An internal library that heavily uses subprocess.Popen() started failing its automated tests when we upgraded from Python 2.7.3 to Python 2.7.5. This library is used in a threaded environment. After debugging the issue, I was able to create a short Python script that demonstrates the error seen as in the failing tests.

This is the script (called "threadedsubprocess.py"):

===
import time
import threading
import subprocess

def subprocesscall():
    p = subprocess.Popen(
        ['ls', '-l'],
        stdin=subprocess.PIPE,
        stdout=subprocess.PIPE,
        stderr=subprocess.PIPE,
        )
    time.sleep(2) # simulate the Popen call takes some time to complete.
    out, err = p.communicate()
    print 'succeeding command in thread:', threading.current_thread().ident

def failingsubprocesscall():
    try:
        p = subprocess.Popen(
            ['thiscommandsurelydoesnotexist'],
            stdin=subprocess.PIPE,
            stdout=subprocess.PIPE,
            stderr=subprocess.PIPE,
            )
    except Exception as e:
        print 'failing command:', e, 'in thread:', threading.current_thread().ident

print 'main thread is:', threading.current_thread().ident

subprocesscall_thread = threading.Thread(target=subprocesscall)
subprocesscall_thread.start()
failingsubprocesscall()
subprocesscall_thread.join()
===

Note: this script does not exit with an IOError when ran from Python 2.7.3. It does fail at least 50% of the times when ran from Python 2.7.5 (both on the same Ubuntu 12.04 64-bit VM).

The error that is raised on Python 2.7.5 is this:

==
/opt/python/2.7.5/bin/python ./threadedsubprocess.py 
main thread is: 139899583563520
failing command: [Errno 2] No such file or directory 139899583563520
Exception in thread Thread-1:
Traceback (most recent call last):
  File "/opt/python/2.7.5/lib/python2.7/threading.py", line 808, in __bootstrap_inner
    self.run()
  File "/opt/python/2.7.5/lib/python2.7/threading.py", line 761, in run
    self.__target(*self.__args, **self.__kwargs)
  File "./threadedsubprocess.py", line 13, in subprocesscall
    out, err = p.communicate()
  File "/opt/python/2.7.5/lib/python2.7/subprocess.py", line 806, in communicate
    return self._communicate(input)
  File "/opt/python/2.7.5/lib/python2.7/subprocess.py", line 1379, in _communicate
    self.stdin.close()
IOError: [Errno 9] Bad file descriptor

close failed in file object destructor:
IOError: [Errno 9] Bad file descriptor
==

When comparing the subprocess module from Python 2.7.3 to Python 2.7.5 I see the Popen()'s __init__() call indeed now explicitly closes the stdin, stdout and stderr file descriptors in case executing the command somehow fails. This seems to be an intended fix applied in Python 2.7.4 to prevent leaking file descriptors (http://hg.python.org/cpython/file/ab05e7dd2788/Misc/NEWS#l629).

The diff between Python 2.7.3 and Python 2.7.5 that seems to be relevant to this issue is in the Popen __init__():

==
@@ -671,12 +702,33 @@
          c2pread, c2pwrite,
          errread, errwrite) = self._get_handles(stdin, stdout, stderr)

-        self._execute_child(args, executable, preexec_fn, close_fds,
-                            cwd, env, universal_newlines,
-                            startupinfo, creationflags, shell,
-                            p2cread, p2cwrite,
-                            c2pread, c2pwrite,
-                            errread, errwrite)
+        try:
+            self._execute_child(args, executable, preexec_fn, close_fds,
+                                cwd, env, universal_newlines,
+                                startupinfo, creationflags, shell,
+                                p2cread, p2cwrite,
+                                c2pread, c2pwrite,
+                                errread, errwrite)
+        except Exception:
+            # Preserve original exception in case os.close raises.
+            exc_type, exc_value, exc_trace = sys.exc_info()
+
+            to_close = []
+            # Only close the pipes we created.
+            if stdin == PIPE:
+                to_close.extend((p2cread, p2cwrite))
+            if stdout == PIPE:
+                to_close.extend((c2pread, c2pwrite))
+            if stderr == PIPE:
+                to_close.extend((errread, errwrite))
+
+            for fd in to_close:
+                try:
+                    os.close(fd)
+                except EnvironmentError:
==

Note: I think to see a similar change in the subprocess.Popen() __init__() from Python-3.3.0 to Python-3.3.1.