Hi all,
greetings from the Debian Med Sprint 2021!
[...]
> /usr/bin/nvcc -M -D__CUDACC__
> /build/relion-cuda-3.1.0/src/acc/cuda/cuda_projector_plan.cu -o
> /build/relion-cuda-3.1.0/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector_plan.cu.o.NVCC-depend
> -ccbin /usr/bin/cc -m64 -DINSTALL_LIBRARY_DIR=/usr/lib/
> -DSOURCE_DIR=/build/relion-cuda-3.1.0/src/ -DACC_CUDA=2 -DACC_CPU=1 -DCUDA
> -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -Xcompiler
> ,\"-g\",\"-O2\",\"-ffile-prefix-map=/build/relion-cuda-3.1.0=.\",\"-fstack-protector-strong\",\"-Wformat\",\"-Werror=format-security\",\"-O3\",\"-DNDEBUG\"
> -arch=sm_35 -D__INTEL_COMPILER --default-stream per-thread
> --disable-warnings -DNVCC -I/usr/include
> -I/usr/lib/x86_64-linux-gnu/openmpi/include
> -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
> -I/build/relion-cuda-3.1.0 -I/usr/lib/fltk -I/usr/include/x86_64-linux-gnu
> nvcc warning : The 'compute_35', 'compute_37', 'compute_50', 'sm_35', 'sm_37'
> and 'sm_50' architectures are deprecated, and may be removed in a future
> release (Use -Wno-deprecated-gpu-targets to suppress warning).
> In file included from /usr/include/thrust/system/cuda/config.h:33,
> from
> /usr/include/thrust/system/cuda/detail/execution_policy.h:35,
> from
> /usr/include/thrust/iterator/detail/device_system_tag.h:23,
> from
> /usr/include/thrust/iterator/detail/iterator_facade_category.h:22,
> from /usr/include/thrust/iterator/iterator_facade.h:37,
> from
> /build/relion-cuda-3.1.0/src/acc/cuda/cub/device/../iterator/arg_index_input_iterator.cuh:48,
> from
> /build/relion-cuda-3.1.0/src/acc/cuda/cub/device/device_reduce.cuh:41,
> from
> /build/relion-cuda-3.1.0/src/acc/cuda/cuda_utils_cub.cuh:16,
> from
> /build/relion-cuda-3.1.0/src/acc/cuda/cuda_projector_plan.cu:10:
> /usr/include/cub/util_namespace.cuh:46:2: error: #error CUB requires a
> definition of CUB_NS_QUALIFIER when CUB_NS_PREFIX/POSTFIX are defined.
>46 | #error CUB requires a definition of CUB_NS_QUALIFIER when
> CUB_NS_PREFIX/POSTFIX are defined.
> | ^
> CMake Error at
> relion_gpu_util_generated_cuda_projector_plan.cu.o.Release.cmake:220
> (message):
> Error generating
>
> /build/relion-cuda-3.1.0/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_projector_plan.cu.o
>
>
> make[4]: *** [src/apps/CMakeFiles/relion_gpu_util.dir/build.make:1439:
> src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector_plan.cu.o]
> Error 1
> make[4]: Leaving directory '/build/relion-cuda-3.1.0/build'
>
>
> This seems to be the Breaking Change described in
> https://github.com/NVIDIA/cub/releases/tag/1.14.0:
>
> #350: When the CUB_NS_[PRE|POST]FIX macros are set, CUB_NS_QUALIFIER
> must also be defined to the fully qualified CUB namespace (e.g.
> #define CUB_NS_QUALIFIER ::foo::cub). Note that this is handled
> automatically when using the new [THRUST_]CUB_WRAPPED_NAMESPACE mechanism.
I updated the relion code to the latest upstream version (3.1.3) and
tried to rebuild in the hope that it changed something: it did, now I get:
[...]
/usr/bin/nvcc -M -D__CUDACC__
/build/relion-cuda-3.1.3/src/acc/cuda/cuda_projector_plan.cu -o
/build/relion-cuda-3.1.3/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector_plan.cu.o.NVCC-depend
-ccbin /usr/bin/cc -m64 -DINSTALL_LIBRARY_DIR=/usr/lib/
-DSOURCE_DIR=/build/relion-cuda-3.1.3/src/ -DACC_CUDA=2 -DACC_CPU=1
-DCUDA -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -Xcompiler
,\"-g\",\"-O2\",\"-ffile-prefix-map=/build/relion-cuda-3.1.3=.\",\"-fstack-protector-strong\",\"-Wformat\",\"-Werror=format-security\",\"-O3\",\"-DNDEBUG\"
-arch=sm_35 -D__INTEL_COMPILER --default-stream per-thread
--disable-warnings -DNVCC -I/usr/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
-I/build/relion-cuda-3.1.3 -I/usr/lib/fltk -I/usr/include/x86_64-linux-gnu
nvcc warning : The 'compute_35', 'compute_37', 'compute_50', 'sm_35',
'sm_37' and 'sm_50' architectures are deprecated, and may be removed in
a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
In file included from
/usr/include/thrust/system/cuda/detail/execution_policy.h:35,
from
/usr/include/thrust/iterator/detail/device_system_tag.h:23,
from
/usr/include/thrust/iterator/detail/iterator_facade_category.h:22,
from /usr/include/thrust/iterator/iterator_facade.h:37,
from
/build/relion-cuda-3.1.3/src/acc/cuda/cub/device/../iterator/arg_index_input_iterator.cuh:48,
from
/build/relion-cuda-3.1.3/src/acc/cuda/cub/device/device_reduce.cuh:41,
from
