Thank you for your answer, but I can't really get you. I am using gromacs 3.3.3. on CentOS with AMD64 clusters with infiniband connection. I have both INTEL and GNU copilers (gcc4.1.2 and gcc3.4) and openmpi (intel and gnu). You are saying I don't have install fftw by myself, aren't you? Then how can I compile? What is the best option for the performance? I did the followings.
====================================== ./configure --prefix=$HOME/gromacs/ --with-fft=fftw2 make make install make clean ./configure --enable-mpi --disable-nice $HOME/gromacs/ --with-fft=fftw2 --program-suffix=_mpi make mdrun make install-mdrun ====================================== Is this wrong? Can I compile it with intel compiler? I'm sorry. I have so many questions. Please let me know how to compile it. Thank you. On Thu, Sep 4, 2008 at 11:40 AM, Roland Schulz <[EMAIL PROTECTED]> wrote: > Hi, > > Gromacs has it's own parallel FFT which only uses FFTW for the local FFT. > Thus a non-MPI FFTW is fine. and FFTW 3 is faster than 2. > > Roland > > On Thu, Sep 4, 2008 at 8:53 AM, Myunggi Yi <[EMAIL PROTECTED]> wrote: > >> Dear gmx users, >> >> fftw3 seems doesn't support MPI. >> Why is the gromacs configuration default fftw3 not fftw2? >> Which version should I use for parallel computing? >> >> Thank you. >> >> >> -- >> Best wishes, >> >> Myunggi Yi >> ================================== >> KLB 419 >> Institute of Molecular Biophysics >> Florida State University >> Tallahassee, FL 32306 >> >> Office: (850) 645-1334 >> http://www.scs.fsu.edu/~myunggi <http://www.scs.fsu.edu/%7Emyunggi> >> [EMAIL PROTECTED] >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> > > > > -- > ORNL/UT Center for Molecular Biophysics cmb.ornl.gov > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Best wishes, Myunggi Yi ================================== KLB 419 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306 Office: (850) 645-1334 http://www.scs.fsu.edu/~myunggi [EMAIL PROTECTED]
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