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The default value of subprocess.Popen "close_fds" parameter changed to True in Python 3. Compared to Python 2, close_fds=True can make Popen 10x slower: see bpo-37790.
A single close(fd) syscall is cheap. But when MAXFDS (maximum file descriptor number) is high, the loop calling close(fd) on each file descriptor can take several milliseconds.
On FreeBSD, the _posixsubprocess could use closefrom() to reduce the number of syscalls.
On Linux, _posixsubprocess lists the content of /proc/self/fd/ to only close open file descriptor, after fork() and before exec().