MCP Timeout when Using Cipher with RooCode (SSE Mode)

[anoosher1]

Hi team,

I'm encountering a timeout issue when running Cipher as an MCP server in SSE mode and connecting it to RooCode in VS Code.

🧩 Environment Details

.env file:

# AWS Credentials
AWS_ACCESS_KEY_ID=<MY_AWS_ACCESS_KEY_ID>
AWS_SECRET_ACCESS_KEY=<MY_AWS_SECRET_ACCESS_KEY>
AWS_SESSION_TOKEN=<MY_AWS_SESSION_TOKEN>
AWS_REGION=eu-central-1
AWS_INFERENCE_PROFILE_ARN=<AWS_INFERENCE_PROFILE_ARN_FOR_MODEL_anthropic.claude-3-5-sonnet>

STORAGE_DATABASE_TYPE=sqlite
STORAGE_DATABASE_PATH=./data/cipher.db

DISABLE_EMBEDDINGS=false

CIPHER_LOG_LEVEL=debug

memAgent/cipher.yml:

mcpServers: {}

llm:
  provider: aws
  model: eu.anthropic.claude-3-5-sonnet-20240620-v1:0
  maxIterations: 50
  aws:
    region: eu-central-1
    accessKeyId: $AWS_ACCESS_KEY_ID
    secretAccessKey: $AWS_SECRET_ACCESS_KEY
    sessionToken: $AWS_SESSION_TOKEN

embedding:
  type: aws-bedrock
  model: amazon.titan-embed-text-v2:0
  region: eu-central-1
  accessKeyId: $AWS_ACCESS_KEY_ID
  secretAccessKey: $AWS_SECRET_ACCESS_KEY
  dimensions: 256  

systemPrompt:
  enabled: true
  content: |
    You are an AI programming assistant focused on coding and reasoning tasks. You excel at:
    - Writing clean, efficient code
    - Debugging and problem-solving
    - Code review and optimization
    - Explaining complex technical concepts
    - Reasoning through programming challenges

    You should call each tool at most once per user request unless explicitly instructed otherwise.

---

⚙️ How I Start the MCP

I start Cipher in MCP mode using:

node dist/src/app/index.cjs --mode mcp --mcp-transport-type sse --mcp-port 4000

---

🧠 RooCode MCP Setup

Inside RooCode’s configuration:

{
  "mcpServers": {
    "cipher-sse": {
      "url": "http://localhost:4000/sse",
      "disabled": false,
      "alwaysAllow": [],
      "timeout": 60,
      "disabledTools": []
    }
  }
}

---

💬 Example Prompt Triggering Timeout

When I send a message like:

{
  "message": "Store this important naming convention for the cipher project: We do not use short format folder names in our testing. For example, 'Lib' is wrong - we should use 'Library' instead. Always use full, descriptive folder names rather than abbreviated versions."
}

RooCode shows:

Error
Error executing MCP tool:
MCP error -32001: Request timed out

---

🪵 Log Output (Excerpt)

The relevant log snippet shows repeated embedding calls and eventually:

Error executing MCP tool:
MCP error -32603: Agent execution failed: Maximum iterations (50) reached without completion

This suggests the agent is repeatedly calling the amazon.titan-embed-text-v2:0 model, possibly stuck in a loop or retry cycle during embedding.

---

✅ Additional Notes

• The SQLite backend issue was previously fixed — the DB now connects successfully.
• The timeout only occurs when Cipher attempts to process embedding or store information via RooCode.
• It seems the embedding process repeatedly triggers inside the same execution loop until the iteration limit is hit.

---

❓Request for Guidance

Could you please advise on:

1. Whether the embedding configuration in cipher.yml might be causing a recursion or repeated call pattern?
2. Any recommended timeout or iteration settings to prevent the loop?
3. If this is a known issue when using SSE transport mode with RooCode?

