Giulio Ermanno Pibiri

I tried another machine of mine (Ubuntu again with gcc) and actually it worked. Very strange indeed. Everything else works correctly on the previous machine.

My machines have 128GB of RAM :) Also, why not including some examples in the readme? I see a lot of people got confused or have no idea about how...

Ok thanks!

Hi @adamant-pwn, and thank you for reaching out! The generalization to arbitrary alphabets would be very interesting. > Would it be of interest for SSHash to merge these changes upstream...

Hi @rob-p and sorry for the late reply to this. I'm interested in distributing SSHash via Bioconda (but I first have to learn how to do it). If distribution currently...

Alright, let's dig into `-march=native` then! I'll do some research and update this thread.

Following from here: https://wiki.gentoo.org/wiki/Safe_CFLAGS#Find_CPU-specific_options, by doing giulio@xor:~$ gcc -v -E -x c /dev/null -o /dev/null -march=native 2>&1 | grep /cc1 | grep mtune I get /usr/lib/gcc/x86_64-linux-gnu/11/cc1 -E -quiet -v -imultiarch...

I think all that is required in the end can be understood from here https://github.com/jermp/pthash/blob/master/include/encoders/util.hpp -- from some special instructions PTHash uses: popcount and parallel-bit-deposit (or `pdep`). For popcount: `_mm_popcnt_u64`...

And it would be instructive to compare the performance of both tools, PTHash and SSHash, with and without those compiler flags to see how much they impact. I did it...

Ok, so it looks we have reduced the problem to - inspect the impact of BMI2 on x86 machines; - and see what are the options for ARM. Will do...