*** glibc detected *** gdb: malloc(): smallbin double linked list

John Reid j.reid at mail.cryst.bbk.ac.uk
Fri Nov 5 20:39:12 CET 2010


Hi,

I've compiled
Python 2.7 (r27:82500, Nov  2 2010, 09:00:37)
[GCC 4.4.3] on linux2

with the following configure options
./configure --prefix=/home/john/local/python-dbg --with-pydebug

I've installed numpy and some other packages but when I try to run my 
extension code under gdb I get the errors below. Does anyone have any 
ideas of how to track down what's happening here? I imagine I've 
misconfigured something somewhere. Is valgrind the answer?

Thanks,
John.



*** glibc detected *** gdb: malloc(): smallbin double linked list 
corrupted: 0x0000000004de7ad0 ***
======= Backtrace: =========
/lib/libc.so.6(+0x775b6)[0x7f0a252215b6]
/lib/libc.so.6(+0x7b8e9)[0x7f0a252258e9]
/lib/libc.so.6(__libc_malloc+0x6e)[0x7f0a2522658e]
gdb(xmalloc+0x18)[0x45bc38]
gdb[0x476df1]
gdb[0x474c9b]
gdb[0x474ee8]
gdb(execute_command+0x2dd)[0x458d1d]
gdb(catch_exception+0x50)[0x535510]
gdb[0x4b5191]
gdb(interp_exec+0x17)[0x535637]
gdb(mi_cmd_interpreter_exec+0x6c)[0x4b9adc]
gdb[0x4ba71a]
gdb(catch_exception+0x50)[0x535510]
gdb(mi_execute_command+0x97)[0x4ba137]
gdb[0x53a0f8]
gdb(gdb_do_one_event+0x29a)[0x53b38a]
gdb(catch_errors+0x5b)[0x53531b]
gdb(start_event_loop+0x1e)[0x53a90e]
gdb[0x44f619]
gdb(catch_errors+0x5b)[0x53531b]
gdb[0x450166]
gdb(catch_errors+0x5b)[0x53531b]
gdb(gdb_main+0x24)[0x44f554]
gdb(main+0x2e)[0x44f51e]
/lib/libc.so.6(__libc_start_main+0xfd)[0x7f0a251c8c4d]
gdb[0x44f429]
======= Memory map: ========
00400000-00818000 r-xp 00000000 08:05 4832730  /usr/bin/gdb
00a17000-00a18000 r--p 00417000 08:05 4832730  /usr/bin/gdb
00a18000-00a25000 rw-p 00418000 08:05 4832730  /usr/bin/gdb
00a25000-00a43000 rw-p 00000000 00:00 0
0287f000-0b920000 rw-p 00000000 00:00 0  [heap]
7f0a1c000000-7f0a1c021000 rw-p 00000000 00:00 0
7f0a1c021000-7f0a20000000 ---p 00000000 00:00 0
7f0a20fc0000-7f0a20fd6000 r-xp 00000000 08:05 3498245  /lib/libgcc_s.so.1
7f0a20fd6000-7f0a211d5000 ---p 00016000 08:05 3498245  /lib/libgcc_s.so.1
7f0a211d5000-7f0a211d6000 r--p 00015000 08:05 3498245  /lib/libgcc_s.so.1
7f0a211d6000-7f0a211d7000 rw-p 00016000 08:05 3498245  /lib/libgcc_s.so.1
7f0a211fd000-7f0a21211000 r--p 000dc000 08:05 4825848 
/usr/lib/libstdc++.so.6.0.13
7f0a21211000-7f0a21218000 r--p 00018000 08:05 4841756 
/usr/lib/debug/lib/librt-2.11.1.so
7f0a21218000-7f0a21226000 r--p 00001000 08:05 4841756 
/usr/lib/debug/lib/librt-2.11.1.so
7f0a21226000-7f0a2123e000 r--p 000bc000 08:05 4653290
/home/john/Dev/MyProjects/Bio/MotifSearch/python/stempy/_debug/libboost_python.so.1.44.0
7f0a2123e000-7f0a21287000 r--p 003dd000 08:05 4653290
/home/john/Dev/MyProjects/Bio/MotifSearch/python/stempy/_debug/libboost_python.so.1.44.0
7f0a21287000-7f0a21299000 r--p 00425000 08:05 4653290
/home/john/Dev/MyProjects/Bio/MotifSearch/python/stempy/_debug/libboost_python.so.1.44.0
7f0a21299000-7f0a213e7000 r--p 0018c000 08:05 4653290
/home/john/Dev/MyProjects/Bio/MotifSearch/python/stempy/_debug/libboost_python.so.1.44.0
7f0a213e7000-7f0a2152f000 r--p 0207c000 08:05 4653324 
/home/john/Dev/MyProjects/Bio/MotifSearch/python/stempy/_debug/_stempy.so
7f0a2152f000-7f0a22027000 r--p 01585000 08:05 4653324 
/home/john/Dev/MyProjects/Bio/MotifSearch/python/stempy/_debug/_stempy.so
