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libcubwt.cu
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/*--
This file is a part of libcubwt, a library for CUDA accelerated
burrows wheeler transform construction and inversion.
Copyright (c) 2022-2025 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 and license details.
--*/
#include "libcubwt.cuh"
#if defined(_MSC_VER) && defined(__INTELLISENSE__)
#define __launch_bounds__(block_size) /* */
#define __CUDACC__
#include <vector_functions.h>
#include <device_functions.h>
#include <device_launch_parameters.h>
#endif
#include <cub/cub.cuh>
#include <cuda.h>
#include <utility>
#if defined(__GNUC__) || defined(__clang__) || defined(__CUDACC__)
#define RESTRICT __restrict__
#elif defined(_MSC_VER) || defined(__INTEL_COMPILER)
#define RESTRICT __restrict
#else
#define RESTRICT /* */
#endif
#ifndef __CUDA_ARCH__
#define CUDA_DEVICE_ARCH 0
#else
#define CUDA_DEVICE_ARCH __CUDA_ARCH__
#endif
#if CUDA_DEVICE_ARCH == 750
#define CUDA_SM_THREADS (1024)
#elif CUDA_DEVICE_ARCH == 860 || CUDA_DEVICE_ARCH == 870 || CUDA_DEVICE_ARCH == 890 || CUDA_DEVICE_ARCH == 1010 || CUDA_DEVICE_ARCH == 1200
#define CUDA_SM_THREADS (1536)
#else
#define CUDA_SM_THREADS (2048)
#endif
#if CUDA_DEVICE_ARCH == 860 || CUDA_DEVICE_ARCH == 870 || CUDA_DEVICE_ARCH == 890 || CUDA_DEVICE_ARCH == 1010 || CUDA_DEVICE_ARCH == 1200
#define CUDA_BLOCK_THREADS (768)
#else
#define CUDA_BLOCK_THREADS (512)
#endif
#define CUDA_WARP_THREADS (32)
#define CUDA_DEVICE_PADDING (12 * 768)
#define ALPHABET_SIZE (256)
template <typename BaseTypeT, typename OffsetTypeT>
struct OffsetToPointerOperator
{
BaseTypeT * d_base;
__host__ __device__ __forceinline__ BaseTypeT * operator()(const OffsetTypeT& offset) const
{
return d_base + offset;
}
};
typedef struct LIBCUBWT_DEVICE_STORAGE
{
void * device_rsort_temp_storage;
size_t device_rsort_temp_storage_size;
void * device_ssort_temp_storage;
size_t device_ssort_temp_storage_size;
uint8_t * device_T;
uint8_t * device_heads;
uint32_t * device_SA;
uint32_t * device_ISA;
uint32_t * device_keys;
uint32_t * device_offsets;
uint32_t * device_temp_SA;
uint32_t * device_temp_ISA;
uint32_t * device_temp_keys;
uint64_t * device_SA_temp_SA;
uint64_t * device_keys_temp_keys;
uint64_t * device_offsets_ISA;
uint4 * device_descriptors_large;
uint4 * device_descriptors_copy;
uint2 * device_descriptors_small;
void * device_storage;
size_t device_storage_size;
int32_t device_L2_cache_bits;
int32_t device_multiprocessor_count;
int32_t device_multiprocessor_max_blocks;
int32_t device_multiprocessor_max_threads;
void * host_pinned_storage;
size_t host_pinned_storage_size;
int64_t max_length;
uint32_t num_unsorted_segments;
uint32_t num_unsorted_suffixes;
uint32_t cuda_block_threads;
cudaStream_t cuda_stream;
} LIBCUBWT_DEVICE_STORAGE;
static int64_t libcubwt_get_error_code(cudaError_t status)
{
return
status == cudaErrorMemoryAllocation ? LIBCUBWT_GPU_NOT_ENOUGH_MEMORY :
status == cudaErrorDevicesUnavailable ? LIBCUBWT_GPU_NOT_SUPPORTED :
status == cudaErrorNoDevice ? LIBCUBWT_GPU_NOT_SUPPORTED :
LIBCUBWT_GPU_ERROR;
}
static cudaError_t libcubwt_cuda_safe_call(const char * filename, int32_t line, cudaError_t result, cudaError_t status = cudaSuccess)
{
#if !defined(NDEBUG)
if (result != cudaSuccess)
{
fprintf(stderr, "%s(%d): libcubwt_cuda_safe_call failed %d: '%s'.\n", filename, line, result, cudaGetErrorString(result));
fflush(stderr);
}
#else
(void)(filename); (void)(line);
#endif
return result != cudaSuccess ? result : status;
}
template <typename T>
static __device__ __forceinline__ T libcubwt_warp_reduce_sum(T value)
{
#if CUDA_DEVICE_ARCH >= 800 && !defined(__CUDA__)
return __reduce_add_sync((uint32_t)-1, value);
#else
#pragma unroll
for (uint32_t mask = CUDA_WARP_THREADS / 2; mask > 0; mask >>= 1)
{
value = cub::Sum()(value, __shfl_xor_sync((uint32_t)-1, value, mask, CUDA_WARP_THREADS));
}
return value;
#endif
}
template <typename T>
static __device__ __forceinline__ T libcubwt_warp_reduce_max(T value)
{
#if CUDA_DEVICE_ARCH >= 800 && !defined(__CUDA__)
return __reduce_max_sync((uint32_t)-1, value);
#else
#pragma unroll
for (uint32_t mask = CUDA_WARP_THREADS / 2; mask > 0; mask >>= 1)
{
value = cub::Max()(value, __shfl_xor_sync((uint32_t)-1, value, mask, CUDA_WARP_THREADS));
}
return value;
#endif
}
template <typename T>
static __device__ __forceinline__ void libcubwt_delay_or_prevent_hoisting(T delay)
