*** glibc detected *** gdb: malloc(): smallbin double linked list
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: 0x04de7ad0 *** === 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: 0040-00818000 r-xp 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 00:00 0 0287f000-0b92 rw-p 00:00 0 [heap] 7f0a1c00-7f0a1c021000 rw-p 00:00 0 7f0a1c021000-7f0a2000 ---p 00:00 0 7f0a20fc-7f0a20fd6000 r-xp 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 1000 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 7f0a22027000-7f0a2240 rw-p 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 0151 08:05 4653324 /home/john/Dev/MyProjects/Bio/MotifSearch/python/stempy/_debug/_stempy.so 7f0a2259c000-7f0a2280c000 r--p 012a 08:05 4653324 /home/john/Dev/MyProjects/Bio/MotifSearch/python/stempy/_debug/_stempy.so 7f0a2280c000-7f0a2343f000 rw-p 00:00 0 7f0a23443000-7f0a2344c000 r--p 0001a000 08:05 6169643 /home/john/local/python-dbg/lib/python2.7/lib-dynload/datetime.so 7f0a2344c000-7f0a2345c000 r--p 002d9000 08:05 4653290 /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 4000 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 /home/john/Dev/MyProjects/Bio/MotifSearch/python/stempy/_debug/_stempy.so 7f0a2350c000-7f0a23555000 r--p 021c3000 08:05 4653324 /home/john/Dev/MyProjects/Bio/MotifSearch/python/stempy/_debug/_stempy.so 7f0a23555000-7f0a2355b000 r--p 00048000 08:05 6169627 /home/john/local/python-dbg/lib/python2.7/lib-dynload
Re: *** glibc detected *** gdb: malloc(): smallbin double linked list
On Fri, 05 Nov 2010 19:39:12 +, John Reid wrote: 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? I imagine that your extension code is trashing the heap, in which case, valgrind is probably the answer. My first guess would be that something is writing to a heap block after it has been deallocated (possibly due to omitting a Py_INCREF). Of course, other causes are possible, but writing to deallocated memory is a common problem when writing extensions for languages with garbage collection. -- http://mail.python.org/mailman/listinfo/python-list
Re: *** glibc detected *** gdb: malloc(): smallbin double linked list
In message pan.2010.11.05.21.30.11.656...@nowhere.com, Nobody wrote: I imagine that your extension code is trashing the heap, in which case, valgrind is probably the answer. Something simpler to try first is to run the code with the MALLOC_CHECK_ environment variable set to 2 or 3. That might give a few more clues. -- http://mail.python.org/mailman/listinfo/python-list
