[gmx-users] GROMACS-GPU enabled installation error

[David van der Spoel]

Den 2018-01-06 kl. 22:20, skrev Joydeep Munshi:
> Hello,
> 
> I am trying to install Gromacs 5.1.5 with GPU enabled version. I have
> Nvidia Geforce GTX1080 GPU card in my system and Cuda 9.1.85 installed as
> my nvcc. While running cmake command as mentioned below, I am succssfully
> able to generate the makefiles in build directory. However, while running
> make after that, I am facing with an error. Could you please help me out
> with resolving the issue?

You need to throw away your CMakeCache.txt file since it has leftovers 
from a previous build. Alternatively, you may have two conflicting CUDA 
installations.

In addition you should consider installing the latest version instead 
(2016.4 for stable or 2018.beta for the upcoming release).

> 
> *cmake *comamnd used before running *make*:
> 
> *cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> -DGMX_GPU=on                -DGMX_BUILD_MDRUN_ONLY=on
> -DGMX_BINARY_SUFFIX=_cuda              -DGMX_LIBS_SUFFIX=_cuda
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-9.1*
> 
> 
> *make *error:
> 
>   */bin/mkdir -p
> '/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/lib/pkgconfig'*
> * /usr/bin/install -c -m 644 fftw3f.pc
> '/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/lib/pkgconfig'*
> *Making install in threads*
> *Making install in tests*
> *Making install in mpi*
> *Making install in doc*
> *Making install in FAQ*
> * /bin/mkdir -p
> '/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/share/info'*
> * /usr/bin/install -c -m 644
> /home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild/doc/fftw3.info
> <http://fftw3.info>
> /home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild/doc/fftw3.info-1
> /home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild/doc/fftw3.info-2
> '/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/share/info'*
> * install-info
> --info-dir='/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/share/info'
> '/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/share/info/fftw3.info
> <http://fftw3.info>'*
> *Making install in tools*
> * /bin/mkdir -p
> '/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/bin'*
> *  /bin/bash ../libtool   --mode=install /usr/bin/install -c fftwf-wisdom
> '/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/bin'*
> *libtool: install: /usr/bin/install -c fftwf-wisdom
> /home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/bin/fftwf-wisdom*
> * /bin/mkdir -p
> '/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/bin'*
> * /usr/bin/install -c fftw-wisdom-to-conf
> '/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/bin'*
> * /bin/mkdir -p
> '/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/share/man/man1'*
> * /usr/bin/install -c -m 644
> /home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild/tools/fftw-wisdom-to-conf.1
> fftwf-wisdom.1
> '/home/joydeep/Downloads/gromacs-5.1.5/build-cuda/src/contrib/fftw/fftwBuild-prefix/share/man/man1'*
> *Making install in m4*
> *[  0%] Completed 'fftwBuild'*
> *[  0%] Built target fftwBuild*
> *[  0%] Generating baseversion-gen.c*
> *[  1%] Building NVCC (Device) object
> src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/cuda_tools/libgromacs_generated_copyrite_gpu.cu.o*
> *nvcc fatal   : Unsupported gpu architecture 'compute_20'*
> *CMake Error at libgromacs_generated_copyrite_gpu.cu.o.cmake:207 (message):*
> *  Error generating*
> *
> /home/joydeep/Downloads/gromacs-5.1.5/build-cuda/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/Makefile2:1291: 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*
> 
> *Thanks and regards,*
> *Joydeep Munshi,*
> *Graduate Research Assistant,*
> *Packard Lab 375,*
> *Mechanical Engineering and Mechanics,*
> *Lehigh University*
> *Contact: (484)-821-6702*
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se