Deadlock flush - malloc - fork - fgets

Deadlock flush - malloc - fork - fgets

[Eduardo Iglesias]

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Context:

Linux ubuntucluster 4.15.0-55-generic #60-Ubuntu SMP Tue Jul 2 18:22:20 
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

# /lib/x86_64-linux-gnu/libc.so.6
GNU C Library (Ubuntu GLIBC 2.27-3ubuntu1) stable release version 2.27.

Lua 5.1

Use PRELOAD Jemalloc 5.3.


Description:

Similar issue based on https://sourceware.org/bugzilla/show_bug.cgi?id=19431


BT Threads:

Thread 377 (Thread 0x7fbcab75b700 (LWP 4403)):
$6 = pthread_mutex_t = {Type = Normal, Status = Acquired, possibly with 
waiters, Owner ID = 3156, Robust = No, Shared = No, Protocol = None}

Thread 368 (Thread 0x7fbcac964700 (LWP 4394)):
$7 = pthread_mutex_t = {Type = Normal, Status = Acquired, possibly with 
waiters, Owner ID = 3156, Robust = No, Shared = No, Protocol = None}

Thread 360 (Thread 0x7fbcad96c700 (LWP 4386)):
$8 = pthread_mutex_t = {Type = Normal, Status = Acquired, possibly with 
waiters, Owner ID = 3156, Robust = No, Shared = No, Protocol = None}

Thread 355 (Thread 0x7fbcae371700 (LWP 4381)):
$2 = pthread_mutex_t = {Type = Normal, Status = Acquired, possibly with 
waiters, Owner ID = 3156, Robust = No, Shared = No, Protocol = None}