{
#if CUDA_DEVICE_ARCH >= 700
__nanosleep(delay);
#else
__threadfence_block(); (void)(delay);
#endif
}
template <int INPUT_BITS>
static __device__ __forceinline__ uint32_t libcubwt_match_any_sync(const uint32_t sync_mask, const uint32_t input)
{
uint32_t peers_mask = sync_mask;
#pragma unroll
for (uint32_t bit = 0; bit < INPUT_BITS; bit += 1)
{
uint32_t peers, bit_mask = 1 << bit;
asm("{\n"
" .reg .pred p;\n"
" and.b32 %0, %1, %2;\n"
" setp.ne.u32 p, %0, 0;\n"
" vote.ballot.sync.b32 %0, p, %3;\n"
" @!p not.b32 %0, %0;\n"
" }"
: "=r"(peers) : "r"(input), "r"(bit_mask), "r"(sync_mask));
peers_mask &= peers;
}
return peers_mask;
}
static __device__ __forceinline__ uint32_t libcubwt_get_lanemask_lt()
{
uint32_t mask;
asm("mov.u32 %0, %%lanemask_lt;" : "=r"(mask));
return mask;
}
static __device__ __forceinline__ uint32_t libcubwt_xxhash32_b32(uint32_t data, uint32_t seed)
{
uint32_t x = (data * 0xc2b2ae3du) + seed + (uint32_t)sizeof(data) + 0x165667b1u;
x = (x << 17) | (x >> 15);
x *= 0x27d4eb2fu; x ^= x >> 15;
x *= 0x85ebca77u; x ^= x >> 13;
x *= 0xc2b2ae3du; x ^= x >> 16;
return x;
}
static __device__ __forceinline__ uint4 libcubwt_shift_left_b128(uint4 v, uint32_t shift)
{
if ((shift & 8) > 0) { v.w = v.y; v.z = v.x; v.y = 0 ; v.x = 0; }
if ((shift & 4) > 0) { v.w = v.z; v.z = v.y; v.y = v.x; v.x = 0; }
shift = (shift << 3) & 0x18u;
v.w = __funnelshift_l(v.z, v.w, shift);
v.z = __funnelshift_l(v.y, v.z, shift);
v.y = __funnelshift_l(v.x, v.y, shift);
v.x = __funnelshift_l(0x0, v.x, shift);
return v;
}
static __device__ __forceinline__ uint4 libcubwt_shift_right_b128(uint4 v, uint32_t shift)
{
if ((shift & 8) > 0) { v.x = v.z; v.y = v.w; v.z = 0 ; v.w = 0; }
if ((shift & 4) > 0) { v.x = v.y; v.y = v.z; v.z = v.w; v.w = 0; }
shift = (shift << 3) & 0x18u;
v.x = __funnelshift_r(v.x, v.y, shift);
v.y = __funnelshift_r(v.y, v.z, shift);
v.z = __funnelshift_r(v.z, v.w, shift);
v.w = __funnelshift_r(v.w, 0x0, shift);
return v;
}
__global__ __launch_bounds__(CUDA_BLOCK_THREADS, CUDA_SM_THREADS / CUDA_BLOCK_THREADS)
static void libcubwt_gather_values_uint32_kernel(const uint32_t * device_idx, const uint32_t * RESTRICT device_src, uint32_t * device_dst, uint32_t m)
{
const uint32_t block_index = blockIdx.x * CUDA_BLOCK_THREADS * 4;
device_idx += block_index; device_dst += block_index; m -= block_index;
if (m >= CUDA_BLOCK_THREADS * 4)
{
const uint4 indexes = *(uint4 *)(device_idx + threadIdx.x * 4);
*(uint4 *)(device_dst + threadIdx.x * 4) = make_uint4(
__ldg(device_src + indexes.x),
__ldg(device_src + indexes.y),
__ldg(device_src + indexes.z),
__ldg(device_src + indexes.w));
}
else
{
for (uint32_t thread_index = threadIdx.x; thread_index < m; thread_index += CUDA_BLOCK_THREADS)
{
device_dst[thread_index] = __ldg(device_src + device_idx[thread_index]);
}
}
}
__global__ __launch_bounds__(CUDA_BLOCK_THREADS, CUDA_SM_THREADS / CUDA_BLOCK_THREADS)
static void libcubwt_scatter_values_uint32_kernel(const uint32_t * RESTRICT device_idx, const uint32_t * RESTRICT device_src, uint32_t * RESTRICT device_dst, uint32_t m)
{
const uint32_t block_index = blockIdx.x * CUDA_BLOCK_THREADS * 4;
device_idx += block_index; device_src += block_index; m -= block_index;
if (m >= CUDA_BLOCK_THREADS * 4)
{
const uint4 indexes = __ldg((uint4 *)(device_idx + threadIdx.x * 4));
const uint4 values = __ldg((uint4 *)(device_src + threadIdx.x * 4));
device_dst[indexes.x] = values.x;
device_dst[indexes.y] = values.y;
device_dst[indexes.z] = values.z;
device_dst[indexes.w] = values.w;
}
else
{
for (uint32_t thread_index = threadIdx.x; thread_index < m; thread_index += CUDA_BLOCK_THREADS)
{
device_dst[__ldg(device_idx + thread_index)] = __ldg(device_src + thread_index);
}
}
}
__global__ __launch_bounds__(CUDA_BLOCK_THREADS, CUDA_SM_THREADS / CUDA_BLOCK_THREADS)
static void libcubwt_permute_block_values_uint32_kernel(const uint32_t * RESTRICT device_idx, const uint32_t * RESTRICT device_src, uint32_t * RESTRICT device_dst, uint32_t n)
{
__shared__ __align__(32) uint32_t cache[16 * CUDA_BLOCK_THREADS];
const uint32_t block_index = blockIdx.x * CUDA_BLOCK_THREADS * 16;
device_idx += block_index; device_src += block_index; device_dst += block_index; n -= block_index;
if (n >= CUDA_BLOCK_THREADS * 16)
{
{
const uint32_t * RESTRICT thread_idx = device_idx + threadIdx.x * 4;
const uint32_t * RESTRICT thread_src = device_src + threadIdx.x * 4;
