我正在尝试调试我编写的程序。我在gdb内运行它，我设法从SIGABRT内抓取calloc()。我完全不知道如何出现这种情况。可能是gcc甚至libc ??
更多细节：我的程序使用OpenMP。我在单线程模式下通过valgrind运行它，没有错误。我还使用mmap()加载40GB文件，但我怀疑这是否相关。在gdb内，我运行了30个线程。几个相同的运行（相同的输入和CL）正确完成，直到我遇到的问题。从表面上看，这表明可能存在某种类型的竞争条件。但是，SIGABRT来自calloc()，这是我无法控制的。以下是一些相关的gdb输出：
(gdb) info threads
[...]
17 Thread 0x7fffec450700 (LWP 73455) 0x00007ffff6b3ce00 in __read_nocancel () from /lib64/libc.so.6
16 Thread 0x7fffece51700 (LWP 73454) _mm_slli_si128 (genome=<value optimized out>, goff=<value optimized out>, glen=50, read=<value optimized out>, rlen=36, genome_ls=<value optimized out>, initbp=-1, is_rna=false) at /usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/emmintrin.h:1155
14 Thread 0x7fffee253700 (LWP 73452) 0x000000000041183e in _mm_prefetch (re=0x7fff291c0f10, st=1, options=0x632014) at /usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/xmmintrin.h:1193
13 Thread 0x7fffeec54700 (LWP 73451) 0x00007ffff6ae5c84 in __memset_sse2 () from /lib64/libc.so.6
12 Thread 0x7fffef655700 (LWP 73450) _mm_cmpeq_epi16 (genome=<value optimized out>, goff=<value optimized out>, glen=33, read=<value optimized out>, rlen=24, genome_ls=<value optimized out>, initbp=-1, is_rna=false) at /usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/emmintrin.h:1263
* 11 Thread 0x7ffff0056700 (LWP 73449) 0x00007ffff6a948a5 in raise () from /lib64/libc.so.6
10 Thread 0x7ffff0a57700 (LWP 73448) _mm_sub_epi16 (genome=<value optimized out>, goff=<value optimized out>, glen=36, read=<value optimized out>, rlen=26, genome_ls=<value optimized out>, initbp=-1, is_rna=false) at /usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/emmintrin.h:1046
5 Thread 0x7ffff3c5c700 (LWP 73443) 0x000000000041183e in _mm_prefetch (re=0x7fff28615010, st=1, options=0x632014) at /usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/xmmintrin.h:1193
2 Thread 0x7ffff5a5f700 (LWP 73440) 0x000000000041e4cd in _mm_max_epi16 (genome=<value optimized out>, goff=<value optimized out>, glen=29, read=<value optimized out>, rlen=21, genome_ls=<value optimized out>, initbp=-1, is_rna=false) at /usr/lib/gcc/x86_64-redhat-linux/4.4.6/include/emmintrin.h:1331
1 Thread 0x7ffff7fdcae0 (LWP 73437) 0x00007ffff6ae5cff in __memset_sse2 () from /lib64/libc.so.6
[...]
