build fails with different versions of g++ and CUDA - which one will work?

[muellan]

I have tried to build the latest nvbio on a Ubuntu 14.04 box with:

• gcc4.7.3
• gcc4.8.4
• gcc4.9.2 and
• CUDA 7.0
• CUDA 7.5

Can anyone give me some advice on how to get the library to compile?

The build fails with these messages (apart from a gazillion warnings about integer conversions and macro redefinitions):

In file included from /usr/local/cuda-7.5/include/thrust/system/cuda/detail/cub/block/specializations/../../block/../util_type.cuh:40:0,
                 from /usr/local/cuda-7.5/include/thrust/system/cuda/detail/cub/block/specializations/../../block/../util_ptx.cuh:37,
                 from /usr/local/cuda-7.5/include/thrust/system/cuda/detail/cub/block/specializations/../../block/block_exchange.cuh:36,
                 from /usr/local/cuda-7.5/include/thrust/system/cuda/detail/cub/block/specializations/../../block/block_radix_sort.cuh:37,
                 from /usr/local/cuda-7.5/include/thrust/system/cuda/detail/cub/block/specializations/block_histogram_sort.cuh:36,
                 from /usr/local/cuda-7.5/include/thrust/system/cuda/detail/cub/block/block_histogram.cuh:36,
                 from /usr/local/cuda-7.5/include/thrust/system/cuda/detail/cub/cub.cuh:38,
                 from /usr/local/cuda-7.5/include/thrust/system/cuda/detail/cub.h:63,
                 from /usr/local/cuda-7.5/include/thrust/system/cuda/detail/detail/stable_radix_sort.inl:28,
                 from /usr/local/cuda-7.5/include/thrust/system/cuda/detail/detail/stable_radix_sort.h:86,
                 from /usr/local/cuda-7.5/include/thrust/system/cuda/detail/detail/stable_primitive_sort.inl:21,
                 from /usr/local/cuda-7.5/include/thrust/system/cuda/detail/detail/stable_primitive_sort.h:81,
                 from /usr/local/cuda-7.5/include/thrust/system/cuda/detail/sort.inl:23,
                 from /usr/local/cuda-7.5/include/thrust/system/cuda/detail/sort.h:59,
                 from /usr/local/cuda-7.5/include/thrust/system/detail/adl/sort.h:32,
                 from /usr/local/cuda-7.5/include/thrust/detail/sort.inl:27,
                 from /usr/local/cuda-7.5/include/thrust/sort.h:1361,
                 from /home/muellan/nvbio/nvbio/basic/primitives.h:40,
                 from /home/muellan/nvbio/nvbio/strings/wavelet_tree.h:32,
                 from /home/muellan/nvbio/nvbio-test/wavelet_test.cu:34:
/usr/local/cuda-7.5/include/thrust/system/cuda/detail/cub/block/specializations/../../block/../util_arch.cuh:190:0: note: this is the location of the previous definition
/home/muellan/nvbio/nvbio/basic/iterator.h(104): error: class "nvbio::iterator_category_system<thrust::detail::iterator_category_with_system_and_traversal<thrust::random_access_device_iterator_tag, thrust::device_system_tag, thrust::random_access_traversal_tag>>" has no member "type"
          detected during:
            instantiation of class "nvbio::iterator_system<iterator> [with iterator=nvbio::PackedStream<thrust::device_ptr<nvbio::uint32>, nvbio::uint8, 1U, true, nvbio::uint32>]"
/home/muellan/nvbio/nvbio/strings/wavelet_tree.h(80): here
            instantiation of class "nvbio::WaveletTree<BitStreamIterator, IndexIterator, SymbolType> [with BitStreamIterator=nvbio::PackedStream<thrust::device_ptr<nvbio::uint32>, nvbio::uint8, 1U, true, nvbio::uint32>, IndexIterator=thrust::detail::normal_iterator<thrust::device_ptr<nvbio::uint32>>, SymbolType=nvbio::uint8]"
/home/muellan/nvbio/nvbio-test/wavelet_test.cu(106): here

