libparasail-sys 0.2.1

/**
 * @file
 *
 * @author jeffrey.daily@gmail.com
 *
 * Copyright (c) 2015 Battelle Memorial Institute.
 */
#include "config.h"

#include <immintrin.h>

#include "parasail/memory.h"
#include "parasail/internal_avx.h"

__m256i * parasail_memalign___m256i(size_t alignment, size_t size)
{
    return (__m256i *) parasail_memalign(alignment, size*sizeof(__m256i));
}

void parasail_memset___m256i(__m256i *b, __m256i c, size_t len)
{
    size_t i;
    for (i=0; i<len; ++i) {
        _mm256_store_si256(&b[i], c);
    }
}

parasail_profile_t * parasail_profile_create_avx_256_8(
        const char * const restrict s1, const int _s1Len,
        const parasail_matrix_t *matrix)
{
    int s1Len = 0;
    int32_t i = 0;
    int32_t j = 0;
    int32_t k = 0;
    int32_t segNum = 0;
    int32_t n = 0; /* number of amino acids in table */
    const int32_t segWidth = 32; /* number of values in vector unit */
    int32_t segLen = 0;
    __m256i* restrict vProfile = NULL;
    int32_t index = 0;
    parasail_profile_t *profile = NULL;

    PARASAIL_CHECK_NULL(matrix);
    /* s1 is ignored for pssm, required for square */
    if (matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) {
        PARASAIL_CHECK_NULL(s1);
    }

    s1Len = matrix->type == PARASAIL_MATRIX_TYPE_SQUARE ? _s1Len : matrix->length;
    n = matrix->size;
    segLen = (s1Len + segWidth - 1) / segWidth;
    vProfile = parasail_memalign___m256i(32, n * segLen);
    if (!vProfile) return NULL;
    profile = parasail_profile_new(s1, s1Len, matrix);
    if (!profile) return NULL;

    for (k=0; k<n; ++k) {
        for (i=0; i<segLen; ++i) {
            __m256i_8_t t;
            j = i;
            for (segNum=0; segNum<segWidth; ++segNum) {
                if (matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) {
                    t.v[segNum] = j >= s1Len ? 0 : matrix->matrix[n*k+matrix->mapper[(unsigned char)s1[j]]];
                }
                else {
                    t.v[segNum] = j >= s1Len ? 0 : matrix->matrix[n*j+matrix->mapper[(unsigned char)matrix->alphabet[k]]];
                }
                j += segLen;
            }
            _mm256_store_si256(&vProfile[index], t.m);
            ++index;
        }
    }

    profile->profile8.score = vProfile;
    profile->free = &parasail_free___m256i;
    return profile;
}

parasail_profile_t * parasail_profile_create_avx_256_16(
        const char * const restrict s1, const int _s1Len,
        const parasail_matrix_t *matrix)
{
    int s1Len = 0;
    int32_t i = 0;
    int32_t j = 0;
    int32_t k = 0;
    int32_t segNum = 0;
    int32_t n = 0; /* number of amino acids in table */
    const int32_t segWidth = 16; /* number of values in vector unit */
    int32_t segLen = 0;
    __m256i* restrict vProfile = NULL;
    int32_t index = 0;
    parasail_profile_t *profile = NULL;

    PARASAIL_CHECK_NULL(matrix);
    /* s1 is ignored for pssm, required for square */
    if (matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) {
        PARASAIL_CHECK_NULL(s1);
    }

    s1Len = matrix->type == PARASAIL_MATRIX_TYPE_SQUARE ? _s1Len : matrix->length;
    n = matrix->size;
    segLen = (s1Len + segWidth - 1) / segWidth;
    vProfile = parasail_memalign___m256i(32, n * segLen);
    if (!vProfile) return NULL;
    profile = parasail_profile_new(s1, s1Len, matrix);
    if (!profile) return NULL;

    for (k=0; k<n; ++k) {
        for (i=0; i<segLen; ++i) {
            __m256i_16_t t;
            j = i;
            for (segNum=0; segNum<segWidth; ++segNum) {
                if (matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) {
                    t.v[segNum] = j >= s1Len ? 0 : matrix->matrix[n*k+matrix->mapper[(unsigned char)s1[j]]];
                }
                else {
                    t.v[segNum] = j >= s1Len ? 0 : matrix->matrix[n*j+matrix->mapper[(unsigned char)matrix->alphabet[k]]];
                }
                j += segLen;
            }
            _mm256_store_si256(&vProfile[index], t.m);
            ++index;
        }
    }

