lib pthread：单线程性能与多线程
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【中文标题】lib pthread：单线程性能与多线程【英文标题】：lib pthread: single threaded performance vs multithreaded 【发布时间】：2012-12-19 08:43:37 【问题描述】：（注意：我看到了这个帖子，如果是同样的问题，请告诉我：C: performance of pthread, low than single thrad）
我正在学习 pthread 库。我编写了同一个 C 程序的两个版本。该程序采用BAM files 的大列表并使用samtools library 计算记录数。
这是单线程程序：
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
#include "bam.h"
/** maximum number of threads */
static const int MAX_COUNT_THREADS=4;
struct Param
char* filename;
;
static void printCount(const char* filename,unsigned long count)
fprintf(stdout,"%s\t%ld\n",filename,count);
static void* scan_bam(void* ptr)
unsigned long count=0;
struct Param* params=(struct Param*)ptr;
bamFile in=bam_open(params->filename, "r") ;
bam_header_t *header= NULL;
bam1_t *b=bam_init1();
time_t rawtime;
time ( &rawtime );
fprintf(stderr,"STARTING : %s %s",params->filename,ctime(&rawtime));
if(in==0)
fprintf(stderr,"Cannot read %s.\n",params->filename);
exit(EXIT_FAILURE);
header= bam_header_read(in);
while((bam_read1(in, b)) > 0)
++count;
bam_destroy1(b);
bam_header_destroy(header);
bam_close(in);
printCount(params->filename,count);
time ( &rawtime );
fprintf(stderr,"end for %s %s",params->filename,ctime(&rawtime));
free(params);
return NULL;
int main(int argc,char** argv)
int optind=1;
while(optind<argc)
struct Param* params=(struct Param*)malloc(sizeof(struct Param));
if(params==0)
fprintf(stderr,"Out of memory.\n");
exit(EXIT_FAILURE);
params->filename=argv[optind++];
scan_bam(params);
return EXIT_SUCCESS;
和多线程程序。该程序最多可以使用 5 个线程，并使用条件锁来计算线程数，并告诉主程序在需要时启动一个新线程。
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <pthread.h>
#include <time.h>
#include "bam.h"
#define VERIFY_ZERO(a) do if(a!=0) \
fprintf(stderr,"Test failed at %s line %d (ret=%d).\n",__FILE__,__LINE__,a);\
exit(EXIT_FAILURE);\
while(0)
/** maximum number of threads */
static const int MAX_COUNT_THREADS=5;
struct Param
pthread_t thread;
char* filename;
;
struct GLOBALS
/** lock to print */
pthread_mutex_t mutex_print;
/** condition: wait for free thread */
pthread_cond_t accept_new_thread;
/** condition lock */
pthread_mutex_t accept_new_thread_lock;
/** number of running threads */
int number_of_threads;
;
static struct GLOBALS globals=
PTHREAD_MUTEX_INITIALIZER,
PTHREAD_COND_INITIALIZER,
PTHREAD_MUTEX_INITIALIZER,
0
;
static void printCount(const char* filename,unsigned long count)
int ret=pthread_mutex_lock(&globals.mutex_print);
VERIFY_ZERO(ret);
fprintf(stdout,"%s\t%ld\n",filename,count);
ret=pthread_mutex_unlock(&globals.mutex_print);
VERIFY_ZERO(ret);
static void* scan_bam(void* ptr)
unsigned long count=0;
struct Param* params=(struct Param*)ptr;
bamFile in=bam_open(params->filename, "r") ;
bam_header_t *header= NULL;
bam1_t *b=bam_init1();
time_t rawtime;
time ( &rawtime );
fprintf(stderr,"STARTING : %s %s",params->filename,ctime(&rawtime));
if(in==0)
fprintf(stderr,"Cannot read %s.\n",params->filename);
exit(EXIT_FAILURE);
header= bam_header_read(in);
while((bam_read1(in, b)) > 0)
++count;
bam_destroy1(b);
bam_header_destroy(header);
bam_close(in);
printCount(params->filename,count);
time ( &rawtime );
