Subject: gdb sometimes miss backtraces
To: NetBSD amd64 <port-amd64@netbsd.org>
From: Nicolas Joly <njoly@pasteur.fr>
List: port-amd64
Date: 10/13/2004 18:10:25
Hi,

I just wanted to report that, our in-tree gdb, sometimes, fail to get
the backtraces on amd64, while examining core files; and only show the
final function. A locally compiled gdb 6.2 does not exhibit that
behaviour.

njoly@lanfeust [~/tmp]> gdb /local/gensoft/bin/blastclust blastclust.core 
GNU gdb 5.3nb1
Copyright 2002 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you are
welcome to change it and/or distribute copies of it under certain conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB.  Type "show warranty" for details.
This GDB was configured as "x86_64--netbsd"...
Core was generated by `blastclust'.
Program terminated with signal 8, Arithmetic exception.
Reading symbols from /usr/libexec/ld.elf_so...done.
Loaded symbols for /usr/libexec/ld.elf_so
Reading symbols from /usr/lib/libpthread.so.0...done.
Loaded symbols for /usr/lib/libpthread.so.0
Reading symbols from /usr/lib/libm.so.0...done.
Loaded symbols for /usr/lib/libm.so.0
Reading symbols from /usr/lib/libc.so.12...done.
Loaded symbols for /usr/lib/libc.so.12
#0  0x0000000040c13cac in __ieee754_exp () from /usr/lib/libm.so.0
(gdb) bt
#0  0x0000000040c13cac in __ieee754_exp () from /usr/lib/libm.so.0
(gdb) 

njoly@lanfeust [~/tmp]> /local/gnu/bin/gdb /local/gensoft/bin/blastclust blastclust.core 
GNU gdb 6.2
Copyright 2004 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you are
welcome to change it and/or distribute copies of it under certain conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB.  Type "show warranty" for details.
This GDB was configured as "x86_64-unknown-netbsd2.99.9"...
Core was generated by `blastclust'.
Program terminated with signal 8, Arithmetic exception.
Reading symbols from /usr/libexec/ld.elf_so...done.
Loaded symbols for /usr/libexec/ld.elf_so
Reading symbols from /usr/lib/libpthread.so.0...done.
Loaded symbols for /usr/lib/libpthread.so.0
Reading symbols from /usr/lib/libm.so.0...done.
Loaded symbols for /usr/lib/libm.so.0
Reading symbols from /usr/lib/libc.so.12...done.
Loaded symbols for /usr/lib/libc.so.12
#0  0x0000000040c13cac in __ieee754_exp () from /usr/lib/libm.so.0
(gdb) bt
#0  0x0000000040c13cac in __ieee754_exp () from /usr/lib/libm.so.0
#1  0x0000000040c053be in exp () from /usr/lib/libm.so.0
#2  0x000000000043943c in BlastKarlinStoE_simple (S=214, kbp=0x347fbc0, 
    searchsp=4305339768) at ../tools/blastkar.c:3934
#3  0x00000000004140a1 in BlastGetNonSumStatsEvalue (search=0x1785000)
    at ../tools/blast.c:11671
#4  0x0000000000465a5d in MegaBlastReevaluateWithAmbiguities (search=0x1785000)
    at ../tools/mblast.c:3740
#5  0x000000000040685e in do_blast_search (ptr=0x1785000)
    at ../tools/blast.c:3350
#6  0x0000000000406def in do_the_blast_run (search=0x1785000)
    at ../tools/blast.c:3565
#7  0x000000000045ef33 in BioseqMegaBlastEngineCore (search=0x1785000, 
    options=0x88ae00) at ../tools/mblast.c:927
#8  0x000000000045ed57 in BioseqMegaBlastEngineByLoc (slp=0x16baf80, 
    progname=0x1785000 "Ôk", database=0x885080 "nidulans.seq", 
    options=0x88ae00, other_returns=0x0, error_returns=0x0, callback=0, 
    seqid_list=0x19e7660, gi_list=0x19e7660, gi_list_total=27162208, 
    results_callback=0x19e7660) at ../tools/mblast.c:867
#9  0x000000000045eb4c in BioseqMegaBlastEngine (bspp=0x918000, 
    progname=0x8908e0 "blastn", database=0x885080 "nidulans.seq", 
    options=0x88ae00, other_returns=0x0, error_returns=0x0, 
    callback=0x19e7660, seqid_list=0x19e7660, gi_list=0x19e7660, 
    gi_list_total=27162208, results_callback=0x19e7660)
    at ../tools/mblast.c:765
#10 0x0000000000404988 in Nlm_Main () at ../demo/blastclust.c:1183
#11 0x00000000005cf162 in main (argc=214, argv=0x347fbc0)
    at ../corelib/ncbimain.c:98
(gdb) 

Regards.

-- 
Nicolas Joly

Biological Software and Databanks.
Institut Pasteur, Paris.