sw_perf/main.c

#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <stdint.h>
#include <assert.h>
#include <time.h>
#include "sys/time.h"
#include "thread_mem.h"
#include "ksw_ext.h"
#include "utils.h"

#define SW_NORMAL 0
#define SW_AVX2 1
#define SW_CUDA 2
#define SW_ALL 3

#define BLOCK_BUF_SIZE 1048576
#define READ_BUF_SIZE 2048
#define SEQ_BUF_SIZE (BLOCK_BUF_SIZE + READ_BUF_SIZE)
#define INIT_ALLOC_SIZE 4096

#define DIVIDE_BY (CLOCKS_PER_SEC * 1.0)

#define KERNEL_NUM 7

#ifdef SHOW_PERF
// 用来调试，计算感兴趣部分的运行时间
// 获取当前毫秒数
int64_t get_mseconds()
{
    // struct timeval tv;
    // gettimeofday(&tv, NULL);
    // return (int64_t)1000 * (tv.tv_sec + ((1e-6) * tv.tv_usec));
    return clock();
}

int64_t time_sw[KERNEL_NUM] = {0};

#endif

#define _PERFORMANCE_TEST_NORMAL(kernel_num, func)    \
    cur_query_pos = 0;                                \
    cur_target_pos = 0;                               \
    for (i = 0; i < block_line_num; ++i)              \
    {                                                 \
        score[kernel_num] = func(                     \
            &tmem[kernel_num],                        \
            info_arr[i][0],                           \
            (uint8_t *)query_arr + cur_query_pos,     \
            info_arr[i][1],                           \
            (uint8_t *)target_arr + cur_target_pos,   \
            5, mat, 6, 1, 6, 1, 100, 5, 100,          \
            info_arr[i][2],                           \
            &qle, &tle, &gtle, &gscore, &max_off[0]); \
        score_total[kernel_num] += score[kernel_num]; \
        cur_query_pos += info_arr[i][0];              \
        cur_target_pos += info_arr[i][1];             \
    }

#define _PERFORMANCE_TEST_AVX2(kernel_num, func)      \
    cur_query_pos = 0;                                \
    cur_target_pos = 0;                               \
    for (i = 0; i < block_line_num; ++i)              \
    {                                                 \
        score[kernel_num] = func(                     \
            &tmem[kernel_num],                        \
            info_arr[i][0],                           \
            (uint8_t *)query_arr + cur_query_pos,     \
            info_arr[i][1],                           \
            (uint8_t *)target_arr + cur_target_pos,   \
            0, 6, 1, 6, 1,                            \
            1, 4,                                     \
            100, 5,                                   \
            info_arr[i][2],                           \
            &qle, &tle, &gtle, &gscore, &max_off[0]); \
        score_total[kernel_num] += score[kernel_num]; \
        cur_query_pos += info_arr[i][0];              \
        cur_target_pos += info_arr[i][1];             \
    }

#ifdef SHOW_PERF
#define PERFORMANCE_TEST_NORMAL(kernel_num, func) \
    start_time = get_mseconds();                  \
    _PERFORMANCE_TEST_NORMAL(kernel_num, func);   \
    time_sw[kernel_num] += get_mseconds() - start_time

#define PERFORMANCE_TEST_AVX2(kernel_num, func) \
    start_time = get_mseconds();                \
    _PERFORMANCE_TEST_AVX2(kernel_num, func);   \
    time_sw[kernel_num] += get_mseconds() - start_time
#else
#define PERFORMANCE_TEST_NORMAL(kernel_num, func) _PERFORMANCE_TEST_NORMAL(kernel_num, func)
#define PERFORMANCE_TEST_AVX2(kernel_num, func) _PERFORMANCE_TEST_AVX2(kernel_num, func)
#endif

// 读取一行序列数据
int read_seq_line(char *read_buf, FILE *f_ptr, char *out_arr)
{
    if (fgets(read_buf, READ_BUF_SIZE, f_ptr) == NULL)
        return 0;
    int line_size = strlen(read_buf);
    assert(line_size < READ_BUF_SIZE);
    if (read_buf[line_size - 1] == '\n')
    {
        read_buf[line_size - 1] = '\0';
        line_size--;
    }
    convert_char_to_2bit(read_buf);
    strncpy(out_arr, read_buf, line_size);
    return line_size;
}

// 程序执行入口
int main(int argc, char *argv[])
{
    const char *qf_path = argv[1];
    const char *tf_path = argv[2];
    const char *if_path = argv[3];

    // 初始化一些全局参数
    int8_t mat[25] = {1, -4, -4, -4, -1,
                      -4, 1, -4, -4, -1,
                      -4, -4, 1, -4, -1,
                      -4, -4, -4, 1, -1,
                      -1, -1, -1, -1, -1};
    int max_off[2];
    int qle, tle, gtle, gscore;
    thread_mem_t tmem[KERNEL_NUM];
    int i, j;
    for (i = 0; i < KERNEL_NUM; ++i)
    {
        thread_mem_init_alloc(tmem + i, INIT_ALLOC_SIZE);
    }
    // 记录计算出的分数
    int score[KERNEL_NUM] = {0};
    int score_total[KERNEL_NUM] = {0};

