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

Fri Aug 24 23:30:44 CEST 2012

2012/8/24 Thomas Evangelidis <tevang3 at gmail.com>:
> Yes there is a fftw3.pc file. I completely removed any fftw3 module from
> Fedora repositories, I set -DPKG_CONFIG_PATH to my home installation, but
> still got an error:
>
> $cmake ../gromacs -DGMX_ACCELERATION=SSE2
> -DPKG_CONFIG_PATH=/home/thomas/Programs/fftw-3.3.2/single_precision_installation_dir/lib/pkgconfig
Sorry, I was not very precise. I meant the environment variable PKG_CONFIG_PATH

export PKG_CONFIG_PATH=/home/thomas/Programs/fftw-3.3.2/single_precision_installation_dir/lib/pkgconfig
(bash)
setenv PKG_CONFIG_PATH
/home/thomas/Programs/fftw-3.3.2/single_precision_installation_dir/lib/pkgconfig
(tcsh)

>
> -- Performing Test GNU_SSE2_CFLAG
> -- Performing Test GNU_SSE2_CFLAG - Success
> -- Performing Test GNU_SSE2_CXXFLAG
> -- Performing Test GNU_SSE2_CXXFLAG - Success
> -- Looking for emmintrin.h
> -- Looking for emmintrin.h - found
> -- Enabling SSE2 Gromacs acceleration, and it will help compiler
> optimization.
>
> -- Found PkgConfig: /usr/bin/pkg-config (found version "0.25")
> -- 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)!
>
>
> It complaints again about that libfftw3f.so file. It also yields an error if
> I define the other two variables you said:
>
> $ cmake ../gromacs -DGMX_ACCELERATION=SSE2
> -DPKG_CONFIG_PATH='/home/thomas/Programs/fftw-3.3.2/single_precision_installation_dir/lib/pkgconfig'
> -DFFTW_LIBRARY='/home/thomas/Programs/fftw-3.3.2/single_precision_installation_dir/lib'
> -DFFTW_INCLUDE_DIR='/home/thomas/Programs/fftw-3.3.2/single_precision_installation_dir/include'
> ........
> ........
>
> -- checking for module 'fftw3f'
> --   package 'fftw3f' not found
> -- Looking for fftwf_plan_r2r_1d in
> /home/thomas/Programs/fftw-3.3.2/single_precision_installation_dir/lib
> WARNING: Target "cmTryCompileExec3758432358" requests linking to directory
> "/home/thomas/Programs/fftw-3.3.2/single_precision_installation_dir/lib".
> Targets may link only to libraries.  CMake is dropping the item.
> -- Looking for fftwf_plan_r2r_1d in
> /home/thomas/Programs/fftw-3.3.2/single_precision_installation_dir/lib - not
> found
> CMake Error at cmake/FindFFTW.cmake:87 (message):
>   Could not find fftwf_plan_r2r_1d in
>   /home/thomas/Programs/fftw-3.3.2/single_precision_installation_dir/lib,
>   take a look at the error message in
>   /home/thomas/Programs/gromacs_cuda_build/CMakeFiles/CMakeError.log to find
>   out what went wrong.  If you are using a static lib (.a) make sure you
> have
>   specified all dependencies of fftw3f in FFTW_LIBRARY by hand (e.g.
>   -DFFTW_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
> Call Stack (most recent call first):
>   CMakeLists.txt:860 (find_package)
>
>
>
> Finally I installed all fftw3 modules from Fedora repository and this is the
> output I get:
>
>
> $ cmake ../gromacs -DGMX_ACCELERATION=SSE2
> -DFFTW_LIBRARY='/usr/lib64/libfftw3f.so.3' -DFFTW_INCLUDE_DIR='/usr/include'
> .........
>
> -- checking for module 'fftw3f'
> --   package 'fftw3f' not found
> -- 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
>
>
> $ 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: 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
>
>
>
> On 24 August 2012 22:16, Christoph Junghans <junghans at votca.org> wrote:
>>
>> 2012/8/24 Thomas Evangelidis <tevang3 at gmail.com>:
>> >
>> >
>> >> >> If you could provide us more information of why your gcc doesn't
>> >> >> understand -mavx that would be useful. Is gcc really 4.7 as cmake
>> >> >> prints?
>> >> >> Gcc 4.7 should support 4.7 thus this is confusing. How did you
>> >> >> obtain
>> >> >> gcc?
>> >> >> Is it from your distribution (if so which one) or did you download
>> >> >> and
>> >> >> compile gcc yourself? If so how?
>> >> >>
>> >> >
>> >> > Yes, its the precompiled gcc 4.7 from Fedora 17 86_64 repositories.
>> >> That odd. Anyone has access to Fedora 17 and can try to reproduce
>> >> this? It seems it would be really nice to have more distributions on
>> >> Jenkins.
>> >>
>> >> >
>> >> > Both command lines failed. cmake is looking for a file a library
>> >> > named
>> >> > "libfftw3f" which does not exist in my fftw installation. What
>> >> > configure
>> >> > options do you use to compile fftw?
>> >> You probably compiled fftw without "--enable-float". You can also use
>> >> the fftw library without sse from before. It will work it just isn't
>> >> won't be quite as fast.
>> >>
>> >
>> > Actually I did. This is the command line I used the last time:
>> >
>> > ./configure --enable-float --enable-threads
>> > --prefix=`pwd`/single_precision_installation_dir --enable-sse
>> >
>> > Here's the list of files in my fftw installation directory matching the
>> > pattern "libfftw3f". I couldn't find any "libfftw3f.so" as the error
>> > says.
>> >
>> > $ find ../fftw-3.3.2/single_precision_installation_dir/ -wholename
>> > "*libfftw3f*"
>> > ../fftw-3.3.2/single_precision_installation_dir/lib/libfftw3f_threads.la
>> > ../fftw-3.3.2/single_precision_installation_dir/lib/libfftw3f.la
>> > ../fftw-3.3.2/single_precision_installation_dir/lib/libfftw3f_threads.a
>> > ../fftw-3.3.2/single_precision_installation_dir/lib/libfftw3f.a
>> Is there a  fftw3f.pc in single_precision_installation_dir? If so, add
>> "/../../../fftw-3.3.2/single_precision_installation_dir/lib/pkgconfig"
>> to your PKG_CONFIG_PATH that will help pkg-config to find the custom
>> installation.
>> Otherwise you will have to set  FFTW_LIBRARY and FFTW_INCLUDE_DIR by
>> hand. And never ever mix FFTW_LIBRARY and FFTW_INCLUDE_DIR of
>> different fftw installations like your did above that will lead to all
>> kind of strange errors.
>>
>> I would always use the system libfftw in the first attempt to compile.
>> You may have to install Fedora's fftw-dev package as well.
>> The error "Your fftw3 seems to be compiled without SSE!" only tells
>> you that the performance is influence a bit.
>>
>> Btw. as far as I remember Gromacs only supports OpenMM version 2.0.
>> (Other developers please correct me!)
>>
>> Christoph
>>
>> > --
>> > gmx-developers mailing list
>> > gmx-developers at gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-developers
>> > Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-developers-request at gromacs.org.
>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>> --
>> gmx-developers mailing list
>> gmx-developers at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-developers-request at gromacs.org.
>
>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
>
> Biomedical Research Foundation, Academy of Athens
>
> 4 Soranou Ephessiou , 115 27 Athens, Greece
>
> email: tevang at bioacademy.gr
>
>           tevang3 at gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
>
>
>
> --
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the
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-- 
Christoph Junghans
Web: http://www.compphys.de