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libsais.c
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/*--
This file is a part of libsais, a library for linear time suffix array,
longest common prefix array and burrows wheeler transform construction.
Copyright (c) 2021-2022 Ilya Grebnov <[email protected]>
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
Please see the file LICENSE for full copyright information.
--*/
#include "libsais.h"
#include <stddef.h>
#include <stdint.h>
#include <stdlib.h>
#include <string.h>
#include <limits.h>
#if defined(LIBSAIS_OPENMP)
#include <omp.h>
#else
#define UNUSED(_x) (void)(_x)
#endif
typedef int32_t sa_sint_t;
typedef uint32_t sa_uint_t;
typedef ptrdiff_t fast_sint_t;
typedef size_t fast_uint_t;
#define SAINT_BIT (32)
#define SAINT_MAX INT32_MAX
#define SAINT_MIN INT32_MIN
#define ALPHABET_SIZE (1 << CHAR_BIT)
#define UNBWT_FASTBITS (17)
#define SUFFIX_GROUP_BIT (SAINT_BIT - 1)
#define SUFFIX_GROUP_MARKER (((sa_sint_t)1) << (SUFFIX_GROUP_BIT - 1))
#define BUCKETS_INDEX2(_c, _s) (((_c) << 1) + (_s))
#define BUCKETS_INDEX4(_c, _s) (((_c) << 2) + (_s))
#define LIBSAIS_PER_THREAD_CACHE_SIZE (24576)
typedef struct LIBSAIS_THREAD_CACHE
{
sa_sint_t symbol;
sa_sint_t index;
} LIBSAIS_THREAD_CACHE;
typedef union LIBSAIS_THREAD_STATE
{
struct
{
fast_sint_t position;
fast_sint_t count;
fast_sint_t m;
fast_sint_t last_lms_suffix;
sa_sint_t * buckets;
LIBSAIS_THREAD_CACHE * cache;
} state;
uint8_t padding[64];
} LIBSAIS_THREAD_STATE;
typedef struct LIBSAIS_CONTEXT
{
sa_sint_t * buckets;
LIBSAIS_THREAD_STATE * thread_state;
fast_sint_t threads;
} LIBSAIS_CONTEXT;
typedef struct LIBSAIS_UNBWT_CONTEXT
{
sa_uint_t * bucket2;
uint16_t * fastbits;
sa_uint_t * buckets;
fast_sint_t threads;
} LIBSAIS_UNBWT_CONTEXT;
#if defined(__GNUC__) || defined(__clang__)
#define RESTRICT __restrict__
#elif defined(_MSC_VER) || defined(__INTEL_COMPILER)
#define RESTRICT __restrict
#else
#error Your compiler, configuration or platform is not supported.
#endif
#if defined(__has_builtin)
#if __has_builtin(__builtin_prefetch)
#define HAS_BUILTIN_PREFETCH
#endif
#elif defined(__GNUC__) && (((__GNUC__ == 3) && (__GNUC_MINOR__ >= 2)) || (__GNUC__ >= 4))
#define HAS_BUILTIN_PREFETCH
#endif
#if defined(__has_builtin)
#if __has_builtin(__builtin_bswap16)
#define HAS_BUILTIN_BSWAP16
#endif
#elif defined(__GNUC__) && (((__GNUC__ == 4) && (__GNUC_MINOR__ >= 8)) || (__GNUC__ >= 5))
#define HAS_BUILTIN_BSWAP16
#endif
#if defined(HAS_BUILTIN_PREFETCH)
#define libsais_prefetchr(address) __builtin_prefetch((const void *)(address), 0, 3)
#define libsais_prefetchw(address) __builtin_prefetch((const void *)(address), 1, 3)
#elif defined (_M_IX86) || defined (_M_AMD64)
#include <intrin.h>
#define libsais_prefetchr(address) _mm_prefetch((const void *)(address), _MM_HINT_T0)
#define libsais_prefetchw(address) _m_prefetchw((const void *)(address))
#elif defined (_M_ARM)
#include <intrin.h>
#define libsais_prefetchr(address) __prefetch((const void *)(address))
#define libsais_prefetchw(address) __prefetchw((const void *)(address))
#elif defined (_M_ARM64)
#include <intrin.h>
#define libsais_prefetchr(address) __prefetch2((const void *)(address), 0)
#define libsais_prefetchw(address) __prefetch2((const void *)(address), 16)
#else
#error Your compiler, configuration or platform is not supported.
#endif
#if !defined(__LITTLE_ENDIAN__) && !defined(__BIG_ENDIAN__)
#if defined(_LITTLE_ENDIAN) \
|| (defined(BYTE_ORDER) && defined(LITTLE_ENDIAN) && BYTE_ORDER == LITTLE_ENDIAN) \
|| (defined(_BYTE_ORDER) && defined(_LITTLE_ENDIAN) && _BYTE_ORDER == _LITTLE_ENDIAN) \
|| (defined(__BYTE_ORDER) && defined(__LITTLE_ENDIAN) && __BYTE_ORDER == __LITTLE_ENDIAN) \
|| (defined(__BYTE_ORDER__) && defined(__ORDER_LITTLE_ENDIAN__) && __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__)
#define __LITTLE_ENDIAN__
#elif defined(_BIG_ENDIAN) \
|| (defined(BYTE_ORDER) && defined(BIG_ENDIAN) && BYTE_ORDER == BIG_ENDIAN) \
|| (defined(_BYTE_ORDER) && defined(_BIG_ENDIAN) && _BYTE_ORDER == _BIG_ENDIAN) \
|| (defined(__BYTE_ORDER) && defined(__BIG_ENDIAN) && __BYTE_ORDER == __BIG_ENDIAN) \
|| (defined(__BYTE_ORDER__) && defined(__ORDER_BIG_ENDIAN__) && __BYTE_ORDER__ == __ORDER_BIG_ENDIAN__)
#define __BIG_ENDIAN__
#elif defined(_WIN32)
#define __LITTLE_ENDIAN__
#endif
#endif
#if defined(__LITTLE_ENDIAN__) && !defined(__BIG_ENDIAN__)
#if defined(HAS_BUILTIN_BSWAP16)
#define libsais_bswap16(x) (__builtin_bswap16(x))
#elif defined(_MSC_VER) && !defined(__INTEL_COMPILER)
#define libsais_bswap16(x) (_byteswap_ushort(x))
#else
#define libsais_bswap16(x) ((uint16_t)(x >> 8) | (uint16_t)(x << 8))
#endif
#elif !defined(__LITTLE_ENDIAN__) && defined(__BIG_ENDIAN__)
#define libsais_bswap16(x) (x)
#else
#error Your compiler, configuration or platform is not supported.
