MCP Server times out on windows #3130

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1. TheFrok

   added

   kind/bug

   status/need-triageIssues that need to be triaged by the triage automation.Issues that need to be triaged by the triage automation.

   on Jul 3, 2025
2. gemini-cli

   added

   area/coreIssues related to User Interface, OS Support, Core FunctionalityIssues related to User Interface, OS Support, Core Functionality

   priority/p2Important but can be addressed in a future release.Important but can be addressed in a future release.

   and removed

   status/need-triageIssues that need to be triaged by the triage automation.Issues that need to be triaged by the triage automation.

   on Jul 3, 2025
3. NTaylorMullen commented on Jul 3, 2025

   

   NTaylorMullen

   on Jul 3, 2025

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   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

   🎉React with 🎉1Reacted by CEORetailManager01
4. TheFrok commented on Jul 3, 2025

   

   TheFrok

   on Jul 3, 2025

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   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.

   🎉React with 🎉1Reacted by CEORetailManager01
5. NTaylorMullen commented on Jul 5, 2025

   

   NTaylorMullen

   on Jul 5, 2025

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   @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?
6. TheFrok commented on Jul 7, 2025

   

   TheFrok

   on Jul 7, 2025

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   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.
7. TheFrok

   closed this as completedon Jul 7, 2025
8. whharris917

   added a commit that references this issue on Feb 1, 2026

   Fix Windows subprocess stdin hang in MCP server

   ...

   3fe2537