uint32_t * RESTRICT thread_cache = cache - block_index;
#pragma unroll
for (uint32_t round = 0; round < 4; round += 1)
{
const uint4 indexes = __ldg((uint4 *)(thread_idx));
const uint4 values = __ldg((uint4 *)(thread_src));
thread_cache[indexes.x] = values.x;
thread_cache[indexes.y] = values.y;
thread_cache[indexes.z] = values.z;
thread_cache[indexes.w] = values.w;
thread_idx += 4 * CUDA_BLOCK_THREADS; thread_src += 4 * CUDA_BLOCK_THREADS;
}
}
__syncthreads();
{
const uint32_t * RESTRICT thread_cache = cache + threadIdx.x * 4;
uint32_t * RESTRICT thread_dst = device_dst + threadIdx.x * 4;
#pragma unroll
for (uint32_t round = 0; round < 4; round += 1)
{
*(uint4 *)(thread_dst) = *(uint4 *)(thread_cache);
thread_cache += 4 * CUDA_BLOCK_THREADS; thread_dst += 4 * CUDA_BLOCK_THREADS;
}
}
}
else
{
{
uint32_t * RESTRICT thread_cache = cache - block_index;
for (uint32_t thread_index = threadIdx.x; thread_index < n; thread_index += CUDA_BLOCK_THREADS)
{
thread_cache[__ldg(device_idx + thread_index)] = __ldg(device_src + thread_index);
}
}
__syncthreads();
{
for (uint32_t thread_index = threadIdx.x; thread_index < n; thread_index += CUDA_BLOCK_THREADS)
{
device_dst[thread_index] = cache[thread_index];
}
}
}
}
__global__ __launch_bounds__(CUDA_BLOCK_THREADS, CUDA_SM_THREADS / CUDA_BLOCK_THREADS)
static void libcubwt_scatter_values_uint64_kernel(const uint32_t * RESTRICT device_idx, const uint64_t * RESTRICT device_src, uint64_t * RESTRICT device_dst, uint32_t m)
{
const uint32_t block_index = blockIdx.x * CUDA_BLOCK_THREADS * 2;
device_idx += block_index; device_src += block_index; m -= block_index;
if (m >= CUDA_BLOCK_THREADS * 2)
{
const uint2 indexes = __ldg((uint2 *)(device_idx + threadIdx.x * 2));
const ulonglong2 values = __ldg((ulonglong2 *)(device_src + threadIdx.x * 2));
device_dst[indexes.x] = values.x;
device_dst[indexes.y] = values.y;
}
else
{
for (uint32_t thread_index = threadIdx.x; thread_index < m; thread_index += CUDA_BLOCK_THREADS)
{
device_dst[__ldg(device_idx + thread_index)] = __ldg(device_src + thread_index);
}
}
}
static cudaError_t libcubwt_gather_scatter_values_uint32(LIBCUBWT_DEVICE_STORAGE * storage, uint32_t * device_src_idx, uint32_t * device_src, uint32_t * device_dst_idx, uint32_t * device_dst, int64_t m, int64_t n, uint32_t * device_temp1, uint32_t * device_temp2)
{
cudaError_t status = cudaSuccess;
cub::DoubleBuffer<uint32_t> db_src_index_value(device_src_idx, device_temp1);
cub::DoubleBuffer<uint32_t> db_dst_index(device_dst_idx, device_temp2);
int32_t sort_end_bit = 0; while ((n - 1) >= ((int64_t)1 << sort_end_bit)) { sort_end_bit += 1; }
int32_t sort_aligned_bits = (sort_end_bit > storage->device_L2_cache_bits - 2) ? (sort_end_bit - storage->device_L2_cache_bits + 2 + 7) & (-8) : 0;
int32_t sort_start_bit = std::max(0, sort_end_bit - sort_aligned_bits);
if (sort_start_bit < sort_end_bit)
{
status = libcubwt_cuda_safe_call(__FILE__, __LINE__, cub::DeviceRadixSort::SortPairs(
storage->device_rsort_temp_storage, storage->device_rsort_temp_storage_size,
db_src_index_value, db_dst_index,
(uint32_t)m,
sort_start_bit, sort_end_bit,
storage->cuda_stream));
}
if (status == cudaSuccess)
{
int64_t n_gather_scatter_blocks = (m + storage->cuda_block_threads * 4 - 1) / (storage->cuda_block_threads * 4);
libcubwt_gather_values_uint32_kernel<<<(uint32_t)n_gather_scatter_blocks, storage->cuda_block_threads, 0, storage->cuda_stream>>>(db_src_index_value.Current(), device_src, db_src_index_value.Current(), (uint32_t)m);
if (sort_start_bit < sort_end_bit)
{
status = libcubwt_cuda_safe_call(__FILE__, __LINE__, cub::DeviceRadixSort::SortPairs(
storage->device_rsort_temp_storage, storage->device_rsort_temp_storage_size,
db_dst_index, db_src_index_value,
(uint32_t)m,
sort_start_bit, sort_end_bit,
storage->cuda_stream));
}
if (status == cudaSuccess)
{
libcubwt_scatter_values_uint32_kernel<<<(uint32_t)n_gather_scatter_blocks, storage->cuda_block_threads, 0, storage->cuda_stream>>>(db_dst_index.Current(), db_src_index_value.Current(), device_dst, (uint32_t)m);
}
}
return status;
}
static cudaError_t libcubwt_scatter_values_uint32(LIBCUBWT_DEVICE_STORAGE * storage, uint32_t * device_idx, uint32_t * device_src, uint32_t * device_dst, int64_t m, int64_t n, uint32_t * device_temp1, uint32_t * device_temp2)
{
cudaError_t status = cudaSuccess;
cub::DoubleBuffer<uint32_t> db_index(device_idx, device_temp1);
