Using transport="stdio" closes real stdio, causing ValueError after server exits

[hyn0027]

Initial Checks

• I confirm that I'm using the latest version of MCP Python SDK
• I confirm that I searched for my issue in https://github.com/modelcontextprotocol/python-sdk/issues before opening this issue

Description

Hi! I ran into an issue where running the server with transport="stdio" causes subsequent stdio operations to fail after the server exits.

Minimal reproduction

from mcp.server.fastmcp import FastMCP

mcp = FastMCP("Demo")
mcp.run(transport="stdio")
print("?")

When using Ctrl+D to exit the server, the final print raises:

Traceback (most recent call last):
  File "...", line 5, in <module>
    print("?")
ValueError: I/O operation on closed file.

I’m not sure if this is intended behavior though.

Likely cause

In stdio.py, stdio is wrapped like this:

python-sdk/src/mcp/server/stdio.py

Lines 44 to 47 in 5301298

	if not stdin:
	stdin = anyio.wrap_file(TextIOWrapper(sys.stdin.buffer, encoding="utf-8"))
	if not stdout:
	stdout = anyio.wrap_file(TextIOWrapper(sys.stdout.buffer, encoding="utf-8"))

When these wrappers are closed, they also close the sys.stdin.buffer / sys.stdout.buffer.

Proposed fix

    if not stdin:
        stdin_fd = os.dup(sys.stdin.fileno())
        stdin_bin = os.fdopen(stdin_fd, "rb", closefd=True)
        stdin = anyio.wrap_file(TextIOWrapper(stdin_bin, encoding="utf-8"))
    if not stdout:
        stdout_fd = os.dup(sys.stdout.fileno())
        stdout_bin = os.fdopen(stdout_fd, "wb", closefd=True)
        stdout = anyio.wrap_file(TextIOWrapper(stdout_bin, encoding="utf-8"))

Python & MCP Python SDK

Python 3.10.15
mcp==1.25.0

[adityuhkapoor]

I can reproduce this on main; root cause is TextIOWrapper closing sys.stdin.buffer/sys.stdout.buffer due to auto garbage collection. os.dup() adds another pointer to the underlying resource and ensures that the stdio process doesn't prematurely get GC'd. Happy to put up a PR if this is up for grabs.

[adityuhkapoor]

Hi, PR #2040 is ready for review, all CI green and regression test is included. The fix uses os.dup() to give TextIOWrapper its own file descriptor so closing it doesn't kill process stdio. @Kludex