Regarding buildit FFT - I believe they say it is slower then other packages. Omer.
Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Thu, Sep 4, 2008 at 21:54, Myunggi Yi <[EMAIL PROTECTED]> wrote: > I have done the compilation. > Thank you so much. > > > > On Thu, Sep 4, 2008 at 12:08 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > >> >> >> Myunggi Yi wrote: >> >>> Thank you for your answer, but I can't really get you. >>> I am using gromacs 3.3.3. <http://3.3.3 <http://3.3.0.3/>.> 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? >>> >> >> Seems reasonable, did it work? >> >> Can I compile it with intel compiler? >>> >> >> It is easy to use gcc, and definitely do *not* use gcc-4.1.2; use 3.4. >> There are step-by-step instructions on how to install both FFTW and Gromacs >> on the Gromacs website: >> >> http://www.gromacs.org/content/view/23/33/ >> >> Following these directly will give you the standard installation, in >> serial and parallel, and single and double precision, if you choose. >> >> -Justin >> >> >>> 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] <mailto: >>> [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] >>> <mailto:[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 <http://www.scs.fsu.edu/~myunggi>> >>> [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> >>> >>> _______________________________________________ >>> gmx-users mailing list gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org> >>> 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] >>> <mailto:[EMAIL PROTECTED]>. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >>> >>> >>> >>> -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov >>> <http://cmb.ornl.gov> >>> >>> _______________________________________________ >>> gmx-users mailing list gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org> >>> 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] >>> <mailto:[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] <mailto:[EMAIL PROTECTED]> >>> >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> gmx-users mailing list gmx-users@gromacs.org >>> 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 >>> >> >> -- >> ======================================== >> >> Justin A. Lemkul >> Graduate Research Assistant >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> 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] > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 >
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