#endif
static void * libsais_align_up(const void * address, size_t alignment)
{
return (void *)((((ptrdiff_t)address) + ((ptrdiff_t)alignment) - 1) & (-((ptrdiff_t)alignment)));
}
static void * libsais_alloc_aligned(size_t size, size_t alignment)
{
void * address = malloc(size + sizeof(short) + alignment - 1);
if (address != NULL)
{
void * aligned_address = libsais_align_up((void *)((ptrdiff_t)address + (ptrdiff_t)(sizeof(short))), alignment);
((short *)aligned_address)[-1] = (short)((ptrdiff_t)aligned_address - (ptrdiff_t)address);
return aligned_address;
}
return NULL;
}
static void libsais_free_aligned(void * aligned_address)
{
if (aligned_address != NULL)
{
free((void *)((ptrdiff_t)aligned_address - ((short *)aligned_address)[-1]));
}
}
static LIBSAIS_THREAD_STATE * libsais_alloc_thread_state(sa_sint_t threads)
{
LIBSAIS_THREAD_STATE * RESTRICT thread_state = (LIBSAIS_THREAD_STATE *)libsais_alloc_aligned((size_t)threads * sizeof(LIBSAIS_THREAD_STATE), 4096);
sa_sint_t * RESTRICT thread_buckets = (sa_sint_t *)libsais_alloc_aligned((size_t)threads * 4 * ALPHABET_SIZE * sizeof(sa_sint_t), 4096);
LIBSAIS_THREAD_CACHE * RESTRICT thread_cache = (LIBSAIS_THREAD_CACHE *)libsais_alloc_aligned((size_t)threads * LIBSAIS_PER_THREAD_CACHE_SIZE * sizeof(LIBSAIS_THREAD_CACHE), 4096);
if (thread_state != NULL && thread_buckets != NULL && thread_cache != NULL)
{
fast_sint_t t;
for (t = 0; t < threads; ++t)
{
thread_state[t].state.buckets = thread_buckets; thread_buckets += 4 * ALPHABET_SIZE;
thread_state[t].state.cache = thread_cache; thread_cache += LIBSAIS_PER_THREAD_CACHE_SIZE;
}
return thread_state;
}
libsais_free_aligned(thread_cache);
libsais_free_aligned(thread_buckets);
libsais_free_aligned(thread_state);
return NULL;
}
static void libsais_free_thread_state(LIBSAIS_THREAD_STATE * thread_state)
{
if (thread_state != NULL)
{
libsais_free_aligned(thread_state[0].state.cache);
libsais_free_aligned(thread_state[0].state.buckets);
libsais_free_aligned(thread_state);
}
}
static LIBSAIS_CONTEXT * libsais_create_ctx_main(sa_sint_t threads)
{
LIBSAIS_CONTEXT * RESTRICT ctx = (LIBSAIS_CONTEXT *)libsais_alloc_aligned(sizeof(LIBSAIS_CONTEXT), 64);
sa_sint_t * RESTRICT buckets = (sa_sint_t *)libsais_alloc_aligned(8 * ALPHABET_SIZE * sizeof(sa_sint_t), 4096);
LIBSAIS_THREAD_STATE * RESTRICT thread_state = threads > 1 ? libsais_alloc_thread_state(threads) : NULL;
if (ctx != NULL && buckets != NULL && (thread_state != NULL || threads == 1))
{
ctx->buckets = buckets;
ctx->threads = threads;
ctx->thread_state = thread_state;
return ctx;
}
libsais_free_thread_state(thread_state);
libsais_free_aligned(buckets);
libsais_free_aligned(ctx);
return NULL;
}
static void libsais_free_ctx_main(LIBSAIS_CONTEXT * ctx)
{
if (ctx != NULL)
{
libsais_free_thread_state(ctx->thread_state);
libsais_free_aligned(ctx->buckets);
libsais_free_aligned(ctx);
}
}
#if defined(LIBSAIS_OPENMP)
static sa_sint_t libsais_count_negative_marked_suffixes(sa_sint_t * RESTRICT SA, fast_sint_t omp_block_start, fast_sint_t omp_block_size)
{
sa_sint_t count = 0;
fast_sint_t i; for (i = omp_block_start; i < omp_block_start + omp_block_size; ++i) { count += (SA[i] < 0); }
return count;
}
static sa_sint_t libsais_count_zero_marked_suffixes(sa_sint_t * RESTRICT SA, fast_sint_t omp_block_start, fast_sint_t omp_block_size)
{
sa_sint_t count = 0;
fast_sint_t i; for (i = omp_block_start; i < omp_block_start + omp_block_size; ++i) { count += (SA[i] == 0); }
return count;
}
static void libsais_place_cached_suffixes(sa_sint_t * RESTRICT SA, LIBSAIS_THREAD_CACHE * RESTRICT cache, fast_sint_t omp_block_start, fast_sint_t omp_block_size)
{
const fast_sint_t prefetch_distance = 32;
fast_sint_t i, j;
for (i = omp_block_start, j = omp_block_start + omp_block_size - prefetch_distance - 3; i < j; i += 4)
{
libsais_prefetchr(&cache[i + 2 * prefetch_distance]);
libsais_prefetchw(&SA[cache[i + prefetch_distance + 0].symbol]);
libsais_prefetchw(&SA[cache[i + prefetch_distance + 1].symbol]);
libsais_prefetchw(&SA[cache[i + prefetch_distance + 2].symbol]);
libsais_prefetchw(&SA[cache[i + prefetch_distance + 3].symbol]);
SA[cache[i + 0].symbol] = cache[i + 0].index;
SA[cache[i + 1].symbol] = cache[i + 1].index;
SA[cache[i + 2].symbol] = cache[i + 2].index;
SA[cache[i + 3].symbol] = cache[i + 3].index;
}
for (j += prefetch_distance + 3; i < j; i += 1)
{
SA[cache[i].symbol] = cache[i].index;
}
}
static void libsais_compact_and_place_cached_suffixes(sa_sint_t * RESTRICT SA, LIBSAIS_THREAD_CACHE * RESTRICT cache, fast_sint_t omp_block_start, fast_sint_t omp_block_size)