    profile->profile16.score = vProfile;
    profile->free = &parasail_free___m256i;
    return profile;
}

parasail_profile_t * parasail_profile_create_avx_256_32(
        const char * const restrict s1, const int _s1Len,
        const parasail_matrix_t *matrix)
{
    int s1Len = 0;
    int32_t i = 0;
    int32_t j = 0;
    int32_t k = 0;
    int32_t segNum = 0;
    int32_t n = 0; /* number of amino acids in table */
    const int32_t segWidth = 8; /* number of values in vector unit */
    int32_t segLen = 0;
    __m256i* restrict vProfile = NULL;
    int32_t index = 0;
    parasail_profile_t *profile = NULL;

    PARASAIL_CHECK_NULL(matrix);
    /* s1 is ignored for pssm, required for square */
    if (matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) {
        PARASAIL_CHECK_NULL(s1);
    }

    s1Len = matrix->type == PARASAIL_MATRIX_TYPE_SQUARE ? _s1Len : matrix->length;
    n = matrix->size;
    segLen = (s1Len + segWidth - 1) / segWidth;
    vProfile = parasail_memalign___m256i(32, n * segLen);
    if (!vProfile) return NULL;
    profile = parasail_profile_new(s1, s1Len, matrix);
    if (!profile) return NULL;

    for (k=0; k<n; ++k) {
        for (i=0; i<segLen; ++i) {
            __m256i_32_t t;
            j = i;
            for (segNum=0; segNum<segWidth; ++segNum) {
                if (matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) {
                    t.v[segNum] = j >= s1Len ? 0 : matrix->matrix[n*k+matrix->mapper[(unsigned char)s1[j]]];
                }
                else {
                    t.v[segNum] = j >= s1Len ? 0 : matrix->matrix[n*j+matrix->mapper[(unsigned char)matrix->alphabet[k]]];
                }
                j += segLen;
            }
            _mm256_store_si256(&vProfile[index], t.m);
            ++index;
        }
    }

    profile->profile32.score = vProfile;
    profile->free = &parasail_free___m256i;
    return profile;
}

parasail_profile_t * parasail_profile_create_avx_256_64(
        const char * const restrict s1, const int _s1Len,
        const parasail_matrix_t *matrix)
{
    int s1Len = 0;
    int32_t i = 0;
    int32_t j = 0;
    int32_t k = 0;
    int32_t segNum = 0;
    int32_t n = 0; /* number of amino acids in table */
    const int32_t segWidth = 4; /* number of values in vector unit */
    int32_t segLen = 0;
    __m256i* restrict vProfile = NULL;
    int32_t index = 0;
    parasail_profile_t *profile = NULL;

    PARASAIL_CHECK_NULL(matrix);
    /* s1 is ignored for pssm, required for square */
    if (matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) {
        PARASAIL_CHECK_NULL(s1);
    }

    s1Len = matrix->type == PARASAIL_MATRIX_TYPE_SQUARE ? _s1Len : matrix->length;
    n = matrix->size;
    segLen = (s1Len + segWidth - 1) / segWidth;
    vProfile = parasail_memalign___m256i(32, n * segLen);
    if (!vProfile) return NULL;
    profile = parasail_profile_new(s1, s1Len, matrix);
    if (!profile) return NULL;

    for (k=0; k<n; ++k) {
        for (i=0; i<segLen; ++i) {
            __m256i_64_t t;
            j = i;
            for (segNum=0; segNum<segWidth; ++segNum) {
                if (matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) {
                    t.v[segNum] = j >= s1Len ? 0 : matrix->matrix[n*k+matrix->mapper[(unsigned char)s1[j]]];
                }
                else {
                    t.v[segNum] = j >= s1Len ? 0 : matrix->matrix[n*j+matrix->mapper[(unsigned char)matrix->alphabet[k]]];
                }
                j += segLen;
            }
            _mm256_store_si256(&vProfile[index], t.m);
            ++index;
        }
    }

