AVX2 and AVX512 implementations for ntHash

[mirounga]

Since the recurrent version of ntHash is a prefix sum with an associative operator, it is possible to compute the hashes in parallel using the prefix scan algorithm. For 64-bit hash the theoretical speedup in 2x for AVX2 and 3x for AVX512. Versions for 32-bit hashes are also included featuring even greater speedup.

[sjackman]

Hi, @mirounga. Cool! Does this code implement ntHash v1 or ntHash v2?

[mirounga]

The code implements the current version of ntHash. I have used the scalar version for validation

[sjackman]

Great. Thanks for confirming, @mirounga.

[mohamadi]

Hi @mirounga

I'm getting the following runtime performance results:

[hmohamadi@hpcg01 ntHash_avx]$ ./nttest_avx -k50 ERR294494_1.part1.fastq 
CPU time (sec) for hash algorithms for kmer=50
nthash	ntavx2	ntavx232	ntavx512	ntavx532	
6.72	2.14	2.25	6.84	6.98

The proper AVX512 and AVX512x32 implementations are not included in nttest_avx.cpp:

void hashSeqAvx512(const string & seq) {
        uint64_t fhVal, rhVal, hVal;
        hVal = NTC64(seq.c_str(), opt::kmerLen, fhVal, rhVal);
        if (hVal)opt::nz++;
        for (size_t i = 1; i < seq.length() - opt::kmerLen + 1; i++) {
                hVal = NTC64(seq[i - 1], seq[i - 1 + opt::kmerLen], opt::kmerLen, fhVal, rhVal);
                if (hVal)opt::nz++;
        }
}

void hashSeqAvx512x32(const string & seq) {
        uint64_t fhVal, rhVal, hVal;
        hVal = NTC64(seq.c_str(), opt::kmerLen, fhVal, rhVal);
        if (hVal)opt::nz++;
        for (size_t i = 1; i < seq.length() - opt::kmerLen + 1; i++) {
                hVal = NTC64(seq[i - 1], seq[i - 1 + opt::kmerLen], opt::kmerLen, fhVal, rhVal);
                if (hVal)opt::nz++;
        }
}

[mirounga]

Hi @mohamadi , fixed the AVX512 functions. When measuring performance please subtract the cost of IO - it is dominating now.

[parham-k]

Closing due to being related to ntHash's old codebase. New ports are welcome!

[rchikhi]

Nice work there! I've expanded this unmerged PR into its own repository, in order to better assess the correctness of results, (keeping the same codebase): https://github.com/rchikhi/ntHash-AVX512

[mohamadi]

@parham-k can you take a look at it and merge if compatible with the new release?

[parham-k]

Sure! Thank you @rchikhi.