[Switching to thread 7 (Thread 0x7fbd273fa700 (LWP 3156))]
#0  __lll_lock_wait_private () at 
../sysdeps/unix/sysv/linux/x86_64/lowlevellock.S:95
95      ../sysdeps/unix/sysv/linux/x86_64/lowlevellock.S: No such file 
or directory.
(gdb) bt
#0  __lll_lock_wait_private () at 
../sysdeps/unix/sysv/linux/x86_64/lowlevellock.S:95
#1  0x00007fbd286c0e2a in __GI__IO_list_lock () at genops.c:1188
#2  0x00007fbd28715965 in __libc_fork () at ../sysdeps/nptl/fork.c:125
#3  0x00007fbd286b16b4 in _IO_new_proc_open (fp=fp@entry=0x7fbc9860ae00, 
command=command@entry=0x7fbc019251f8 "lsb_release -i", mode=<optimized 
out>, mode@entry=0x7fbc37e03df8 "r") at iopopen.c:122
#4  0x00007fbd286b1938 in _IO_new_popen 
(command=command@entry=0x7fbc019251f8 "lsb_release -i", 
mode=mode@entry=0x7fbc37e03df8 "r") at iopopen.c:206
#5  0x000056156400b4f2 in io_popen (L=0x7fbc019f8000) at liolib.c:178
#6  0x0000561563ff9f48 in luaD_precall (L=L@entry=0x7fbc019f8000, 
func=func@entry=0x7fbba9e04490, nresults=nresults@entry=-1) at ldo.c:320
#7  0x0000561564003602 in luaV_execute (L=L@entry=0x7fbc019f8000, 
nexeccalls=6, nexeccalls@entry=1) at lvm.c:591
#8  0x0000561563ffa2ad in luaD_call (L=0x7fbc019f8000, 
func=0x7fbba9e04380, nResults=<optimized out>) at ldo.c:378
#9  0x0000561563ff971e in luaD_rawrunprotected 
(L=L@entry=0x7fbc019f8000, f=f@entry=0x561563ff5b80 <f_call>, 
ud=ud@entry=0x7fbd273f8490) at ldo.c:116
#10 0x0000561563ffa41b in luaD_pcall (L=L@entry=0x7fbc019f8000, 
func=func@entry=0x561563ff5b80 <f_call>, u=u@entry=0x7fbd273f8490, 
old_top=896, ef=<optimized out>) at ldo.c:464
#11 0x0000561563ff79d5 in lua_pcall (L=L@entry=0x7fbc019f8000, 
nargs=nargs@entry=0, nresults=nresults@entry=-1, 
errfunc=errfunc@entry=1) at lapi.c:821
#12 0x000056156400893c in luaB_xpcall (L=0x7fbc019f8000) at lbaselib.c:389
#13 0x0000561563ff9f48 in luaD_precall (L=L@entry=0x7fbc019f8000, 
func=func@entry=0x7fbba9e04360, nresults=nresults@entry=2) at ldo.c:320
#14 0x0000561564003602 in luaV_execute (L=L@entry=0x7fbc019f8000, 
nexeccalls=5, nexeccalls@entry=1) at lvm.c:591
#15 0x0000561563ffa2ad in luaD_call (L=0x7fbc019f8000, 
func=0x7fbba9e041b0, nResults=<optimized out>) at ldo.c:378
#16 0x0000561563ff971e in luaD_rawrunprotected 
(L=L@entry=0x7fbc019f8000, f=f@entry=0x561563ff5b80 <f_call>, 
ud=ud@entry=0x7fbd273f8740) at ldo.c:116
#17 0x0000561563ffa41b in luaD_pcall (L=L@entry=0x7fbc019f8000, 
func=func@entry=0x561563ff5b80 <f_call>, u=u@entry=0x7fbd273f8740, 
old_top=432, ef=<optimized out>) at ldo.c:464
#18 0x0000561563ff79d5 in lua_pcall (L=L@entry=0x7fbc019f8000, 
nargs=nargs@entry=0, nresults=nresults@entry=-1, 
errfunc=errfunc@entry=1) at lapi.c:821
#19 0x000056156400893c in luaB_xpcall (L=0x7fbc019f8000) at lbaselib.c:389
#20 0x0000561563ff9f48 in luaD_precall (L=L@entry=0x7fbc019f8000, 
func=func@entry=0x7fbba9e04190, nresults=nresults@entry=-1) at ldo.c:320
#21 0x000056156400359f in luaV_execute (L=L@entry=0x7fbc019f8000, 
nexeccalls=3, nexeccalls@entry=1) at lvm.c:612
#22 0x0000561563ffa2ad in luaD_call (L=0x7fbc019f8000, 
func=0x7fbba9e04040, nResults=<optimized out>) at ldo.c:378
#23 0x0000561563ff971e in luaD_rawrunprotected 
(L=L@entry=0x7fbc019f8000, f=f@entry=0x561563ff5b80 <f_call>, 
ud=ud@entry=0x7fbd273f89f0) at ldo.c:116
#24 0x0000561563ffa41b in luaD_pcall (L=L@entry=0x7fbc019f8000, 
func=func@entry=0x561563ff5b80 <f_call>, u=u@entry=0x7fbd273f89f0, 
old_top=64, ef=<optimized out>) at ldo.c:464
#25 0x0000561563ff79d5 in lua_pcall (L=0x7fbc019f8000, nargs=<optimized 
out>, nresults=-1, errfunc=<optimized out>) at lapi.c:821


