1、引言
"数据同步算法研究"一文研究了在网络上高效同步数据的方法，其中有个前提是文件A和B非常相似，即两者之间存在大量相同的数据。如果两个文件相似性很低，虽然这种方法依然可以正常工作，但数据同步性能却不会得到提高，甚至会有所降低。因为会产生部分元数据和网络通信消耗，这在两个文件完全不相关时尤为明显。因此，同步数据前需要计算种子文件(seed file)与目标文件之间的相似性，如果相似性大于指定阈值(通常应大于50%)则应用该数据同步算法，否则接传输文件即可。如此，可使得数据同步算法则具有较好的自适应性，在数据具有不同相似性的情形下均可进行高性能的数据同步。另外，在数据相似性检测的基础之上，可对于相似性高的数据进行数据编码处理(如Delta编码)，通过一个文件给另一个文件编码的方式进行数据压缩，这是一种基于相似数据检测与编码的重复数据删除技术。
2、相似性计算
Unix diff对文档进行逐行对比来检测相似文件，它采用经典的LCS(Longest Common Subsequence，最长公共子串)算法，运用动态规划方法来计算相似性。LCS的含义是同时包含在字符串里的一个最长字符序列，LCS的长度作为这两个字符串相似性的度量。Diff算法以整行作为"字符"来计算最长公共子串，性能上比字符级的LCS算法快很多。这种方法效率很低，而且只适用文本文件的相似比较，不能直接适用于二进制文件。
目前通常的做法是将文件相似性问题转换为集合相似性问题，如基于shingle的计算方法和基于bloom filter的计算方法，这两种方法都可适用于任何格式的数据文件。这种方式的核心思想是为每个文件提取组特征值，以特征值集合来计算相似性，从而降低计算复杂性来提高性能。shingle用特征值交集来计算相似性会导致高计算和空间开销，bloom filter技术在计算开销和匹配精度上更具势。Bloom filter所定义的集合元素是文件按照CDC(content-defined chunking)算法所切分数据块的指纹值，其相似性定义如下：
|fingerprints(f1) ∩ fingerprints(f2)|
Sim(f1, f2) = --------------------------------------------- (公式1)
|fingerprints(f1) ∪ fingerprints(f2)|
另外一种方法，是将二进制文件进行切块，使用数据块指纹来表示数据块，然后将数据块映射为"字符"，再应用LCS算法寻找最大公共子串并计算出相似度。其相似性定义如下：
2 * length(LCS(fingerprints(f1), fingerprints(f2)))
Sim(f1, f2) = ------------------------------------------------------------------ (公式2)
length(fingerprints(f1)) + length(fingerprints(f2))
上面两种相似性算法中均采用数据切分技术，数据块可以是定长或变长。为了相似性计算的精确性，实现中采用以数据块长度作为权的加权计算方法。
3、Bloom filter算法
该文件相似性计算流程如下：
(1) 采用CDC算法将文件切分成数据块集，并为每个数据块计算MD5指纹；
(2) 计算两个指纹集合的交集和并集，通过hashtable来实现；
(3) 按照公式1计算文件相似性，考虑重复数据块和数据块长度来提高计算精确度。
详细参见附录bsim源码中的file_chunk，chunk_file_process和similarity_detect函数实现。
4、LCS算法
该文件相似性计算流程如下：
(1) 采用CDC算法将文件切分成数据块集，并为每个数据块计算MD5指纹；
(2) 将MD5指纹串映射为"字符"，则文件转换为"字符串"表示；
(3) 应用LCS算法计算出最长公共子串，并计算其加权长度；
(4) 按照公式2计算文件相似性，考虑重复数据块和数据块长度来提高计算精确度。
详细参见附录bsim源码中的file_chunk，chunk_file_process，LCS和similarity_detect函数实现。
5、算法分析比较
两种算法都对文件进行切分操作，假设文件f1切为m个块，文件f2切分成n个块。Bloom filter算法没有考虑数据块顺序，因此在相似性精确度方面要低于LCS算法，其时间和空间复杂性都是O(m + n)。相反，LCS算法考虑了数据块顺序问题，相似性度量相对精确，然而其时间和空间复杂性是O(mn)，这个大大限制了应用规模。综合来看，Bloom filter算法精确度比LCS算法要低，但计算消耗要小很多，性能和适用性非常好。LCS比较适合精确的文件相似性计算，这些文件往往比较小，50MB以内比较合适。对于重复数据删除和网络数据同步来说，消重效果和性能与数据块顺序性无关，因此Bloom filter算法计算的数据相似性更适用，性能也更高。
附录：bsim.c源码
(完整源码请参见deduputil源码)
- /* Copyright (C) 2010 Aigui Liu
- *
- * This program is free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along
- * with this program; if not, visit the http://fsf.org website.
