On Wed, May 9, 2012 at 12:59 PM, Geoff Hutchison
<ge...@geoffhutchison.net> wrote:
>
> > I'm currently working with the development branch, SVN revision 4744
> > (snapshot from about two weeks ago). If I run "make; make install; make
> > test", almost every test crashes with a segmentation violation. This makes
> > me nervous.
>
> CDash suggests that everything except MinGW should be fine:
> http://my.cdash.org/index.php?project=Open+Babel&display=project
>
> Can you run a test through GDB and see what happens?
> e.g., from your build directory:
>
> gdb bin/test_aromatest
Does the backtrace below ring any bells? I'm happy to dig in further,
but I don't want to waste a bunch of time if it's some trivial
configuration problem.
Thanks,
Craig
(Note: I renamed the version to 5 in CMakeLists.txt (i.e.
libopenbabel.so.5) so that I could have two versions installed at the
same time. Otherwise I've made no changes.)
LD_LIBRARY_PATH=/home/cjames/openbabel-2.3.x/lib:/usr/local/pgsql/lib
PATH=/home/cjames/bin:/usr/local/bin:/usr/local/pgsql/bin:/bin:/usr/bin:/usr/bin/X11:/usr/X11R6/bin:/sbin/:/usr/sbin:/home/cjames/openbabel-2.3.x/bin:.
BABEL_DATADIR=/home/cjames/openbabel-2.3.x/share/openbabel/2.3.90
BABEL_LIBDIR=/home/cjames/openbabel-2.3.x/lib/openbabel/2.3.90
$ gdb bin/test_aromatest
...
ok 339
ok 340
ok 341
1..341
*** glibc detected ***
/home/cjames/openbabel-2.3.x-r4744/build-g/bin/test_aromatest: free():
invalid pointer: 0x00000000006beb68 ***
======= Backtrace: =========
/lib/libc.so.6(+0x77806)[0x7ffff7ad1806]
/lib/libc.so.6(cfree+0x73)[0x7ffff7ad80d3]
/usr/lib/libstdc++.so.6(_ZNSsD1Ev+0x39)[0x7ffff6d5b129]
/home/cjames/openbabel-2.3.x/lib/libopenbabel.so.5(_ZN9OpenBabel7OBErrorD1Ev+0x8d)[0x7ffff76d197b]
/home/cjames/openbabel-2.3.x/lib/libopenbabel.so.5(_ZSt8_DestroyIN9OpenBabel7OBErrorEEvPT_+0x18)[0x7ffff76d19e6]
/home/cjames/openbabel-2.3.x/lib/libopenbabel.so.5(_ZNSt12_Destroy_auxILb0EE9__destroyIPN9OpenBabel7OBErrorEEEvT_S5_+0x1e)[0x7ffff76d17a7]
/home/cjames/openbabel-2.3.x/lib/libopenbabel.so.5(_ZSt8_DestroyIPN9OpenBabel7OBErrorEEvT_S3_+0x23)[0x7ffff76d14ef]
/home/cjames/openbabel-2.3.x/lib/libopenbabel.so.5(_ZSt8_DestroyIPN9OpenBabel7OBErrorES1_EvT_S3_RSaIT0_E+0x27)[0x7ffff76d109f]
/home/cjames/openbabel-2.3.x/lib/libopenbabel.so.5(_ZNSt5dequeIN9OpenBabel7OBErrorESaIS1_EE19_M_destroy_data_auxESt15_Deque_iteratorIS1_RS1_PS1_ES7_+0x6d)[0x7ffff76d0131]
/home/cjames/openbabel-2.3.x/lib/libopenbabel.so.5(_ZNSt5dequeIN9OpenBabel7OBErrorESaIS1_EE15_M_destroy_dataESt15_Deque_iteratorIS1_RS1_PS1_ES7_RKS2_+0x55)[0x7ffff76ce93d]
/home/cjames/openbabel-2.3.x/lib/libopenbabel.so.5(_ZNSt5dequeIN9OpenBabel7OBErrorESaIS1_EED1Ev+0x5e)[0x7ffff76d486a]
/home/cjames/openbabel-2.3.x/lib/libopenbabel.so.5(_ZN9OpenBabel16OBMessageHandlerD1Ev+0x70)[0x7ffff76d35a8]
/lib/libc.so.6(__cxa_finalize+0xa0)[0x7ffff7a93630]
/home/cjames/openbabel-2.3.x/lib/libopenbabel.so.5(+0x1b7bb6)[0x7ffff7598bb6]
======= Memory map: ========
00400000-00403000 r-xp 00000000 00:15 29500700
/home/cjames/openbabel-2.3.x-r4744/build-g/bin/test_aromatest
