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:<br><br>$cmake ../gromacs -DGMX_ACCELERATION=SSE2 -DPKG_CONFIG_PATH=/home/thomas/Programs/fftw-3.3.2/single_precision_installation_dir/lib/pkgconfig<br>
-- Performing Test GNU_SSE2_CFLAG<br>-- Performing Test GNU_SSE2_CFLAG - Success<br>-- Performing Test GNU_SSE2_CXXFLAG<br>-- Performing Test GNU_SSE2_CXXFLAG - Success<br>-- Looking for emmintrin.h<br>-- Looking for emmintrin.h - found<br>
-- Enabling SSE2 Gromacs acceleration, and it will help compiler optimization.<br>-- Found PkgConfig: /usr/bin/pkg-config (found version "0.25") <br>-- checking for module 'fftw3f'<br>-- package 'fftw3f' not found<br>
Could not find fftw3f library named libfftw3f, please specify its location in FFTW_LIBRARY by hand (e.g. -DFFTW_LIBRARY='/path/to/libfftw3f.so')<br>CMake Error at CMakeLists.txt:863 (MESSAGE):<br> Cannot find FFTW3 (with correct precision - libfftw3f for single precision<br>
GROMACS or libfftw3 for double precision GROMACS). Fix it, choose another<br> FFT library, or use the Gromacs built-in fftpack (slower)!<br><br><br>It complaints again about that libfftw3f.so file. It also yields an error if I define the other two variables you said:<br>
<br>$ 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'<br>
........<br>........<br>-- checking for module 'fftw3f'<br>-- package 'fftw3f' not found<br>-- Looking for fftwf_plan_r2r_1d in /home/thomas/Programs/fftw-3.3.2/single_precision_installation_dir/lib<br>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.<br>
-- Looking for fftwf_plan_r2r_1d in /home/thomas/Programs/fftw-3.3.2/single_precision_installation_dir/lib - not found<br>CMake Error at cmake/FindFFTW.cmake:87 (message):<br> Could not find fftwf_plan_r2r_1d in<br> /home/thomas/Programs/fftw-3.3.2/single_precision_installation_dir/lib,<br>
take a look at the error message in<br> /home/thomas/Programs/gromacs_cuda_build/CMakeFiles/CMakeError.log to find<br> out what went wrong. If you are using a static lib (.a) make sure you have<br> specified all dependencies of fftw3f in FFTW_LIBRARY by hand (e.g.<br>
-DFFTW_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !<br>Call Stack (most recent call first):<br> CMakeLists.txt:860 (find_package)<br><br><br><br>Finally I installed all fftw3 modules from Fedora repository and this is the output I get:<br>
<br><br>$ cmake ../gromacs -DGMX_ACCELERATION=SSE2 -DFFTW_LIBRARY='/usr/lib64/libfftw3f.so.3' -DFFTW_INCLUDE_DIR='/usr/include'<br>.........<br>-- checking for module 'fftw3f'<br>-- package 'fftw3f' not found<br>
-- Looking for fftwf_plan_r2r_1d in /usr/lib64/libfftw3f.so.3<br>-- Looking for fftwf_plan_r2r_1d in /usr/lib64/libfftw3f.so.3 - found<br>-- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so.3<br>-- Looking for fftwf_have_simd_sse2 in /usr/lib64/libfftw3f.so.3 - not found<br>
-- Looking for fftw_have_simd_sse2 in /usr/lib64/libfftw3f.so.3<br>-- Looking for fftw_have_simd_sse2 in /usr/lib64/libfftw3f.so.3 - not found<br>-- Looking for fftwf_have_sse in /usr/lib64/libfftw3f.so.3<br>-- Looking for fftwf_have_sse in /usr/lib64/libfftw3f.so.3 - not found<br>
-- Looking for fftw_have_sse2 in /usr/lib64/libfftw3f.so.3<br>-- Looking for fftw_have_sse2 in /usr/lib64/libfftw3f.so.3 - not found<br>-- Using internal BLAS library<br>-- LAPACK requires BLAS<br>-- Using internal LAPACK library<br>
-- Checking for dlopen<br>-- Performing Test HAVE_DLOPEN<br>-- Performing Test HAVE_DLOPEN - Success<br>-- Checking for dlopen - found<br>-- 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).<br>
-- Checking for suitable VMD version<br>-- VMD plugins not found. Path to VMD can be set with VMDDIR.<br>-- Configuring done<br>-- Generating done<br>-- Build files have been written to: /home/thomas/Programs/gromacs_cuda_build<br>
<br><br>$ make mdrun<br>[ 0%] Building NVCC (Device) object src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//./nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o<br>cc1plus: error: unrecognized command line option "-fexcess-precision=fast"<br>
CMake Error at nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o.cmake:198 (message):<br> Error generating<br> /home/thomas/Programs/gromacs_cuda_build/src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//./nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o<br>
<br><br>make[3]: *** [src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir/./nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o] Error 1<br>make[2]: *** [src/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir/all] Error 2<br>make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2<br>
