Hi Anton,
You need to be using CUDA 8.0 with Pascal (GTX-1080) GPUs. CUDA 7.5 does not support Pascal GPUs. Make sure nvcc -v returns 8.0 and then try again.
That said the error you are getting is from /usr/include/string.h which is not part of AMBER. Are you sure other C and C++ programs can be compiled correctly on this system?
A simple google of the error shows you are not the only one and it is not unique to AMBER:
/usr/include/string.h:652:42: error: ‘memcpy’ was not declared in this scope
https://www.google.com/search?client=safari&rls=en&q=/usr/include/string.h:652:42:+error:+%E2%80%98memcpy%E2%80%99+was+not+declared+in+this+scope&ie=UTF-8&oe=UTF-8 <
https://www.google.com/search?client=safari&rls=en&q=/usr/include/string.h:652:42:+error:+%E2%80%98memcpy%E2%80%99+was+not+declared+in+this+scope&ie=UTF-8&oe=UTF-8>
You might want to consider Ubuntu 14.04 or Centos instead. I try to stay away from the bleeding edge Ubuntu builds unless there is a real compelling reason.
All the best
Ross
> On Feb 1, 2017, at 23:06, Anton Perera <antonsperera.ichemc.edu.lk> wrote:
>
> Hi!
> I'm trying to compile pmemd.cuda in ubuntu 16.04 with CUDA 7.5 for a
> GTX1080.(However I have installed CUDA 8.0 as *well
> ref:https://www.pugetsystems.com/labs/hpc/Install-Ubuntu-16-04-or-14-04-and-CUDA-8-and-7-5-for-NVIDIA-Pascal-GPU-825/
> <https://www.pugetsystems.com/labs/hpc/Install-Ubuntu-16-04-or-14-04-and-CUDA-8-and-7-5-for-NVIDIA-Pascal-GPU-825/>*
> )
> The AMBER versions I use are as follows
>
> AmberTools version 15.06
> Amber version 14.13
>
> I get the following error when compiling. Any support in this regard is
> much appreciated.
>
> make -C ./cuda
> make[5]: Entering directory
> '/media/iti_gpu_01/Workspace/AMBER/amber14/src/pmemd/src/cuda'
> gfortran -DBINTRAJ -DEMIL -DPUBFFT -O3 -mtune=native -DCUDA -Duse_SPFP
> -I/usr/local/cuda-7.5/include -IB40C -IB40C/KernelCommon -c cuda_info.F90
> f951: Warning: Nonexistent include directory ‘B40C/KernelCommon’
> [-Wmissing-include-dirs]
> gcc -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ
> -DCUDA -Duse_SPFP -I/usr/local/cuda-7.5/include -IB40C
> -IB40C/KernelCommon -c gpu.cpp
> gcc -O3 -mtune=native -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ
> -DCUDA -Duse_SPFP -I/usr/local/cuda-7.5/include -IB40C
> -IB40C/KernelCommon -c gputypes.cpp
> /usr/local/cuda-7.5/bin/nvcc -gencode arch=compute_20,code=sm_20 -gencode
> arch=compute_30,code=sm_30 -gencode arch=compute_50,code=sm_50
> -use_fast_math -O3 -DCUDA -Duse_SPFP -I/usr/local/cuda-7.5/include -IB40C
> -IB40C/KernelCommon -c kForcesUpdate.cu
> /usr/include/string.h: In function ‘void* __mempcpy_inline(void*, const
> void*, size_t)’:
> /usr/include/string.h:652:42: error: ‘memcpy’ was not declared in this scope
> return (char *) memcpy (__dest, __src, __n) + __n;
> ^
> Makefile:35: recipe for target 'kForcesUpdate.o' failed
> make[5]: *** [kForcesUpdate.o] Error 1
> make[5]: Leaving directory
> '/media/iti_gpu_01/Workspace/AMBER/amber14/src/pmemd/src/cuda'
> Makefile:136: recipe for target 'cuda/cuda.a' failed
> make[4]: *** [cuda/cuda.a] Error 2
> make[4]: Leaving directory
> '/media/iti_gpu_01/Workspace/AMBER/amber14/src/pmemd/src'
> Makefile:23: recipe for target 'cuda' failed
> make[3]: *** [cuda] Error 2
> make[3]: Leaving directory
> '/media/iti_gpu_01/Workspace/AMBER/amber14/src/pmemd'
> Makefile:37: recipe for target 'cuda' failed
> make[2]: *** [cuda] Error 2
> make[2]: Leaving directory '/media/iti_gpu_01/Workspace/AMBER/amber14/src'
> Makefile:321: recipe for target 'cuda' failed
> make[1]: [cuda] Error 2 (ignored)
> make[1]: Leaving directory
> '/media/iti_gpu_01/Workspace/AMBER/amber14/AmberTools/src'
> make[1]: Entering directory '/media/iti_gpu_01/Workspace/AMBER/amber14/src'
> Starting installation of Amber14 (cuda) at 2017 පෙබරවාරි 2 වැනි
> බ්රහස්පතින්දා 00:34:03 +0530.
> cd pmemd && make cuda
> make[2]: Entering directory
> '/media/iti_gpu_01/Workspace/AMBER/amber14/src/pmemd'
> make -C src/ cuda
> make[3]: Entering directory
> '/media/iti_gpu_01/Workspace/AMBER/amber14/src/pmemd/src'
> make -C ./cuda
> make[4]: Entering directory
> '/media/iti_gpu_01/Workspace/AMBER/amber14/src/pmemd/src/cuda'
> /usr/local/cuda-7.5/bin/nvcc -gencode arch=compute_20,code=sm_20 -gencode
> arch=compute_30,code=sm_30 -gencode arch=compute_50,code=sm_50
> -use_fast_math -O3 -DCUDA -Duse_SPFP -I/usr/local/cuda-7.5/include -IB40C
> -IB40C/KernelCommon -c kForcesUpdate.cu
> /usr/include/string.h: In function ‘void* __mempcpy_inline(void*, const
> void*, size_t)’:
> /usr/include/string.h:652:42: error: ‘memcpy’ was not declared in this scope
> return (char *) memcpy (__dest, __src, __n) + __n;
> ^
> Makefile:35: recipe for target 'kForcesUpdate.o' failed
> make[4]: *** [kForcesUpdate.o] Error 1
> make[4]: Leaving directory
> '/media/iti_gpu_01/Workspace/AMBER/amber14/src/pmemd/src/cuda'
> Makefile:136: recipe for target 'cuda/cuda.a' failed
> make[3]: *** [cuda/cuda.a] Error 2
> make[3]: Leaving directory
> '/media/iti_gpu_01/Workspace/AMBER/amber14/src/pmemd/src'
> Makefile:23: recipe for target 'cuda' failed
> make[2]: *** [cuda] Error 2
> make[2]: Leaving directory
> '/media/iti_gpu_01/Workspace/AMBER/amber14/src/pmemd'
> Makefile:37: recipe for target 'cuda' failed
> make[1]: *** [cuda] Error 2
> make[1]: Leaving directory '/media/iti_gpu_01/Workspace/AMBER/amber14/src'
> Makefile:7: recipe for target 'install' failed
> make: *** [install] Error 2
> iti_gpu_01.ITIGPU01:/media/iti_gpu_01/Workspace/AMBER/amber14$
>
> Kind regards,
> Anton
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Received on Wed Feb 01 2017 - 20:30:04 PST