    // 读取测试数据
    char *query_arr = (char *)malloc(SEQ_BUF_SIZE);
    char *target_arr = (char *)malloc(SEQ_BUF_SIZE);
    int *info_buf = (int *)malloc(SEQ_BUF_SIZE * sizeof(int));
    int **info_arr = (int **)malloc(SEQ_BUF_SIZE * sizeof(int *));

    FILE *query_f = 0, *target_f = 0, *info_f = 0;
    FILE *normal_out_f = 0, *avx2_out_f = 0, *avx2_u8_out_f = 0;

    query_f = fopen(qf_path, "r");
    target_f = fopen(tf_path, "r");
    info_f = fopen(if_path, "r");

    // 将每次比对的得分等信息写入文件，进行debug
    // normal_out_f = fopen("normal_out.txt", "w");
    // avx2_out_f = fopen("avx2_out.txt", "w");
    // avx2_u8_out_f = fopen("avx2_u8_out.txt", "w");

    // 每次读取一定量的数据，然后执行，直到处理完所有数据
    int total_line_num = 0; // 目前处理的总的数据行数
    int block_line_num = 0; // 当前循环包含的数据行数
    int cur_query_pos, cur_target_pos;
    int64_t start_time;
    char read_buf[READ_BUF_SIZE]; // 读文件缓存

    // 初始化info_arr数组
    i = 0;
    j = 0;
    while (1)
    {
        if (j > BLOCK_BUF_SIZE)
            break;
        info_arr[i] = &info_buf[j];
        i += 1;
        j += 3;
    }

    while (!feof(target_f))
    {
        block_line_num = 0; // 记录每次读取的行数
        // target序列一般占用存储最多，先读取target，看一个buf能读多少行，query和info就按照这个行数来读
        int cur_read_size = 0;
        while (!feof(target_f) && cur_read_size < BLOCK_BUF_SIZE)
        {
            int line_size = read_seq_line(read_buf, target_f, target_arr + cur_read_size);
            if (line_size == 0)
                break;
            cur_read_size += line_size;
            ++block_line_num;
            ++total_line_num;
        }

        // 读query
        cur_read_size = 0;
        for (i = 0; i < block_line_num; ++i)
        {
            int line_size = read_seq_line(read_buf, query_f, query_arr + cur_read_size);
            if (line_size == 0)
                break;
            cur_read_size += line_size;
        }

        // 读info
        cur_read_size = 0;
        for (i = 0; i < block_line_num; ++i)
        {
            if (fgets(read_buf, READ_BUF_SIZE, info_f) == NULL)
                break;
            const int line_size = strlen(read_buf);
            assert(line_size < READ_BUF_SIZE);
            sscanf(read_buf, "%d %d %d\n", &info_arr[i][0], &info_arr[i][1], &info_arr[i][2]);
            cur_read_size += line_size;
            // fprintf(stderr, "%-8d%-8d%-8d\n", info_arr[i][0], info_arr[i][1], info_arr[i][2]);
            // fprintf(stderr, "%s\n", read_buf);
        }

        // 性能测试

        // normal sw
        PERFORMANCE_TEST_NORMAL(0, ksw_extend_normal);

        // avx2
        PERFORMANCE_TEST_AVX2(1, ksw_extend_avx2);

        // avx2 u8
        PERFORMANCE_TEST_AVX2(2, ksw_extend_avx2_u8);

        // avx2 heuristics
        PERFORMANCE_TEST_AVX2(3, ksw_extend_avx2_heuristics);

        // avx2 u8 heuristics
        PERFORMANCE_TEST_AVX2(4, ksw_extend_avx2_u8_heuristics);

        // avx2 mem aligned
        PERFORMANCE_TEST_AVX2(5, ksw_extend_avx2_aligned);

        // avx2 u8 mem aligned
        PERFORMANCE_TEST_AVX2(6, ksw_extend_avx2_u8_aligned);
    }

#ifdef SHOW_PERF
    char *kernel_names[7] = {
        "normal",
        "avx2",
        "avx2_u8",
        "avx2_heuristics",
        "avx2_u8_heuristics",
        "avx2_aligned",
        "avx2_u8_aligned"};

    for (i = 0; i < KERNEL_NUM; ++i)
    {
        fprintf(stderr, "[%18s] time: %9.6f s; score: %d\n", kernel_names[i], time_sw[i] / DIVIDE_BY, score_total[i]);
    }
#endif

    if (query_f != 0)
        fclose(query_f);
    if (target_f != 0)
        fclose(target_f);
    if (info_f != 0)
        fclose(info_f);
    if (avx2_out_f != 0)
        fclose(avx2_out_f);
    if (avx2_u8_out_f != 0)
        fclose(avx2_u8_out_f);
    if (normal_out_f != 0)
        fclose(normal_out_f);
}