[gmx-developers] GROMACS 4.6 error in file src/gromacs/analysisdata/analysisdata.cpp:45:0

[Szilárd Páll]

On Fri, Aug 24, 2012 at 12:15 PM, Thomas Evangelidis <tevang3 at gmail.com> wrote:
>
>> if you want to get the new native gpu feature you need no special cmake
>> flags so
>> cmake .
>> should work. But I got confused when claiming you should get release-4-6.
>> Instead you need to get:
>> git fetch https://gerrit.gromacs.org/gromacs refs/changes/84/1284/14 &&
>> git checkout FETCH_HEAD
>> (for other download options see https://gerrit.gromacs.org/#/c/1284/)
>> It will be in 4.6 but is not (quite) in it yet.
>> As far as I know the OpenMM GPU option hasn't been updated for 4.6 and
>> thus for OpenMM you could as well use the 4.5 version.
>>

I've tried to reproduce your errors with the same compiler, CUDA 4.2,
and fftw 3.3 and for me it all works fine.

> OK, here's what I did:
>
> $git clone https://gerrit.gromacs.org/gromacs
> $cd gromacs
> $git fetch https://gerrit.gromacs.org/gromacs refs/changes/84/1284/14 && git
> checkout FETCH_HEAD
> $cd ../
> $mkdir gromacs_cuda_build
> $cd gromacs_cuda_build
> $cmake ../gromacs
> -- The C compiler identification is GNU 4.7.0
> -- The CXX compiler identification is GNU 4.7.0
> .....
> .....
> -- checking for module 'fftw3f'
> --   package 'fftw3f' not found
> Could not find fftw3f library named libfftw3f, please specify its location
> in FFTW_LIBRARY by hand (e.g. -DFFTW_LIBRARY='/path/to/libfftw3f.so')
> CMake Error at CMakeLists.txt:863 (MESSAGE):
>   Cannot find FFTW3 (with correct precision - libfftw3f for single precision
>   GROMACS or libfftw3 for double precision GROMACS).  Fix it, choose another
>   FFT library, or use the Gromacs built-in fftpack (slower)!
>
> These are the only files that match the pattern "libfftw3f.so":
> /usr/lib64/libfftw3f.so.3
> /usr/lib64/libfftw3f.so.3.3.1
>
> So I reran cmake using:

Note that you can hint search path to CMake using the
CMAKE_PREFIX_PATH variable.

> $cmake ../gromacs -DFFTW_LIBRARY='/usr/lib64/libfftw3f.so.3'
> Could not the fftw3f header fftw3.h, please specify its path in
> FFTW_INCLUDE_DIR by hand (e.g. -DFFTW_INCLUDE_DIR='/path/to/include')
> CMake Error at CMakeLists.txt:863 (MESSAGE):
>   Cannot find FFTW3 (with correct precision - libfftw3f for single precision
>   GROMACS or libfftw3 for double precision GROMACS).  Fix it, choose another
>   FFT library, or use the Gromacs built-in fftpack (slower)!
>
> Finally I added another flag to designate the FFTW include folder:
>
> $ cmake ../gromacs -DFFTW_LIBRARY='/usr/lib64/libfftw3f.so.3'
> -DFFTW_INCLUDE_DIR='/home/thomas/Programs/fftw-3.3.2/single_precision_installation_dir/include'
> -- Looking for fftwf_plan_r2r_1d in /usr/lib64/libfftw3f.so.3
> -- Looking for fftwf_plan_r2r_1d in /usr/lib64/libfftw3f.so.3 - found
> -- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so.3
> -- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so.3 - not found
> -- Looking for fftw_have_simd_sse2 in /usr/lib64/libfftw3f.so.3
> -- Looking for fftw_have_simd_sse2 in /usr/lib64/libfftw3f.so.3 - not found
> -- Looking for fftwf_have_sse in /usr/lib64/libfftw3f.so.3
> -- Looking for fftwf_have_sse in /usr/lib64/libfftw3f.so.3 - not found
> -- Looking for fftw_have_sse2 in /usr/lib64/libfftw3f.so.3
> -- Looking for fftw_have_sse2 in /usr/lib64/libfftw3f.so.3 - not found

Your fftw3 seems to be compiled without SSE!

