how to set close-on-exec by default

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No and no.

You simply need to be careful and set close-on-exec on all file descriptors you care about.

Setting it is easy, though:

#include <fcntl.h>
fcntl(fd, F_SETFD, fcntl(fd, F_GETFD) | FD_CLOEXEC);

#include <unistd.h>
/* please don't do this */
for (i = getdtablesize(); i --> 3;) {
    if ((flags = fcntl(i, F_GETFD)) != -1)
        fcntl(fd, F_SETFD, flags | FD_CLOEXEC);
}

If you are running Linux kernel ≥2.6.23 and glibc ≥2.7, open (along with other similar syscalls) accepts a new flag O_CLOEXEC:

#include <unistd.h>
fd = open("...", ... | O_CLOEXEC);

If you are running Linux kernel ≥2.6.24 and glibc ≥2.7, fcntl accepts a new argument F_DUPFD_CLOEXEC:

#include <fcntl.h>
newfd = fcntl(oldfd, F_DUPFD_CLOEXEC);

If you are running Linux kernel ≥2.6.27 and glibc ≥2.9, there are new syscalls pipe2, dup3, etc., and many more syscalls gain new *_CLOEXEC flags:

#define _GNU_SOURCE
#include <unistd.h>
pipe2(pipefds, O_CLOEXEC);
dup3(oldfd, newfd, O_CLOEXEC);

Note that POSIX specifies that

The popen() function shall ensure that any streams from previous popen() calls that remain open in the parent process are closed in the new child process.

so if you’re worried about that leak, don’t be.

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