I;ve created index through phpMyadmin. There is already option on right side to 'add index' with simple clicking on 'add index'. (i hope that it is same instead of running query to add index to columns 'ip' and 'counter')
I see directly improvement in speed. Before was under 1second and now is 2x faster.
Great and thanks again. Your input to help me was excellent.
I will monitor through Cpanel (Resources Usage) of CPU raising to 100% has been dropped.