/home/muellan/nvbio/nvbio/basic/iterator.h(104): error: class "nvbio::iterator_category_system<thrust::detail::iterator_category_with_system_and_traversal<thrust::random_access_device_iterator_tag, thrust::device_system_tag, thrust::random_access_traversal_tag>>" has no member "type"
          detected during:
            instantiation of class "nvbio::iterator_system<iterator> [with iterator=thrust::device_ptr<nvbio::uint32>]"
/home/muellan/nvbio/nvbio/basic/packedstream_inl.h(1414): here
            instantiation of "void nvbio::assign(IndexType, InputIterator, nvbio::PackedStream<InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType>) [with InputIterator=thrust::transform_iterator<nvbio::select_bit_functor<nvbio::uint8>, thrust::detail::normal_iterator<thrust::device_ptr<nvbio::uint8>>, thrust::use_default, thrust::use_default>, InputStream=thrust::device_ptr<nvbio::uint32>, Symbol=nvbio::uint8, SYMBOL_SIZE_T=1U, BIG_ENDIAN_T=true, IndexType=nvbio::uint32]"
/home/muellan/nvbio/nvbio/strings/wavelet_tree_inl.h(197): here
            instantiation of "void nvbio::setup(index_type, const string_iterator &, nvbio::WaveletTreeStorage<system_tag, index_type, symbol_type> &) [with system_tag=nvbio::device_tag, string_iterator=thrust::detail::normal_iterator<thrust::device_ptr<nvbio::uint8>>, index_type=nvbio::uint32, symbol_type=nvbio::uint8]"
/home/muellan/nvbio/nvbio-test/wavelet_test.cu(97): here

/home/muellan/nvbio/nvbio/basic/iterator.h(104): error: class "nvbio::iterator_category_system<thrust::detail::iterator_category_with_system_and_traversal<thrust::random_access_device_iterator_tag, thrust::device_system_tag, thrust::random_access_traversal_tag>>" has no member "type"
          detected during:
            instantiation of class "nvbio::iterator_system<iterator> [with iterator=nvbio::PackedStream<thrust::device_ptr<const nvbio::uint32>, nvbio::uint8, 1U, true, nvbio::uint32>]"
/home/muellan/nvbio/nvbio/strings/wavelet_tree.h(80): here
            instantiation of class "nvbio::WaveletTree<BitStreamIterator, IndexIterator, SymbolType> [with BitStreamIterator=nvbio::PackedStream<thrust::device_ptr<const nvbio::uint32>, nvbio::uint8, 1U, true, nvbio::uint32>, IndexIterator=thrust::detail::normal_iterator<thrust::device_ptr<const nvbio::uint32>>, SymbolType=nvbio::uint8]"
/home/muellan/nvbio/nvbio/strings/wavelet_tree.h(343): here
            instantiation of "nvbio::WaveletTreeStorage<SystemTag, IndexType, SymbolType>::plain_view_type nvbio::plain_view(nvbio::WaveletTreeStorage<SystemTag, IndexType, SymbolType> &) [with SystemTag=nvbio::device_tag, IndexType=nvbio::uint32, SymbolType=nvbio::uint8]"
/home/muellan/nvbio/nvbio-test/wavelet_test.cu(106): here

3 errors detected in the compilation of "/tmp/tmpxft_0000c633_00000000-7_wavelet_test.cpp1.ii".
CMake Error at nvbio-test_generated_wavelet_test.cu.o.cmake:264 (message):
  Error generating file
  /home/muellan/nvbio/build/nvbio-test/CMakeFiles/nvbio-test.dir//./nvbio-test_generated_wavelet_test.cu.o

[nsubtil]

The supported configuration is gcc 4.8 with CUDA 6.5.

There have been some fixes for CUDA 7.x recently, but unfortunately the build still doesn't work with the latest toolkit versions.

[muellan]

Ah, OK, thanks.

[vmiheer]

Is this repository not maintained? (I am wondering if this repository is moved to some other location and/or will there be ever support for newer cuda versions?) Thanking you. +miheer