[gmx-users] Building gromacs on CRAY XC40

[kevin chen]

Dear Gromacs users,

I am trying to build gromacs on our latest supercomputer CRAY XC40, but the
following errors using gcc and fftw. Here's my list of module loaded and
install script, can anyone give any instructions?

=========================================================================
Currently Loaded Modulefiles:
  1) modules/3.2.6.7                       8) gcc/4.9.3
       15) xpmem/0.1-2.0502.55507.3.2.ari
  2) eswrap/1.1.0-1.020200.1231.0          9) cray-libsci/13.1.0
        16) dvs/2.5_0.9.0-1.0502.1873.1.145.ari
  3) switch/1.0-1.0502.54233.2.96.ari     10)
udreg/2.3.2-1.0502.9275.1.12.ari     17) alps/5.2.1-2.0502.9041.11.6.ari
  4) craype-network-aries                 11) ugni/5.0-1.0502.9685.4.24.ari
       18) rca/1.0.0-2.0502.53711.3.127.ari
  5) craype/2.4.1                         12)
pmi/5.0.8-1.0000.10843.170.1.ari     19) atp/1.8.3
  6) cray-mpich/7.2.4                     13)
dmapp/7.0.1-1.0502.9501.5.219.ari    20) PrgEnv-gnu/5.2.40
  7) craype-ivybridge                     14)
gni-headers/3.0-1.0502.9684.5.2.ari  21) fftw/3.3.4.4
===========================================================================
export CXX=`which cc`
export CC=`which cc`
export MPICC=`which cc`
export F77=`which ftn`
export INSTALL_PATH=/home1/03024/chenk/Software/Gromacs/install

mkdir g_single_parallel
cd g_single_parallel


/home1/03024/chenk/Software/cmake/install/bin/cmake .. \
-DCMAKE_INSTALL_PREFIX=$INSTALL_PATH \
-DGMX_FFT_LIBRARY=fftw3 \
-DGMX_X11=OFF \
-DBUILD_SHARED_LIBS=OFF \
-DGMX_PREFER_STATIC_LIBS=ON \
-DGMX_BUILD_MDRUN_ONLY=OFF \
-DGMX_MPI=ON -DGMX_OPENMP=ON \
-DGMX_XML=OFF \
-DGMX_SOFTWARE_INVSQRT=OFF \
-DGMX_SKIP_DEFAULT_CFLAGS=ON \
-DCMAKE_C_COMPILER=cc \
-DCMAKE_C_FLAGS="-fomit-frame-pointer -finline-functions -funroll-all-loops
-O3 " \
-DCMAKE_CXX_COMPILER=cc \
-DCMAKE_CXX_FLAGS="-O3" \
-DGMX_DEFAULT_SUFFIX=ON \
-DGMX_EXTERNAL_BOOST=OFF \
-DGMX_BUILD_SHARED_EXE=off

make -j 12
make install
=========================================================================
Error messages:

In file included from
/opt/gcc/4.9.3/snos/lib/gcc/x86_64-suse-linux/4.9.3/include/immintrin.h:61:0,
                 from
/home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h:40,
                 from
/home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd.h:118,
                 from
/home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/gmxlib/bondfree.c:62:
/home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd_math.h:
In function 'gmx_simd_rsqrt_iter_f':
/opt/gcc/4.9.3/snos/lib/gcc/x86_64-suse-linux/4.9.3/include/fmaintrin.h:159:1:
error: inlining failed in call to always_inline '_mm256_fnmadd_ps': target
specific option mismatch
 _mm256_fnmadd_ps (__m256 __A, __m256 __B, __m256 __C)
 ^
In file included from
/home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd.h:118:0,
                 from
/home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/gmxlib/bondfree.c:62:
/home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h:61:36:
error: called from here
 #define gmx_simd_fmadd_f           _mm256_fmadd_ps
                                    ^
/home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd_math.h:146:12:
note: in expansion of macro 'gmx_simd_fmadd_f'
     return gmx_simd_fmadd_f(gmx_simd_fnmadd_f(x, gmx_simd_mul_f(lu, lu),
gmx_simd_set1_f(1.0f)), gmx_simd_mul_f(lu, gmx_simd_set1_f(0.5f)), lu);
            ^
In file included from
/opt/gcc/4.9.3/snos/lib/gcc/x86_64-suse-linux/4.9.3/include/immintrin.h:61:0,
                 from
/home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h:40,
                 from
/home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd.h:118,
                 from
/home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/gmxlib/bondfree.c:62:
/opt/gcc/4.9.3/snos/lib/gcc/x86_64-suse-linux/4.9.3/include/fmaintrin.h:63:1:
error: inlining failed in call to always_inline '_mm256_fmadd_ps': target
specific option mismatch
 _mm256_fmadd_ps (__m256 __A, __m256 __B, __m256 __C)
 ^
In file included from
/home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/gmxlib/bondfree.c:63:0:
/home1/03024/chenk/Software/Gromacs/GNU_FFTW/gromacs-5.0.6/src/gromacs/simd/simd_math.h:146:5:
error: called from here
     return gmx_simd_fmadd_f(gmx_simd_fnmadd_f(x, gmx_simd_mul_f(lu, lu),
gmx_simd_set1_f(1.0f)), gmx_simd_mul_f(lu, gmx_simd_set1_f(0.5f)), lu);
     ^
[ 51%] Building C object
src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/nrnb.c.o
make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/bondfree.c.o]
Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [all] Error 2
[  0%] Building C object
src/gromacs/CMakeFiles/libgromacs.dir/gmxlib/bondfree.c.o
In file included from
/opt/gcc/4.9.3/snos/lib/gcc/x86_64-suse-linux/4.9.3/include/immintrin.h:61:0,

=========================================================================

Thanks in advance!

Kevin