[gmx-users] Gromacs error

Vytautas Rakeviius vytautas1987 at yahoo.com
Mon Oct 30 12:51:54 CET 2017

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:  
I have the following problems

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

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


  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


  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

/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


recipe for target

make[2]: ***
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
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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