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 - 01:00:02 PDT