    profile->profile64.score = vProfile;
    profile->free = &parasail_free___m256i;
    return profile;
}

parasail_profile_t* parasail_profile_create_avx_256_sat(
        const char * const restrict s1, const int s1Len,
        const parasail_matrix_t *matrix)
{
    parasail_profile_t *profile8 = parasail_profile_create_avx_256_8(s1, s1Len, matrix);
    parasail_profile_t *profile16 = parasail_profile_create_avx_256_16(s1, s1Len, matrix);
    parasail_profile_t *profile32 = parasail_profile_create_avx_256_32(s1, s1Len, matrix);
    profile8->profile16 = profile16->profile16;
    profile8->profile32 = profile32->profile32;
    free(profile16);
    free(profile32);

    return profile8;
}

parasail_profile_t * parasail_profile_create_stats_avx_256_8(
        const char * const restrict s1, const int _s1Len,
        const parasail_matrix_t *matrix)
{
    int s1Len = 0;
    int32_t i = 0;
    int32_t j = 0;
    int32_t k = 0;
    int32_t segNum = 0;
    int32_t n = 0;
    const int32_t segWidth = 32; /* number of values in vector unit */
    int32_t segLen = 0;
    __m256i* restrict vProfile = NULL;
    __m256i* restrict vProfileM = NULL;
    __m256i* restrict vProfileS = NULL;
    int32_t index = 0;
    parasail_profile_t *profile = NULL;

    PARASAIL_CHECK_NULL(matrix);
    /* s1 is required for both pssm and square */
    PARASAIL_CHECK_NULL(s1);

    s1Len = matrix->type == PARASAIL_MATRIX_TYPE_SQUARE ? _s1Len : matrix->length;
    n = matrix->size; /* number of amino acids in table */
    segLen = (s1Len + segWidth - 1) / segWidth;
    vProfile = parasail_memalign___m256i(32, n * segLen);
    if (!vProfile) return NULL;
    vProfileM = parasail_memalign___m256i(32, n * segLen);
    if (!vProfileM) return NULL;
    vProfileS = parasail_memalign___m256i(32, n * segLen);
    if (!vProfileS) return NULL;
    profile = parasail_profile_new(s1, s1Len, matrix);
    if (!profile) return NULL;

    for (k=0; k<n; ++k) {
        for (i=0; i<segLen; ++i) {
            __m256i_8_t p;
            __m256i_8_t m;
            __m256i_8_t s;
            j = i;
            for (segNum=0; segNum<segWidth; ++segNum) {
                if (matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) {
                    p.v[segNum] = j >= s1Len ? 0 : matrix->matrix[n*k+matrix->mapper[(unsigned char)s1[j]]];
                }
                else {
                    p.v[segNum] = j >= s1Len ? 0 : matrix->matrix[n*j+matrix->mapper[(unsigned char)matrix->alphabet[k]]];
                }
                m.v[segNum] = j >= s1Len ? 0 : (k == matrix->mapper[(unsigned char)s1[j]]);
                s.v[segNum] = p.v[segNum] > 0;
                j += segLen;
            }
            _mm256_store_si256(&vProfile[index], p.m);
            _mm256_store_si256(&vProfileM[index], m.m);
            _mm256_store_si256(&vProfileS[index], s.m);
            ++index;
        }
    }

    profile->profile8.score = vProfile;
    profile->profile8.matches = vProfileM;
    profile->profile8.similar = vProfileS;
    profile->free = &parasail_free___m256i;
    return profile;
}

parasail_profile_t * parasail_profile_create_stats_avx_256_16(
        const char * const restrict s1, const int _s1Len,
        const parasail_matrix_t *matrix)
{
    int s1Len = 0;
    int32_t i = 0;
    int32_t j = 0;
    int32_t k = 0;
    int32_t segNum = 0;
    int32_t n = 0;
    const int32_t segWidth = 16; /* number of values in vector unit */
    int32_t segLen = 0;
    __m256i* restrict vProfile = NULL;
    __m256i* restrict vProfileM = NULL;
    __m256i* restrict vProfileS = NULL;
    int32_t index = 0;
    parasail_profile_t *profile = NULL;

