Re: pthreads+bproc (was Re: [BProc] Re: bpslave dies)

[Nicholas H. <he...@se...>]

Following are the backtraces in gdb from each of the threads. I also
noticed that these processes obeyed kill -9 ( from the node side -- all
this has been ), but if gdb is attached -- the process remains in state
'T', and ignores kill -9. Is there a good way to attach gdb to LWP's ?


0x40082bb5 in __sigsuspend (set=0xbffff390) at ../sysdeps/unix/sysv/linux/sigsuspend.c:45
45      ../sysdeps/unix/sysv/linux/sigsuspend.c: No such file or directory.
        in ../sysdeps/unix/sysv/linux/sigsuspend.c
(gdb) bt
#0  0x40082bb5 in __sigsuspend (set=0xbffff390) at ../sysdeps/unix/sysv/linux/sigsuspend.c:45
#1  0x40048179 in __pthread_wait_for_restart_signal (self=0x40050f20) at pthread.c:978
#2  0x40044bac in pthread_cond_wait (cond=0x82ac8ec, mutex=0x82ac8d4) at restart.h:34
#3  0x0804b17a in NlmSemaWait ()
#4  0x0804af5e in NlmThreadJoinAll ()
#5  0x08088da1 in RPSBlastSearchMT ()
#6  0x0804a957 in Nlm_Main ()
#7  0x08178470 in main ()
#8  0x40070657 in __libc_start_main (main=0x8178454 <main>, argc=11, ubp_av=0xbffff5b4, init=0x80496d4 <_init>, fini=0x818a164 <_fini>,
    rtld_fini=0x4000dcd4 <_dl_fini>, stack_end=0xbffff5ac) at ../sysdeps/generic/libc-start.c:129



0x4013a427 in __poll (fds=0x82ae784, nfds=1, timeout=2000) at ../sysdeps/unix/sysv/linux/poll.c:63
63      ../sysdeps/unix/sysv/linux/poll.c: No such file or directory.
        in ../sysdeps/unix/sysv/linux/poll.c
(gdb) bt
#0  0x4013a427 in __poll (fds=0x82ae784, nfds=1, timeout=2000) at ../sysdeps/unix/sysv/linux/poll.c:63
#1  0x400458f0 in __pthread_manager (arg=0x7) at manager.c:140
   


0x40082bb5 in __sigsuspend (set=0x599ac88c) at ../sysdeps/unix/sysv/linux/sigsuspend.c:45
45      ../sysdeps/unix/sysv/linux/sigsuspend.c: No such file or directory.
        in ../sysdeps/unix/sysv/linux/sigsuspend.c
(gdb) bt
#0  0x40082bb5 in __sigsuspend (set=0x599ac88c) at ../sysdeps/unix/sysv/linux/sigsuspend.c:45
#1  0x40048179 in __pthread_wait_for_restart_signal (self=0x599acbe0) at pthread.c:978
#2  0x400499cc in __pthread_lock (lock=0x40188bf0, self=0x599acbe0) at spinlock.c:149
#3  0x40046d16 in __pthread_mutex_lock (mutex=0x40188be0) at mutex.c:109
#4  0x400d0f70 in _IO_link_in (fp=0x82bb5f8) at genops.c:97
#5  0x400d0bb0 in _IO_new_file_init (fp=0x82bb5f8) at fileops.c:150
#6  0x400c5db3 in _IO_new_fopen (filename=0x82b3180 "rpsblast.log", mode=0x81b1664 "a+") at iofopen.c:63
#7  0x08177c0a in Nlm_FileOpen ()
#8  0x08174bf8 in Nlm_ErrSetLogfile ()
#9  0x0804abfa in NlmThreadWrapper ()
#10 0x40045c3f in pthread_start_thread (arg=0x599acbe0) at manager.c:284
    
Nic
-- 
Nicholas Henke
Penguin Herder & Linux Cluster System Programmer
Liniac Project - Univ. of Pennsylvania