{
const fast_sint_t prefetch_distance = 32;
fast_sint_t i, j, l;
for (i = omp_block_start, j = omp_block_start + omp_block_size - 3, l = omp_block_start; i < j; i += 4)
{
libsais_prefetchw(&cache[i + prefetch_distance]);
cache[l] = cache[i + 0]; l += cache[l].symbol >= 0;
cache[l] = cache[i + 1]; l += cache[l].symbol >= 0;
cache[l] = cache[i + 2]; l += cache[l].symbol >= 0;
cache[l] = cache[i + 3]; l += cache[l].symbol >= 0;
}
for (j += 3; i < j; i += 1)
{
cache[l] = cache[i]; l += cache[l].symbol >= 0;
}
libsais_place_cached_suffixes(SA, cache, omp_block_start, l - omp_block_start);
}
static void libsais_accumulate_counts_s32_2(sa_sint_t * RESTRICT bucket00, fast_sint_t bucket_size, fast_sint_t bucket_stride)
{
sa_sint_t * RESTRICT bucket01 = bucket00 - bucket_stride;
fast_sint_t s; for (s = 0; s < bucket_size; s += 1) { bucket00[s] = bucket00[s] + bucket01[s]; }
}
static void libsais_accumulate_counts_s32_3(sa_sint_t * RESTRICT bucket00, fast_sint_t bucket_size, fast_sint_t bucket_stride)
{
sa_sint_t * RESTRICT bucket01 = bucket00 - bucket_stride;
sa_sint_t * RESTRICT bucket02 = bucket01 - bucket_stride;
fast_sint_t s; for (s = 0; s < bucket_size; s += 1) { bucket00[s] = bucket00[s] + bucket01[s] + bucket02[s]; }
}
static void libsais_accumulate_counts_s32_4(sa_sint_t * RESTRICT bucket00, fast_sint_t bucket_size, fast_sint_t bucket_stride)
{
sa_sint_t * RESTRICT bucket01 = bucket00 - bucket_stride;
sa_sint_t * RESTRICT bucket02 = bucket01 - bucket_stride;
sa_sint_t * RESTRICT bucket03 = bucket02 - bucket_stride;
fast_sint_t s; for (s = 0; s < bucket_size; s += 1) { bucket00[s] = bucket00[s] + bucket01[s] + bucket02[s] + bucket03[s]; }
}
static void libsais_accumulate_counts_s32_5(sa_sint_t * RESTRICT bucket00, fast_sint_t bucket_size, fast_sint_t bucket_stride)
{
sa_sint_t * RESTRICT bucket01 = bucket00 - bucket_stride;
sa_sint_t * RESTRICT bucket02 = bucket01 - bucket_stride;
sa_sint_t * RESTRICT bucket03 = bucket02 - bucket_stride;
sa_sint_t * RESTRICT bucket04 = bucket03 - bucket_stride;
fast_sint_t s; for (s = 0; s < bucket_size; s += 1) { bucket00[s] = bucket00[s] + bucket01[s] + bucket02[s] + bucket03[s] + bucket04[s]; }
}
static void libsais_accumulate_counts_s32_6(sa_sint_t * RESTRICT bucket00, fast_sint_t bucket_size, fast_sint_t bucket_stride)
{
sa_sint_t * RESTRICT bucket01 = bucket00 - bucket_stride;
sa_sint_t * RESTRICT bucket02 = bucket01 - bucket_stride;
sa_sint_t * RESTRICT bucket03 = bucket02 - bucket_stride;
sa_sint_t * RESTRICT bucket04 = bucket03 - bucket_stride;
sa_sint_t * RESTRICT bucket05 = bucket04 - bucket_stride;
fast_sint_t s; for (s = 0; s < bucket_size; s += 1) { bucket00[s] = bucket00[s] + bucket01[s] + bucket02[s] + bucket03[s] + bucket04[s] + bucket05[s]; }
}
static void libsais_accumulate_counts_s32_7(sa_sint_t * RESTRICT bucket00, fast_sint_t bucket_size, fast_sint_t bucket_stride)
{
sa_sint_t * RESTRICT bucket01 = bucket00 - bucket_stride;
sa_sint_t * RESTRICT bucket02 = bucket01 - bucket_stride;
sa_sint_t * RESTRICT bucket03 = bucket02 - bucket_stride;
sa_sint_t * RESTRICT bucket04 = bucket03 - bucket_stride;
sa_sint_t * RESTRICT bucket05 = bucket04 - bucket_stride;
sa_sint_t * RESTRICT bucket06 = bucket05 - bucket_stride;
fast_sint_t s; for (s = 0; s < bucket_size; s += 1) { bucket00[s] = bucket00[s] + bucket01[s] + bucket02[s] + bucket03[s] + bucket04[s] + bucket05[s] + bucket06[s]; }
}
static void libsais_accumulate_counts_s32_8(sa_sint_t * RESTRICT bucket00, fast_sint_t bucket_size, fast_sint_t bucket_stride)
{
sa_sint_t * RESTRICT bucket01 = bucket00 - bucket_stride;
sa_sint_t * RESTRICT bucket02 = bucket01 - bucket_stride;
sa_sint_t * RESTRICT bucket03 = bucket02 - bucket_stride;
sa_sint_t * RESTRICT bucket04 = bucket03 - bucket_stride;
sa_sint_t * RESTRICT bucket05 = bucket04 - bucket_stride;
sa_sint_t * RESTRICT bucket06 = bucket05 - bucket_stride;
sa_sint_t * RESTRICT bucket07 = bucket06 - bucket_stride;
fast_sint_t s; for (s = 0; s < bucket_size; s += 1) { bucket00[s] = bucket00[s] + bucket01[s] + bucket02[s] + bucket03[s] + bucket04[s] + bucket05[s] + bucket06[s] + bucket07[s]; }
}
static void libsais_accumulate_counts_s32_9(sa_sint_t * RESTRICT bucket00, fast_sint_t bucket_size, fast_sint_t bucket_stride)
{
sa_sint_t * RESTRICT bucket01 = bucket00 - bucket_stride;
sa_sint_t * RESTRICT bucket02 = bucket01 - bucket_stride;
sa_sint_t * RESTRICT bucket03 = bucket02 - bucket_stride;
sa_sint_t * RESTRICT bucket04 = bucket03 - bucket_stride;
sa_sint_t * RESTRICT bucket05 = bucket04 - bucket_stride;
