[gmx-users] Error while re-compiling Gromacs 5.1.2 with GPU and gcc 5.3.1

[Diogo Martins de Sá]

Hi guys,

 

I am running kubuntu 16.04 and installed CUDA toolkit 7.5 like was done here:

 

https://www.pugetsystems.com/labs/articles/NVIDIA-CUDA-with-Ubuntu-16-04-beta-on-a-laptop-if-you-just-cannot-wait-775/

 

I used cmake with the following command line:

 

cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on -DGPU_DEPLOYMENT_KIT_ROOT_DIR=/usr/local/cuda-7.5

 

No errors occured.

 

Then I ran make and I got the following msg:

 

Making install in m4
[  1%] Completed 'fftwBuild'
[  1%] Built target fftwBuild
[  1%] Generating baseversion-gen.c
[  2%] Building NVCC (Device) object src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_copyrite_gpu.cu.o
/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;
                                          ^
CMake Error at libgromacs_generated_copyrite_gpu.cu.o.cmake:266 (message):
  Error generating file
  /home/biofisica/Downloads/gromacs-5.1.2/build/src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/./libgromacs_generated_copyrite_gpu.cu.o


src/gromacs/CMakeFiles/libgromacs.dir/build.make:63: recipe for target 'src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_copyrite_gpu.cu.o' failed
make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_copyrite_gpu.cu.o] Error 1
CMakeFiles/Makefile2:2026: recipe for target 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2

 

Any clues how to proceed?

 

Best regards,

Diogo

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