[gmx-users] installation and fftw

[Myunggi Yi]

I have done the compilation.
Thank you so much.


On Thu, Sep 4, 2008 at 12:08 PM, Justin A. Lemkul <jalemkul at vt.edu> 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 <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><
>> http://www.scs.fsu.edu/%7Emyunggi>
>>        myunggi at gmail.com <mailto:myunggi at gmail.com>
>>
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>>
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>>    <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 <http://www.scs.fsu.edu/%7Emyunggi>
>> myunggi at gmail.com <mailto:myunggi at gmail.com>
>>
>>
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>>
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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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-- 
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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