sa_sint_t * RESTRICT bucket06 = bucket05 - bucket_stride;
sa_sint_t * RESTRICT bucket07 = bucket06 - bucket_stride;
sa_sint_t * RESTRICT bucket08 = bucket07 - bucket_stride;
fast_sint_t s; for (s = 0; s < bucket_size; s += 1) { bucket00[s] = bucket00[s] + bucket01[s] + bucket02[s] + bucket03[s] + bucket04[s] + bucket05[s] + bucket06[s] + bucket07[s] + bucket08[s]; }
}
static void libsais_accumulate_counts_s32(sa_sint_t * RESTRICT buckets, fast_sint_t bucket_size, fast_sint_t bucket_stride, fast_sint_t num_buckets)
{
while (num_buckets >= 9)
{
libsais_accumulate_counts_s32_9(buckets - (num_buckets - 9) * bucket_stride, bucket_size, bucket_stride); num_buckets -= 8;
}
switch (num_buckets)
{
case 1: break;
case 2: libsais_accumulate_counts_s32_2(buckets, bucket_size, bucket_stride); break;
case 3: libsais_accumulate_counts_s32_3(buckets, bucket_size, bucket_stride); break;
case 4: libsais_accumulate_counts_s32_4(buckets, bucket_size, bucket_stride); break;
case 5: libsais_accumulate_counts_s32_5(buckets, bucket_size, bucket_stride); break;
case 6: libsais_accumulate_counts_s32_6(buckets, bucket_size, bucket_stride); break;
case 7: libsais_accumulate_counts_s32_7(buckets, bucket_size, bucket_stride); break;
case 8: libsais_accumulate_counts_s32_8(buckets, bucket_size, bucket_stride); break;
}
}
#endif
static void libsais_gather_lms_suffixes_8u(const uint8_t * RESTRICT T, sa_sint_t * RESTRICT SA, sa_sint_t n, fast_sint_t m, fast_sint_t omp_block_start, fast_sint_t omp_block_size)
{
if (omp_block_size > 0)
{
const fast_sint_t prefetch_distance = 128;
fast_sint_t i, j = omp_block_start + omp_block_size, c0 = T[omp_block_start + omp_block_size - 1], c1 = -1;
while (j < n && (c1 = T[j]) == c0) { ++j; }
fast_uint_t s = c0 >= c1;
for (i = omp_block_start + omp_block_size - 2, j = omp_block_start + 3; i >= j; i -= 4)
{
libsais_prefetchr(&T[i - prefetch_distance]);
c1 = T[i - 0]; s = (s << 1) + (fast_uint_t)(c1 > (c0 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i + 1); m -= ((s & 3) == 1);
c0 = T[i - 1]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i - 0); m -= ((s & 3) == 1);
c1 = T[i - 2]; s = (s << 1) + (fast_uint_t)(c1 > (c0 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i - 1); m -= ((s & 3) == 1);
c0 = T[i - 3]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i - 2); m -= ((s & 3) == 1);
}
for (j -= 3; i >= j; i -= 1)
{
c1 = c0; c0 = T[i]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i + 1); m -= ((s & 3) == 1);
}
SA[m] = (sa_sint_t)(i + 1);
}
}
static void libsais_gather_lms_suffixes_8u_omp(const uint8_t * RESTRICT T, sa_sint_t * RESTRICT SA, sa_sint_t n, sa_sint_t threads, LIBSAIS_THREAD_STATE * RESTRICT thread_state)
{
#if defined(LIBSAIS_OPENMP)
#pragma omp parallel num_threads(threads) if(threads > 1 && n >= 65536 && omp_get_dynamic() == 0)
#endif
{
#if defined(LIBSAIS_OPENMP)
fast_sint_t omp_thread_num = omp_get_thread_num();
fast_sint_t omp_num_threads = omp_get_num_threads();
#else
UNUSED(threads); UNUSED(thread_state);
fast_sint_t omp_thread_num = 0;
fast_sint_t omp_num_threads = 1;
#endif
fast_sint_t omp_block_stride = (n / omp_num_threads) & (-16);
fast_sint_t omp_block_start = omp_thread_num * omp_block_stride;
fast_sint_t omp_block_size = omp_thread_num < omp_num_threads - 1 ? omp_block_stride : n - omp_block_start;
if (omp_num_threads == 1)
{
libsais_gather_lms_suffixes_8u(T, SA, n, (fast_sint_t)n - 1, omp_block_start, omp_block_size);
}
#if defined(LIBSAIS_OPENMP)
else
{
fast_sint_t t, m = 0; for (t = omp_num_threads - 1; t > omp_thread_num; --t) { m += thread_state[t].state.m; }
libsais_gather_lms_suffixes_8u(T, SA, n, (fast_sint_t)n - 1 - m, omp_block_start, omp_block_size);
#pragma omp barrier
if (thread_state[omp_thread_num].state.m > 0)
{
SA[(fast_sint_t)n - 1 - m] = (sa_sint_t)thread_state[omp_thread_num].state.last_lms_suffix;
}
}
#endif
}
}
static sa_sint_t libsais_gather_lms_suffixes_32s(const sa_sint_t * RESTRICT T, sa_sint_t * RESTRICT SA, sa_sint_t n)
{
const fast_sint_t prefetch_distance = 32;
sa_sint_t i = n - 2;
sa_sint_t m = n - 1;
fast_uint_t s = 1;
fast_sint_t c0 = T[n - 1];
fast_sint_t c1 = 0;
for (; i >= 3; i -= 4)
{
libsais_prefetchr(&T[i - prefetch_distance]);
c1 = T[i - 0]; s = (s << 1) + (fast_uint_t)(c1 > (c0 - (fast_sint_t)(s & 1))); SA[m] = i + 1; m -= ((s & 3) == 1);
c0 = T[i - 1]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1))); SA[m] = i - 0; m -= ((s & 3) == 1);
c1 = T[i - 2]; s = (s << 1) + (fast_uint_t)(c1 > (c0 - (fast_sint_t)(s & 1))); SA[m] = i - 1; m -= ((s & 3) == 1);
