[gmx-users] Gromacs error

[Vytautas Rakeviius]

You really need cuda? IF no you can try:cmake .. -DGMX_GPU=OFF
 

    On Sunday, October 29, 2017, 7:26:04 AM GMT+2, Kunal Dutta <kunal_lifesc at mail.vidyasagar.ac.in> wrote:  
 
 Hi,
I have the following problems

kunal at kunal-HP-Pavilion-Notebook:~/Downloads/gromacs-5.0/build$ cmake ..
-DGMX_BUILD_OWN_FFTW=ON

CMake Warning at src/contrib/fftw/CMakeLists.txt:79 (message):

  The GROMACS build will download FFTW 3.3.3 as requested, but it will not

  know the file it receives is correct.  If you now use



  make



  GROMACS will build and link to FFTW anyway, but there is a possible
security risk if you execute a GROMACS tool that calls this library.
Instead, you can use



  make fftwBuild



  to do just the download and build of FFTW, and then run



  md5sum src/contrib/fftw/fftwBuild-prefix/src/fftw-3.3.3.tar.gz



  to see if it matches 0a05ca9c7b3bfddc8278e7c40791a1c2.  If so, everything

  is OK and you should use



  make



  to proceed with the rest of the GROMACS build. Alternatively, you could
stop using GMX_BUILD_OWN_FFTW, and instead follow the GROMACS installation
instructions to build FFTW yourself.





-- The GROMACS-managed build of FFTW 3 will configure with the following
optimizations: --enable-sse2

-- Configuring done

-- Generating done

-- Build files have been written to: /home/kunal/Downloads/gromacs-5.0/build

kunal at kunal-HP-Pavilion-Notebook:~/Downloads/gromacs-5.0/build$ make

[  1%] Built target fftwBuild

[  1%] Building NVCC (Device) object
src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.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 cuda_tools_generated_cudautils.cu.o.cmake:264 (message):

  Error generating file


/home/kunal/Downloads/gromacs-5.0/build/src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o





src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/build.make:383:
recipe for target
'src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_cudautils.cu.o'
failed

make[2]: ***
[src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_cudautils.cu.o]
Error 1

CMakeFiles/Makefile2:1609: recipe for target
'src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all' failed

make[1]: *** [src/gromacs/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all]
Error 2

Makefile:147: recipe for target 'all' failed

make: *** [all] Error 2
-- 
---------------------------------------------------------
Regards.
Kunal Dutta
Senior Research Scholar
Microbiology and Immunology Laboratory
Department of Human Physiology with Community Health
Vidyasagar University, Medinipur-721102
West Bengal, India.
Cell: 9126181933
--------------------------------------------
ORCID ID: 0000-0002-0818-8787
RG: https://www.researchgate.net/profile/Kunal_Dutta2
GS: https://scholar.google.co.in/citations?user=ULby284AAAAJ&hl=en

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