(gdb)f 1
(gdb)p list_all_lock

$6 = {lock = 2, cnt = 1, owner = 0x7fbd223d2700}

[Switching to thread 47 (Thread 0x7fbd223d2700 (LWP 3196))]
#0  __lll_lock_wait_private () at 
../sysdeps/unix/sysv/linux/x86_64/lowlevellock.S:95
#1  0x00007fbd286c0274 in _IO_flush_all_lockp (do_lock=do_lock@entry=1) 
at genops.c:762
#2  0x00007fbd286c06fa in __GI__IO_flush_all () at genops.c:790
#3  0x00007fbd286af895 in __GI__IO_fflush (fp=fp@entry=0x0) at iofflush.c:34
#4  0x000056156400b4e7 in io_popen (L=0x7fbc2905e780) at liolib.c:178
#5  0x0000561563ff9f48 in luaD_precall (L=L@entry=0x7fbc2905e780, 
func=func@entry=0x7fbc08418c90, nresults=nresults@entry=-1) at ldo.c:320
#6  0x0000561564003602 in luaV_execute (L=L@entry=0x7fbc2905e780, 
nexeccalls=6, nexeccalls@entry=1) at lvm.c:591
#7  0x0000561563ffa2ad in luaD_call (L=0x7fbc2905e780, 
func=0x7fbc08418b80, nResults=<optimized out>) at ldo.c:378
#8  0x0000561563ff971e in luaD_rawrunprotected 
(L=L@entry=0x7fbc2905e780, f=f@entry=0x561563ff5b80 <f_call>, 
ud=ud@entry=0x7fbd223d0490) at ldo.c:116
#9  0x0000561563ffa41b in luaD_pcall (L=L@entry=0x7fbc2905e780, 
func=func@entry=0x561563ff5b80 <f_call>, u=u@entry=0x7fbd223d0490, 
old_top=896, ef=<optimized out>) at ldo.c:464
#10 0x0000561563ff79d5 in lua_pcall (L=L@entry=0x7fbc2905e780, 
nargs=nargs@entry=0, nresults=nresults@entry=-1, 
errfunc=errfunc@entry=1) at lapi.c:821
#11 0x000056156400893c in luaB_xpcall (L=0x7fbc2905e780) at lbaselib.c:389
#12 0x0000561563ff9f48 in luaD_precall (L=L@entry=0x7fbc2905e780, 
func=func@entry=0x7fbc08418b60, nresults=nresults@entry=2) at ldo.c:320
#13 0x0000561564003602 in luaV_execute (L=L@entry=0x7fbc2905e780, 
nexeccalls=5, nexeccalls@entry=1) at lvm.c:591
#14 0x0000561563ffa2ad in luaD_call (L=0x7fbc2905e780, 
func=0x7fbc084189b0, nResults=<optimized out>) at ldo.c:378
#15 0x0000561563ff971e in luaD_rawrunprotected 
(L=L@entry=0x7fbc2905e780, f=f@entry=0x561563ff5b80 <f_call>, 
ud=ud@entry=0x7fbd223d0740) at ldo.c:116
#16 0x0000561563ffa41b in luaD_pcall (L=L@entry=0x7fbc2905e780, 
func=func@entry=0x561563ff5b80 <f_call>, u=u@entry=0x7fbd223d0740, 
old_top=432, ef=<optimized out>) at ldo.c:464
#17 0x0000561563ff79d5 in lua_pcall (L=L@entry=0x7fbc2905e780, 
nargs=nargs@entry=0, nresults=nresults@entry=-1, 
errfunc=errfunc@entry=1) at lapi.c:821
#18 0x000056156400893c in luaB_xpcall (L=0x7fbc2905e780) at lbaselib.c:389
#19 0x0000561563ff9f48 in luaD_precall (L=L@entry=0x7fbc2905e780, 
func=func@entry=0x7fbc08418990, nresults=nresults@entry=-1) at ldo.c:320
#20 0x000056156400359f in luaV_execute (L=L@entry=0x7fbc2905e780, 
nexeccalls=3, nexeccalls@entry=1) at lvm.c:612
#21 0x0000561563ffa2ad in luaD_call (L=0x7fbc2905e780, 
func=0x7fbc08418840, nResults=<optimized out>) at ldo.c:378
#22 0x0000561563ff971e in luaD_rawrunprotected 
(L=L@entry=0x7fbc2905e780, f=f@entry=0x561563ff5b80 <f_call>, 
ud=ud@entry=0x7fbd223d09f0) at ldo.c:116
#23 0x0000561563ffa41b in luaD_pcall (L=L@entry=0x7fbc2905e780, 
func=func@entry=0x561563ff5b80 <f_call>, u=u@entry=0x7fbd223d09f0, 
old_top=64, ef=<optimized out>) at ldo.c:464
#24 0x0000561563ff79d5 in lua_pcall (L=0x7fbc2905e780, nargs=<optimized 
out>, nresults=-1, errfunc=<optimized out>) at lapi.c:821


