The simple solution is to NOT use fgets() when you're on a deadline, because of the greedy read semantic.

Use fread() instead, in conjunction with stream_select() (which is what is used internally to implement the timeout).

Here's an example from our test suite:

function system_with_timeout($commandline)
{
	$data = "";
	
	$proc = proc_open($commandline, array(
		0 => array('pipe', 'r'),
		1 => array('pipe', 'w'),
		2 => array('pipe', 'w')
		), $pipes, null, null, array("suppress_errors" => true));

	if (!$proc)
		return false;

	fclose($pipes[0]);

	while (true) {
		/* hide errors from interrupted syscalls */
		$r = $pipes;
		$w = null;
		$e = null;
		$n = @stream_select($r, $w, $e, 60);

		if ($n === 0) {
			/* timed out */
			$data .= "\n ** ERROR: process timed out **\n";
			proc_terminate($proc);
			return $data;
		} else if ($n > 0) {
			$line = fread($pipes[1], 8192);
			if (strlen($line) == 0) {
				/* EOF */
				break;
			}
			$data .= $line;
		}
	}
	$stat = proc_get_status($proc);
	if ($stat['signaled']) {
		$data .= "\nTermsig=".$stat['stopsig'];
	}
	$code = proc_close($proc);
	return $data;
}

I have a couple of notes on that example. The function
attempts to fread 8Kbytes, whilst a positive response from
stream_select only guarantees that 1 byte can be read w/o
blocking. Further, 60 secs is really eons.

I'm using this:

   function guarded_fgets($pipes)
   {
      $line = "";
      $time = 2;
      $c = "c";
      while ($time >= 0 && ord($c) != 10)
      {
         $read = array($pipes[1]);
         while (!feof($read[0]) &&
            ($n = stream_select($read, $w = NULL, $e = NULL, $time)) !== FALSE &&
            $n > 0 &&
            strlen($c = fgetc($read[0])) > 0 &&
            ord($c) != 10)
               $line .= $c;
         --$time;
      }

      if (ord($c) != 10)
      {
         // error handling
      }

      return $line;
   }

For the record I just created an issue that should address this problem once implemented: https://github.com/php/php-src/issues/10171 .