#1069691 libmaus2: FTBFS on arm64: what(): AutoArray<unsigned long,alloc_type_memalign_cacheline> failed to allocate 1398102 elements (11184816 bytes)

Package:
src:libmaus2
Source:
src:libmaus2
Submitter:
Sebastian Ramacher
Date:
2025-01-05 11:15:02 UTC
Severity:
normal
Tags:
#1069691#5
Date:
2024-04-22 19:39:47 UTC
From:
To:
Source: libmaus2
Version: 2.0.813+ds-2
Severity: serious
Tags: ftbfs
Justification: fails to build from source (but built successfully in the past)
X-Debbugs-Cc: sramacher@debian.org

https://buildd.debian.org/status/fetch.php?pkg=libmaus2&arch=arm64&ver=2.0.813%2Bds-2&stamp=1713374325&raw=0

   libmaus2 2.0.813: test/test-suite.log
===========================================

# TOTAL: 13
# PASS:  11
# SKIP:  0
# XFAIL: 0
# FAIL:  2
# XPASS: 0
# ERROR: 0

.. contents:: :depth: 2

FAIL: testRank.sh
=================

/<<PKGBUILDDIR>>/test /<<PKGBUILDDIR>>/test
/<<PKGBUILDDIR>>/test
[V] testing FastRank...done.
[V] testing RunLengthBitVector...done.
[V] testing E2Append:
	[V]rank class libmaus2::rank::ERank222BAppend writer type libmaus2::bitio::BitWriterTemplate<unsigned long, unsigned long*, 9223372036854775808ul> data type unsigned long
		[V] loop 1
		[V] libmaus2::rank::ERank222BAppendDynamic loop 1
		[V] loop 2
		[V] libmaus2::rank::ERank222BAppendDynamic loop 2
		[V] loop 3
		[V] libmaus2::rank::ERank222BAppendDynamic loop 3
		[V] loop 4
		[V] libmaus2::rank::ERank222BAppendDynamic loop 4
		[V] loop 5
		[V] libmaus2::rank::ERank222BAppendDynamic loop 5
[V] testing WaveletTree rank/select random (size 128)...done.
[V] testing WaveletTree smaller/larger...done.
[V] testing CacheLineRank:
terminate called after throwing an instance of 'libmaus2::exception::LibMausException'
  what():  AutoArray<unsigned long,alloc_type_memalign_cacheline> failed to allocate 1398102 elements (11184816 bytes)
current total allocation 11521707

/<<PKGBUILDDIR>>/src/.libs/libmaus2_stacktrace.so.2(libmaus2::stacktrace::StackTrace::StackTrace()+0x74)[0xffffb4644b88]
/<<PKGBUILDDIR>>/src/.libs/libmaus2_exception.so.2(libmaus2::exception::LibMausException::LibMausException()+0x40)[0xffffb4e42b40]
/<<PKGBUILDDIR>>/src/.libs/testRank(libmaus2::autoarray::AutoArrayAllocate<unsigned long, (libmaus2::autoarray::alloc_type)2>::allocate(unsigned long)+0xc4)[0xaaaae833c2c4]
/<<PKGBUILDDIR>>/src/.libs/testRank(testCacheLineRank()+0x88)[0xaaaae831d318]
/<<PKGBUILDDIR>>/src/.libs/testRank(main+0x134)[0xaaaae830b834]
/lib/aarch64-linux-gnu/libc.so.6(+0x26dc4)[0xffffb4886dc4]
/lib/aarch64-linux-gnu/libc.so.6(__libc_start_main+0x98)[0xffffb4886e98]
/<<PKGBUILDDIR>>/src/.libs/testRank(_start+0x30)[0xaaaae830c5f0]

./testRank.sh: line 7: 355775 Aborted                 ../src/testRank
Exiting with return code 134
FAIL testRank.sh (exit status: 134)

FAIL: testdnarank.sh
====================

/<<PKGBUILDDIR>>/test /<<PKGBUILDDIR>>/test
/<<PKGBUILDDIR>>/test
[V] running short tests...
AutoArray<unsigned long,alloc_type_memalign_cacheline> failed to allocate 16 elements (128 bytes)
current total allocation 341115

/<<PKGBUILDDIR>>/src/.libs/libmaus2_stacktrace.so.2(libmaus2::stacktrace::StackTrace::StackTrace()+0x74)[0xffffa4e64b88]
/<<PKGBUILDDIR>>/src/.libs/libmaus2_exception.so.2(libmaus2::exception::LibMausException::LibMausException()+0x40)[0xffffa55b2b40]
/<<PKGBUILDDIR>>/src/.libs/testdnarank(libmaus2::autoarray::AutoArrayAllocate<unsigned long, (libmaus2::autoarray::alloc_type)2>::allocate(unsigned long)+0xc4)[0xaaaac76d0e24]
/<<PKGBUILDDIR>>/src/.libs/testdnarank(libmaus2::rank::DNARankTemplate<64u>::loadFromRunLength(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, unsigned long)+0x108)[0xaaaac76dcfd8]
/<<PKGBUILDDIR>>/src/.libs/testdnarank(void testShort<libmaus2::rank::DNARankTemplate<64u> >(unsigned long)+0x27c)[0xaaaac77008bc]
/<<PKGBUILDDIR>>/src/.libs/testdnarank(main+0x15c)[0xaaaac76b16cc]
/lib/aarch64-linux-gnu/libc.so.6(+0x26dc4)[0xffffa50a6dc4]
/lib/aarch64-linux-gnu/libc.so.6(__libc_start_main+0x98)[0xffffa50a6e98]
/<<PKGBUILDDIR>>/src/.libs/testdnarank(_start+0x30)[0xaaaac76b1970]

Exiting with return code 1
FAIL testdnarank.sh (exit status: 1)

Cheers
#1069691#10
Date:
2024-04-24 18:09:43 UTC
From:
To:
Control: found -1 2.0.813+ds-3

Hmn, this is annoying.  I do not manage to reproduce the error
with qemu-user.  The test error is reproducible on buildd's real
hardware in the meantime[1], or at least on two of the Arm build
machines hosted by Conova.  There could be something hardware
specific.  I'd have to check how things go on porterbox next.

[1]: https://buildd.debian.org/status/fetch.php?pkg=libmaus2&arch=arm64&ver=2.0.813%2Bds-3&stamp=1713977128&raw=0

Have a nice day,  :)
#1069691#17
Date:
2024-05-12 11:20:19 UTC
From:
To:
Control: tags -1 + confirmed upstream
Control: forwarded -1 https://gitlab.com/german.tischler/libmaus2/-/issues/40

In the end, I could reproduce the test failures affecting
libmaus2 on amdahl and informed upstream.  We'll see how things
go.

Have a nice day,  :)
#1069691#28
Date:
2024-09-04 09:32:18 UTC
From:
To:
Control: severity -1 normal

Hi,

I reduce the severity of this ftbfs bug on arm64, as the
libmaus2 and it's reverse dependency biobambam2 have been
removed from this architecture.  See #1079718 and #1079456.

Have a nice day,  :)