c0 = T[i - 3]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1))); SA[m] = i - 2; m -= ((s & 3) == 1);
}
for (; i >= 0; i -= 1)
{
c1 = c0; c0 = T[i]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1))); SA[m] = i + 1; m -= ((s & 3) == 1);
}
return n - 1 - m;
}
static sa_sint_t libsais_gather_compacted_lms_suffixes_32s(const sa_sint_t * RESTRICT T, sa_sint_t * RESTRICT SA, sa_sint_t n)
{
const fast_sint_t prefetch_distance = 32;
sa_sint_t i = n - 2;
sa_sint_t m = n - 1;
fast_uint_t s = 1;
fast_sint_t c0 = T[n - 1];
fast_sint_t c1 = 0;
for (; i >= 3; i -= 4)
{
libsais_prefetchr(&T[i - prefetch_distance]);
c1 = T[i - 0]; s = (s << 1) + (fast_uint_t)(c1 > (c0 - (fast_sint_t)(s & 1))); SA[m] = i + 1; m -= ((fast_sint_t)(s & 3) == (c0 >= 0));
c0 = T[i - 1]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1))); SA[m] = i - 0; m -= ((fast_sint_t)(s & 3) == (c1 >= 0));
c1 = T[i - 2]; s = (s << 1) + (fast_uint_t)(c1 > (c0 - (fast_sint_t)(s & 1))); SA[m] = i - 1; m -= ((fast_sint_t)(s & 3) == (c0 >= 0));
c0 = T[i - 3]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1))); SA[m] = i - 2; m -= ((fast_sint_t)(s & 3) == (c1 >= 0));
}
for (; i >= 0; i -= 1)
{
c1 = c0; c0 = T[i]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1))); SA[m] = i + 1; m -= ((fast_sint_t)(s & 3) == (c1 >= 0));
}
return n - 1 - m;
}
#if defined(LIBSAIS_OPENMP)
static void libsais_count_lms_suffixes_32s_4k(const sa_sint_t * RESTRICT T, sa_sint_t n, sa_sint_t k, sa_sint_t * RESTRICT buckets)
{
const fast_sint_t prefetch_distance = 32;
memset(buckets, 0, 4 * (size_t)k * sizeof(sa_sint_t));
sa_sint_t i = n - 2;
fast_uint_t s = 1;
fast_sint_t c0 = T[n - 1];
fast_sint_t c1 = 0;
for (; i >= prefetch_distance + 3; i -= 4)
{
libsais_prefetchr(&T[i - 2 * prefetch_distance]);
libsais_prefetchw(&buckets[BUCKETS_INDEX4(T[i - prefetch_distance - 0], 0)]);
libsais_prefetchw(&buckets[BUCKETS_INDEX4(T[i - prefetch_distance - 1], 0)]);
libsais_prefetchw(&buckets[BUCKETS_INDEX4(T[i - prefetch_distance - 2], 0)]);
libsais_prefetchw(&buckets[BUCKETS_INDEX4(T[i - prefetch_distance - 3], 0)]);
c1 = T[i - 0]; s = (s << 1) + (fast_uint_t)(c1 > (c0 - (fast_sint_t)(s & 1)));
buckets[BUCKETS_INDEX4((fast_uint_t)c0, s & 3)]++;
c0 = T[i - 1]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1)));
buckets[BUCKETS_INDEX4((fast_uint_t)c1, s & 3)]++;
c1 = T[i - 2]; s = (s << 1) + (fast_uint_t)(c1 > (c0 - (fast_sint_t)(s & 1)));
buckets[BUCKETS_INDEX4((fast_uint_t)c0, s & 3)]++;
c0 = T[i - 3]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1)));
buckets[BUCKETS_INDEX4((fast_uint_t)c1, s & 3)]++;
}
for (; i >= 0; i -= 1)
{
c1 = c0; c0 = T[i]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1)));
buckets[BUCKETS_INDEX4((fast_uint_t)c1, s & 3)]++;
}
buckets[BUCKETS_INDEX4((fast_uint_t)c0, (s << 1) & 3)]++;
}
#endif
static void libsais_count_lms_suffixes_32s_2k(const sa_sint_t * RESTRICT T, sa_sint_t n, sa_sint_t k, sa_sint_t * RESTRICT buckets)
{
const fast_sint_t prefetch_distance = 32;
memset(buckets, 0, 2 * (size_t)k * sizeof(sa_sint_t));
sa_sint_t i = n - 2;
fast_uint_t s = 1;
fast_sint_t c0 = T[n - 1];
fast_sint_t c1 = 0;
for (; i >= prefetch_distance + 3; i -= 4)
{
libsais_prefetchr(&T[i - 2 * prefetch_distance]);
libsais_prefetchw(&buckets[BUCKETS_INDEX2(T[i - prefetch_distance - 0], 0)]);
libsais_prefetchw(&buckets[BUCKETS_INDEX2(T[i - prefetch_distance - 1], 0)]);
libsais_prefetchw(&buckets[BUCKETS_INDEX2(T[i - prefetch_distance - 2], 0)]);
libsais_prefetchw(&buckets[BUCKETS_INDEX2(T[i - prefetch_distance - 3], 0)]);
c1 = T[i - 0]; s = (s << 1) + (fast_uint_t)(c1 > (c0 - (fast_sint_t)(s & 1)));
buckets[BUCKETS_INDEX2((fast_uint_t)c0, (s & 3) == 1)]++;
c0 = T[i - 1]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1)));
buckets[BUCKETS_INDEX2((fast_uint_t)c1, (s & 3) == 1)]++;
c1 = T[i - 2]; s = (s << 1) + (fast_uint_t)(c1 > (c0 - (fast_sint_t)(s & 1)));
buckets[BUCKETS_INDEX2((fast_uint_t)c0, (s & 3) == 1)]++;
c0 = T[i - 3]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1)));
buckets[BUCKETS_INDEX2((fast_uint_t)c1, (s & 3) == 1)]++;
}
for (; i >= 0; i -= 1)
{
c1 = c0; c0 = T[i]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1)));
buckets[BUCKETS_INDEX2((fast_uint_t)c1, (s & 3) == 1)]++;
}
buckets[BUCKETS_INDEX2((fast_uint_t)c0, 0)]++;
}
#if defined(LIBSAIS_OPENMP)
static void libsais_count_compacted_lms_suffixes_32s_2k(const sa_sint_t * RESTRICT T, sa_sint_t n, sa_sint_t k, sa_sint_t * RESTRICT buckets)
{
const fast_sint_t prefetch_distance = 32;
memset(buckets, 0, 2 * (size_t)k * sizeof(sa_sint_t));