    PARASAIL_CHECK_NULL(matrix);
    /* s1 is required for both pssm and square */
    PARASAIL_CHECK_NULL(s1);

    s1Len = matrix->type == PARASAIL_MATRIX_TYPE_SQUARE ? _s1Len : matrix->length;
    n = matrix->size; /* number of amino acids in table */
    segLen = (s1Len + segWidth - 1) / segWidth;
    vProfile = parasail_memalign___m256i(32, n * segLen);
    if (!vProfile) return NULL;
    vProfileM = parasail_memalign___m256i(32, n * segLen);
    if (!vProfileM) return NULL;
    vProfileS = parasail_memalign___m256i(32, n * segLen);
    if (!vProfileS) return NULL;
    profile = parasail_profile_new(s1, s1Len, matrix);
    if (!profile) return NULL;

    for (k=0; k<n; ++k) {
        for (i=0; i<segLen; ++i) {
            __m256i_16_t p;
            __m256i_16_t m;
            __m256i_16_t s;
            j = i;
            for (segNum=0; segNum<segWidth; ++segNum) {
                if (matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) {
                    p.v[segNum] = j >= s1Len ? 0 : matrix->matrix[n*k+matrix->mapper[(unsigned char)s1[j]]];
                }
                else {
                    p.v[segNum] = j >= s1Len ? 0 : matrix->matrix[n*j+matrix->mapper[(unsigned char)matrix->alphabet[k]]];
                }
                m.v[segNum] = j >= s1Len ? 0 : (k == matrix->mapper[(unsigned char)s1[j]]);
                s.v[segNum] = p.v[segNum] > 0;
                j += segLen;
            }
            _mm256_store_si256(&vProfile[index], p.m);
            _mm256_store_si256(&vProfileM[index], m.m);
            _mm256_store_si256(&vProfileS[index], s.m);
            ++index;
        }
    }

    profile->profile16.score = vProfile;
    profile->profile16.matches = vProfileM;
    profile->profile16.similar = vProfileS;
    profile->free = &parasail_free___m256i;
    return profile;
}

parasail_profile_t * parasail_profile_create_stats_avx_256_32(
        const char * const restrict s1, const int _s1Len,
        const parasail_matrix_t *matrix)
{
    int s1Len = 0;
    int32_t i = 0;
    int32_t j = 0;
    int32_t k = 0;
    int32_t segNum = 0;
    int32_t n = 0;
    const int32_t segWidth = 8; /* number of values in vector unit */
    int32_t segLen = 0;
    __m256i* restrict vProfile = NULL;
    __m256i* restrict vProfileM = NULL;
    __m256i* restrict vProfileS = NULL;
    int32_t index = 0;
    parasail_profile_t *profile = NULL;

    PARASAIL_CHECK_NULL(matrix);
    /* s1 is required for both pssm and square */
    PARASAIL_CHECK_NULL(s1);

    s1Len = matrix->type == PARASAIL_MATRIX_TYPE_SQUARE ? _s1Len : matrix->length;
    n = matrix->size; /* number of amino acids in table */
    segLen = (s1Len + segWidth - 1) / segWidth;
    vProfile = parasail_memalign___m256i(32, n * segLen);
    if (!vProfile) return NULL;
    vProfileM = parasail_memalign___m256i(32, n * segLen);
    if (!vProfileM) return NULL;
    vProfileS = parasail_memalign___m256i(32, n * segLen);
    if (!vProfileS) return NULL;
    profile = parasail_profile_new(s1, s1Len, matrix);
    if (!profile) return NULL;

    for (k=0; k<n; ++k) {
        for (i=0; i<segLen; ++i) {
            __m256i_32_t p;
            __m256i_32_t m;
            __m256i_32_t s;
            j = i;
            for (segNum=0; segNum<segWidth; ++segNum) {
                if (matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) {
                    p.v[segNum] = j >= s1Len ? 0 : matrix->matrix[n*k+matrix->mapper[(unsigned char)s1[j]]];
                }
                else {
                    p.v[segNum] = j >= s1Len ? 0 : matrix->matrix[n*j+matrix->mapper[(unsigned char)matrix->alphabet[k]]];
                }
                m.v[segNum] = j >= s1Len ? 0 : (k == matrix->mapper[(unsigned char)s1[j]]);
                s.v[segNum] = p.v[segNum] > 0;
                j += segLen;
            }
            _mm256_store_si256(&vProfile[index], p.m);
            _mm256_store_si256(&vProfileM[index], m.m);
            _mm256_store_si256(&vProfileS[index], s.m);
            ++index;
        }
    }