00602000-00603000 r--p 00002000 00:15 29500700
/home/cjames/openbabel-2.3.x-r4744/build-g/bin/test_aromatest
00603000-00604000 rw-p 00003000 00:15 29500700
/home/cjames/openbabel-2.3.x-r4744/build-g/bin/test_aromatest
00604000-006cc000 rw-p 00000000 00:00 0 [heap]
7fffe0000000-7fffe0021000 rw-p 00000000 00:00 0
7fffe0021000-7fffe4000000 ---p 00000000 00:00 0
7fffe7099000-7fffe70ac000 r-xp 00000000 00:15 28583351
/home/cjames/openbabel-2.3.x-r4744/build-g/lib/cacaoformat.so
7fffe70ac000-7fffe72ab000 ---p 00013000 00:15 28583351
/home/cjames/openbabel-2.3.x-r4744/build-g/lib/cacaoformat.so
7fffe72ab000-7fffe72ac000 r--p 00012000 00:15 28583351
/home/cjames/openbabel-2.3.x-r4744/build-g/lib/cacaoformat.so
7fffe72ac000-7fffe72ad000 rw-p 00013000 00:15 28583351
/home/cjames/openbabel-2.3.x-r4744/build-g/lib/cacaoformat.so
7fffe72ad000-7fffe72b9000 r-xp 00000000 00:15 28583353
/home/cjames/openbabel-2.3.x-r4744/build-g/lib/carformat.so
7fffe72b9000-7fffe74b8000 ---p 0000c000 00:15 28583353
/home/cjames/openbabel-2.3.x-r4744/build-g/lib/carformat.so
7fffe74b8000-7fffe74b9000 r--p 0000b000 00:15 28583353
/home/cjames/openbabel-2.3.x-r4744/build-g/lib/carformat.so
7fffe74b9000-7fffe74ba000 rw-p 0000c000 00:15 28583353
/home/cjames/openbabel-2.3.x-r4744/build-g/lib/carformat.so
7fffe74ba000-7fffe74cb000 r-xp 00000000 00:15 28583416
/home/cjames/openbabel-2.3.x-r4744/build-g/lib/pwscfformat.so
7fffe74cb000-7fffe76ca000 ---p 00011000 00:15 28583416
/home/cjames/openbabel-2.3.x-r4744/build-g/lib/pwscfformat.so
7fffe76ca000-7fffe76cb000 r--p 00010000 00:15 28583416
/home/cjames/openbabel-2.3.x-r4744/build-g/lib/pwscfformat.so
7fffe76cb000-7fffe76cc000 rw-p 00011000 00:15 28583416
/home/cjames/openbabel-2.3.x-r4744/build-g/lib/pwscfformat.so
7fffe76cc000-7fffe7700000 r-xp 00000000 00:15 28583383
/home/cjames/openbabel-2.3.x-r4744/build-g/lib/gaussformat.so
7fffe7700000-7fffe7900000 ---p 00034000 00:15 28583383
/home/cjames/openbabel-2.3.x-r4744/build-g/lib/gaussformat.so
7fffe7900000-7fffe7901000 r--p 00034000 00:15 28583383
/home/cjames/openbabel-2.3.x-r4744/build-g/lib/gaussformat.so
7fffe7901000-7fffe7903000 rw-p 00035000 00:15 28583383
/home/cjames/openbabel-2.3.x-r4744/build-g/lib/gaussformat.so
7fffe7903000-7fffe7968000 r-xp 00000000 00:15 28583362
/home/cjames/openbabel-2.3.x-r4744/build-g/lib/cifformat.so
7fffe7968000-7fffe7b68000 ---p 00065000 00:15 28583362
/home/cjames/openbabel-2.3.x-r4744/build-g/lib/cifformat.so
7fffe7b68000-7fffe7b69000 r--p 00065000 00:15 28583362
/home/cjames/openbabel-2.3.x-r4744/build-g/lib/cifformat.so
7fffe7b69000-7fffe7b6c000 rw-p 00066000 00:15 28583362
/home/cjames/openbabel-2.3.x-r4744/build-g/lib/cifformat.so
7fffe7b6c000-7fffe7b7c000 r-xp 00000000 00:15 28583336
/home/cjames/openbabel-2.3.x-r4744/build-g/lib/MNAformat.so
7fffe7b7c000-7fffe7d7b000 ---p 00010000 00:15 28583336
/home/cjames/openbabel-2.3.x-r4744/build-g/lib/MNAformat.so
7fffe7d7b000-7fffe7d7c000 r--p 0000f000 00:15 28583336
/home/cjames/openbabel-2.3.x-r4744/build-g/lib/MNAformat.so
Program received signal SIGABRT, Aborted.