7f0a22027000-7f0a22400000 rw-p 00000000 00:00 0
7f0a22408000-7f0a224d1000 r--p 00315000 08:05 4653290
/home/john/Dev/MyProjects/Bio/MotifSearch/python/stempy/_debug/libboost_python.so.1.44.0
7f0a224d1000-7f0a224ff000 r--p 002e8000 08:05 4653290
/home/john/Dev/MyProjects/Bio/MotifSearch/python/stempy/_debug/libboost_python.so.1.44.0
7f0a224ff000-7f0a22526000 r--p 00038000 08:05 4653310
/home/john/Dev/MyProjects/Bio/MotifSearch/python/stempy/_debug/myrrh_pylib-d
7f0a22526000-7f0a2259c000 r--p 01510000 08:05 4653324 
/home/john/Dev/MyProjects/Bio/MotifSearch/python/stempy/_debug/_stempy.so
7f0a2259c000-7f0a2280c000 r--p 012a0000 08:05 4653324 
/home/john/Dev/MyProjects/Bio/MotifSearch/python/stempy/_debug/_stempy.so
7f0a2280c000-7f0a2343f000 rw-p 00000000 00:00 0
7f0a23443000-7f0a2344c000 r--p 0001a000 08:05 6169643 
/home/john/local/python-dbg/lib/python2.7/lib-dynload/datetime.so
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/home/john/Dev/MyProjects/Bio/MotifSearch/python/stempy/_debug/libboost_python.so.1.44.0
7f0a2345c000-7f0a23461000 r--p 0005e000 08:05 4653310
/home/john/Dev/MyProjects/Bio/MotifSearch/python/stempy/_debug/myrrh_pylib-d
7f0a23461000-7f0a23477000 r--p 0001f000 08:05 4653310
/home/john/Dev/MyProjects/Bio/MotifSearch/python/stempy/_debug/myrrh_pylib-d
7f0a23477000-7f0a2347d000 r--p 00004000 08:05 4653095
/home/john/Dev/MyProjects/Bio/MotifSearch/python/stempy/_debug/libboost_system.so.1.44.0
7f0a2347d000-7f0a2350c000 r--p 00757000 08:05 4653324 
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/home/john/Dev/MyProjects/Bio/MotifSearch/python/stempy/_debug/_stempy.so
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7f0a2356f000-7f0a23575000 r--p 000b1000 08:05 3489898
/home/john/local/python-dbg/lib/python2.7/site-packages/numpy-1.5.1rc1-py2.7-linux-x86_64.egg/numpy/random/mtrand.so
7f0a23575000-7f0a2357c000 r--p 000ab000 08:05 3489898
/home/john/local/python-dbg/lib/python2.7/site-packages/numpy-1.5.1rc1-py2.7-linux-x86_64.egg/numpy/random/mtrand.so
7f0a2357c000-7f0a2358d000 r--p 0009b000 08:05 3489898
/home/john/local/python-dbg/lib/python2.7/site-packages/numpy-1.5.1rc1-py2.7-linux-x86_64.egg/numpy/random/mtrand.so
7f0a2358d000-7f0a2359b000 r--p 000dd000 08:05 4827887 
/usr/lib/libgfortran.so.3.0.0
7f0a2359b000-7f0a235ac000 r--p 00416000 08:05 6709644
/home/john/local/python-dbg/lib/python2.7/site-packages/numpy-1.5.1rc1-py2.7-linux-x86_64.egg/numpy/linalg/lapack_lite.so
7f0a235ac000-7f0a23668000 rw-p 00000000 00:00 0
7f0a23668000-7f0a2366d000 r--p 00033000 08:05 3180358
/home/john/local/python-dbg/lib/python2.7/site-packages/numpy-1.5.1rc1-py2.7-linux-x86_64.egg/numpy/core/scalarmath.so
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/home/john/local/python-dbg/lib/python2.7/site-packages/numpy-1.5.1rc1-py2.7-linux-x86_64.egg/numpy/core/scalarmath.so
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/home/john/local/python-dbg/lib/python2.7/site-packages/numpy-1.5.1rc1-py2.7-linux-x86_64.egg/numpy/core/scalarmath.so
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/home/john/local/python-dbg/lib/python2.7/site-packages/numpy-1.5.1rc1-py2.7-linux-x86_64.egg/numpy/core/scalarmath.so
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/home/john/local/python-dbg/lib/python2.7/site-packages/numpy-1.5.1rc1-py2.7-linux-x86_64.egg/numpy/core/_sort.so