cub::DoubleBuffer<uint32_t> db_value(device_src, device_temp2);
int32_t sort_end_bit = 0; while ((n - 1) >= ((int64_t)1 << sort_end_bit)) { sort_end_bit += 1; }
int32_t sort_aligned_bits = (sort_end_bit > storage->device_L2_cache_bits - 2) ? (sort_end_bit - storage->device_L2_cache_bits + 2 + 7) & (-8) : 0;
int32_t sort_start_bit = std::max(0, sort_end_bit - sort_aligned_bits);
if (sort_start_bit < sort_end_bit)
{
status = libcubwt_cuda_safe_call(__FILE__, __LINE__, cub::DeviceRadixSort::SortPairs(
storage->device_rsort_temp_storage, storage->device_rsort_temp_storage_size,
db_index, db_value,
(uint32_t)m,
sort_start_bit, sort_end_bit,
storage->cuda_stream));
}
if (status == cudaSuccess)
{
int64_t n_scatter_blocks = (m + storage->cuda_block_threads * 4 - 1) / (storage->cuda_block_threads * 4);
libcubwt_scatter_values_uint32_kernel<<<(uint32_t)n_scatter_blocks, storage->cuda_block_threads, 0, storage->cuda_stream>>>(db_index.Current(), db_value.Current(), device_dst, (uint32_t)m);
}
return status;
}
static cudaError_t libcubwt_permute_values_uint32(LIBCUBWT_DEVICE_STORAGE * storage, uint32_t * device_idx, uint32_t * device_src, uint32_t * device_dst, int64_t n, uint32_t * device_temp1, uint32_t * device_temp2)
{
cudaError_t status = cudaSuccess;
cub::DoubleBuffer<uint32_t> db_index(device_idx, device_temp1);
cub::DoubleBuffer<uint32_t> db_value(device_src, device_temp2);
int32_t sort_end_bit = 0; while ((n - 1) >= ((int64_t)1 << sort_end_bit)) { sort_end_bit += 1; }
int32_t sort_aligned_bits = (sort_end_bit > storage->device_L2_cache_bits - 2) ? (sort_end_bit - storage->device_L2_cache_bits + 2 + 7) & (-8) : 0;
int32_t sort_start_bit = std::max(0, sort_end_bit - sort_aligned_bits);
if (sort_start_bit < sort_end_bit)
{
status = libcubwt_cuda_safe_call(__FILE__, __LINE__, cub::DeviceRadixSort::SortPairs(
storage->device_rsort_temp_storage, storage->device_rsort_temp_storage_size,
db_index, db_value,
(uint32_t)n,
sort_start_bit, sort_end_bit,
storage->cuda_stream));
}
if (status == cudaSuccess)
{
if (((storage->cuda_block_threads * 16) % ((int64_t)1 << sort_start_bit)) == 0)
{
int64_t n_permute_blocks = (n + storage->cuda_block_threads * 16 - 1) / (storage->cuda_block_threads * 16);
libcubwt_permute_block_values_uint32_kernel<<<(uint32_t)n_permute_blocks, storage->cuda_block_threads, 0, storage->cuda_stream>>>(db_index.Current(), db_value.Current(), device_dst, (uint32_t)n);
}
else
{
int64_t n_scatter_blocks = (n + storage->cuda_block_threads * 4 - 1) / (storage->cuda_block_threads * 4);
libcubwt_scatter_values_uint32_kernel<<<(uint32_t)n_scatter_blocks, storage->cuda_block_threads, 0, storage->cuda_stream>>>(db_index.Current(), db_value.Current(), device_dst, (uint32_t)n);
}
}
return status;
}
static cudaError_t libcubwt_scatter_values_uint64(LIBCUBWT_DEVICE_STORAGE * storage, cub::DoubleBuffer<uint32_t> & db_index, cub::DoubleBuffer<uint64_t> & db_value, int64_t m, int64_t n, int64_t k = 0)
{
cudaError_t status = cudaSuccess;
int32_t sort_end_bit = 0; while ((n - 1) >= ((int64_t)1 << sort_end_bit)) { sort_end_bit += 1; }
int32_t sort_aligned_bits = (sort_end_bit > storage->device_L2_cache_bits - 3) ? (sort_end_bit - storage->device_L2_cache_bits + 3 + 7) & (-8) : 0;
int32_t sort_start_bit = std::max(0, sort_end_bit - sort_aligned_bits);
if (sort_start_bit < sort_end_bit)
{
status = libcubwt_cuda_safe_call(__FILE__, __LINE__, cub::DeviceRadixSort::SortPairs(
storage->device_rsort_temp_storage, storage->device_rsort_temp_storage_size,
db_index, db_value,
(uint32_t)m,
sort_start_bit, sort_end_bit,
storage->cuda_stream));
}
if (status == cudaSuccess)
{
int64_t n_scatter_blocks = (m + storage->cuda_block_threads * 2 - 1) / (storage->cuda_block_threads * 2);
libcubwt_scatter_values_uint64_kernel<<<(uint32_t)n_scatter_blocks, storage->cuda_block_threads, 0, storage->cuda_stream>>>(db_index.Current(), db_value.Current(), db_value.Alternate() - k, (uint32_t)m);
db_index.selector ^= 1;
db_value.selector ^= 1;
}
return status;
}
template <bool extra_sentinel_bits>
__global__ __launch_bounds__(CUDA_BLOCK_THREADS, CUDA_SM_THREADS / CUDA_BLOCK_THREADS)
static void libcubwt_initialize_device_arrays_kernel(const uint8_t * RESTRICT device_T, uint32_t * RESTRICT device_SA, uint64_t * RESTRICT device_keys)
{
__shared__ __align__(32) uint4 prefixes[4 * CUDA_BLOCK_THREADS];
{
device_T += blockIdx.x * CUDA_BLOCK_THREADS * 12 + threadIdx.x * 16;
