Source: seqan2 Version: 2.4.0+dfsg-9 Severity: important User: [email protected] Usertags: alignment
Hi! I've been doing a full rebuild of the Debian archive, building all source packages targeting armel and armhf using arm64 hardware. We are planning in future to move all of our 32-bit armel/armhf builds to using arm64 machines, so this rebuild is to identify packages that might have problems with this configuration. A feature of the arm64 kernel is that it does *not* support fixing up code with broken alignment, so code that might have built and run OK on our older armel/armhf build machines due to kernel fixups will now fail. When building your package, I've found a bus error (aka alignment fault). The full log is online at https://www.einval.com/debian/arm/rebuild-logs/armel/FAIL/seqan2_2.4.0+dfsg-9_armel.log for reference I've done a quick bit of debugging to find the source of the bug. Here's a gdb stacktrace and variable printout to demonstrate the problem. (sid-armel)steve@mjolnir:~/debian/build/seqan2/seqan2-2.4.0+dfsg$ gdb obj-arm-linux-gnueabi/bin/test_index_fm_rank_dictionary obj-arm-linux-gnueabi/tests/index/core ... Core was generated by `/home/steve/debian/build/seqan2/seqan2-2.4.0+dfsg/obj-arm-linux-gnueabi/bin/tes'. Program terminated with signal SIGBUS, Bus error. #0 0x00bf7d24 in seqan::_getWordRank<bool, void, seqan::LevelsRDConfig<unsigned int, seqan::Alloc<void>, 2u, 2u>, unsigned long long, unsigned int> ( word=@0x234df2a: 6741939070857683030, c=true, posInWord=63) at ./include/seqan/misc/bit_twiddling.h:346 346 _popCountImpl(TWord word, WordSize_<64> const & /*tag*/) (gdb) bt #0 0x00bf7d24 in seqan::_getWordRank<bool, void, seqan::LevelsRDConfig<unsigned int, seqan::Alloc<void>, 2u, 2u>, unsigned long long, unsigned int> ( word=@0x234df2a: 6741939070857683030, c=true, posInWord=63) at ./include/seqan/misc/bit_twiddling.h:346 #1 seqan::_getWordRank<bool, void, seqan::LevelsRDConfig<unsigned int, seqan::Alloc<void>, 2u, 2u>, unsigned long long> (dict=..., word=@0x234df2a: 6741939070857683030, c=true) at ./include/seqan/index/index_fm_rank_dictionary_levels.h:1139 #2 seqan::_getValueRank<bool, void, seqan::LevelsRDConfig<unsigned int, seqan::Alloc<void>, 2u, 2u>, seqan::Tuple<seqan::Tuple<bool, 64u, seqan::BitPacked<16u, 16u> >, 2u, void>, unsigned int> (c=true, dict=..., posInBlock=127, values=...) at ./include/seqan/index/index_fm_rank_dictionary_levels.h:1261 #3 seqan::_getValuesRanks<void, seqan::LevelsRDConfig<unsigned int, seqan::Alloc<void>, 2u, 2u>, unsigned int> (pos=<optimized out>, dict=...) at ./include/seqan/index/index_fm_rank_dictionary_levels.h:1349 #4 seqan::updateRanks<bool, void, seqan::LevelsRDConfig<unsigned int, seqan::Alloc<void>, 2u, 2u> > (dict=...) at ./include/seqan/index/index_fm_rank_dictionary_levels.h:1711 #5 seqan::createRankDictionary<bool, seqan::Levels<void, seqan::LevelsRDConfig<unsigned int, seqan::Alloc<void>, 2u, 2u> >, seqan::String<bool, seqan::Alloc<void> > > ( dict=..., text=...) at ./include/seqan/index/index_fm_rank_dictionary_base.h:268 #6 0x00bf8cfc in seqan::RankDictionary<bool, seqan::Levels<void, seqan::LevelsRDConfig<unsigned int, seqan::Alloc<void>, 2u, 2u> > >::RankDictionary<seqan::String<bool, seqan::Alloc<void> > > (text=..., this=0xffd11048) at ./include/seqan/index/index_fm_rank_dictionary_levels.h:430 #7 RankDictionaryTest__Constructor<seqan::RankDictionary<bool, seqan::Levels<void, seqan::LevelsRDConfig<unsigned int, seqan::Alloc<void>, 2u, 2u> > > >::runTest ( this=0x232df30) at ./tests/index/test_index_fm_rank_dictionary.cpp:186 #8 0x00bc2074 in seqan::TestSystem::runAll () at /usr/include/c++/8/bits/unique_ptr.h:342 #9 0xf783a474 in __libc_start_main (main=0xffd11244, argc=-141082624, argv=0xf783a474 <__libc_start_main+268>, init=<optimized out>, fini=0xc45368 <__libc_csu_fini>, rtld_fini=0xf7c9e66c <_dl_fini>, stack_end=0xffd11244) at libc-start.c:308 #10 0x00bb40ac in _start () at ./include/seqan/basic/debug_test_system.h:502 Backtrace stopped: previous frame identical to this frame (corrupt stack?) (gdb) list 341 // GCC or CLANG implementations. 342 // SSE4.2 popcnt is emitted when compiling with -mpopcnt or -march=corei7 343 344 template <typename TWord> 345 inline unsigned 346 _popCountImpl(TWord word, WordSize_<64> const & /*tag*/) 347 { 348 return __builtin_popcountll(static_cast<uint64_t>(word)); 349 } 350 (gdb) p word $1 = (const unsigned long long &) @0x234df2a: 6741939070857683030 This is classic buggy code for alignment faults - simply casting a uint64_t over the unaligned address 0x234df2a is not safe. -- System Information: Debian Release: 9.6 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable-debug'), (500, 'stable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.9.0-8-amd64 (SMP w/4 CPU cores) Locale: LANG=en_GB.UTF-8, LC_CTYPE=en_GB.UTF-8 (charmap=UTF-8), LANGUAGE=en_GB.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system)