make: *** [mdrun] Error 2<br><br><br><br><div class="gmail_quote">On 24 August 2012 22:16, Christoph Junghans <span dir="ltr"><<a href="mailto:junghans@votca.org" target="_blank">junghans@votca.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">2012/8/24 Thomas Evangelidis <<a href="mailto:tevang3@gmail.com">tevang3@gmail.com</a>>:<br>
<div><div class="h5">><br>
><br>
>> >> If you could provide us more information of why your gcc doesn't<br>
>> >> understand -mavx that would be useful. Is gcc really 4.7 as cmake<br>
>> >> prints?<br>
>> >> Gcc 4.7 should support 4.7 thus this is confusing. How did you obtain<br>
>> >> gcc?<br>
>> >> Is it from your distribution (if so which one) or did you download and<br>
>> >> compile gcc yourself? If so how?<br>
>> >><br>
>> ><br>
>> > Yes, its the precompiled gcc 4.7 from Fedora 17 86_64 repositories.<br>
>> That odd. Anyone has access to Fedora 17 and can try to reproduce<br>
>> this? It seems it would be really nice to have more distributions on<br>
>> Jenkins.<br>
>><br>
>> ><br>
>> > Both command lines failed. cmake is looking for a file a library named<br>
>> > "libfftw3f" which does not exist in my fftw installation. What configure<br>
>> > options do you use to compile fftw?<br>
>> You probably compiled fftw without "--enable-float". You can also use<br>
>> the fftw library without sse from before. It will work it just isn't<br>
>> won't be quite as fast.<br>
>><br>
><br>
> Actually I did. This is the command line I used the last time:<br>
><br>
> ./configure --enable-float --enable-threads<br>
> --prefix=`pwd`/single_precision_installation_dir --enable-sse<br>
><br>
> Here's the list of files in my fftw installation directory matching the<br>
> pattern "libfftw3f". I couldn't find any "libfftw3f.so" as the error says.<br>
><br>
> $ find ../fftw-3.3.2/single_precision_installation_dir/ -wholename<br>
> "*libfftw3f*"<br>
> ../fftw-3.3.2/single_precision_installation_dir/lib/<a href="http://libfftw3f_threads.la" target="_blank">libfftw3f_threads.la</a><br>
> ../fftw-3.3.2/single_precision_installation_dir/lib/<a href="http://libfftw3f.la" target="_blank">libfftw3f.la</a><br>
> ../fftw-3.3.2/single_precision_installation_dir/lib/libfftw3f_threads.a<br>
> ../fftw-3.3.2/single_precision_installation_dir/lib/libfftw3f.a<br>
</div></div>Is there a fftw3f.pc in single_precision_installation_dir? If so, add<br>
"/../../../fftw-3.3.2/single_precision_installation_dir/lib/pkgconfig"<br>
to your PKG_CONFIG_PATH that will help pkg-config to find the custom<br>
installation.<br>
Otherwise you will have to set FFTW_LIBRARY and FFTW_INCLUDE_DIR by<br>
hand. And never ever mix FFTW_LIBRARY and FFTW_INCLUDE_DIR of<br>
different fftw installations like your did above that will lead to all<br>
kind of strange errors.<br>
<br>
I would always use the system libfftw in the first attempt to compile.<br>
You may have to install Fedora's fftw-dev package as well.<br>
The error "Your fftw3 seems to be compiled without SSE!" only tells<br>
you that the performance is influence a bit.<br>
<br>
Btw. as far as I remember Gromacs only supports OpenMM version 2.0.<br>
(Other developers please correct me!)<br>
<br>
Christoph<br>
<div class="im HOEnZb"><br>
> --<br>
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<br>
<br>
<br>
</div><span class="HOEnZb"><font color="#888888">--<br>
Christoph Junghans<br>
Web: <a href="http://www.compphys.de" target="_blank">http://www.compphys.de</a><br>
</font></span><div class="HOEnZb"><div class="h5">--<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>
<p style="margin-bottom:0cm" align="LEFT">======================================================================</p>
<p style="margin-bottom:0cm" align="LEFT">Thomas Evangelidis</p>
<p style="margin-bottom:0cm" align="LEFT">PhD student</p>
<p style="margin-bottom:0cm" align="LEFT">Biomedical Research
Foundation, Academy of Athens</p>
<p style="margin-bottom:0cm" align="LEFT">4 Soranou Ephessiou , 115 27
Athens, Greece<br><br>email: <a href="mailto:tevang@bioacademy.gr" target="_blank">tevang@bioacademy.gr</a></p>
<p style="margin-bottom:0cm" align="LEFT"> <a href="mailto:tevang3@gmail.com" target="_blank">tevang3@gmail.com</a></p>
<p style="margin-bottom:0cm" align="LEFT"><br>website:
<a href="https://sites.google.com/site/thomasevangelidishomepage/" target="_blank">https://sites.google.com/site/thomasevangelidishomepage/</a></p>
<p style="margin-bottom:0cm" align="LEFT"><br>
</p>
<br>