if (threadIdx.x < (12 * CUDA_BLOCK_THREADS + 8 + 15) / 16) { prefixes[threadIdx.x] = __ldg((uint4 *)device_T); }
__syncthreads();
}
{
uint32_t * RESTRICT thread_cache = ((uint32_t *)prefixes) + threadIdx.x * 3;
uint4 * RESTRICT thread_prefixes = ((uint4 * )prefixes) + threadIdx.x * 4;
const uint32_t b0 = thread_cache[0];
const uint32_t b1 = thread_cache[1];
const uint32_t b2 = thread_cache[2];
const uint32_t b3 = thread_cache[3];
const uint32_t b4 = thread_cache[4];
__syncthreads();
thread_prefixes[0] = make_uint4
(
__byte_perm(b1, b2, 0x1234) | (extra_sentinel_bits ? (uint32_t)7 : (uint32_t)1), __byte_perm(b0, b1, 0x1234),
__byte_perm(b1, b2, 0x2345) | (extra_sentinel_bits ? (uint32_t)7 : (uint32_t)1), __byte_perm(b0, b1, 0x2345)
);
thread_prefixes[1] = make_uint4
(
__byte_perm(b2, b3, 0x0123) | (extra_sentinel_bits ? (uint32_t)7 : (uint32_t)1), __byte_perm(b1, b2, 0x0123),
__byte_perm(b2, b3, 0x1234) | (extra_sentinel_bits ? (uint32_t)7 : (uint32_t)1), __byte_perm(b1, b2, 0x1234)
);
thread_prefixes[2] = make_uint4
(
__byte_perm(b2, b3, 0x3456) | (extra_sentinel_bits ? (uint32_t)7 : (uint32_t)1), __byte_perm(b1, b2, 0x3456),
__byte_perm(b3, b4, 0x0123) | (extra_sentinel_bits ? (uint32_t)7 : (uint32_t)1), __byte_perm(b2, b3, 0x0123)
);
thread_prefixes[3] = make_uint4
(
__byte_perm(b3, b4, 0x2345) | (extra_sentinel_bits ? (uint32_t)7 : (uint32_t)1), __byte_perm(b2, b3, 0x2345),
__byte_perm(b3, b4, 0x3456) | (extra_sentinel_bits ? (uint32_t)7 : (uint32_t)1), __byte_perm(b2, b3, 0x3456)
);
__syncwarp();
}
{
const uint32_t block_index = blockIdx.x * CUDA_BLOCK_THREADS * 8;
{
uint32_t thread_index = block_index + threadIdx.x * 4; device_SA += thread_index;
((uint4 *)device_SA)[0] = make_uint4(thread_index + 0, thread_index + 1, thread_index + 2, thread_index + 3);
thread_index += CUDA_BLOCK_THREADS * 4; device_SA += CUDA_BLOCK_THREADS * 4;
((uint4 *)device_SA)[0] = make_uint4(thread_index + 0, thread_index + 1, thread_index + 2, thread_index + 3);
}
{
device_keys += block_index;
uint4 * RESTRICT thread_prefixes = (uint4 *)prefixes + ((threadIdx.x / CUDA_WARP_THREADS) * CUDA_WARP_THREADS * 4) + (threadIdx.x % CUDA_WARP_THREADS);
uint4 * RESTRICT thread_keys = (uint4 *)device_keys + ((threadIdx.x / CUDA_WARP_THREADS) * CUDA_WARP_THREADS * 4) + (threadIdx.x % CUDA_WARP_THREADS);
thread_keys[0] = thread_prefixes[0]; thread_keys += CUDA_WARP_THREADS; thread_prefixes += CUDA_WARP_THREADS;
thread_keys[0] = thread_prefixes[0]; thread_keys += CUDA_WARP_THREADS; thread_prefixes += CUDA_WARP_THREADS;
thread_keys[0] = thread_prefixes[0]; thread_keys += CUDA_WARP_THREADS; thread_prefixes += CUDA_WARP_THREADS;
thread_keys[0] = thread_prefixes[0];
}
}
}
__global__ __launch_bounds__(CUDA_BLOCK_THREADS, 1)
static void libcubwt_set_sentinel_values_kernel(uint8_t * RESTRICT device_T_end, uint64_t * RESTRICT device_keys_end, uint64_t k0, uint64_t k1, uint64_t k2, uint64_t k3, uint64_t k4, uint64_t k5, uint64_t k6, uint64_t k7)
{
device_T_end[0] = 0;
device_T_end[1] = 0;
device_T_end[2] = 0;
device_keys_end[-8] = k0;
device_keys_end[-7] = k1;
device_keys_end[-6] = k2;
device_keys_end[-5] = k3;
device_keys_end[-4] = k4;
device_keys_end[-3] = k5;
device_keys_end[-2] = k6;
device_keys_end[-1] = k7;
}
static cudaError_t libcubwt_initialize_device_arrays(LIBCUBWT_DEVICE_STORAGE * storage, const uint8_t * T, int64_t reduced_n, int64_t expanded_n, int64_t input_n)
{
cudaError_t status = cudaSuccess;
if ((status = libcubwt_cuda_safe_call(__FILE__, __LINE__, cudaMemcpyAsync(storage->device_T, T, (size_t)input_n, cudaMemcpyHostToDevice, storage->cuda_stream))) == cudaSuccess)
{
int64_t n_initialize_blocks = 1 + (expanded_n / (storage->cuda_block_threads * 12));
bool extra_sentinel_bits = (expanded_n - input_n >= 2) || (T[input_n - 1] == 0);
if (extra_sentinel_bits)
{
libcubwt_initialize_device_arrays_kernel<true><<<(uint32_t)n_initialize_blocks, storage->cuda_block_threads, 0, storage->cuda_stream>>>(storage->device_T, storage->device_SA, storage->device_keys_temp_keys);
}
else
{
libcubwt_initialize_device_arrays_kernel<false><<<(uint32_t)n_initialize_blocks, storage->cuda_block_threads, 0, storage->cuda_stream>>>(storage->device_T, storage->device_SA, storage->device_keys_temp_keys);
}
{
uint64_t c0 = (expanded_n - 11 < input_n) ? T[expanded_n - 11] : (uint64_t)0;
uint64_t c1 = (expanded_n - 10 < input_n) ? T[expanded_n - 10] : (uint64_t)0;
