[gmx-developers] GROMACS 4.6 error in file src/gromacs/analysisdata/analysisdata.cpp:45:0
Thomas Evangelidis
tevang3 at gmail.com
Fri Aug 24 12:15:29 CEST 2012
> 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.
>
>
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:
$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
-- 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
And after that hell was unleashed again:
$ 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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