[gmx-users] installation and fftw

[Justin A. Lemkul]

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 <roland at utk.edu 
> <mailto:roland at utk.edu>> 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 <myunggi at gmail.com
>     <mailto:myunggi at gmail.com>> 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>
>         myunggi at gmail.com <mailto:myunggi at gmail.com>
> 
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> 
> 
>     -- 
>     ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
>     <http://cmb.ornl.gov>
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> 
> 
> 
> -- 
> 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
> myunggi at gmail.com <mailto:myunggi at gmail.com>
> 
> 
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-- 
========================================

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

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