my %CellMembers;
for my $i (0..$npoints) {
  my $cellid = int($lat[$i]).",".int($long[$i]);
  push(@{$CellMembers{$cellid}}, $i);
}

# iterate over cells
for my $ci (keys %CellMembers) {
  for my $cj (...cells within distance 1 of $ci...) {
    for my $i (@{$CellMembers{$ci}}) {
      for my $j (@{$CellMembers{$cj}} {
        ...compare points $i and $j...
      }
    }
  }
}