Hi
I found that this problem was posted by 'Hashemi, Mohtadin' and a solution
was posted by 'Scott Brozell'.
Link: http://archive.ambermd.org/202206/0040.html
-Nitin
On Mon, Oct 31, 2022 at 1:23 PM Nitin Kulhar <bo18resch11002.iith.ac.in>
wrote:
> Hello
>
> Installation of Amber for GPU failed after successful installation/testing
> of serial and MPI versions. output of `$make install` :
>
> [ 89%] Building NVCC (Device) object
> src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/pmemd_xray_cuda_generated_BulkMaskGPU.cu.o
> cd
> /home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray
> && /home/opt_ohpc_pub/utils/cmake/3.15.4/bin/cmake -E make_directory
> /home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/.
> cd
> /home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray
> && /home/opt_ohpc_pub/utils/cmake/3.15.4/bin/cmake -D verbose:BOOL=1 -D
> build_configuration:STRING=Debug -D
> generated_file:STRING=/home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/./pmemd_xray_cuda_generated_BulkMaskGPU.cu.o
> -D
> generated_cubin_file:STRING=/home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/./pmemd_xray_cuda_generated_BulkMaskGPU.cu.o.cubin.txt
> -P
> /home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/pmemd_xray_cuda_generated_BulkMaskGPU.cu.o.Debug.cmake
> -- Removing
> /home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/./pmemd_xray_cuda_generated_BulkMaskGPU.cu.o
> /home/opt_ohpc_pub/utils/cmake/3.15.4/bin/cmake -E remove
> /home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/./pmemd_xray_cuda_generated_BulkMaskGPU.cu.o
> -- Generating dependency file:
> /home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/pmemd_xray_cuda_generated_BulkMaskGPU.cu.o.NVCC-depend
> /opt/ohpc/pub/cuda/cuda-11.2/bin/nvcc -M -D__CUDACC__
> /home/nitin.bt.iith/Amber22/amber22_src/src/pmemd/src/xray/cuda/src/xray/BulkMaskGPU.cu
> -o
> /home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/pmemd_xray_cuda_generated_BulkMaskGPU.cu.o.NVCC-depend
> -ccbin /opt/ohpc/pub/compiler/gcc/10.2.0/bin/g++ -m64 -DCUDA -DUSE_MKSTEMP
> -D_GNU_SOURCE -DBINTRAJ -gencode arch=compute_35,code=sm_35 -gencode
> arch=compute_50,code=sm_50 -gencode arch=compute_52,code=sm_52 -gencode
> arch=compute_53,code=sm_53 -gencode arch=compute_60,code=sm_60 -gencode
> arch=compute_61,code=sm_61 -gencode arch=compute_70,code=sm_70 -gencode
> arch=compute_75,code=sm_75 -gencode arch=compute_80,code=sm_80
> -Wno-deprecated-gpu-targets -Wno-deprecated-declarations -DNVCC
> -I/opt/ohpc/pub/cuda/cuda-11.2/include
> -I/home/nitin.bt.iith/Amber22/amber22_src/src/pmemd/src/xray/cuda/src
> -- Generating temporary cmake readable file:
> /home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/pmemd_xray_cuda_generated_BulkMaskGPU.cu.o.depend.tmp
> /home/opt_ohpc_pub/utils/cmake/3.15.4/bin/cmake -D
> input_file:FILEPATH=/home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/pmemd_xray_cuda_generated_BulkMaskGPU.cu.o.NVCC-depend
> -D
> output_file:FILEPATH=/home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/pmemd_xray_cuda_generated_BulkMaskGPU.cu.o.depend.tmp
> -D verbose=1 -P
> /home/opt_ohpc_pub/utils/cmake/3.15.4/share/cmake-3.15/Modules/FindCUDA/make2cmake.cmake
> -- Copy if different
> /home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/pmemd_xray_cuda_generated_BulkMaskGPU.cu.o.depend.tmp
> to
> /home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/pmemd_xray_cuda_generated_BulkMaskGPU.cu.o.depend
> /home/opt_ohpc_pub/utils/cmake/3.15.4/bin/cmake -E copy_if_different
> /home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/pmemd_xray_cuda_generated_BulkMaskGPU.cu.o.depend.tmp
> /home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/pmemd_xray_cuda_generated_BulkMaskGPU.cu.o.depend
> -- Removing
> /home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/pmemd_xray_cuda_generated_BulkMaskGPU.cu.o.depend.tmp
> and
> /home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/pmemd_xray_cuda_generated_BulkMaskGPU.cu.o.NVCC-depend
