One way to improve execution time of your code would be this:
$num = 1000;
for($j = 2; $j <= $num; $j++)
{
$cond = sqrt($j);
for($k = 2; $k <= $cond; $k++)
{
if($j % $k == 0)
{
break;
}
}
if($k > $cond)
{
echo 'Prime number: ' . $j . '<br>';
}
}
But there is no need to calculate prime numbers from the begining each time. You can remember every 30 seconds or so where you were, save the result to a database, file, or an array, and then restart the script, which should the continue from where it stopped.