In my experience (at least with Apache) you need to close STDERR in addition to STDOUT, because Apache (or mod_cgi to be more precise) sets up
two pipes to the CGI program (STDERR is connected to Apache's
error log), which get duplicated when the CGI process forks... If you
don't close them before starting the long-running process, Apache will
wait for those handles to be closed by that forked process before it finishes the request
cycle.
Preferably start the long-running process via fork/exec,
in which case you can conveniently close STDOUT/STDERR after the fork (so
the handles remain functional in the main CGI), but before doing the exec.
(A similar question came up recently, btw.)
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