[Debian-med-packaging] Bug#986592: [Help] Re: Bug#986592: kleborate: flaky arm64 autopkgtest: Mutex is not owned by current thread

[Andreas Tille]

Hi Aaron,

On Fri, Apr 09, 2021 at 12:01:21AM -0400, Aaron M. Ucko wrote:
> Never mind, this appears to be a different issue, per a backtrace
> obtained with EXCEPTION_STACK_TRACE_LEVEL=Error and a great deal of
> patience:
> 
> Error: tblastn encountered an error:
> terminate called after throwing an instance of 'ncbi::CMutexException'
>   what():  NCBI C++ Exception:
>     T29 "c++/include/corelib/ncbidiag.hpp", line 417: Error: (CMutexException::eOwner) ncbi::ncbi_namespace_mutex_mt::SSystemMutex::ThrowNotOwned() - Mutex is not owned by current thread
>      Stack trace:
>       /usr/lib/ncbi-blast+/libxncbi.so ???:0 ncbi::CMutexException::CMutexException(ncbi::CDiagCompileInfo const&, ncbi::CException const*, ncbi::CMutexException::EErrCode, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, ncbi::EDiagSev) offset=0x3C addr=0xffff83061d9c
>       /usr/lib/ncbi-blast+/libxncbi.so ???:0 ncbi::ncbi_namespace_mutex_mt::SSystemMutex::ThrowNotOwned() offset=0x88 addr=0xffff82f76534
>       /usr/lib/ncbi-blast+/libxncbi.so ???:0 ncbi::ncbi_namespace_mutex_mt::SSystemMutex::Unlock(ncbi::ncbi_namespace_mutex_mt::SSystemFastMutex::ELockSemantics) offset=0x78 addr=0xffff83057938
>       /usr/lib/ncbi-blast+/libseqdb.so ???:0 ncbi::CSeqDBLockHold::~CSeqDBLockHold() offset=0x30 addr=0xffff84305fa0
>       /usr/lib/ncbi-blast+/libseqdb.so ???:0 ncbi::CSeqDBImpl::GetSeqLength(int) const offset=0x48 addr=0xffff8432ca1c
>       /usr/lib/ncbi-blast+/libblast.so ???:0 BLAST_SetupPartialFetching offset=0x134 addr=0xffff84442904
>       /usr/lib/ncbi-blast+/libblast.so ???:0  offset=0x27938 addr=0xffff8441f938
>       /usr/lib/aarch64-linux-gnu/libgomp.so.1 ???:0  offset=0x18CB0 addr=0xffff81f19cb0
>       /lib/aarch64-linux-gnu/libpthread.so.0 ???:0  offset=0x8628 addr=0xffff82027628
>       /lib/aarch64-linux-gnu/libc.so.6 ???:0  offset=0xD601C addr=0xffff82c2001c

Thanks a lot for your investigation.  Unfortunately I have no idea how
to proceed from here.  Does anybody have an idea?  I mean a better idea
than just stating this package does not work on arm64 which would
probably some last resort.

Kind regards

     Andreas.

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