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

Fri Aug 24 22:45:18 CEST 2012

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
-- 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
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>

-- 

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

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/
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