> -- Using internal BLAS library
> -- LAPACK requires BLAS
> -- Using internal LAPACK library
> -- Checking for dlopen
> -- Performing Test HAVE_DLOPEN
> -- Performing Test HAVE_DLOPEN - Success
> -- Checking for dlopen - found
> -- Found the ability to use plug-ins when building shared libaries, so will
> compile to use plug-ins (e.g. to read VMD-supported file formats).
> -- Checking for suitable VMD version
> -- VMD plugins not found. Path to VMD can be set with VMDDIR.
> -- Configuring done
> -- Generating done
> -- Build files have been written to:
> /home/thomas/Programs/gromacs_cuda_build
>
> Then I did:
>
> $ make mdrun
> [  0%] Building NVCC (Device) object
> src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//./nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o
> cc1plus: error: invalid option `avx'
>
> cc1plus: error: unrecognized command line option "-fexcess-precision=fast"
> CMake Error at nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o.cmake:198
> (message):
>   Error generating
>
> /home/thomas/Programs/gromacs_cuda_build/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//./nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o
>
>
> make[3]: ***
> [src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir/./nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o]
> Error 1
> make[2]: *** [src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir/all] Error 2
>
> make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2
> make: *** [mdrun] Error 2
>
> I corrected them both by doing:
>
> $for fname in $(grep -lR "\-fexcess\-precision=fast" *); do perl -pi -e
> "s/\-fexcess\-precision=fast//g" $fname; done
> $for fname in $(grep -lR "\-mavx" *); do perl -pi -e "s/\-mavx//g" $fname;
> done

You shouldn't have to do that. Do you happen to be using some ancient
CUDA version?

> And after that hell was unleashed again:

And the errors below are also pretty suspicious.