uint64_t c2 = (expanded_n - 9 < input_n) ? T[expanded_n - 9] : (uint64_t)0;
uint64_t c3 = (expanded_n - 8 < input_n) ? T[expanded_n - 8] : (uint64_t)0;
uint64_t c4 = (expanded_n - 7 < input_n) ? T[expanded_n - 7] : (uint64_t)0;
uint64_t c5 = (expanded_n - 6 < input_n) ? T[expanded_n - 6] : (uint64_t)0;
uint64_t c6 = (expanded_n - 5 < input_n) ? T[expanded_n - 5] : (uint64_t)0;
uint64_t c7 = (expanded_n - 4 < input_n) ? T[expanded_n - 4] : (uint64_t)0;
uint64_t c8 = (expanded_n - 3 < input_n) ? T[expanded_n - 3] : (uint64_t)0;
uint64_t c9 = (expanded_n - 2 < input_n) ? T[expanded_n - 2] : (uint64_t)0;
uint64_t ca = (expanded_n - 1 < input_n) ? T[expanded_n - 1] : (uint64_t)0;
uint64_t k0 = (c0 << 56) | (c1 << 48) | (c2 << 40) | (c3 << 32) | (c4 << 24) | (c5 << 16) | (c6 << 8) | (c7 << 0) | (extra_sentinel_bits ? 7 : 1);
uint64_t k1 = (c1 << 56) | (c2 << 48) | (c3 << 40) | (c4 << 32) | (c5 << 24) | (c6 << 16) | (c7 << 8) | (c8 << 0) | (extra_sentinel_bits ? 7 : 1);
uint64_t k2 = (c3 << 56) | (c4 << 48) | (c5 << 40) | (c6 << 32) | (c7 << 24) | (c8 << 16) | (c9 << 8) | (ca << 0) | (extra_sentinel_bits ? 7 : 0);
uint64_t k3 = (c4 << 56) | (c5 << 48) | (c6 << 40) | (c7 << 32) | (c8 << 24) | (c9 << 16) | (ca << 8) | (extra_sentinel_bits ? 6 : 0);
uint64_t k4 = (c6 << 56) | (c7 << 48) | (c8 << 40) | (c9 << 32) | (ca << 24) | (extra_sentinel_bits ? 4 : 0);
uint64_t k5 = (c7 << 56) | (c8 << 48) | (c9 << 40) | (ca << 32) | (extra_sentinel_bits ? 3 : 0);
uint64_t k6 = (c9 << 56) | (ca << 48) | (extra_sentinel_bits ? 1 : 0);
uint64_t k7 = (ca << 56);
libcubwt_set_sentinel_values_kernel<<<1, 1, 0, storage->cuda_stream>>>(storage->device_T + input_n, storage->device_keys_temp_keys + reduced_n, k0, k1, k2, k3, k4, k5, k6, k7);
}
storage->num_unsorted_segments = (uint32_t)1;
storage->num_unsorted_suffixes = (uint32_t)reduced_n;
}
return status;
}
static cudaError_t libcubwt_sort_suffixes_by_prefix(LIBCUBWT_DEVICE_STORAGE * storage, int64_t n)
{
cub::DoubleBuffer<uint64_t> db_keys(storage->device_keys_temp_keys, storage->device_offsets_ISA);
cub::DoubleBuffer<uint32_t> db_SA(storage->device_SA, storage->device_temp_SA);
cudaError_t status = libcubwt_cuda_safe_call(__FILE__, __LINE__, cub::DeviceRadixSort::SortPairs(
storage->device_rsort_temp_storage, storage->device_rsort_temp_storage_size,
db_keys, db_SA,
(uint32_t)n,
0, 64,
storage->cuda_stream));
if (db_keys.selector)
{
std::swap(storage->device_keys_temp_keys, storage->device_offsets_ISA);
std::swap(storage->device_keys, storage->device_offsets);
std::swap(storage->device_temp_keys, storage->device_ISA);
}
if (db_SA.selector)
{
std::swap(storage->device_SA, storage->device_temp_SA);
}
return status;
}
__global__ __launch_bounds__(CUDA_BLOCK_THREADS, CUDA_SM_THREADS / CUDA_BLOCK_THREADS)
static void libcubwt_rank_and_segment_suffixes_initialization_kernel(uint32_t * RESTRICT device_SA, uint64_t * RESTRICT device_keys, uint8_t * RESTRICT device_heads, uint4 * RESTRICT device_descriptors_large, uint2 * RESTRICT device_descriptors_small, uint32_t n)
{
const uint32_t thread_index = blockIdx.x * CUDA_BLOCK_THREADS + threadIdx.x;
device_descriptors_large += thread_index;
device_descriptors_small += thread_index;
device_descriptors_large[0] = make_uint4(0, 0, 0, 0);
device_descriptors_small[0] = make_uint2(0, 0);
if (blockIdx.x == 0)
{
if (threadIdx.x < CUDA_WARP_THREADS)
{
device_descriptors_large[-CUDA_WARP_THREADS] = make_uint4((uint32_t)-1, 0, 0, 0);
device_descriptors_small[-CUDA_WARP_THREADS] = make_uint2((uint32_t)-1, 0);
}
{
uint64_t key = (threadIdx.x % 2 == 0) ? 0 : (uint64_t)-1;
device_SA += threadIdx.x; device_keys += threadIdx.x; device_heads += threadIdx.x;
if (threadIdx.x < 2)
{
device_keys [-2] = key;
device_heads[-2] = 1;
}
device_SA += n; device_keys += n; device_heads += n;
device_SA [0 * CUDA_BLOCK_THREADS] = n + threadIdx.x + 0 * CUDA_BLOCK_THREADS;
device_SA [1 * CUDA_BLOCK_THREADS] = n + threadIdx.x + 1 * CUDA_BLOCK_THREADS;
device_SA [2 * CUDA_BLOCK_THREADS] = n + threadIdx.x + 2 * CUDA_BLOCK_THREADS;
device_SA [3 * CUDA_BLOCK_THREADS] = n + threadIdx.x + 3 * CUDA_BLOCK_THREADS;
device_keys [0 * CUDA_BLOCK_THREADS] = key;
device_keys [1 * CUDA_BLOCK_THREADS] = key;
device_keys [2 * CUDA_BLOCK_THREADS] = key;
device_keys [3 * CUDA_BLOCK_THREADS] = key;
device_heads[0 * CUDA_BLOCK_THREADS] = 1;
device_heads[1 * CUDA_BLOCK_THREADS] = 1;
