[c++] Replacing a 32-bit loop counter with 64-bit introduces crazy performance deviations with _mm_popcnt_u64 on Intel CPUs

Have you tried moving the reduction step outside the loop? Right now you have a data dependency that really isn't needed.

Try:

  uint64_t subset_counts[4] = {};
  for( unsigned k = 0; k < 10000; k++){
     // Tight unrolled loop with unsigned
     unsigned i=0;
     while (i < size/8) {
        subset_counts[0] += _mm_popcnt_u64(buffer[i]);
        subset_counts[1] += _mm_popcnt_u64(buffer[i+1]);
        subset_counts[2] += _mm_popcnt_u64(buffer[i+2]);
        subset_counts[3] += _mm_popcnt_u64(buffer[i+3]);
        i += 4;
     }
  }
  count = subset_counts[0] + subset_counts[1] + subset_counts[2] + subset_counts[3];

You also have some weird aliasing going on, that I'm not sure is conformant to the strict aliasing rules.

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