NVBIO CUDA Compatibility

[ioeddk]

Which CUDA version does NVBIO currently support? I was trying to build it with nvcc 12.2 and aimed to run on CUDA 12.0 targeting SM86 compute capability.

I used cmake -DGPU_ARCHITECTURE=sm_86 .. to generate the build files and the output is:

-- The C compiler identification is GNU 10.5.0
-- The CXX compiler identification is GNU 10.5.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Building Release
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Found CUDA: /usr/local/cuda-12.2 (found version "12.2") 
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) 
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of off64_t
-- Check size of off64_t - done
-- Looking for fseeko
-- Looking for fseeko - found
-- Looking for unistd.h
-- Looking for unistd.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /home/[email protected]/repo/nvbio/build

Then I got the following errors resulting in build failure:

/usr/local/cuda-12.2/include/cub/detail/type_traits.cuh:58:1: error: ‘CUB_NAMESPACE_END’ does not name a type
   58 | CUB_NAMESPACE_END
      | ^~~~~~~~~~~~~~~~~

/home/[email protected]/repo/nvbio/contrib/cub/cub/util_device.cuh:151:90: error: cannot resolve overloaded function ‘EmptyKernel’ based on conversion to type ‘const void*’
  151 |         if (CubDebug(error = cudaFuncGetAttributes(&empty_kernel_attrs, EmptyKernel<void>))) break;

Is there a simple workaround for this problem?