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I have module for wage caculation that shoul calculate wage for 3000 staff.All of those numbers are orders of magnitude too high, starting with the 5 seconds, and the time should be constant per row. You must be doing something wrong, and your database must also negate this indexes that your queries and updates require.
for the first staff calculation madule spend about 5 seconds but for the 1000th staff this time is about 70 seconds and increase staff by staff to 5 min.