[gmx-users] installation and fftw

Sun Sep 7 11:51:39 CEST 2008

Regarding buildit FFT - I believe they say it is slower then other packages.
Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/

On Thu, Sep 4, 2008 at 21:54, Myunggi Yi <myunggi at gmail.com> wrote:

> 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 <http://3.3.0.3/>.> 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/~myunggi>>
>>>        myunggi at gmail.com <mailto:myunggi at gmail.com>
>>>
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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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>
>
>
> --
> 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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