(gdb) f 1
#1  0x00007fbd286c0274 in _IO_flush_all_lockp (do_lock=do_lock@entry=1) 
at genops.c:762
762     genops.c: No such file or directory.
(gdb) p list_all_lock
$7 = {lock = 2, cnt = 1, owner = 0x7fbd223d2700}
(gdb) p *fp
$8 = {_flags = -72539000, _IO_read_ptr = 0x0, _IO_read_end = 0x0, 
_IO_read_base = 0x0, _IO_write_base = 0x0, _IO_write_ptr = 0x0, 
_IO_write_end = 0x0, _IO_buf_base = 0x0, _IO_buf_end = 0x0, 
_IO_save_base = 0x0, _IO_backup_base = 0x0,
   _IO_save_end = 0x0, _markers = 0x0, _chain = 0x7fbc8ce14f80, _fileno 
= 1331, _flags2 = 128, _old_offset = 5788344089832285558, _cur_column = 
0, _vtable_offset = 46 '.', _shortbuf = "1", _lock = 0x7fbca8219160, 
_offset = -1,
   _codecvt = 0x722d302e33207465, _wide_data = 0x7fbca8219170, 
_freeres_list = 0x0, _freeres_buf = 0x313930353d544e45, __pad5 = 
3979268027835692085, _mode = -1, _unused2 = "bba22cd111cb426c\" ti"}
(gdb) p *(fp._lock)
$9 = {lock = 2, cnt = 1, owner = 0x7fbd219cd700}


