[gmx-users] install Gromacs with MPI?

[David van der Spoel]

On Wed, 2004-02-11 at 17:16, Wu Xun wrote:
> Thanks Choon-Peng, David and Erik.
> 
> I changed the fftw to the directory containing MPI
> version and compile, it still doesn't work, saying
> that sfftw.h and fftw.h can't be found.
you only have double precision fftw apparently. ask your sysadmin to
install single precision as well, or do it yourself, or install gromacs
in double precision with --disable-float
> 
> setenv LDFLAGS "-L/usr/local/vmi/mpich/lib/gcc
> -L/usr/apps/math/fftw/fftw-2.1.5/mpi"
> setenv CPPFLAGS "-I/usr/local/vmi/mpich/include
> -I/usr/apps/math/fftw/fftw-2.1.5/mpi"
> ./configure --enable-mpi --prefix=where/I/want". 
> 
> Shouldn't the script be looking for "sfftw_mpi.h"
> instead of "sfftw.h"? otherwise I have to find some
> way to ask it to look for "sfftw_mpi.h".
> 
> Thanks,
> Weihua
>  
> --- Chng Choon Peng <cpchng at bii.a-star.edu.sg> wrote:
> > Hi Weihua,
> > 
> >    What you did is correct. This is puzzling...
> > But sfftw.h is for the sequential version.
> > You should be using the FFTw include and library
> > files for
> > the parallel compilation.
> > 
> > Can we have your Gromacs "./configure" options?
> > 
> > Maybe you would like to find some simple programs
> > that calls the FFTw
> > libraries to see how to compile a code to use the
> > library.
> > I have some if you wish to try them.
> > 
> > regards,
> > Choon-Peng
> > 
> > On 2/11/04 9:02 AM, "Wu Xun" <wxun2000 at yahoo.com>
> > wrote:
> > 
> > > 
> > > From the FAQ I found some info about how to
> > install
> > > gromacs with MPI, but it seems not able to find
> > the
> > > fftw files. Here is the commands I used:
> > > 
> > > setenv LDFLAGS "-L/usr/local/vmi/mpich/lib/gcc
> > > -L/usr/apps/math/fftw/fftw-2.1.5/icc7/lib"
> > > 
> > > setenv CPPFLAGS "-I/usr/local/vmi/mpich/include
> > > -I/usr/apps/math/fftw/fftw-2.1.5/icc7/include"
> > > 
> > > setenv LIBS "-lmpich -lvmi -ldl -lpthread"
> > > setenv CC gcc
> > > setenv MPICC gcc
> > > ./configure --enable-mpi
> > > --prefix=/u/ncsa/weihua/Gromacs/gromacs_mpi
> > > 
> > > The configure output gives
> > > "error: Cannot find any single precision sfftw.h
> > or
> > > fftw.h".
> > > 
> > > The above directories does contain the sfftw.h and
> > > fftw.h files. I also tried the directories with
> > > sfftw_mpi.h and fftw_mpi.h and they don't work
> > either.
> > > 
> > > 
> > > Therefore, I believe that the way I setup the
> > flags
> > > was wrong.  Could anyone tell me how to setup
> > multiple
> > > libraries for the same flag? I am using C shell.
> > > 
> > > Thanks,
> > > Weihua
> > > 
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> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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