> $ make mdrun
> -- Configuring done
> -- Generating done
> -- Build files have been written to:
> /home/thomas/Programs/gromacs_cuda_build
> [  0%] Building NVCC (Device) object
> src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o
> [  0%] Building NVCC (Device) object
> src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o
> Scanning dependencies of target gpu_utils
> Linking CXX static library libgpu_utils.a
> [  0%] Built target gpu_utils
> Scanning dependencies of target gmx_version
>
> [  0%] Generating version information
> [  0%] Built target gmx_version
> [  0%] Building NVCC (Device) object
> src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_cudautils.cu.o
> /home/thomas/Programs/gromacs/src/gmxlib/cuda_tools/cudautils.cu: In
> function `void cu_realloc_buffered(void**, void*, size_t, int*, int*, int,
> CUstream_st*, gmx_bool)':
> /home/thomas/Programs/gromacs/src/gmxlib/cuda_tools/cudautils.cu:293:
> warning: converting to `int' from `double'
> [  0%] Building NVCC (Device) object
> src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o
> Scanning dependencies of target cuda_tools
> Linking CXX static library libcuda_tools.a
> [  0%] Built target cuda_tools
> Scanning dependencies of target gmx
> [  0%] Building C object src/gmxlib/CMakeFiles/gmx.dir/txtdump.c.o
> [  0%] Building C object src/gmxlib/CMakeFiles/gmx.dir/tcontrol.c.o
> [  0%] Building C object src/gmxlib/CMakeFiles/gmx.dir/sighandler.c.o
> [  0%] Building C object src/gmxlib/CMakeFiles/gmx.dir/random.c.o
> [  0%] Building C object src/gmxlib/CMakeFiles/gmx.dir/trnio.c.o
> [  0%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_arpack.c.o
> [  0%] Building C object src/gmxlib/CMakeFiles/gmx.dir/sparsematrix.c.o
> [  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/gmx_random.c.o
> [  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/sortwater.c.o
> [  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/string2.c.o
> [  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/matio.c.o
> [  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/writeps.c.o
> [  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/names.c.o
> [  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/xdrd.c.o
> [  1%] Building C object src/gmxlib/CMakeFiles/gmx.dir/bondfree.c.o
> In file included from
> /home/thomas/Programs/gromacs/include/gmx_x86_simd_single.h:27:0,
>                  from
> /home/thomas/Programs/gromacs/src/gmxlib/bondfree.c:60:
> /home/thomas/Programs/gromacs/include/gmx_x86_avx_256.h:136:37: error:
> unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_x86_avx_256.h:145:40: error:
> unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_x86_avx_256.h:155:37: error:
> unknown type name ‘__m256d’
> /home/thomas/Programs/gromacs/include/gmx_x86_avx_256.h:164:40: error:
> unknown type name ‘__m256d’
> /home/thomas/Programs/gromacs/include/gmx_x86_avx_256.h:175:40: error:
> unknown type name ‘__m256i’
> In file included from
> /home/thomas/Programs/gromacs/include/gmx_x86_simd_single.h:28:0,
>                  from
> /home/thomas/Programs/gromacs/src/gmxlib/bondfree.c:60:
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:41:1:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:41:22:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:66:1:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:66:19:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:97:1:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:97:18:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:119:1:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:119:18:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:136:1:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:136:18:
> error: unknown type name ‘__m256’
> In file included from
> /home/thomas/Programs/gromacs/include/gmx_x86_simd_single.h:28:0,
>                  from
> /home/thomas/Programs/gromacs/src/gmxlib/bondfree.c:60:
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:330:1:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:330:19:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h: In
> function ‘gmx_mm_exp2_ps’:
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:412:5:
> warning: implicit declaration of function ‘_mm_round_ps’
> [-Wimplicit-function-declaration]
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:412:30:
> error: ‘_MM_FROUND_TO_NEAREST_INT’ undeclared (first use in this function)
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:412:30:
> note: each undeclared identifier is reported only once for each function it
> appears in
> In file included from
> /home/thomas/Programs/gromacs/include/gmx_x86_simd_single.h:28:0,
>                  from
> /home/thomas/Programs/gromacs/src/gmxlib/bondfree.c:60:
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h: At top
> level:
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:448:1:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:448:18:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h: In
> function ‘gmx_mm_exp_ps’:
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:546:30:
> error: ‘_MM_FROUND_TO_NEAREST_INT’ undeclared (first use in this function)
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h: At top
> level:
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:581:1:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:581:18:
> error: unknown type name ‘__m256’
> In file included from
> /home/thomas/Programs/gromacs/include/gmx_x86_simd_single.h:28:0,
>                  from
> /home/thomas/Programs/gromacs/src/gmxlib/bondfree.c:60:
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h: In
> function ‘gmx_mm_erf_ps’:
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:894:5:
> warning: implicit declaration of function ‘_mm_blendv_ps’
> [-Wimplicit-function-declaration]
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:894:14:
> error: incompatible types when assigning to type ‘__m128’ from type ‘int’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:899:14:
> error: incompatible types when assigning to type ‘__m128’ from type ‘int’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:903:9:
> error: incompatible types when assigning to type ‘__m128’ from type ‘int’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h: At top
> level:
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:913:1:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:913:19:
> error: unknown type name ‘__m256’
> In file included from
> /home/thomas/Programs/gromacs/include/gmx_x86_simd_single.h:28:0,
>                  from
> /home/thomas/Programs/gromacs/src/gmxlib/bondfree.c:60:
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h: In
> function ‘gmx_mm_erfc_ps’:
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1224:14:
> error: incompatible types when assigning to type ‘__m128’ from type ‘int’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1229:14:
> error: incompatible types when assigning to type ‘__m128’ from type ‘int’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1233:9:
> error: incompatible types when assigning to type ‘__m128’ from type ‘int’
> In file included from
> /home/thomas/Programs/gromacs/include/gmx_x86_simd_single.h:28:0,
>                  from
> /home/thomas/Programs/gromacs/src/gmxlib/bondfree.c:60:
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h: At top
> level:
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1309:1:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1309:23:
> error: unknown type name ‘__m256’
> In file included from
> /home/thomas/Programs/gromacs/include/gmx_x86_simd_single.h:28:0,
>                  from
> /home/thomas/Programs/gromacs/src/gmxlib/bondfree.c:60:
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1438:1:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1438:23:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1532:21:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1533:21:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1534:21:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h: In
> function ‘gmx_mm_sincos_ps’:
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1677:24:
> error: ‘_MM_FROUND_TO_ZERO’ undeclared (first use in this function)
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1710:13:
> error: incompatible types when assigning to type ‘__m128’ from type ‘int’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1711:13:
> error: incompatible types when assigning to type ‘__m128’ from type ‘int’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1719:13:
> error: incompatible types when assigning to type ‘__m128’ from type ‘int’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1720:13:
> error: incompatible types when assigning to type ‘__m128’ from type ‘int’
> In file included from
> /home/thomas/Programs/gromacs/include/gmx_x86_simd_single.h:28:0,
>                  from
> /home/thomas/Programs/gromacs/src/gmxlib/bondfree.c:60:
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h: At top
> level:
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1733:1:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1733:18:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1754:1:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1754:18:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1771:1:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1771:18:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1798:1:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1798:19:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1934:1:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1934:19:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h: In
> function ‘gmx_mm_acos_ps’:
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1990:7:
> error: incompatible types when assigning to type ‘__m128’ from type ‘int’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1997:7:
> error: incompatible types when assigning to type ‘__m128’ from type ‘int’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:1998:7:
> error: incompatible types when assigning to type ‘__m128’ from type ‘int’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h: At top
> level:
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:2005:1:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:2005:19:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h: In
> function ‘gmx_mm_atan_ps’:
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:2090:7:
> error: incompatible types when assigning to type ‘__m128’ from type ‘int’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:2092:7:
> error: incompatible types when assigning to type ‘__m128’ from type ‘int’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:2093:7:
> error: incompatible types when assigning to type ‘__m128’ from type ‘int’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h: At top
> level:
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:2117:1:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:2117:20:
> error: unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_math_x86_avx_256_single.h:2117:30:
> error: unknown type name ‘__m256’
> In file included from
> /home/thomas/Programs/gromacs/src/gmxlib/bondfree.c:60:0:
> /home/thomas/Programs/gromacs/include/gmx_x86_simd_single.h:61:1: error:
> unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_x86_simd_single.h:61:23: error:
> unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_x86_simd_single.h:61:34: error:
> unknown type name ‘__m256’
> /home/thomas/Programs/gromacs/include/gmx_x86_simd_single.h:61:45: error:
> unknown type name ‘__m256’
> make[3]: *** [src/gmxlib/CMakeFiles/gmx.dir/bondfree.c.o] Error 1
> make[2]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
>
> make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2
> make: *** [mdrun] Error 2
>
> --
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