[gmx-users] Building gromacs on CRAY XC40
Mark Abraham
mark.j.abraham at gmail.com
Mon Oct 5 12:37:50 CEST 2015
Hi,
Often the XC40 has a different kind of login vs compute node. Here it looks
like you have configured for the compute node, but are actually using a
toolchain to build for the login node. Use the Cray MPI wrapper compiler
configured to use gcc as its back end as the compiler to give to CMake, and
you should be fine.
Mark
On Mon, Oct 5, 2015 at 6:15 AM kevin chen <fch6699 at gmail.com> wrote:
> 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
> --
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