One problem · bounded diagnostic

MCP server not responding: locate the timeout

Separate a server startup failure from an initialization failure and a slow tool call before changing timeouts.

Check startup first

Confirm that the server process stays running. For stdio transports, diagnostic logs belong on stderr: ordinary text on stdout can corrupt protocol messages. Keep a sanitized startup exit code.

Identify the failing boundary

Record whether the failure happens during initialization, tool listing or one specific tool call. A successful tools/list result narrows the problem to invocation or the downstream dependency.

Test one bounded call

Use one small known input and one retry at most. Note elapsed time and whether a response eventually arrives. Increasing a timeout does not fix a crashed process or an unreachable dependency.

Evidence to keep

Transport type, failing method, elapsed time and a sanitized error message. Do not send credentials or private endpoints.

Scope of this check

The free probe classifies the symptom. It does not connect to your server or prove that a downstream dependency is healthy.

Example: isolate the failing MCP stage

Illustrative diagnostic record, not a customer repair or live server test. Fill in each result from your own client.

initialize: record success or exact error
tools/list: record success or exact error
tools/call (one small input): record elapsed time and exact error

If initialization and tool listing succeed but one call fails, inspect that tool and its downstream dependency. If startup fails, preserve the process exit code and stderr. Raising all timeouts does not identify the cause.

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Related troubleshooting guides

Try the free probe

Use a sanitized symptom or a synthetic sample. The request goes to the existing NAIF diagnostic API. No payment or repair is started.

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Use this guide with an AI agent
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Existing agent discovery