Part of the logs as follows

   ~/repos/cipher  on   main !4 ?4  node dist/src/app/index.cjs --mode mcp --mcp-transport-type sse --mcp-port 4000  ✔  at 20:59:28 
[CIPHER-MCP] Log redirection activated: /var/folders/ts/dhcpj54x7p512cnr753l_6nh0000gn/T/cipher-mcp.log
20:59:33 INFO: MCP Manager: MCPManager initialized
20:59:33 INFO: MCP Manager: Initializing 0 servers (0 disabled)
20:59:33 INFO: MCP Manager: Initialization complete
accessKeyId <My_AWS_accessKeyId>
secretAccessKey <My_AWS_secretAccessKey>
20:59:33 DEBUG: Overriding vector store dimension from agent config
20:59:33 DEBUG: Creating new dual collection vector store instance
20:59:33 INFO: [VectorStoreFactory] Creating dual collection vector storage from environment
20:59:33 INFO: DualCollectionVectorManager: Initialized with dual collections
20:59:33 INFO: DualCollectionVectorManager: Connecting collections...
20:59:33 INFO: [VectorStoreManager] Vector storage system connected
20:59:33 INFO: DualCollectionVectorManager: Knowledge collection connected
20:59:33 INFO: [VectorStoreManager] Vector storage system connected
20:59:33 INFO: DualCollectionVectorManager: Reflection collection connected
20:59:33 INFO: [KG-Factory] Knowledge graph is disabled in environment
logging to check if it is initializing postgres
doesnt seem to be initializing postgres
20:59:33 INFO: [StorageManager] Initialized with configuration
20:59:33 INFO: [StorageManager] Starting connection attempt 1
20:59:33 INFO: InMemoryBackend connected
20:59:33 INFO: [StorageManager:Cache] Connected successfully
20:59:33 INFO: SQLite backend connected successfully
20:59:33 INFO: [StorageManager:Database] Connected successfully
20:59:33 INFO: [StorageManager] Storage system connected
Tools config args {
enableInternalTools: true,
enableMcpTools: true,
conflictResolution: 'prefix-internal',
executionTimeout: 30000,
mode: 'cli'
}
🔍 [7lalji] search_memory tool called with: {
query: 'Portal tribe naming conventions or rules, especially related to folder naming',
top_k: 3,
similarity_threshold: undefined,
sessionId: undefined,
toolName: 'cipher_memory_search'
}
aws bedrock embedder received: Portal tribe naming conventions or rules, especially related to folder naming
aws bedrock embedder body: {
"inputText": "Portal tribe naming conventions or rules, especially related to folder naming",
"dimensions": 256
}
aws bedrock embedder calling: InvokeModelCommand {
middlewareStack: {
add: [Function: add],
addRelativeTo: [Function: addRelativeTo],
clone: [Function: clone],
use: [Function: use],
remove: [Function: remove],
removeByTag: [Function: removeByTag],
concat: [Function: concat],
applyToStack: [Function: cloneTo],
identify: [Function: identify],
identifyOnResolve: [Function: identifyOnResolve],
resolve: [Function: resolve]
},
schema: undefined,
input: {
modelId: 'amazon.titan-embed-text-v2:0',
body: '{"inputText":"Portal tribe naming conventions or rules, especially related to folder naming","dimensions":256}',
contentType: 'application/json',
accept: 'application/json'
},
serialize: [AsyncFunction: se_InvokeModelCommand],
deserialize: [AsyncFunction: de_InvokeModelCommand]
}
aws bedrock embedder model: amazon.titan-embed-text-v2:0
aws bedrock embedder region: eu-central-1
aws bedrock embedder client config: {
"region": "eu-central-1",
"credentials": {
"accessKeyId": "SET",
"secretAccessKey": "SET"
}
}
aws bedrock embedder responsed: {
embedding: [
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0.0027261183131486177, 0.02574128843843937, 0.1524674892425537,
0.030407236889004707,
... 156 more items
],
embeddingsByType: {
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0.030407236889004707,
... 156 more items
]
},
inputTextTokenCount: 13
}
🔍 [ftdb63] search_memory tool called with: {
query: 'Portal tribe naming conventions or rules, specifically about folder naming',
top_k: 3,
similarity_threshold: undefined,
sessionId: undefined,
toolName: 'cipher_memory_search'
}
aws bedrock embedder received: Portal tribe naming conventions or rules, specifically about folder naming
aws bedrock embedder body: {
"inputText": "Portal tribe naming conventions or rules, specifically about folder naming",
"dimensions": 256
}
aws bedrock embedder calling: InvokeModelCommand {
middlewareStack: {
add: [Function: add],
addRelativeTo: [Function: addRelativeTo],
clone: [Function: clone],
use: [Function: use],
remove: [Function: remove],
removeByTag: [Function: removeByTag],
concat: [Function: concat],
applyToStack: [Function: cloneTo],
identify: [Function: identify],
identifyOnResolve: [Function: identifyOnResolve],
resolve: [Function: resolve]
},
schema: undefined,
input: {
modelId: 'amazon.titan-embed-text-v2:0',
body: '{"inputText":"Portal tribe naming conventions or rules, specifically about folder naming","dimensions":256}',
contentType: 'application/json',
accept: 'application/json'
},
serialize: [AsyncFunction: se_InvokeModelCommand],
deserialize: [AsyncFunction: de_InvokeModelCommand]
}
aws bedrock embedder model: amazon.titan-embed-text-v2:0
aws bedrock embedder region: eu-central-1
aws bedrock embedder client config: {
"region": "eu-central-1",
"credentials": {
"accessKeyId": "SET",
"secretAccessKey": "SET"
}
}
aws bedrock embedder responsed: {
embedding: [
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],
embeddingsByType: {
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... 156 more items
]
},
inputTextTokenCount: 12
}
🔍 [nd9iw] search_memory tool called with: {
query: 'Portal tribe naming conventions or rules, especially related to folder naming',
top_k: 3,
similarity_threshold: undefined,
sessionId: undefined,
toolName: 'cipher_memory_search'
}
aws bedrock embedder received: Portal tribe naming conventions or rules, especially related to folder naming
.
.
.
.

Thanks in advance for your time and support! 🙏