--- Begin Message ---
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)
--- End Message ---
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