sa_sint_t i = n - 2;
fast_uint_t s = 1;
fast_sint_t c0 = T[n - 1];
fast_sint_t c1 = 0;
for (; i >= prefetch_distance + 3; i -= 4)
{
libsais_prefetchr(&T[i - 2 * prefetch_distance]);
libsais_prefetchw(&buckets[BUCKETS_INDEX2(T[i - prefetch_distance - 0] & SAINT_MAX, 0)]);
libsais_prefetchw(&buckets[BUCKETS_INDEX2(T[i - prefetch_distance - 1] & SAINT_MAX, 0)]);
libsais_prefetchw(&buckets[BUCKETS_INDEX2(T[i - prefetch_distance - 2] & SAINT_MAX, 0)]);
libsais_prefetchw(&buckets[BUCKETS_INDEX2(T[i - prefetch_distance - 3] & SAINT_MAX, 0)]);
c1 = T[i - 0]; s = (s << 1) + (fast_uint_t)(c1 > (c0 - (fast_sint_t)(s & 1)));
c0 &= SAINT_MAX; buckets[BUCKETS_INDEX2((fast_uint_t)c0, (s & 3) == 1)]++;
c0 = T[i - 1]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1)));
c1 &= SAINT_MAX; buckets[BUCKETS_INDEX2((fast_uint_t)c1, (s & 3) == 1)]++;
c1 = T[i - 2]; s = (s << 1) + (fast_uint_t)(c1 > (c0 - (fast_sint_t)(s & 1)));
c0 &= SAINT_MAX; buckets[BUCKETS_INDEX2((fast_uint_t)c0, (s & 3) == 1)]++;
c0 = T[i - 3]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1)));
c1 &= SAINT_MAX; buckets[BUCKETS_INDEX2((fast_uint_t)c1, (s & 3) == 1)]++;
}
for (; i >= 0; i -= 1)
{
c1 = c0; c0 = T[i]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1)));
c1 &= SAINT_MAX; buckets[BUCKETS_INDEX2((fast_uint_t)c1, (s & 3) == 1)]++;
}
c0 &= SAINT_MAX; buckets[BUCKETS_INDEX2((fast_uint_t)c0, 0)]++;
}
#endif
static sa_sint_t libsais_count_and_gather_lms_suffixes_8u(const uint8_t * RESTRICT T, sa_sint_t * RESTRICT SA, sa_sint_t n, sa_sint_t * RESTRICT buckets, fast_sint_t omp_block_start, fast_sint_t omp_block_size)
{
memset(buckets, 0, 4 * ALPHABET_SIZE * sizeof(sa_sint_t));
fast_sint_t m = omp_block_start + omp_block_size - 1;
if (omp_block_size > 0)
{
const fast_sint_t prefetch_distance = 128;
fast_sint_t i, j = m + 1, c0 = T[m], c1 = -1;
while (j < n && (c1 = T[j]) == c0) { ++j; }
fast_uint_t s = c0 >= c1;
for (i = m - 1, j = omp_block_start + 3; i >= j; i -= 4)
{
libsais_prefetchr(&T[i - prefetch_distance]);
c1 = T[i - 0]; s = (s << 1) + (fast_uint_t)(c1 > (c0 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i + 1); m -= ((s & 3) == 1);
buckets[BUCKETS_INDEX4((fast_uint_t)c0, s & 3)]++;
c0 = T[i - 1]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i - 0); m -= ((s & 3) == 1);
buckets[BUCKETS_INDEX4((fast_uint_t)c1, s & 3)]++;
c1 = T[i - 2]; s = (s << 1) + (fast_uint_t)(c1 > (c0 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i - 1); m -= ((s & 3) == 1);
buckets[BUCKETS_INDEX4((fast_uint_t)c0, s & 3)]++;
c0 = T[i - 3]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i - 2); m -= ((s & 3) == 1);
buckets[BUCKETS_INDEX4((fast_uint_t)c1, s & 3)]++;
}
for (j -= 3; i >= j; i -= 1)
{
c1 = c0; c0 = T[i]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i + 1); m -= ((s & 3) == 1);
buckets[BUCKETS_INDEX4((fast_uint_t)c1, s & 3)]++;
}
c1 = (i >= 0) ? T[i] : -1; s = (s << 1) + (fast_uint_t)(c1 > (c0 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i + 1); m -= ((s & 3) == 1);
buckets[BUCKETS_INDEX4((fast_uint_t)c0, s & 3)]++;
}
return (sa_sint_t)(omp_block_start + omp_block_size - 1 - m);
}
static sa_sint_t libsais_count_and_gather_lms_suffixes_8u_omp(const uint8_t * RESTRICT T, sa_sint_t * RESTRICT SA, sa_sint_t n, sa_sint_t * RESTRICT buckets, sa_sint_t threads, LIBSAIS_THREAD_STATE * RESTRICT thread_state)
{
sa_sint_t m = 0;
#if defined(LIBSAIS_OPENMP)
#pragma omp parallel num_threads(threads) if(threads > 1 && n >= 65536 && omp_get_dynamic() == 0)
#endif
{
#if defined(LIBSAIS_OPENMP)
fast_sint_t omp_thread_num = omp_get_thread_num();
fast_sint_t omp_num_threads = omp_get_num_threads();
#else
UNUSED(threads); UNUSED(thread_state);
fast_sint_t omp_thread_num = 0;
fast_sint_t omp_num_threads = 1;
#endif
fast_sint_t omp_block_stride = (n / omp_num_threads) & (-16);
fast_sint_t omp_block_start = omp_thread_num * omp_block_stride;
fast_sint_t omp_block_size = omp_thread_num < omp_num_threads - 1 ? omp_block_stride : n - omp_block_start;
if (omp_num_threads == 1)
{
m = libsais_count_and_gather_lms_suffixes_8u(T, SA, n, buckets, omp_block_start, omp_block_size);
}
#if defined(LIBSAIS_OPENMP)
else
{
{
thread_state[omp_thread_num].state.position = omp_block_start + omp_block_size;
thread_state[omp_thread_num].state.m = libsais_count_and_gather_lms_suffixes_8u(T, SA, n, thread_state[omp_thread_num].state.buckets, omp_block_start, omp_block_size);
if (thread_state[omp_thread_num].state.m > 0)
{
thread_state[omp_thread_num].state.last_lms_suffix = SA[thread_state[omp_thread_num].state.position - 1];
