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.

Hi,

But other 32bit architectures like armel and armhf are passing[2].  So I
fail to see why exactly i386 is failing.  Is this possibly an effect of
bug #917851?

Kind regards

     Andreas.

[2] https://buildd.debian.org/status/package.php?p=seqan2

Am 12.02.2021 um 11:01 teilte Andreas Tille mit:

Hi,
Maybe the memory of the whole builder is exhausted. In this case it may
help to limit the amount of parallel running processes. On i386 we have
"make -j4" on armel just "make -j1" .

H.
-- 
sigfault

Then it would get an OOM, not a *virtual* memory error.

Andreas Tille <tille@debian.org> writes:

Probably not; dropping the bug to a Bcc.  Experimentation in an i386
chroot reveals the problem to be specifically with yara_mapper, which
https://salsa.debian.org/med-team/seqan2/-/blob/master/debian/patches/skip-some-apps-on-some-archs
explicitly excludes (along with yara_indexer) on several other 32-bit
platforms.  We could go the same route for i386, but AFAICT it suffices
to drop the optimization level back down to -O2 for this specific
application, by adding

# Drop back from global -O3 on i386 to avoid
# "virtual memory exhausted: Operation not permitted"
if ("$ENV{DEB_BUILD_ARCH}" STREQUAL "i386")
    target_compile_options (yara_mapper PRIVATE "-O2")
endif ()

to apps/yara/CMakeLists.txt following the add_executable call for
yara_mapper.  (If and when debian/rules honors noopt, we should further
conditionalize this call accordingly, but I'm not familiar enough with
cmake to come up with the correct syntax offhand.)  We could perhaps try
doing the same for other affected platforms in an upload to
experimental.

We believe that the bug you reported is fixed in the latest version of
seqan2, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 917851@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated seqan2 package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Wed, 03 Dec 2025 14:49:24 +0100
Source: seqan2
Architecture: source
Version: 2.4.0+dfsg-17
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Closes: 917851 1047218
Changes:
 seqan2 (2.4.0+dfsg-17) unstable; urgency=medium
 .
   [ Santiago Vila ]
   * Fix clean target. Closes: #1047218
 .
   [ Andreas Tille ]
   * d/watch: version=5
   * Standards-Version: 4.7.2 (routine-update)
   * Rely on pre-initialized dpkg-architecture variables.
   * Build-Depends: architecture-is-64-bit
     Closes: #917851
   * Disable i386 build on Salsa CI
   * Enable building with CMake 4
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 9c3bc3de665d30dabf6f485a2f522acd0e925df6 30084 seqan2_2.4.0+dfsg-17.debian.tar.xz
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Files:
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 4e44700a8806353a065ccfc8084c93d4 30084 science optional seqan2_2.4.0+dfsg-17.debian.tar.xz
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