR: Error updating index service configuration: Option 'embeddingUpdateInterval' doesn't exist
trilium-1  | Created option "embeddingDimensionStrategy" with default value "auto"
trilium-1  | AI settings changed, updating index service configuration
trilium-1  | ERROR: Error updating index service configuration: Option 'embeddingUpdateInterval' doesn't exist
trilium-1  | Created option "embeddingSelectedProvider" with default value "openai"
trilium-1  | AI settings changed, updating index service configuration
trilium-1  | ERROR: Error updating index service configuration: Option 'embeddingUpdateInterval' doesn't exist
trilium-1  | Created option "embeddingSimilarityThreshold" with default value "0.75"
trilium-1  | Created option "enableAutomaticIndexing" with default value "true"
trilium-1  | Created option "maxNotesPerLlmQuery" with default value "3"
trilium-1  | AI settings changed, updating index service configuration
trilium-1  | ERROR: Error updating index service configuration: Option 'embeddingUpdateInterval' doesn't exist
trilium-1  | Created option "embeddingBatchSize" with default value "10"
trilium-1  | AI settings changed, updating index service configuration
trilium-1  | Created option "embeddingUpdateInterval" with default value "5000"
trilium-1  | AI settings changed, updating index service configuration
trilium-1  | Created option "embeddingDefaultDimension" with default value "1536"
trilium-1  | AI settings changed, updating index service configuration
trilium-1  | Created option "embeddingGenerationLocation" with default value "client"
trilium-1  |
trilium-1  | <--- Last few GCs --->
trilium-1  |
trilium-1  | [1:0x7ff0609f2000]    20056 ms: Mark-Compact 4052.3 (4130.5) -> 4049.2 (4130.5) MB, pooled: 0 MB, 814.13 / 2.57 ms  (average mu = 0.415, current mu = 0.182) allocation failure; scavenge might not succeed
trilium-1  | [1:0x7ff0609f2000]    21438 ms: Mark-Compact 4064.9 (4130.5) -> 4061.7 (4156.2) MB, pooled: 8 MB, 1327.86 / 2.56 ms  (average mu = 0.221, current mu = 0.039) allocation failure; scavenge might not succeed
trilium-1  |
trilium-1  |
trilium-1  | <--- JS stacktrace --->
trilium-1  |
trilium-1  | FATAL ERROR: Reached heap limit Allocation failed - JavaScript heap out of memory
trilium-1  | ----- Native stack trace -----
trilium-1  |
trilium-1 exited with code 0

It's running fine now, so there might simply be a bug in the upgrade code, dunno. Perhaps a side-effect of the still-missing options?

The desktop client never showed its GUI either (not blank, simply no window), while steadily allocating more memory. I could reproduce this issue on two Windows 11 devices.

[dosubot[bot]]

Hi @fuzzykiller! I'm Dosu and I’m helping the Notes team.

The out-of-memory crash you saw right after upgrading from 0.93 to 0.94.1 is likely related to the major architectural changes in the embedding/LLM system introduced in 0.94.x. During the first startup after migration, the app needs to create new tables and options for embeddings and AI features. The errors about missing options like aiEnabled and embeddingUpdateInterval are expected during this phase—these options are created on-the-fly if missing, which can trigger repeated config reloads and some noisy logs until all defaults are in place.

There are no known persistent bugs causing memory leaks or crashes tied directly to these options, but the initial migration and embedding system initialization can be resource-intensive, especially if you have a large note database. The code processes embeddings in batches to avoid memory issues, but if the system is under heavy load or the options are missing during the first run, it may temporarily spike memory usage and even crash once before stabilizing on subsequent runs. This matches your experience, and the fact that things are running fine now suggests the migration completed and all options are now set up as expected.

There is a related issue where LLM embedding changes in 0.94.x caused high CPU or sync loops for some users, which was fixed in recent updates (see here). The blank GUI on the desktop client was also addressed in 0.94.1 (see here).

Unless you see repeated crashes or memory growth, you can consider this a one-time migration hiccup. If you do see recurring issues, it could be worth checking your embedding/AI settings and batch sizes, especially if you have a very large note set or custom config.

To reply, just mention @dosu.

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