Oh and yes I see AMBER 14 now I look properly.
AMBER 14 does NOT support CUDA 8.0 OR Pascal GPUs (GTX1070/1080/Titan-XP). You will need to upgrade to AMBER 16.
All the best
Ross
> On Feb 1, 2017, at 23:14, Ross Walker <ross.rosswalker.co.uk> wrote:
>
> 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 <mailto: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/>
>> <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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>
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Received on Wed Feb 01 2017 - 20:30:04 PST