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/home/john/local/python-dbg/lib/python2.7/site-packages/numpy-1.5.1rc1-py2.7-linux-x86_64.egg/numpy/core/umath.so
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/home/john/local/python-dbg/lib/python2.7/site-packages/numpy-1.5.1rc1-py2.7-linux-x86_64.egg/numpy/core/umath.so
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/home/john/local/python-dbg/lib/python2.7/site-packages/numpy-1.5.1rc1-py2.7-linux-x86_64.egg/numpy/core/umath.so
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7f0a2608e000-7f0a260a4000 r-xp 00000000 08:05 2900157  /lib/libz.so.1.2.3.3
7f0a260a4000-7f0a262a3000 ---p 00016000 08:05 2900157  /lib/libz.so.1.2.3.3
7f0a262a3000-7f0a262a4000 r--p 00015000 08:05 2900157  /lib/libz.so.1.2.3.3
7f0a262a4000-7f0a262a5000 rw-p 00016000 08:05 2900157  /lib/libz.so.1.2.3.3
7f0a262a5000-7f0a262e3000 r-xp 00000000 08:05 3498266 
/lib/libncurses.so.5.7
7f0a262e3000-7f0a264e3000 ---p 0003e000 08:05 3498266 
/lib/libncurses.so.5.7
7f0a264e3000-7f0a264e7000 r--p 0003e000 08:05 3498266 
/lib/libncurses.so.5.7
7f0a264e7000-7f0a264e8000 rw-p 00042000 08:05 3498266 
/lib/libncurses.so.5.7
7f0a264e8000-7f0a26521000 r-xp 00000000 08:05 3498308 
/lib/libreadline.so.6.1
7f0a26521000-7f0a26720000 ---p 00039000 08:05 3498308 
/lib/libreadline.so.6.1
7f0a26720000-7f0a26722000 r--p 00038000 08:05 3498308 
/lib/libreadline.so.6.1
7f0a26722000-7f0a26728000 rw-p 0003a000 08:05 3498308 
/lib/libreadline.so.6.1
7f0a26728000-7f0a26729000 rw-p 00000000 00:00 0
7f0a26729000-7f0a26749000 r-xp 00000000 08:05 2900131  /lib/ld-2.11.1.so
7f0a26749000-7f0a2674f000 r--p 00013000 08:05 6169622 
/home/john/local/python-dbg/lib/python2.7/lib-dynload/itertools.so
7f0a2674f000-7f0a26758000 r--p 0004c000 08:05 4841753 
/usr/lib/debug/lib/ld-2.11.1.so
7f0a26758000-7f0a267a4000 r--p 00001000 08:05 4841753 
/usr/lib/debug/lib/ld-2.11.1.so
7f0a267a4000-7f0a26857000 rw-p 00000000 00:00 0
7f0a26857000-7f0a26858000 r--p 00000000 08:05 5792628 
/usr/share/locale-langpack/en_GB/LC_MESSAGES/libc.mo
7f0a26858000-7f0a268da000 rw-p 00000000 00:00 0
7f0a268da000-7f0a26919000 r--p 00000000 08:05 4874536 
/usr/lib/locale/en_GB.utf8/LC_CTYPE
7f0a26919000-7f0a26920000 rw-p 00000000 00:00 0
7f0a26922000-7f0a26928000 r--p 0005e000 08:05 4841753 
/usr/lib/debug/lib/ld-2.11.1.so
7f0a26928000-7f0a26933000 r--p 00054000 08:05 4841753 
/usr/lib/debug/lib/ld-2.11.1.so
7f0a26935000-7f0a26938000 rw-p 00000000 00:00 0
7f0a26938000-7f0a2693e000 r--p 00000000 08:05 5792627 
/usr/share/locale-langpack/en_GB/LC_MESSAGES/gdb.mo
7f0a2693e000-7f0a26945000 r--s 00000000 08:05 5417899 
/usr/lib/gconv/gconv-modules.cache
7f0a26945000-7f0a26946000 r--p 00000000 08:05 4875999 
/usr/lib/locale/en_GB.utf8/LC_MESSAGES/SYS_LC_MESSAGES
7f0a26946000-7f0a26948000 rw-p 00000000 00:00 0
7f0a26948000-7f0a26949000 r--p 0001f000 08:05 2900131  /lib/ld-2.11.1.so
7f0a26949000-7f0a2694a000 rw-p 00020000 08:05 2900131  /lib/ld-2.11.1.so
7f0a2694a000-7f0a2694b000 rw-p 00000000 00:00 0
7ffff92d6000-7ffff92f8000 rw-p 00000000 00:00 0  [stack]
7ffff93ff000-7ffff9400000 r-xp 00000000 00:00 0  [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0  [vsyscall]





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