<div dir="ltr">Regarding buildit FFT - I believe they say it is slower then other packages. Omer.<br clear="all"><br>Koby Levy research group,<br>Weizmann Institute of Science. <br><a href="http://www.weizmann.ac.il/sb/faculty_pages/Levy/">http://www.weizmann.ac.il/sb/faculty_pages/Levy/</a><br>
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<div class="gmail_quote">On Thu, Sep 4, 2008 at 21:54, Myunggi Yi <span dir="ltr"><<a href="mailto:myunggi@gmail.com">myunggi@gmail.com</a>></span> wrote:<br>
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<div dir="ltr">I have done the compilation.<br>Thank you so much.
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<div class="Wj3C7c"><br><br><br>
<div class="gmail_quote">On Thu, Sep 4, 2008 at 12:08 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid"><br><br>Myunggi Yi wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid">
<div>Thank you for your answer, but I can't really get you.<br></div>I am using gromacs <a href="http://3.3.3./" target="_blank">3.3.3.</a> <<a href="http://3.3.0.3/" target="_blank">http://3.3.3</a>.> on CentOS with AMD64 clusters with infiniband connection.
<div><br>I have both INTEL and GNU copilers (gcc4.1.2 and gcc3.4) and openmpi (intel and gnu).<br>You are saying I don't have install fftw by myself, aren't you?<br>Then how can I compile? What is the best option for the performance?<br>
I did the followings.<br><br>======================================<br>./configure --prefix=$HOME/gromacs/ --with-fft=fftw2<br>make<br>make install<br><br>make clean<br>./configure --enable-mpi --disable-nice $HOME/gromacs/ --with-fft=fftw2 --program-suffix=_mpi<br>
make mdrun<br>make install-mdrun<br>======================================<br><br>Is this wrong?<br></div></blockquote><br>Seems reasonable, did it work?
<div><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid">Can I compile it with intel compiler?<br></blockquote><br></div>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:<br>
<br><a href="http://www.gromacs.org/content/view/23/33/" target="_blank">http://www.gromacs.org/content/view/23/33/</a><br><br>Following these directly will give you the standard installation, in serial and parallel, and single and double precision, if you choose.<br>
<br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid">
<div><br>I'm sorry. I have so many questions.<br>Please let me know how to compile it.<br><br>Thank you.<br><br><br></div>
<div>On Thu, Sep 4, 2008 at 11:40 AM, Roland Schulz <<a href="mailto:roland@utk.edu" target="_blank">roland@utk.edu</a> <mailto:<a href="mailto:roland@utk.edu" target="_blank">roland@utk.edu</a>>> wrote:<br><br>
Hi,<br><br> Gromacs has it's own parallel FFT which only uses FFTW for the local<br> FFT. Thus a non-MPI FFTW is fine. and FFTW 3 is faster than 2.<br><br> Roland<br><br> On Thu, Sep 4, 2008 at 8:53 AM, Myunggi Yi <<a href="mailto:myunggi@gmail.com" target="_blank">myunggi@gmail.com</a><br>
</div>
<div> <mailto:<a href="mailto:myunggi@gmail.com" target="_blank">myunggi@gmail.com</a>>> wrote:<br><br> Dear gmx users,<br><br> fftw3 seems doesn't support MPI.<br> Why is the gromacs configuration default fftw3 not fftw2?<br>
Which version should I use for parallel computing?<br><br> Thank you.<br><br><br> -- Best wishes,<br><br> Myunggi Yi<br> ==================================<br> KLB 419<br> Institute of Molecular Biophysics<br>
Florida State University<br> Tallahassee, FL 32306<br><br> Office: (850) 645-1334<br></div> <a href="http://www.scs.fsu.edu/~myunggi" target="_blank">http://www.scs.fsu.edu/~myunggi</a> <<a href="http://www.scs.fsu.edu/~myunggi" target="_blank">http://www.scs.fsu.edu/%7Emyunggi</a>><br>
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</div></blockquote><br>-- <br>========================================<br><br>Justin A. Lemkul<br>Graduate Research Assistant<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br>
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