(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 -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: https://lists.debian.org/[email protected]