device_heads[2 * CUDA_BLOCK_THREADS] = 1;
device_heads[3 * CUDA_BLOCK_THREADS] = 1;
}
}
}
template <bool scatter_ranks_directly>
__global__ __launch_bounds__(CUDA_BLOCK_THREADS, CUDA_SM_THREADS / CUDA_BLOCK_THREADS)
static void libcubwt_rank_and_segment_suffixes_initiatory_kernel(
const uint32_t * RESTRICT device_SA,
const uint64_t * RESTRICT device_keys,
uint8_t * RESTRICT device_heads,
uint32_t * RESTRICT device_ISA,
uint32_t * RESTRICT device_offsets_begin,
uint32_t * RESTRICT device_offsets_end,
uint4 * RESTRICT device_descriptors
)
{
__shared__ __align__(32) uint2 warp_state[1 + CUDA_WARP_THREADS];
uint32_t thread_exclusive_suffix_rank;
uint32_t thread_suffix_rank[4];
uint32_t thread_exclusive_segment_index;
uint32_t thread_segment_index[4];
{
__shared__ __align__(32) ulonglong2 cache[1 + 2 * CUDA_BLOCK_THREADS];
{
device_keys += blockIdx.x * CUDA_BLOCK_THREADS * 4 + threadIdx.x * 2;
if (threadIdx.x == 0) { cache[0] = __ldg((ulonglong2 *)(device_keys - 2)); }
cache[1 + threadIdx.x + 0 * CUDA_BLOCK_THREADS] = __ldg((ulonglong2 *)(device_keys + 0 * CUDA_BLOCK_THREADS));
cache[1 + threadIdx.x + 1 * CUDA_BLOCK_THREADS] = __ldg((ulonglong2 *)(device_keys + 2 * CUDA_BLOCK_THREADS));
}
__syncthreads();
{
const uint32_t block_index = blockIdx.x * CUDA_BLOCK_THREADS * 4;
const uint32_t thread_index = block_index + threadIdx.x * 4;
ulonglong2 key_a = cache[2 * threadIdx.x + 0];
ulonglong2 key_b = cache[2 * threadIdx.x + 1];
ulonglong2 key_c = cache[2 * threadIdx.x + 2];
uchar4 thread_new_heads = make_uchar4(
(key_a.y != key_b.x) ? (uint8_t)1 : (uint8_t)0,
(key_b.x != key_b.y) ? (uint8_t)1 : (uint8_t)0,
(key_b.y != key_c.x) ? (uint8_t)1 : (uint8_t)0,
(key_c.x != key_c.y) ? (uint8_t)1 : (uint8_t)0);
*(uchar4 *)(device_heads + thread_index) = thread_new_heads;
thread_suffix_rank[0] = (thread_new_heads.x != 0) ? (thread_index + 0) : 0;
thread_suffix_rank[1] = (thread_new_heads.y != 0) ? (thread_index + 1) : thread_suffix_rank[0];
thread_suffix_rank[2] = (thread_new_heads.z != 0) ? (thread_index + 2) : thread_suffix_rank[1];
thread_suffix_rank[3] = (thread_new_heads.w != 0) ? (thread_index + 3) : thread_suffix_rank[2];
thread_segment_index[0] = ((thread_new_heads.x != 0) && (key_a.x == key_a.y));
thread_segment_index[1] = thread_segment_index[0] + ((thread_new_heads.y != 0) && (thread_new_heads.x == 0));
thread_segment_index[2] = thread_segment_index[1] + ((thread_new_heads.z != 0) && (thread_new_heads.y == 0));
thread_segment_index[3] = thread_segment_index[2] + ((thread_new_heads.w != 0) && (thread_new_heads.z == 0));
}
}
{
uint32_t thread_inclusive_suffix_rank;
uint32_t thread_inclusive_segment_index;
typedef cub::WarpScan<uint32_t> WarpScan;
__shared__ typename WarpScan::TempStorage warp_scan_storage[CUDA_WARP_THREADS];
WarpScan(warp_scan_storage[threadIdx.x / CUDA_WARP_THREADS]).Scan(thread_suffix_rank[3] , thread_inclusive_suffix_rank , thread_exclusive_suffix_rank , (uint32_t)0, cub::Max());
WarpScan(warp_scan_storage[threadIdx.x / CUDA_WARP_THREADS]).Scan(thread_segment_index[3], thread_inclusive_segment_index, thread_exclusive_segment_index, (uint32_t)0, cub::Sum());
if ((threadIdx.x % CUDA_WARP_THREADS) == (CUDA_WARP_THREADS - 1))
{
warp_state[threadIdx.x / CUDA_WARP_THREADS] = make_uint2(thread_inclusive_suffix_rank, thread_inclusive_segment_index);
}
__syncthreads();
}
{
if (threadIdx.x < CUDA_WARP_THREADS)
{
uint32_t block_exclusive_suffix_rank = 0;
uint32_t block_exclusive_segment_index = 0;
uint32_t warp_inclusive_suffix_rank;
uint32_t warp_inclusive_segment_index;
{
typedef cub::WarpScan<uint32_t> WarpScan;
__shared__ typename WarpScan::TempStorage warp_scan_storage;
uint2 warp_inclusive_state = warp_state[threadIdx.x];
WarpScan(warp_scan_storage).InclusiveScan(warp_inclusive_state.x, warp_inclusive_suffix_rank , cub::Max());
WarpScan(warp_scan_storage).InclusiveScan(warp_inclusive_state.y, warp_inclusive_segment_index, cub::Sum());
}
{
const uint32_t descriptor_status_aggregate_not_ready = 0;
const uint32_t descriptor_status_partial_aggregate_ready = 1;
const uint32_t descriptor_status_full_aggregate_ready = 4;
if (threadIdx.x == ((CUDA_BLOCK_THREADS / CUDA_WARP_THREADS) - 1))
{
cub::ThreadStore<cub::STORE_CG>(device_descriptors + blockIdx.x, make_uint4(descriptor_status_partial_aggregate_ready, 0, warp_inclusive_suffix_rank, warp_inclusive_segment_index));
}
{
uint4 * RESTRICT descriptors_lookback = device_descriptors + blockIdx.x + threadIdx.x;
