Hello, it seems FFTW3 is not installed in the LD_LIBRARY_PATH and/or the fftw3 headers can not be found. On Ubuntu, most likely the headers are not installed (available in the package libfftw3-dev). However it is really easy to compile FFTW3 yourself and install it inside your $HOME. Then you do not get in conflict with your system libraries and no administrator privileges are necessary. Furthermore you can compile FFTW3 with the desired flags for example: ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared --enable-float
make -j make install which will install shared fftw3 libs and headers in $HOME/local/fftw3. The flag -sse enables assembler optimization and --enable-float finally gives a single precision library libfftw3f.so . It is strongly suggested to enable assembler to optimize the performance of the FFTW3. Now for the configuration and installation of GROMACS in single precision you can use CMake and or the autotools. For the usage of autotools, the same scheme as describe above applies, however as FFTW3 is not in a standard location, the configure script must be told where to find the required files: CPPFLAGS=-I$HOME/local/fftw3/include LDFLAGS=-L $HOME/local/fftw3/lib ./configure --prefix=$HOME/local/gromacs --enable-shared make -j make install This should install a single-precision version of gromacs with shared libraries in $HOME/local/gromacs. For further specifications ./configure --helps gives many options to choose for example --enable-mpi For CMake the input scheme varies a little bit, but the procedure is the same mkdir build cd build cmake -DFFTW3F_INCLUDE_DIR=$HOME/local/fftw3/include -DFFTW3F_LIBRARIES= $HOME/local/fftw3/lib -DCMAKE_INSTALL_PREFIX=$HOME/local/gromacs make -j make install For CMake a shared build is enabled by default. /Flo On Mon, 2011-03-14 at 13:15 +0100, Diego Enry wrote: > The most basic question is: did you install FFTW as root or superuser ? > > sudo make install > > > If so, try to provide fftw /lib and /include locations (using CPPFLAGS > and LDFLAGS) while configuring GMX. (from the Installation > Instructions) > > setenv CPPFLAGS -I/home/joe/fftw/include > setenv LDFLAGS -L/home/joe/fftw/lib > > If your shell is bash: > > export CPPFLAGS="-I/home/joe/fftw/include" > export LDFLAGS="-L/home/joe/fftw/lib" > > > *If that does not work. Follow cmake instructions. > http://www.gromacs.org/Developer_Zone/Cmake > > > ** I have this problem with ubuntu 10.04, even though FFTW is ok I can > only Cmake finds fftw. (even providing CPPFLAGS and LDFLAGS) > > > > On Mon, Mar 14, 2011 at 1:05 PM, Thomas Koller <[email protected]> wrote: > > Hello, > > > > I want to install Gromacs 4.5.3 in my computer. Therefore I downloaded fftw > > 3.2.2 and did as in the instructions: > > > > ./configure --enable-float > > make > > make install > > > > After that I ran: > > > > ./configure > > > > with Gromacs, but I always get: > > > > checking for fftw3.h... configure: error: Cannot find the default external > > FFT library (fftw3). > > Other alternatives are 'fftw2', or 'mkl' for Intel MKL. > > You are STRONGLY recommended to use one of these - fftw is free. > > > > make is not working after this: > > > > make: *** No targets specified and no makefile found. Stop. > > > > What is going wrong? > > > > Thomas > > -- > > Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir > > belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [email protected]. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > Diego Enry B. Gomes > Laboratório de Modelagem e Dinamica Molecular > Universidade Federal do Rio de Janeiro - Brasil. -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: [email protected] Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658
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