与Python相比，具有动态分配的结构数组在C中的运行速度非常慢 [英] Array of structs with dynamic allocation runs very slow in C in comparison to Python

问题描述

我(在其他SO用户的帮助下)粘合"了一个小型C程序，该程序将字符串标签映射到边缘列表数据结构中的整数标签.例如，对于输入文件

I "glue" together (with a help of other SO users) a small C program that maps string labels to integer labels in a edgelist data structure. For instance, for input file

Mike Andrew
Mike Jane
John Jane

程序输出

1 2
1 3
4 3

但是，我映射了巨大的边缘列表文件，不幸的是，与Python替代版本相比，该程序运行非常慢.下面，我用C和Python粘贴了这两个程序.请问如何提高C程序速度的指针.

However, I mapped huge edgelist files and unfortunately the program runs very slow in comparison to Python alternative. Below I pasted both programs, in C and Python. I kindly ask for a pointers how to improve speed of the C program.

#include <stdio.h>
#include <stdlib.h>

// Initial number of maximal lines in a file
enum { MAXL = 200};

typedef struct {
    unsigned int first;
    unsigned int second;
} edge;

typedef struct {
    unsigned int hashed;
     char **map;
} hash;


int insertInMap(hash *map, char *entry)
{
  int i =0;
  for (i=0;i<map->hashed;i++)
  {
    if (strcmp(map->map[i],entry) == 0)
    return i+1;
  }
  /* Warning no boundary check is added */
  map->map[map->hashed++] = strdup(entry);   
  return map->hashed;
}

int main() {
  FILE *fp = NULL;
  char node1[30];
  char node2[30];
  int idx = 0;
  int i, n = 0, maxl = MAXL;

  edge *edges;
  hash map;

  edges = malloc(MAXL * sizeof(edge));
  map.map = malloc(MAXL * sizeof(char*));
  map.hashed = 0;

  fp = fopen("./test.txt", "r");

  while (fscanf(fp, "%s %s", &node1, &node2) == 2) {
    if (++n == maxl) { /* if limit reached, realloc lines  */
      void *tmp = realloc (edges, (maxl + 40) * sizeof *edges);
      void *tmp1 = realloc (map.map, (maxl + 80) * sizeof(char*));
      if (!tmp) {     /* validate realloc succeeded */
        fprintf (stderr, "error: realloc - virtual memory exhausted.\n");
        break;      /* on failure, exit with existing data */
      }
      edges = tmp;    /* assign reallocated block to lines */

      map.map = tmp1;
      maxl += 40;     /* update maxl to reflect new size */
    }
    edges[idx].first = insertInMap(&map,node1);
    edges[idx].second = insertInMap(&map,node2);
    idx++;
  }

  fclose(fp);

  for (int i = 0; i < idx; i++) {
    printf("%d -- %d\n", edges[i].first, edges[i].second);
  }


  free(edges);

  return 0;
}

相应的Python替代方法:

The corresponding Python alternative:

import fileinput

i = 0
cui2int = {}

for line in fileinput.input():    
    (cui1, cui2) = line.split()
    if cui1 in cui2int:
        int1 = cui2int[cui1]
    else:
        i += 1
        cui2int[cui1] = i
        int1 = i

    if cui2 in cui2int:
        int2 = cui2int[cui2]
    else:
        i += 1
        cui2int[cui2] = i
        int2 = i

    print(int1, int2)

已编辑并添加

以下是使用GLib哈希实现的修改后的代码.我提高了性能，但不幸的是输出仍然有问题

Below is modified code using the GLib hash implementation. I improved performance, but unfortunately still have troubles with the output which should be

1 2
1 3
4 3

代替

0 0
0 1
1 1

有人可以看看吗?

#include <stdio.h>
#include <stdlib.h>
#include <glib.h>
#include <stdint.h>

int main() {
  GHashTable *table;
  table = g_hash_table_new(g_int_hash, g_int_equal);

  FILE *fp = NULL;
  char node1[30];
  char node2[30];

  fp = fopen("./test.txt", "r");
  int i = 0;
  while (fscanf(fp, "%s %s", &node1, &node2) == 2) {
    char *key1 = malloc(sizeof(char)*1024);
    char *key2 = malloc(sizeof(char)*1024);
    uint32_t* value = (uint32_t *)malloc(sizeof(uint32_t));
    key1 = g_strdup(node1);
    key2 = g_strdup(node2);
    *value = i;

    uint32_t *x;
    if (g_hash_table_contains(table, key1)) {
      x = (uint32_t *)g_hash_table_lookup(table, key1);
    } else {
      i++;
      g_hash_table_insert(table, (gpointer)key1, (gpointer)value);
      x = (uint32_t *)value;
    }

    uint32_t *y;
    if (g_hash_table_contains(table, key2)) {
      y = (uint32_t *)g_hash_table_lookup(table, key2);
    } else {
      g_hash_table_insert(table, (gpointer)key2, (gpointer)value);
      y = (uint32_t *)value;
    }
    printf("%d -- %d\n", *x, *y);
  }

  fclose(fp);

  g_hash_table_destroy(table);
  table = NULL;
  return 0;
}

推荐答案

这两个程序使用的是根本不同的数据结构，具有不同的时间复杂度. python程序使用的字典是高度优化的哈希表，具有摊销性能的 O ( 1 )用于查找和删除.

The two programs are using fundamentally different data structures with different time complexity. The python program is using a dictionary which is a highly tuned hash- table with O(1) amortized performance for lookup and deletion.

因此python程序以 O (字数)渐近复杂性运行.

So the python program is running with O(number of words) asymptotic complexity.

现在，谈论您要尝试创建的C程序，本质上只是一个键-值对数组.在这里插入或检索键需要 O (数组的大小)，因为您可以循环遍历数组直到最后找到匹配项.

Now, talking about your C program what you have tried to create is essentially just an array of key-value pairs. Inserting or retrieving the keys takes O(size of the array) here since you can potentially loop through the array till the end to find a match.

如果做一些数学运算，结果就是 O (((i)单词数) ² ).

If you do some math, it turns out to be O((number of words)²).

C ++具有名为 unordered_map 的内置哈希表实现，您如果您可以顺利切换到C ++，可以使用它.或在SO上检查此问题，以学习在C中编写自己的哈希表.

C++ has built-in Hash-table implementation named unordered_map, you can use that if you have no trouble switching to C++. Or check out this question on SO to learn writing your own hash table in C. What is a hash table and how do you make it in C?

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