int32_t full_aggregate_lane, delay = 8;
do
{
descriptors_lookback -= CUDA_WARP_THREADS;
uint4 block_descriptor;
do
{
libcubwt_delay_or_prevent_hoisting(delay <<= 1);
block_descriptor = cub::ThreadLoad<cub::LOAD_CG>(descriptors_lookback);
} while (__any_sync((uint32_t)-1, block_descriptor.x == descriptor_status_aggregate_not_ready));
delay = 0;
{
full_aggregate_lane = 31 - __clz((int32_t)__ballot_sync((uint32_t)-1, block_descriptor.x != descriptor_status_partial_aggregate_ready));
block_descriptor.z = (((int32_t)threadIdx.x) >= full_aggregate_lane) ? block_descriptor.z : 0;
block_descriptor.w = (((int32_t)threadIdx.x) >= full_aggregate_lane) ? block_descriptor.w : 0;
}
{
block_exclusive_suffix_rank = cub::Max()(block_exclusive_suffix_rank , libcubwt_warp_reduce_max(block_descriptor.z));
block_exclusive_segment_index = cub::Sum()(block_exclusive_segment_index, libcubwt_warp_reduce_sum(block_descriptor.w));
}
} while (full_aggregate_lane == -1);
warp_inclusive_suffix_rank = cub::Max()(warp_inclusive_suffix_rank , block_exclusive_suffix_rank );
warp_inclusive_segment_index = cub::Sum()(warp_inclusive_segment_index, block_exclusive_segment_index);
}
if (threadIdx.x == ((CUDA_BLOCK_THREADS / CUDA_WARP_THREADS) - 1))
{
cub::ThreadStore<cub::STORE_CG>(device_descriptors + blockIdx.x, make_uint4(descriptor_status_full_aggregate_ready, 0, warp_inclusive_suffix_rank, warp_inclusive_segment_index));
}
}
{
if (threadIdx.x == 0)
{
warp_state[0] = make_uint2(block_exclusive_suffix_rank, block_exclusive_segment_index);
}
warp_state[1 + threadIdx.x] = make_uint2(warp_inclusive_suffix_rank, warp_inclusive_segment_index);
}
}
__syncthreads();
}
{
uint2 warp_exclusive_state = warp_state[threadIdx.x / CUDA_WARP_THREADS];
thread_exclusive_suffix_rank = cub::Max()(thread_exclusive_suffix_rank , warp_exclusive_state.x);
thread_exclusive_segment_index = cub::Sum()(thread_exclusive_segment_index, warp_exclusive_state.y);
thread_suffix_rank[0] = cub::Max()(thread_suffix_rank[0], thread_exclusive_suffix_rank);
thread_suffix_rank[1] = cub::Max()(thread_suffix_rank[1], thread_exclusive_suffix_rank);
thread_suffix_rank[2] = cub::Max()(thread_suffix_rank[2], thread_exclusive_suffix_rank);
thread_suffix_rank[3] = cub::Max()(thread_suffix_rank[3], thread_exclusive_suffix_rank);
thread_segment_index[0] = cub::Sum()(thread_segment_index[0], thread_exclusive_segment_index);
thread_segment_index[1] = cub::Sum()(thread_segment_index[1], thread_exclusive_segment_index);
thread_segment_index[2] = cub::Sum()(thread_segment_index[2], thread_exclusive_segment_index);
thread_segment_index[3] = cub::Sum()(thread_segment_index[3], thread_exclusive_segment_index);
const uint32_t thread_index = blockIdx.x * CUDA_BLOCK_THREADS * 4 + threadIdx.x * 4;
if (thread_exclusive_segment_index != thread_segment_index[0]) { device_offsets_begin[thread_segment_index[0]] = thread_exclusive_suffix_rank; device_offsets_end[thread_segment_index[0]] = thread_index + 0; }
if (thread_segment_index[0] != thread_segment_index[1]) { device_offsets_begin[thread_segment_index[1]] = thread_suffix_rank[0]; device_offsets_end[thread_segment_index[1]] = thread_index + 1; }
if (thread_segment_index[1] != thread_segment_index[2]) { device_offsets_begin[thread_segment_index[2]] = thread_suffix_rank[1]; device_offsets_end[thread_segment_index[2]] = thread_index + 2; }
if (thread_segment_index[2] != thread_segment_index[3]) { device_offsets_begin[thread_segment_index[3]] = thread_suffix_rank[2]; device_offsets_end[thread_segment_index[3]] = thread_index + 3; }
if (scatter_ranks_directly)
{
const uint4 indexes = __ldg((uint4 *)(device_SA + thread_index));
device_ISA[indexes.x] = thread_suffix_rank[0];
device_ISA[indexes.y] = thread_suffix_rank[1];
device_ISA[indexes.z] = thread_suffix_rank[2];
device_ISA[indexes.w] = thread_suffix_rank[3];
}
else
{
*(uint4 *)(device_ISA + thread_index) = make_uint4(thread_suffix_rank[0], thread_suffix_rank[1], thread_suffix_rank[2], thread_suffix_rank[3]);
}
}
}
template <bool alternate_block_descriptor_statuses, bool scatter_ranks_directly>
__global__ __launch_bounds__(CUDA_BLOCK_THREADS, CUDA_SM_THREADS / CUDA_BLOCK_THREADS)
static void libcubwt_rank_and_segment_suffixes_incremental_kernel(
const uint32_t * RESTRICT device_SA,
const uint32_t * RESTRICT device_keys,
uint8_t * RESTRICT device_heads,
uint32_t * RESTRICT device_out_SA,