[gmx-users] installation of gromacs
dommert at icp.uni-stuttgart.de
Mon Mar 14 14:05:13 CET 2011
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
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:
$HOME/local/fftw3/lib ./configure --prefix=$HOME/local/gromacs
This should install a single-precision version of gromacs with shared
libraries in $HOME/local/gromacs. For further specifications ./configure
--helps gives many options to choose for example --enable-mpi
For CMake the input scheme varies a little bit, but the procedure is the
cmake -DFFTW3F_INCLUDE_DIR=$HOME/local/fftw3/include -DFFTW3F_LIBRARIES=
For CMake a shared build is enabled by default.
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
> 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.
> ** 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 <koller-thomas at gmx.de> 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
> > --
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> Diego Enry B. Gomes
> Laboratório de Modelagem e Dinamica Molecular
> Universidade Federal do Rio de Janeiro - Brasil.
Dipl. - Phys.
Institute for Computational Physics
EMail: dommert at icp.uni-stuttgart.de
Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
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