Re: hdf5 error with cmake on a few platforms (including mips)

(I thought I sent this before but I think my mail client messed it up -
sorry if you receive it twice)

On Thu, 16 Oct 2014 12:54:16 +0200 Olivier Sallou wrote:
> I have FTBS errors with hdf5 using cmake on a few platforms (mips,
> powerpc, sparc).
> 
> The error is:
> 
> CMake Warning (dev) at thirdparty/gatb-core/CMakeLists.txt:201 (ADD_DEPENDENCIES):
>   Policy CMP0046 is not set: Error on non-existent dependency in
>   add_dependencies.  Run "cmake --help-policy CMP0046" for policy details.
>   Use the cmake_policy command to set the policy and suppress this warning.
> 
>   The dependency target "hdf5" of target "gatbcore-static" does not exist.
> This warning is for project developers.  Use -Wno-dev to suppress it

Hi,

That isn't the error causing the FTBFS (infact that warning appears on
all arches - you should look into that). The real error is:

> [ 97%] Building CXX object ext/gatb-core/tools/CMakeFiles/dbgh5.dir/dbgh5.cpp.o
> Linking CXX executable ../bin/dbgh5
> ../lib/libgatbcore.a(Storage.cpp.o): In function `gatb::core::tools::storage::impl::BagHDF5<gatb::core::tools::math::NativeInt8>::insert(gatb::core::tools::math::NativeInt8 const*, unsigned int)':
> /«BUILDDIR»/mapsembler2-2.2.3+dfsg/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:102: undefined reference to `__sync_fetch_and_add_8'
> ../lib/libgatbcore.a(SortingCountAlgorithmTemplates2.cpp.o): In function `gatb::core::tools::storage::impl::BagHDF5<gatb::core::tools::math::LargeInt<2> >::insert(gatb::core::tools::math::LargeInt<2> const*, unsigned int)':
> /«BUILDDIR»/mapsembler2-2.2.3+dfsg/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:102: undefined reference to `__sync_fetch_and_add_8'
> ../lib/libgatbcore.a(SortingCountAlgorithmTemplates2.cpp.o): In function `gatb::core::tools::storage::impl::BagHDF5<gatb::core::kmer::impl::Kmer<64u>::Count>::insert(gatb::core::kmer::impl::Kmer<64u>::Count const*, unsigned int)':
> /«BUILDDIR»/mapsembler2-2.2.3+dfsg/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:102: undefined reference to `__sync_fetch_and_add_8'
> ../lib/libgatbcore.a(SortingCountAlgorithmTemplates2.cpp.o): In function `gatb::core::tools::storage::impl::BagHDF5<gatb::core::tools::misc::IHistogram::Entry>::insert(gatb::core::tools::misc::IHistogram::Entry const*, unsigned int)':
> /«BUILDDIR»/mapsembler2-2.2.3+dfsg/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:102: undefined reference to `__sync_fetch_and_add_8'
> ../lib/libgatbcore.a(SortingCountAlgorithmTemplates2.cpp.o): In function `gatb::core::tools::storage::impl::BagHDF5<gatb::core::tools::math::NativeInt64>::insert(gatb::core::tools::math::NativeInt64 const*, unsigned int)':
> /«BUILDDIR»/mapsembler2-2.2.3+dfsg/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:102: undefined reference to `__sync_fetch_and_add_8'
> ../lib/libgatbcore.a(SortingCountAlgorithmTemplates1.cpp.o):/«BUILDDIR»/mapsembler2-2.2.3+dfsg/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:102: more undefined references to `__sync_fetch_and_add_8' follow
> collect2: error: ld returned 1 exit status

MIPS 32-bit (and probably the other arches) have no hardware support for
8-byte atomic operations. Either you should remove / disable 8-byte
calls to __sync* functions on these arches, or you can use the __atomic
functions from libatomic which should work everywhere. 

https://gcc.gnu.org/onlinedocs/gcc-4.9.1/gcc/_005f_005fatomic-Builtins.html#_005f_005fatomic-Builtins

Also, the functions in stdatomic.h from C11 map almost exactly to gcc's
__atomic functions (requires gcc 4.9).

http://en.cppreference.com/w/c/atomic

You can use the most restrictive memory model __ATOMIC_SEQ_CST to get
the same behaviour as the __sync functions. You'll also need to link
with -latomic.

Thanks,
James