- */
- #include <stdio.h>
- #include <stdlib.h>
- #include <string.h>
- #include <sys/types.h>
- #include <sys/stat.h>
- #include <fcntl.h>
- #include <unistd.h>
- #include "hashtable.h"
- #include "sync.h"
- #define NEITHER 0
- #define UP 1
- #define LEFT 2
- #define UP_AND_LEFT 3
- #define MAX(x, y) (((x) > (y)) ? (x) : (y))
- #define MIN(x, y) (((x) < (y)) ? (x) : (y))
- #define MD5_LEN 17
- enum {
- FILE1 = 0,
- FILE2
- };
- enum {
- LCS_NOT = 0,
- LCS_YES
- };
- typedef struct {
- uint32_t nr1;
- uint32_t nr2;
- uint32_t len;
- } hash_entry;
- typedef struct {
- char **str;
- uint32_t len;
- } lcs_entry;
- static uint32_t sim_union = 0;
- static uint32_t sim_intersect = 0;
- static void usage()
- {
- fprintf(stderr, "Usage: bsim FILE1 FILE2 CHUNK_ALGO LCS/n/n");
- fprintf(stderr, "Similarity detect between FILE1 and FILE2 based on block level./n");
- fprintf(stderr, "CHUNK_ALGO:/n");
- fprintf(stderr, " FSP - fixed-size partition/n");
- fprintf(stderr, " CDC - content-defined chunking/n");
- fprintf(stderr, " SBC - slide block chunking/n/n");
- fprintf(stderr, "LCS:/n");
- fprintf(stderr, " LCS_NOT - do not use LCS(longest lommon subsequence) algorithms/n");
- fprintf(stderr, " LCS_YES - use LCS algorithms/n/n");
- fprintf(stderr, "Report bugs to <Aigui.Liu@gmail.com>./n");
- }
- static int parse_arg(char *argname)
- {
- if (0 == strcmp(argname, "FSP"))
- return CHUNK_FSP;
- else if (0 == strcmp(argname, "CDC"))
- return CHUNK_CDC;
- else if (0 == strcmp(argname, "SBC"))
- return CHUNK_SBC;
- else if (0 == strcmp(argname, "LCS_NOT"))
- return LCS_NOT;
- else if (0 == strcmp(argname, "LCS_YES"))
- return LCS_YES;
- else
- return -1;
- }
- static char **alloc_2d_array(int row, int col)
- {
- int i;
- char *p, **pp;
- p = (char *)malloc(row * col * sizeof(char));
- pp = (char **)malloc(row * sizeof(char *));
- if (p == NULL || pp == NULL)
- return NULL;
- for (i = 0; i < row; i++) {
- pp[i] = p + col * i;
- }
- return pp;
- }
- static void free_2d_array(char **str)
- {
- free(str[0]);
- free(str);
- }
- static void show_md5_hex(unsigned char md5_checksum[16])
- {
- int i;
- for (i = 0; i < 16; i++) {
- printf("%02x", md5_checksum[i]);
- }
- printf("/n");
- }
- static int chunk_file_process(char *chunk_file, hashtable *htab, int which, int sim_algo, lcs_entry *le)
- {
- int fd, i, ret = 0;
- ssize_t rwsize;
- chunk_file_header chunk_file_hdr;
- chunk_block_entry chunk_bentry;
- hash_entry *he = NULL;
- /* parse chunk file */
- fd = open(chunk_file, O_RDONLY);
- if (-1 == fd) {
- return -1;
- }
- rwsize = read(fd, &chunk_file_hdr, CHUNK_FILE_HEADER_SZ);