(gdb) thread 11
[Switching to thread 11 (Thread 0x7ffff0056700 (LWP 73449))]#0 0x00007ffff6a948a5 in raise () from /lib64/libc.so.6
(gdb) bt
#0 0x00007ffff6a948a5 in raise () from /lib64/libc.so.6
#1 0x00007ffff6a96085 in abort () from /lib64/libc.so.6
#2 0x00007ffff6ad1fe7 in __libc_message () from /lib64/libc.so.6
#3 0x00007ffff6ad7916 in malloc_printerr () from /lib64/libc.so.6
#4 0x00007ffff6adb79f in _int_malloc () from /lib64/libc.so.6
#5 0x00007ffff6adbdd6 in calloc () from /lib64/libc.so.6
#6 0x000000000040e87f in my_calloc (re=0x7fff2867ef10, st=0, options=0x632020) at gmapper/../gmapper/../common/my-alloc.h:286
#7 read_get_hit_list_per_strand (re=0x7fff2867ef10, st=0, options=0x632020) at gmapper/mapping.c:1046
#8 0x000000000041308a in read_get_hit_list (re=<value optimized out>, options=0x632010, n_options=1) at gmapper/mapping.c:1239
#9 handle_read (re=<value optimized out>, options=0x632010, n_options=1) at gmapper/mapping.c:1806
#10 0x0000000000404f35 in launch_scan_threads (.omp_data_i=<value optimized out>) at gmapper/gmapper.c:557
#11 0x00007ffff7230502 in ?? () from /usr/lib64/libgomp.so.1
#12 0x00007ffff6dfc851 in start_thread () from /lib64/libpthread.so.0
#13 0x00007ffff6b4a11d in clone () from /lib64/libc.so.6
(gdb) f 6
#6 0x000000000040e87f in my_calloc (re=0x7fff2867ef10, st=0, options=0x632020) at gmapper/../gmapper/../common/my-alloc.h:286
286 res = calloc(size, 1);
(gdb) p size
$2 = 814080
(gdb)
函数my_calloc()只是一个包装器，但问题不存在，因为真正的calloc()调用看似合法。这些是shell中设置的限制：
$ ulimit -a
core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 2067285
max locked memory (kbytes, -l) 64
max memory size (kbytes, -m) unlimited
open files (-n) 1024
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 10240
cpu time (seconds, -t) unlimited
max user processes (-u) 1024
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited
程序没有内存不足，它在256GB可用的机器上使用41GB：
$ top -b -n 1 | grep gmapper
73437 user 20 0 41.5g 16g 15g T 0.0 6.6 55:17.24 gmapper-ls
$ free -m
total used free shared buffers cached
Mem: 258437 195567 62869 0 82 189677
-/+ buffers/cache: 5807 252629
Swap: 0 0 0
我使用g++ (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4)编译，标记为-g -O2 -DNDEBUG -mmmx -msse -msse2 -fopenmp -Wall -Wno-deprecated -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS。
编辑：我收到的详细错误消息如下。我将其截断，未显示的行与最后一行相似。
*** glibc detected *** /tmp/t/gmapper-ls: corrupted double-linked list: 0x0000000009447380 ***
*** glibc detected *** /tmp/t/gmapper-ls: corrupted double-linked list: 0x0000000009447380 ***
======= Backtrace: =========
======= Backtrace: =========
/lib64/libc.so.6(+0x75916)[0x7ffff6ad7916]
/lib64/libc.so.6(+0x75916)[0x7ffff6ad7916]
/lib64/libc.so.6(+0x7979f)[0x7ffff6adb79f]
/lib64/libc.so.6(+0x7979f)[0x7ffff6adb79f]
/lib64/libc.so.6(__libc_malloc+0x71)[0x7ffff6adc141]
/lib64/libc.so.6(__libc_calloc+0xc6)[0x7ffff6adbdd6]
/usr/lib64/libgomp.so.1(+0x8502)[0x7ffff7230502]
/usr/lib64/libgomp.so.1(+0x8502)[0x7ffff7230502]
/lib64/libc.so.6(clone+0x6d)[0x7ffff6b4a11d]
/lib64/libpthread.so.0(+0x7851)[0x7ffff6dfc851]
/lib64/libc.so.6(clone+0x6d)[0x7ffff6b4a11d]
======= Memory map: ========
00400000-00430000 r-xp 00000000 00:14 927268870 /tmp/t/gmapper
00630000-00631000 rw-p 00030000 00:14 927268870 /tmp/t/gmapper
00631000-2f461000 rw-p 00000000 00:00 0 [heap]
7f749d9be000-7f7e2053b000 r--p 00000000 00:0f 1278724 /dev/shm/hg19-ls
7fff24000000-7fff2727a000 rw-p 00000000 00:00 0
7fff2727a000-7fff28000000 ---p 00000000 00:00 0
7fff285ce000-7fff2c000000 rw-p 00000000 00:00 0
7fff2c000000-7fff2f547000 rw-p 00000000 00:00 0
7fff2f547000-7fff30000000 ---p 00000000 00:00 0
[...]
Edit2 ：我为所有线程添加了线程信息，这些线程在看似“非常重要”的位置停止（10/30）。
答案 0 :(得分：1)
请注意，您的GCC版本已经过时了。目前的海湾合作委员会是4.7.2
出于调试目的，您可以使用较少的优化进行编译：而不是使用-g -O2 -NDEBUG -mmmx -msse -msse2 -fopenmp -Wall，只需使用-g -Wall。
使gdb调试器更加快乐
然后，使用valgrind和gdb调试您的程序。