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 - 20:30:03 PST
