[gmx-users] Gromacs 2019.3 compilation with GPU support

[Prithwish Nandi]

Hi,
I am trying to compile Gromacs-2019.3 at our HPC cluster. I successfully compiled the single and double precision versions, but it’s producing error for GPU support. (The error message is pasted below)

I am using Intel/2018 update 4 and CUDA/10.0. The base gcc version is 4.8.5. Using MKL as the FFTW lib and mliicc as the C compiler, and mpiicpc as the CXX compiler.

The error I am getting is given below.

Do you have any clue for this?

Thanks, //PN

The error message:

  Error generating file
  /xxx/xxx/gromacs/intel/2019.3/kay/gromacs-2019.3/build_gpu/src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/./libgromacs_generated_nbnxn_cuda_kernel_pruneonly.cu.o


make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_cuda/libgromacs_generated_nbnxn_cuda_kernel_pruneonly.cu.o] Error 1
/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(68): error: identifier "_mm_set1_epi64x" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(70): error: identifier "_mm_set1_pd" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(112): error: identifier "_mm_set_epi64x" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(123): error: identifier "_mm_set_epi64x" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(123): error: identifier "_mm_and_si128" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(172): error: identifier "_mm_set_epi64x" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(175): error: identifier "_mm_or_si128" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(176): error: identifier "_mm_sub_pd" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(177): error: identifier "_mm_mul_pd" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(178): error: identifier "_mm_hadd_pd" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(178): error: identifier "_mm_cvtsd_f64" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(185): error: identifier "_mm_mul_pd" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(185): error: identifier "_mm_add_pd" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(187): error: identifier "_mm_storeu_pd" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(68): error: identifier "_mm_set1_epi64x" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(70): error: identifier "_mm_set1_pd" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(112): error: identifier "_mm_set_epi64x" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(123): error: identifier "_mm_set_epi64x" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(123): error: identifier "_mm_and_si128" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(172): error: identifier "_mm_set_epi64x" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(175): error: identifier "_mm_or_si128" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(176): error: identifier "_mm_sub_pd" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(177): error: identifier "_mm_mul_pd" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(178): error: identifier "_mm_hadd_pd" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(178): error: identifier "_mm_cvtsd_f64" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(185): error: identifier "_mm_mul_pd" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(185): error: identifier "_mm_add_pd" is undefined

/usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(187): error: identifier "_mm_storeu_pd" is undefined

14 errors detected in the compilation of "/localscratch/397189/tmpxft_00006280_00000000-6_gpubonded-impl.cpp4.ii".