0x7fbd219cd700 (thread 52)
#0  __lll_lock_wait () at 
../sysdeps/unix/sysv/linux/x86_64/lowlevellock.S:135
#1  0x00007fbd29836025 in __GI___pthread_mutex_lock 
(mutex=mutex@entry=0x7fbca8415d68) at ../nptl/pthread_mutex_lock.c:80
#2  0x00007fbd2a7c4fde in malloc_mutex_lock_final (mutex=0x7fbca8415d28) 
at include/jemalloc/internal/mutex.h:151
#3  je_malloc_mutex_lock_slow (mutex=mutex@entry=0x7fbca8415d28) at 
src/mutex.c:90
#4  0x00007fbd2a764b66 in malloc_mutex_lock (mutex=<optimized out>, 
tsdn=<optimized out>) at include/jemalloc/internal/mutex.h:217
#5  je_arena_cache_bin_fill_small (tsdn=tsdn@entry=0x7fbd219ccca8, 
arena=arena@entry=0x7fbca8401040, 
cache_bin=cache_bin@entry=0x7fbd219cd2a8, cache_bin_info=<optimized 
out>, binind=binind@entry=28, nfill=<optimized out>)
     at src/arena.c:972
#6  0x00007fbd2a7d1329 in je_tcache_alloc_small_hard 
(tsdn=tsdn@entry=0x7fbd219ccca8, arena=arena@entry=0x7fbca8401040, 
tcache=tcache@entry=0x7fbd219cd000, 
cache_bin=cache_bin@entry=0x7fbd219cd2a8, binind=binind@entry=28,
     tcache_success=tcache_success@entry=0x7fbd219c8d00) at src/tcache.c:238
#7  0x00007fbd2a75a9df in tcache_alloc_small (slow_path=<optimized out>, 
zero=false, binind=28, size=<optimized out>, tcache=0x7fbd219cd000, 
arena=<optimized out>, tsd=<optimized out>) at 
include/jemalloc/internal/tcache_inlines.h:68
#8  arena_malloc (slow_path=<optimized out>, tcache=0x7fbd219cd000, 
zero=false, ind=28, size=<optimized out>, arena=0x0, tsdn=<optimized 
out>) at include/jemalloc/internal/arena_inlines_b.h:151
#9  iallocztm (slow_path=<optimized out>, arena=0x0, is_internal=false, 
tcache=0x7fbd219cd000, zero=false, ind=28, size=<optimized out>, 
tsdn=<optimized out>) at 
include/jemalloc/internal/jemalloc_internal_inlines_c.h:55
#10 imalloc_no_sample (ind=28, usize=4096, size=<optimized out>, 
tsd=0x7fbd219ccca8, dopts=<synthetic pointer>, sopts=<synthetic 
pointer>) at src/jemalloc.c:2398
#11 imalloc_body (tsd=0x7fbd219ccca8, dopts=<synthetic pointer>, 
sopts=<synthetic pointer>) at src/jemalloc.c:2573
#12 imalloc (dopts=<synthetic pointer>, sopts=<synthetic pointer>) at 
src/jemalloc.c:2687
#13 je_malloc_default (size=<optimized out>) at src/jemalloc.c:2722
#14 0x00007fbd2a75b14d in imalloc_fastpath 
(fallback_alloc=0x7fbd2a75a820 <je_malloc_default>, 
size=size@entry=4096) at 
include/jemalloc/internal/jemalloc_internal_inlines_c.h:266
#15 malloc (size=size@entry=4096) at src/jemalloc.c:2746
#16 0x00007fbd286af13c in __GI__IO_file_doallocate (fp=0x7fbca8219080) 
at filedoalloc.c:101
#17 0x00007fbd286bf329 in __GI__IO_doallocbuf 
(fp=fp@entry=0x7fbca8219080) at genops.c:365
#18 0x00007fbd286be204 in _IO_new_file_underflow (fp=0x7fbca8219080) at 
fileops.c:495
#19 0x00007fbd286bf3a2 in __GI__IO_default_uflow (fp=0x7fbca8219080) at 
genops.c:380
#20 0x00007fbd286b0e12 in __GI__IO_getline_info (eof=0x0, 
extract_delim=<optimized out>, delim=10, n=1023, buf=0x7fbd219c8f80 "", 
fp=0x7fbca8219080, fp@entry=0x0) at iogetline.c:60
#21 __GI__IO_getline (fp=fp@entry=0x7fbca8219080, 
buf=buf@entry=0x7fbd219c8f80 "", n=<optimized out>, 
delim=delim@entry=10, extract_delim=extract_delim@entry=1) at iogetline.c:34
#22 0x00007fbd286afb7d in _IO_fgets (buf=0x7fbd219c8f80 "", n=<optimized 
out>, fp=0x7fbca8219080) at iofgets.c:53



$5 = pthread_mutex_t = {Type = Normal, Status = Acquired, possibly with 
waiters, Owner ID = 3156, Robust = No, Shared = No, Protocol = None}

[Switching to thread 7 (Thread 0x7fbd273fa700 (LWP 3156))]

The initial Thread....


==> genops.c

int
_IO_flush_all_lockp (int do_lock)
{
   int result = 0;
   struct _IO_FILE *fp;

#ifdef _IO_MTSAFE_IO
   _IO_cleanup_region_start_noarg (flush_cleanup);
   _IO_lock_lock (list_all_lock);
#endif

   for (fp = (_IO_FILE *) _IO_list_all; fp != NULL; fp = fp->_chain)
     {
       run_fp = fp;
       if (do_lock)
     _IO_flockfile (fp);

       if (((fp->_mode <= 0 && fp->_IO_write_ptr > fp->_IO_write_base)
        || (_IO_vtable_offset (fp) == 0
            && fp->_mode > 0 && (fp->_wide_data->_IO_write_ptr
                     > fp->_wide_data->_IO_write_base))
        )
       && _IO_OVERFLOW (fp, EOF) == EOF)
     result = EOF;

       if (do_lock)
     _IO_funlockfile (fp);
       run_fp = NULL;
     }

#ifdef _IO_MTSAFE_IO
   _IO_lock_unlock (list_all_lock);
   _IO_cleanup_region_end (0);
#endif

   return result;
}

Regards

@7i77an


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