MCP Server times out on windows

[TheFrok]

What happened?

I constantly getting the McpError: MCP error -32001: Request timed out when I try my MCP on windows, while working fine on linux.

What did you expect to happen?

I wanted the MCP to finish running and return the result.

Client information

• CLI Version: 0.1.9
• Git Commit: 34935d6
• Operating System: win32 v22.17.0
• Sandbox Environment: no sandbox
• Model Version: gemini-2.5-pro
• Memory Usage: 131.2 MB

Login information

I use vertex AI credentials

Anything else we need to know?

This using FastMCP, and the tool invokes a different process to get its stdout.
The MCP transport is stdio.

[NTaylorMullen]

Few questions:

• What's your MCP server config look like?
• If you run the command to start it locally does it work?
• If you boot Gemini CLI with the -d parameter and then hit ctrl + o (will open the output pane) could you share the output there

[TheFrok]

My settings.json is this (I that's the server config you meant):

{ 
  "theme": "Default",
  "selectedAuthType": "vertex-ai",
  "mcpServers": {
    "my_server": {
      "command": "C:\\Users\\admin\\venv\\Scripts\\python", 
      "args": [
        "C:\\Users\\admin\\server.py"
      ],
      "cwd": "C:\\Users\\admin",
      "timeout": 600000,
      "trust": true
    }
  }
}

If I run the server.py script (with the right python environment) I get 07/03/25 20:34:34] INFO Starting MCP server 'my-server' with transport 'stdio' server.py:1246, which I assumed is correct since I have the same result on Linux.
Also if I import server.py to the python interpreter and run call the function of the tools they return immediately.

When running with gemini -d and prompting to use the version tool of the server I get:

Debug Console (ctrl+o to close)

ℹ  Authenticated via "vertex-ai".
ℹ  Flushing log events to Clearcut. (x7)
✖  MCP ERROR (my_server): Error: Received a response for an unknown message ID: {"jsonrpc":"2.0","id":2,"result":{"content":[{"type":"text","text":"my_tool version 0.3.4\n"}],"isError":false}}
ℹ  Flushing log events to Clearcut. (x3)

And "my_tool version 0.3.4\n" is the correct result from using the tool.

[NTaylorMullen]

@TheFrok hmmm, so based on that error it seems your MCP server is misbehaving. How Json RPC typically works is that for each request you are given an id and each response must contain the corresponding id parameter. Does this MCP server work with other MCP clients by chance?

[TheFrok]

This was indeed an issue on my side. The subprocess I invoked raced with the server on reading from stdin.
Passing stdin=subprocess.DEVNULL when invoking the command solved it for me.