fprintf(stderr,"end1 for %s %s",params->filename,ctime(&rawtime));
pthread_mutex_lock( &globals.accept_new_thread_lock);
globals.number_of_threads--;
pthread_cond_signal(&globals.accept_new_thread);
pthread_mutex_unlock(&globals.accept_new_thread_lock);
time ( &rawtime );
fprintf(stderr,"end2 for %s %s",params->filename,ctime(&rawtime));
free(params);
return NULL;
int main(int argc,char** argv)
int optind=1;
while(optind<argc)
struct Param* params=(struct Param*)malloc(sizeof(struct Param));
if(params==0)
fprintf(stderr,"Out of memory.\n");
exit(EXIT_FAILURE);
pthread_mutex_lock(&globals.accept_new_thread_lock);
while (globals.number_of_threads > MAX_COUNT_THREADS)
pthread_cond_wait(&globals.accept_new_thread, &globals.accept_new_thread_lock);
globals.number_of_threads++;
pthread_mutex_unlock(&globals.accept_new_thread_lock);
params->filename=argv[optind++];
fprintf(stderr,"creating %s\n",params->filename);
pthread_create (&(params->thread), NULL, scan_bam,params);
pthread_detach(params->thread);
pthread_mutex_lock(&globals.accept_new_thread_lock);
while (globals.number_of_threads > 0)
pthread_cond_wait(&globals.accept_new_thread, &globals.accept_new_thread_lock);
pthread_mutex_unlock(&globals.accept_new_thread_lock);
pthread_cond_destroy(&globals.accept_new_thread);
return EXIT_SUCCESS;
编译运行多线程程序
gcc -O3 -Wall jeter.c -pthread -I/usr/local/package/samtools-0.1.18 -L/usr/local/package/samtools-0.1.18/ -lbam -lz
$ time (find .// -name "*recal.bam" | grep Item1[0-9] | xargs ./a.out )
creating ./Item10/recal.bam
creating ./Item11/recal.bam
creating ./Item12/recal.bam
creating ./Item13/recal.bam
creating ./Item14/recal.bam
creating ./Item15/recal.bam
STARTING : ./Item10/recal.bam Tue Dec 18 15:12:48 2012
STARTING : ./Item11/recal.bam Tue Dec 18 15:12:48 2012
STARTING : ./Item12/recal.bam Tue Dec 18 15:12:48 2012
STARTING : ./Item14/recal.bam Tue Dec 18 15:12:48 2012
STARTING : ./Item13/recal.bam Tue Dec 18 15:12:48 2012
STARTING : ./Item15/recal.bam Tue Dec 18 15:12:48 2012
./Item10/recal.bam 185784310
end1 for ./Item10/recal.bam Tue Dec 18 15:38:16 2012
end2 for ./Item10/recal.bam Tue Dec 18 15:38:16 2012
creating ./Item16/recal.bam
STARTING : ./Item16/recal.bam Tue Dec 18 15:38:16 2012
./Item11/recal.bam 204408906
end1 for ./Item11/recal.bam Tue Dec 18 15:41:52 2012
end2 for ./Item11/recal.bam Tue Dec 18 15:41:52 2012
creating ./Item17/recal.bam
STARTING : ./Item17/recal.bam Tue Dec 18 15:41:52 2012
./Item12/recal.bam 207766317
end1 for ./Item12/recal.bam Tue Dec 18 15:42:17 2012
end2 for ./Item12/recal.bam Tue Dec 18 15:42:17 2012
creating ./Item18/recal.bam
STARTING : ./Item18/recal.bam Tue Dec 18 15:42:17 2012
./Item15/recal.bam 224957522
end1 for ./Item15/recal.bam Tue Dec 18 15:44:54 2012
end2 for ./Item15/recal.bam Tue Dec 18 15:44:54 2012
creating ./Item19/recal.bam
STARTING : ./Item19/recal.bam Tue Dec 18 15:44:54 2012
./Item13/recal.bam 224548326
end1 for ./Item13/recal.bam Tue Dec 18 15:45:32 2012
end2 for ./Item13/recal.bam Tue Dec 18 15:45:32 2012
./Item14/recal.bam 241267346
end1 for ./Item14/recal.bam Tue Dec 18 15:48:28 2012
end2 for ./Item14/recal.bam Tue Dec 18 15:48:28 2012
./Item16/recal.bam 227446579
