shell_exec() timeout management & exec()

I would suggest you look into using proc_open. You can configure it to return a stream resource, manually keep a timer, and if the timer expires before the process completes, you can terminate it with proc_terminate. If it does complete before the timer expires, then you can use proc_close then stream_get_contents to grab the data that would have otherwise been written to stdout.

See http://www.php.net/manual/en/function.proc-open.php

I write some working piece of code for such task. Function returns exit code (0 - OK, >0 - error) and writes stdout, stderr to reference variables.

/*execute program and write all output to $out
terminate program if it runs more than 30 seconds */
execute("program --option", null, $out, $out, 30);
echo $out;

function execute($cmd, $stdin=null, &$stdout, &$stderr, $timeout=false)
{
    $pipes = array();
    $process = proc_open(
        $cmd,
        array(array('pipe','r'),array('pipe','w'),array('pipe','w')),
        $pipes
    );
    $start = time();
    $stdout = '';
    $stderr = '';

    if(is_resource($process))
    {
        stream_set_blocking($pipes[0], 0);
        stream_set_blocking($pipes[1], 0);
        stream_set_blocking($pipes[2], 0);
        fwrite($pipes[0], $stdin);
        fclose($pipes[0]);
    }

    while(is_resource($process))
    {
        //echo ".";
        $stdout .= stream_get_contents($pipes[1]);
        $stderr .= stream_get_contents($pipes[2]);

        if($timeout !== false && time() - $start > $timeout)
        {
            proc_terminate($process, 9);
            return 1;
        }

        $status = proc_get_status($process);
        if(!$status['running'])
        {
            fclose($pipes[1]);
            fclose($pipes[2]);
            proc_close($process);
            return $status['exitcode'];
        }

        usleep(100000);
    }

    return 1;
}