[gmx-users] installation and fftw

[Myunggi Yi]

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 <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> 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
>>
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>
>
>
> --
> ORNL/UT Center for Molecular Biophysics 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
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