end1 for ./Item16/recal.bam Tue Dec 18 16:12:15 2012
end2 for ./Item16/recal.bam Tue Dec 18 16:12:15 2012
./Item17/recal.bam 215307379
end1 for ./Item17/recal.bam Tue Dec 18 16:13:05 2012
end2 for ./Item17/recal.bam Tue Dec 18 16:13:05 2012
./Item18/recal.bam 225914723
end1 for ./Item18/recal.bam Tue Dec 18 16:13:48 2012
end2 for ./Item18/recal.bam Tue Dec 18 16:13:48 2012
./Item19/recal.bam 225509630
end1 for ./Item19/recal.bam Tue Dec 18 16:14:06 2012
end2 for ./Item19/recal.bam Tue Dec 18 16:14:06 2012
。
real 61m17.560s
user 66m0.476s
sys 4m5.980s
编译运行单线程程序
$ gcc -O3 -Wall jeter2.c -I/usr/local/package/samtools-0.1.18 -L/usr/local/package/samtools-0.1.18/ -lbam -lz
time (find .// -name "*recal.bam" | grep Item1[0-9] | xargs ./a.out )
STARTING : ./Item10/recal.bam Tue Dec 18 16:15:25 2012
./Item10/recal.bam 185784310
end for ./Item10/recal.bam Tue Dec 18 16:20:43 2012
STARTING : ./Item11/recal.bam Tue Dec 18 16:20:43 2012
./Item11/recal.bam 204408906
end for ./Item11/recal.bam Tue Dec 18 16:26:20 2012
STARTING : ./Item12/recal.bam Tue Dec 18 16:26:20 2012
./Item12/recal.bam 207766317
end for ./Item12/recal.bam Tue Dec 18 16:31:56 2012
STARTING : ./Item13/recal.bam Tue Dec 18 16:31:56 2012
./Item13/recal.bam 224548326
end for ./Item13/recal.bam Tue Dec 18 16:38:05 2012
STARTING : ./Item14/recal.bam Tue Dec 18 16:38:05 2012
./Item14/recal.bam 241267346
end for ./Item14/recal.bam Tue Dec 18 16:44:59 2012
STARTING : ./Item15/recal.bam Tue Dec 18 16:44:59 2012
./Item15/recal.bam 224957522
end for ./Item15/recal.bam Tue Dec 18 16:50:56 2012
STARTING : ./Item16/recal.bam Tue Dec 18 16:50:56 2012
./Item16/recal.bam 227446579
end for ./Item16/recal.bam Tue Dec 18 16:58:07 2012
STARTING : ./Item17/recal.bam Tue Dec 18 16:58:07 2012
./Item17/recal.bam 215307379
end for ./Item17/recal.bam Tue Dec 18 17:04:58 2012
STARTING : ./Item18/recal.bam Tue Dec 18 17:04:58 2012
./Item18/recal.bam 225914723
end for ./Item18/recal.bam Tue Dec 18 17:11:31 2012
STARTING : ./Item19/recal.bam Tue Dec 18 17:11:31 2012
./Item19/recal.bam 225509630
end for ./Item19/recal.bam Tue Dec 18 17:18:19 2012
.
real 62m54.503s
user 53m39.529s
sys 3m44.580s
这两个程序都已运行了 ~1H00。所以 MT 程序的运行速度比另一个慢。为什么 ？是否可以加速该代码？
【问题讨论】：
这里的问题可能是文件系统。在线程程序中，您尝试同时读取多个文件，可能从同一个磁盘读取，效率不高。 @JoachimPileborg - 我希望有人会为这种磁盘操作生成一些实际的统计数据。海报一直说使用多个线程要么无济于事，要么实际上减慢了速度，但我没有看到任何数字/图表。如果有人真的用一个本地微调器、一个本地 SSD 和一个网络磁盘（也许还有一些组合）来尝试这个，那就太好了。 【参考方案1】：看起来 I/O 操作（从文件中读取）在您的程序中占主导地位，因此很可能您不会从线程中获得太多好处，无论它做得多么好。
还要注意，多线程变体实际上要快一点；你需要比较实时。 用户时间由于多线程而更大，因为它总结了所有线程在用户模式下花费的时间。 内核时间也是如此。
【讨论】：
+1，尽管我要补充一点，如果文件位于不同的磁盘上，尤其是众所周知的延迟和容易断开连接的网络磁盘，则可以实现更大的加速。另外，我想知道如果重新设计应用程序以池化线程并避免痛苦的持续创建/终止/销毁线程会产生什么影响？【参考方案2】：首先我想澄清一点：
多线程并不一定意味着您的程序会运行得更快！
这可能意味着，但这取决于您的程序可以真正执行的并行度。
我在您的 MT 代码中看到您正在等待条件变量，这意味着那里可能存在争用点，并且这里没有真正的并行性。
当你的线程每个都可以做一大堆工作而不必等待其他线程时，实际上可以通过线程获得真正的加速。如果它们可以完全独立完成，您可能会得到一些加速。
然后，该加速还取决于诸如错误共享之类的事情，即（假设是多核 CPU），如果您在内存中有一些数组并且线程 A 需要该数组中的元素 2，而另一个运行的线程 B 也需要元素 4在那个数组中，元素是 sizeof(int) 例如，那么你就会知道你遇到了缓存问题。每次任何一个线程写入数组时，都需要更新缓存。假设高速缓存行是 64k。这是虚假分享。这可能会导致相当严重的减速。
还有其他原因导致您的 MT 程序无法比单线程程序加速。你应该问的最终问题是：
我可以让线程做不依赖于任何其他线程的工作吗？
从你让你的线程做的所有等待来看，似乎没有。
【讨论】：
我明白了。感谢您提供有用的答案。稍后我会验证最佳答案。以上是关于lib pthread：单线程性能与多线程的主要内容，如果未能解决你的问题，请参考以下文章