0x00007ffff7a8da75 in *__GI_raise (sig=<value optimized out>) at
../nptl/sysdeps/unix/sysv/linux/raise.c:64
64 ../nptl/sysdeps/unix/sysv/linux/raise.c: No such file or directory.
in ../nptl/sysdeps/unix/sysv/linux/raise.c
(gdb) bt
#0 0x00007ffff7a8da75 in *__GI_raise (sig=<value optimized out>) at
../nptl/sysdeps/unix/sysv/linux/raise.c:64
#1 0x00007ffff7a915c0 in *__GI_abort () at abort.c:92
#2 0x00007ffff7ac774b in __libc_message (do_abort=<value optimized
out>, fmt=<value optimized out>)
at ../sysdeps/unix/sysv/linux/libc_fatal.c:189
#3 0x00007ffff7ad1806 in malloc_printerr (action=3,
str=0x7ffff7ba2153 "free(): invalid pointer", ptr=<value optimized
out>)
at malloc.c:6266
#4 0x00007ffff7ad80d3 in *__GI___libc_free (mem=<value optimized
out>) at malloc.c:3738
#5 0x00007ffff6d5b129 in std::basic_string<char,
std::char_traits<char>, std::allocator<char> >::~basic_string() ()
from /usr/lib/libstdc++.so.6
#6 0x00007ffff76d197b in ~OBError (this=0x6a4570, __in_chrg=<value
optimized out>)
at /home/cjames/openbabel-2.3.x-r4744/source/include/openbabel/oberror.h:53
#7 0x00007ffff76d19e6 in std::_Destroy<OpenBabel::OBError>
(__pointer=0x6a4570) at /usr/include/c++/4.4/bits/stl_construct.h:83
#8 0x00007ffff76d17a7 in
std::_Destroy_aux<false>::__destroy<OpenBabel::OBError*>
(__first=0x6a4570, __last=0x6a4750)
at /usr/include/c++/4.4/bits/stl_construct.h:93
#9 0x00007ffff76d14ef in std::_Destroy<OpenBabel::OBError*>
(__first=0x6a4570, __last=0x6a4750)
at /usr/include/c++/4.4/bits/stl_construct.h:116
#10 0x00007ffff76d109f in std::_Destroy<OpenBabel::OBError*,
OpenBabel::OBError> (__first=0x6a4570, __last=0x6a4750)
at /usr/include/c++/4.4/bits/stl_construct.h:142
#11 0x00007ffff76d0131 in std::deque<OpenBabel::OBError,
std::allocator<OpenBabel::OBError> >::_M_destroy_data_aux
(this=0x7ffff7a58ff8,
__first=..., __last=...) at /usr/include/c++/4.4/bits/deque.tcc:728
#12 0x00007ffff76ce93d in std::deque<OpenBabel::OBError,
std::allocator<OpenBabel::OBError> >::_M_destroy_data
(this=0x7ffff7a58ff8,
__first=..., __last=...) at /usr/include/c++/4.4/bits/stl_deque.h:1653
#13 0x00007ffff76d486a in ~deque (this=0x7ffff7a58ff8,
__in_chrg=<value optimized out>) at
/usr/include/c++/4.4/bits/stl_deque.h:790
#14 0x00007ffff76d35a8 in ~OBMessageHandler (this=0x7ffff7a58fe0,
__in_chrg=<value optimized out>)
at /home/cjames/openbabel-2.3.x-r4744/source/src/oberror.cpp:161
#15 0x00007ffff7a93630 in __cxa_finalize (d=0x7ffff7a55420) at cxa_finalize.c:56
#16 0x00007ffff7598bb6 in __do_global_dtors_aux () from
/home/cjames/openbabel-2.3.x/lib/libopenbabel.so.5
#17 0x0000000000000000 in ?? ()
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