}
}
#pragma omp barrier
#pragma omp master
{
memset(buckets, 0, 4 * ALPHABET_SIZE * sizeof(sa_sint_t));
fast_sint_t t;
for (t = omp_num_threads - 1; t >= 0; --t)
{
m += (sa_sint_t)thread_state[t].state.m;
if (t != omp_num_threads - 1 && thread_state[t].state.m > 0)
{
memcpy(&SA[n - m], &SA[thread_state[t].state.position - thread_state[t].state.m], (size_t)thread_state[t].state.m * sizeof(sa_sint_t));
}
{
sa_sint_t * RESTRICT temp_bucket = thread_state[t].state.buckets;
fast_sint_t s; for (s = 0; s < 4 * ALPHABET_SIZE; s += 1) { sa_sint_t A = buckets[s], B = temp_bucket[s]; buckets[s] = A + B; temp_bucket[s] = A; }
}
}
}
}
#endif
}
return m;
}
static sa_sint_t libsais_count_and_gather_lms_suffixes_32s_4k(const sa_sint_t * RESTRICT T, sa_sint_t * RESTRICT SA, sa_sint_t n, sa_sint_t k, sa_sint_t * RESTRICT buckets, fast_sint_t omp_block_start, fast_sint_t omp_block_size)
{
memset(buckets, 0, 4 * (size_t)k * sizeof(sa_sint_t));
fast_sint_t m = omp_block_start + omp_block_size - 1;
if (omp_block_size > 0)
{
const fast_sint_t prefetch_distance = 32;
fast_sint_t i, j = m + 1, c0 = T[m], c1 = -1;
while (j < n && (c1 = T[j]) == c0) { ++j; }
fast_uint_t s = c0 >= c1;
for (i = m - 1, j = omp_block_start + prefetch_distance + 3; i >= j; i -= 4)
{
libsais_prefetchr(&T[i - 2 * prefetch_distance]);
libsais_prefetchw(&buckets[BUCKETS_INDEX4(T[i - prefetch_distance - 0], 0)]);
libsais_prefetchw(&buckets[BUCKETS_INDEX4(T[i - prefetch_distance - 1], 0)]);
libsais_prefetchw(&buckets[BUCKETS_INDEX4(T[i - prefetch_distance - 2], 0)]);
libsais_prefetchw(&buckets[BUCKETS_INDEX4(T[i - prefetch_distance - 3], 0)]);
c1 = T[i - 0]; s = (s << 1) + (fast_uint_t)(c1 > (c0 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i + 1); m -= ((s & 3) == 1);
buckets[BUCKETS_INDEX4((fast_uint_t)c0, s & 3)]++;
c0 = T[i - 1]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i - 0); m -= ((s & 3) == 1);
buckets[BUCKETS_INDEX4((fast_uint_t)c1, s & 3)]++;
c1 = T[i - 2]; s = (s << 1) + (fast_uint_t)(c1 > (c0 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i - 1); m -= ((s & 3) == 1);
buckets[BUCKETS_INDEX4((fast_uint_t)c0, s & 3)]++;
c0 = T[i - 3]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i - 2); m -= ((s & 3) == 1);
buckets[BUCKETS_INDEX4((fast_uint_t)c1, s & 3)]++;
}
for (j -= prefetch_distance + 3; i >= j; i -= 1)
{
c1 = c0; c0 = T[i]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i + 1); m -= ((s & 3) == 1);
buckets[BUCKETS_INDEX4((fast_uint_t)c1, s & 3)]++;
}
c1 = (i >= 0) ? T[i] : -1; s = (s << 1) + (fast_uint_t)(c1 > (c0 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i + 1); m -= ((s & 3) == 1);
buckets[BUCKETS_INDEX4((fast_uint_t)c0, s & 3)]++;
}
return (sa_sint_t)(omp_block_start + omp_block_size - 1 - m);
}
static sa_sint_t libsais_count_and_gather_lms_suffixes_32s_2k(const sa_sint_t * RESTRICT T, sa_sint_t * RESTRICT SA, sa_sint_t n, sa_sint_t k, sa_sint_t * RESTRICT buckets, fast_sint_t omp_block_start, fast_sint_t omp_block_size)
{
memset(buckets, 0, 2 * (size_t)k * sizeof(sa_sint_t));
fast_sint_t m = omp_block_start + omp_block_size - 1;
if (omp_block_size > 0)
{
const fast_sint_t prefetch_distance = 32;
fast_sint_t i, j = m + 1, c0 = T[m], c1 = -1;
while (j < n && (c1 = T[j]) == c0) { ++j; }
fast_uint_t s = c0 >= c1;
for (i = m - 1, j = omp_block_start + prefetch_distance + 3; i >= j; i -= 4)
{
libsais_prefetchr(&T[i - 2 * prefetch_distance]);
libsais_prefetchw(&buckets[BUCKETS_INDEX2(T[i - prefetch_distance - 0], 0)]);
libsais_prefetchw(&buckets[BUCKETS_INDEX2(T[i - prefetch_distance - 1], 0)]);
libsais_prefetchw(&buckets[BUCKETS_INDEX2(T[i - prefetch_distance - 2], 0)]);
libsais_prefetchw(&buckets[BUCKETS_INDEX2(T[i - prefetch_distance - 3], 0)]);
c1 = T[i - 0]; s = (s << 1) + (fast_uint_t)(c1 > (c0 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i + 1); m -= ((s & 3) == 1);
buckets[BUCKETS_INDEX2((fast_uint_t)c0, (s & 3) == 1)]++;
c0 = T[i - 1]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i - 0); m -= ((s & 3) == 1);
buckets[BUCKETS_INDEX2((fast_uint_t)c1, (s & 3) == 1)]++;
c1 = T[i - 2]; s = (s << 1) + (fast_uint_t)(c1 > (c0 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i - 1); m -= ((s & 3) == 1);
buckets[BUCKETS_INDEX2((fast_uint_t)c0, (s & 3) == 1)]++;
c0 = T[i - 3]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i - 2); m -= ((s & 3) == 1);
buckets[BUCKETS_INDEX2((fast_uint_t)c1, (s & 3) == 1)]++;
}
for (j -= prefetch_distance + 3; i >= j; i -= 1)
{
c1 = c0; c0 = T[i]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i + 1); m -= ((s & 3) == 1);
