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.> 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/%7Emyunggi> >> [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[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] >> <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 [email protected] >> <mailto:[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] >> <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 <http://www.scs.fsu.edu/%7Emyunggi> >> [EMAIL PROTECTED] <mailto:[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 >> > > -- > ======================================== > > 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 [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]
_______________________________________________ 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