- if (rwsize != CHUNK_FILE_HEADER_SZ) {
- ret = -1;
- goto _CHUNK_FILE_PROCESS_EXIT;
- }
- if (sim_algo == LCS_YES) {
- le->str = alloc_2d_array(chunk_file_hdr.block_nr, MD5_LEN);
- if (le->str == NULL) {
- ret = -1;
- goto _CHUNK_FILE_PROCESS_EXIT;
- }
- le->len = chunk_file_hdr.block_nr;
- }
- for(i = 0; i < chunk_file_hdr.block_nr; i++) {
- rwsize = read(fd, &chunk_bentry, CHUNK_BLOCK_ENTRY_SZ);
- if (rwsize != CHUNK_BLOCK_ENTRY_SZ) {
- ret = -1;
- goto _CHUNK_FILE_PROCESS_EXIT;
- }
- he = (hash_entry *)hash_value((void *)chunk_bentry.md5, htab);
- if (he == NULL) {
- he = (hash_entry *)malloc(sizeof(hash_entry));
- he->nr1 = he->nr2 = 0;
- he->len = chunk_bentry.len;
- }
- (which == FILE1) ? he->nr1++ : he->nr2++;
- /* insert or update hash entry */
- hash_insert((void *)strdup(chunk_bentry.md5), (void *)he, htab);
- if (sim_algo == LCS_YES) {
- memcpy(le->str[i], chunk_bentry.md5, MD5_LEN);
- }
- }
- _CHUNK_FILE_PROCESS_EXIT:
- close(fd);
- return ret;
- }
- uint32_t LCS(char** a, int n, char** b, int m, hashtable *htab)
- {
- int** S;
- int** R;
- int ii;
- int jj;
- int pos;
- uint32_t len = 0;
- hash_entry *he = NULL;
- /* Memory allocation */
- S = (int **)malloc( (n+1) * sizeof(int *) );
- R = (int **)malloc( (n+1) * sizeof(int *) );
- if (S == NULL || R == NULL) {
- perror("malloc for S and R in LCS");
- exit(0);
- }
- for(ii = 0; ii <= n; ++ii) {
- S[ii] = (int*) malloc( (m+1) * sizeof(int) );
- R[ii] = (int*) malloc( (m+1) * sizeof(int) );
- if (S[ii] == NULL || R[ii] == NULL) {
- perror("malloc for S[ii] and R[ii] in LCS");
- exit(0);
- }
- }
- /* It is important to use <=, not <. The next two for-loops are initialization */
- for(ii = 0; ii <= n; ++ii) {
- S[ii][0] = 0;
- R[ii][0] = UP;
- }
- for(jj = 0; jj <= m; ++jj) {
- S[0][jj] = 0;
- R[0][jj] = LEFT;
- }
- /* This is the main dynamic programming loop that computes the score and */
- /* backtracking arrays. */
- for(ii = 1; ii <= n; ++ii) {
- for(jj = 1; jj <= m; ++jj) {
- if (strcmp(a[ii-1], b[jj-1]) == 0) {
- S[ii][jj] = S[ii-1][jj-1] + 1;
- R[ii][jj] = UP_AND_LEFT;
- }
- else {
- S[ii][jj] = S[ii-1][jj-1] + 0;
- R[ii][jj] = NEITHER;
- }
- if( S[ii-1][jj] >= S[ii][jj] ) {
- S[ii][jj] = S[ii-1][jj];
- R[ii][jj] = UP;
- }
- if( S[ii][jj-1] >= S[ii][jj] ) {
- S[ii][jj] = S[ii][jj-1];
- R[ii][jj] = LEFT;
- }
- }
- }
- /* The length of the longest substring is S[n][m] */
- ii = n;
- jj = m;
- pos = S[ii][jj];
- /* Trace the backtracking matrix. */
- while( ii > 0 || jj > 0 ) {
- if( R[ii][jj] == UP_AND_LEFT ) {
- ii--;
- jj--;