buckets[BUCKETS_INDEX2((fast_uint_t)c1, (s & 3) == 1)]++;
}
c1 = (i >= 0) ? T[i] : -1; s = (s << 1) + (fast_uint_t)(c1 > (c0 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i + 1); m -= ((s & 3) == 1);
buckets[BUCKETS_INDEX2((fast_uint_t)c0, (s & 3) == 1)]++;
}
return (sa_sint_t)(omp_block_start + omp_block_size - 1 - m);
}
static sa_sint_t libsais_count_and_gather_compacted_lms_suffixes_32s_2k(const sa_sint_t * RESTRICT T, sa_sint_t * RESTRICT SA, sa_sint_t n, sa_sint_t k, sa_sint_t * RESTRICT buckets, fast_sint_t omp_block_start, fast_sint_t omp_block_size)
{
memset(buckets, 0, 2 * (size_t)k * sizeof(sa_sint_t));
fast_sint_t m = omp_block_start + omp_block_size - 1;
if (omp_block_size > 0)
{
const fast_sint_t prefetch_distance = 32;
fast_sint_t i, j = m + 1, c0 = T[m], c1 = -1;
while (j < n && (c1 = T[j]) == c0) { ++j; }
fast_uint_t s = c0 >= c1;
for (i = m - 1, j = omp_block_start + prefetch_distance + 3; i >= j; i -= 4)
{
libsais_prefetchr(&T[i - 2 * prefetch_distance]);
libsais_prefetchw(&buckets[BUCKETS_INDEX2(T[i - prefetch_distance - 0] & SAINT_MAX, 0)]);
libsais_prefetchw(&buckets[BUCKETS_INDEX2(T[i - prefetch_distance - 1] & SAINT_MAX, 0)]);
libsais_prefetchw(&buckets[BUCKETS_INDEX2(T[i - prefetch_distance - 2] & SAINT_MAX, 0)]);
libsais_prefetchw(&buckets[BUCKETS_INDEX2(T[i - prefetch_distance - 3] & SAINT_MAX, 0)]);
c1 = T[i - 0]; s = (s << 1) + (fast_uint_t)(c1 > (c0 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i + 1); m -= ((fast_sint_t)(s & 3) == (c0 >= 0));
c0 &= SAINT_MAX; buckets[BUCKETS_INDEX2((fast_uint_t)c0, (s & 3) == 1)]++;
c0 = T[i - 1]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i - 0); m -= ((fast_sint_t)(s & 3) == (c1 >= 0));
c1 &= SAINT_MAX; buckets[BUCKETS_INDEX2((fast_uint_t)c1, (s & 3) == 1)]++;
c1 = T[i - 2]; s = (s << 1) + (fast_uint_t)(c1 > (c0 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i - 1); m -= ((fast_sint_t)(s & 3) == (c0 >= 0));
c0 &= SAINT_MAX; buckets[BUCKETS_INDEX2((fast_uint_t)c0, (s & 3) == 1)]++;
c0 = T[i - 3]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i - 2); m -= ((fast_sint_t)(s & 3) == (c1 >= 0));
c1 &= SAINT_MAX; buckets[BUCKETS_INDEX2((fast_uint_t)c1, (s & 3) == 1)]++;
}
for (j -= prefetch_distance + 3; i >= j; i -= 1)
{
c1 = c0; c0 = T[i]; s = (s << 1) + (fast_uint_t)(c0 > (c1 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i + 1); m -= ((fast_sint_t)(s & 3) == (c1 >= 0));
c1 &= SAINT_MAX; buckets[BUCKETS_INDEX2((fast_uint_t)c1, (s & 3) == 1)]++;
}
c1 = (i >= 0) ? T[i] : -1; s = (s << 1) + (fast_uint_t)(c1 > (c0 - (fast_sint_t)(s & 1))); SA[m] = (sa_sint_t)(i + 1); m -= ((fast_sint_t)(s & 3) == (c0 >= 0));
c0 &= SAINT_MAX; buckets[BUCKETS_INDEX2((fast_uint_t)c0, (s & 3) == 1)]++;
}
return (sa_sint_t)(omp_block_start + omp_block_size - 1 - m);
}
#if defined(LIBSAIS_OPENMP)
static fast_sint_t libsais_get_bucket_stride(fast_sint_t free_space, fast_sint_t bucket_size, fast_sint_t num_buckets)
{
fast_sint_t bucket_size_1024 = (bucket_size + 1023) & (-1024); if (free_space / (num_buckets - 1) >= bucket_size_1024) { return bucket_size_1024; }
fast_sint_t bucket_size_16 = (bucket_size + 15) & (-16); if (free_space / (num_buckets - 1) >= bucket_size_16) { return bucket_size_16; }
return bucket_size;
}
static sa_sint_t libsais_count_and_gather_lms_suffixes_32s_4k_fs_omp(const sa_sint_t * RESTRICT T, sa_sint_t * RESTRICT SA, sa_sint_t n, sa_sint_t k, sa_sint_t * RESTRICT buckets, sa_sint_t threads, LIBSAIS_THREAD_STATE * RESTRICT thread_state)
{
sa_sint_t m = 0;
#if defined(LIBSAIS_OPENMP)
#pragma omp parallel num_threads(threads) if(threads > 1 && n >= 65536)
#endif
{
#if defined(LIBSAIS_OPENMP)
fast_sint_t omp_thread_num = omp_get_thread_num();
fast_sint_t omp_num_threads = omp_get_num_threads();
#else
UNUSED(threads); UNUSED(thread_state);
fast_sint_t omp_thread_num = 0;
fast_sint_t omp_num_threads = 1;
#endif
fast_sint_t omp_block_stride = (n / omp_num_threads) & (-16);
fast_sint_t omp_block_start = omp_thread_num * omp_block_stride;
fast_sint_t omp_block_size = omp_thread_num < omp_num_threads - 1 ? omp_block_stride : n - omp_block_start;
if (omp_num_threads == 1)
{
m = libsais_count_and_gather_lms_suffixes_32s_4k(T, SA, n, k, buckets, omp_block_start, omp_block_size);
}
#if defined(LIBSAIS_OPENMP)
else
{
fast_sint_t bucket_size = 4 * (fast_sint_t)k;
fast_sint_t bucket_stride = libsais_get_bucket_stride(buckets - &SA[n], bucket_size, omp_num_threads);
{
thread_state[omp_thread_num].state.position = omp_block_start + omp_block_size;