You don't even need your own mainloop, as AnyEvent brings its own main loop with it.

I would rewrite your main loop as follows:

my $loop = AnyEvent->condvar;
my $a = 0;

sub heartbeat {
    open( $fh, '>>', $msg_log );
        print $fh "looping $a\n";
    close $fh;
};

AnyEvent->timer( interval => 5, cb => \&heartbeat );
$loop->recv;
exit 0;
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I would move reacting to IO out of the main loop as well:

$iocv->cb( \&on_io );

sub on_io {
    open( $fh, '>>', $msg_log );
        print $fh "loop data: $data\n";
    close $fh;
    undef( $iocv );
    $iocv = AnyEvent->condvar;
    $iocv->cb( \&on_io );
};
[download]

Ideally, you don't have your own main loop and only have callbacks and let AnyEvent decide, which callback to run, depending on what kind of event has arrived.