> /home/opt_ohpc_pub/utils/cmake/3.15.4/bin/cmake -E remove
> /home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/pmemd_xray_cuda_generated_BulkMaskGPU.cu.o.depend.tmp
> /home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/pmemd_xray_cuda_generated_BulkMaskGPU.cu.o.NVCC-depend
> -- Generating
> /home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/./pmemd_xray_cuda_generated_BulkMaskGPU.cu.o
> /opt/ohpc/pub/cuda/cuda-11.2/bin/nvcc
> /home/nitin.bt.iith/Amber22/amber22_src/src/pmemd/src/xray/cuda/src/xray/BulkMaskGPU.cu
> -c -o
> /home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/./pmemd_xray_cuda_generated_BulkMaskGPU.cu.o
> -ccbin /opt/ohpc/pub/compiler/gcc/10.2.0/bin/g++ -m64 -DCUDA -DUSE_MKSTEMP
> -D_GNU_SOURCE -DBINTRAJ -gencode arch=compute_35,code=sm_35 -gencode
> arch=compute_50,code=sm_50 -gencode arch=compute_52,code=sm_52 -gencode
> arch=compute_53,code=sm_53 -gencode arch=compute_60,code=sm_60 -gencode
> arch=compute_61,code=sm_61 -gencode arch=compute_70,code=sm_70 -gencode
> arch=compute_75,code=sm_75 -gencode arch=compute_80,code=sm_80
> -Wno-deprecated-gpu-targets -Wno-deprecated-declarations -DNVCC
> -I/opt/ohpc/pub/cuda/cuda-11.2/include
> -I/home/nitin.bt.iith/Amber22/amber22_src/src/pmemd/src/xray/cuda/src
> /opt/ohpc/pub/cuda/cuda-11.2/include/thrust/detail/allocator/allocator_traits.h(245):
> error: class "thrust::detail::device_delete_allocator" has no member
> "value_type"
> detected during:
> instantiation of class
> "thrust::detail::allocator_traits<Alloc> [with
> Alloc=thrust::detail::device_delete_allocator]"
> (402): here
> instantiation of class
> "thrust::detail::allocator_system<Alloc> [with
> Alloc=thrust::detail::device_delete_allocator]"
> /opt/ohpc/pub/cuda/cuda-11.2/include/thrust/detail/allocator/destroy_range.inl(137):
> here
> instantiation of
> "thrust::detail::allocator_traits_detail::enable_if_destroy_range_case2<Allocator,
> Pointer>::type
> thrust::detail::allocator_traits_detail::destroy_range(Allocator &,
> Pointer, Size) [with Allocator=thrust::detail::device_delete_allocator,
> Pointer=thrust::device_ptr<xray::Sym33>, Size=size_t]"
> /opt/ohpc/pub/cuda/cuda-11.2/include/thrust/detail/allocator/destroy_range.inl(158):
> here
> instantiation of "void thrust::detail::destroy_range(Allocator
> &, Pointer, Size) [with Allocator=thrust::detail::device_delete_allocator,
> Pointer=thrust::device_ptr<xray::Sym33>, Size=size_t]"
> /opt/ohpc/pub/cuda/cuda-11.2/include/thrust/detail/device_delete.inl(42):
> here
> instantiation of "void
> thrust::device_delete(thrust::device_ptr<T>, size_t) [with T=xray::Sym33]"
> /home/nitin.bt.iith/Amber22/amber22_src/src/pmemd/src/xray/cuda/src/xray/BulkMaskGPU.cu(116):
> here
>
> .
> .
> .
>
> 26 errors detected in the compilation of
> "/home/nitin.bt.iith/Amber22/amber22_src/src/pmemd/src/xray/cuda/src/xray/BulkMaskGPU.cu".
> -- Removing
> /home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/./pmemd_xray_cuda_generated_BulkMaskGPU.cu.o
> /home/opt_ohpc_pub/utils/cmake/3.15.4/bin/cmake -E remove
> /home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/./pmemd_xray_cuda_generated_BulkMaskGPU.cu.o
> CMake Error at pmemd_xray_cuda_generated_BulkMaskGPU.cu.o.Debug.cmake:277
> (message):
> Error generating file
>
> /home/nitin.bt.iith/Amber22/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/./pmemd_xray_cuda_generated_BulkMaskGPU.cu.o
>
>
> make[2]: ***
> [src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/pmemd_xray_cuda_generated_BulkMaskGPU.cu.o]
> Error 1
> make[2]: Leaving directory `/home/nitin.bt.iith/Amber22/amber22_src/build'
> make[1]: *** [src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/all]
> Error 2
> make[1]: Leaving directory `/home/nitin.bt.iith/Amber22/amber22_src/build'
> make: *** [all] Error 2
>
> Please help me to troubleshoot this.
> Many thanks!
> -nitin
>
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Received on Mon Oct 31 2022 - 23:00:02 PDT