    profile->profile32.score = vProfile;
    profile->profile32.matches = vProfileM;
    profile->profile32.similar = vProfileS;
    profile->free = &parasail_free___m256i;
    return profile;
}

parasail_profile_t * parasail_profile_create_stats_avx_256_64(
        const char * const restrict s1, const int _s1Len,
        const parasail_matrix_t *matrix)
{
    int s1Len = 0;
    int32_t i = 0;
    int32_t j = 0;
    int32_t k = 0;
    int32_t segNum = 0;
    int32_t n = 0;
    const int32_t segWidth = 4; /* number of values in vector unit */
    int32_t segLen = 0;
    __m256i* restrict vProfile = NULL;
    __m256i* restrict vProfileM = NULL;
    __m256i* restrict vProfileS = NULL;
    int32_t index = 0;
    parasail_profile_t *profile = NULL;

    PARASAIL_CHECK_NULL(matrix);
    /* s1 is required for both pssm and square */
    PARASAIL_CHECK_NULL(s1);

    s1Len = matrix->type == PARASAIL_MATRIX_TYPE_SQUARE ? _s1Len : matrix->length;
    n = matrix->size; /* number of amino acids in table */
    segLen = (s1Len + segWidth - 1) / segWidth;
    vProfile = parasail_memalign___m256i(32, n * segLen);
    if (!vProfile) return NULL;
    vProfileM = parasail_memalign___m256i(32, n * segLen);
    if (!vProfileM) return NULL;
    vProfileS = parasail_memalign___m256i(32, n * segLen);
    if (!vProfileS) return NULL;
    profile = parasail_profile_new(s1, s1Len, matrix);
    if (!profile) return NULL;

    for (k=0; k<n; ++k) {
        for (i=0; i<segLen; ++i) {
            __m256i_64_t p;
            __m256i_64_t m;
            __m256i_64_t s;
            j = i;
            for (segNum=0; segNum<segWidth; ++segNum) {
                if (matrix->type == PARASAIL_MATRIX_TYPE_SQUARE) {
                    p.v[segNum] = j >= s1Len ? 0 : matrix->matrix[n*k+matrix->mapper[(unsigned char)s1[j]]];
                }
                else {
                    p.v[segNum] = j >= s1Len ? 0 : matrix->matrix[n*j+matrix->mapper[(unsigned char)matrix->alphabet[k]]];
                }
                m.v[segNum] = j >= s1Len ? 0 : (k == matrix->mapper[(unsigned char)s1[j]]);
                s.v[segNum] = p.v[segNum] > 0;
                j += segLen;
            }
            _mm256_store_si256(&vProfile[index], p.m);
            _mm256_store_si256(&vProfileM[index], m.m);
            _mm256_store_si256(&vProfileS[index], s.m);
            ++index;
        }
    }

    profile->profile64.score = vProfile;
    profile->profile64.matches = vProfileM;
    profile->profile64.similar = vProfileS;
    profile->free = &parasail_free___m256i;
    return profile;
}

parasail_profile_t* parasail_profile_create_stats_avx_256_sat(
        const char * const restrict s1, const int s1Len,
        const parasail_matrix_t *matrix)
{
    parasail_profile_t *profile8 = parasail_profile_create_stats_avx_256_8(s1, s1Len, matrix);
    parasail_profile_t *profile16 = parasail_profile_create_stats_avx_256_16(s1, s1Len, matrix);
    parasail_profile_t *profile32 = parasail_profile_create_stats_avx_256_32(s1, s1Len, matrix);
    profile8->profile16 = profile16->profile16;
    profile8->profile32 = profile32->profile32;
    free(profile16);
    free(profile32);

    return profile8;
}

void parasail_free___m256i(void *ptr)
{
    parasail_free((__m256i*)ptr);
}