- //lcs[pos--] = a[ii];
- he = (hash_entry *)hash_value((void *)a[ii], htab);
- len += ((he == NULL) ? 0: he->len);
- }
- else if( R[ii][jj] == UP ) {
- ii--;
- }
- else if( R[ii][jj] == LEFT ) {
- jj--;
- }
- }
- for(ii = 0; ii <= n; ++ii ) {
- free(S[ii]);
- free(R[ii]);
- }
- free(S);
- free(R);
- return len;
- }
- int hash_callback(void *key, void *data)
- {
- hash_entry *he = (hash_entry *)data;
- sim_union += (he->len * (he->nr1 + he->nr2));
- sim_intersect += (he->len * MIN(he->nr1, he->nr2));
- }
- static float similarity_detect(hashtable *htab, char **str1, int n, char **str2, int m, int sim_algo)
- {
- uint32_t lcs_len = 0;
- hash_for_each_do(htab, hash_callback);
- if (sim_algo == LCS_YES) {
- lcs_len = LCS(str1, n, str2, m, htab);
- return lcs_len * 2.0 / sim_union;
- } else { /* LCS_NOT */
- return sim_intersect * 2.0 / sim_union;
- }
- }
- int main(int argc, char *argv[])
- {
- int chunk_algo = CHUNK_CDC;
- int sim_algo = LCS_NOT;
- char *file1 = NULL;
- char *file2 = NULL;
- lcs_entry le1, le2;
- char tmpname[NAME_MAX_SZ] = {0};
- char template[] = "deduputil_bsim_XXXXXX";
- hashtable *htab = NULL;
- int ret = 0;
- if (argc < 5) {
- usage();
- return -1;
- }
- /* parse chunk algorithms */
- file1 = argv[1];
- file2 = argv[2];
- chunk_algo = parse_arg(argv[3]);
- sim_algo = parse_arg(argv[4]);
- if (chunk_algo == -1 || sim_algo == -1) {
- usage();
- return -1;
- }
- htab = create_hashtable(HASHTABLE_BUCKET_SZ);
- if (htab == NULL) {
- fprintf(stderr, "create hashtabke failed/n");
- return -1;
- }
- /* chunk file1 and file2 into blocks */
- sprintf(tmpname, "/tmp/%s_%d", mktemp(template), getpid());
- ret = file_chunk(file1, tmpname, chunk_algo);
- if (0 != ret) {
- fprintf(stderr, "chunk %s failed/n", file1);
- goto _BENCODE_EXIT;
- }
- le1.str = NULL;
- ret = chunk_file_process(tmpname, htab, FILE1, sim_algo, &le1);
- if (ret != 0) {
- fprintf(stderr, "pasre %s failed/n", file1);
- goto _BENCODE_EXIT;
- }
- ret = file_chunk(file2, tmpname, chunk_algo);
- if (0 != ret){
- fprintf(stderr, "chunk %s failed/n", file2);
- goto _BENCODE_EXIT;
- }
- le2.str = NULL;
- ret = chunk_file_process(tmpname, htab, FILE2, sim_algo, &le2);
- if (ret != 0) {
- fprintf(stderr, "pasre %s failed/n", file2);
- goto _BENCODE_EXIT;
- }
- fprintf(stderr, "similarity = %.4f/n", similarity_detect(htab, le1.str, le1.len, le2.str, le2.len, sim_algo));
- _BENCODE_EXIT:
- unlink(tmpname);
- hash_free(htab);
- if (le1.str) free_2d_array(le1.str);
- if (le2.str) free_2d_array(le2.str);
- return ret;
- }
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