AMBER Archive (2008)

Subject: Re: AMBER: installing pmemd with fftw

From: Robert Duke (rduke_at_email.unc.edu)
Date: Sun Apr 13 2008 - 08:57:36 CDT

YangMingjun -
Answers to your questions in order:
1.) PMEMD must be configured and compiled separately. Read the README under
$AMBERHOME/src/pmemd; run ./configure -help there.
2.) Serial fftw is used with pmemd. No need to worry about parallel fftw.
Unless you are using pmemd on a single processor pentium machine, or are
just in love with fftw, my "public" fft implementation works about as well,
and especially at higher scaling (more processors) it is doubtful that the
gain associated with using fftw is worth the bother.
3.) Use the same mpi library for amber and for pmemd; you don't need to
compile parallel fftw.
4.) Per above, you don't need parallel fftw.
Regards - Bob Duke

----- Original Message -----
From: "YangMingjun" <mjyang_at_dicp.ac.cn>
To: "amber" <amber_at_scripps.edu>
Sent: Sunday, April 13, 2008 9:07 AM
Subject: AMBER: installing pmemd with fftw

> Dear all,
>
> I have some questions when installing amber9 with pmemd.
> 1. when amber was compiled with parallel, should the pmemd be compiled
> with parallel too?
> 2. when compiling the parallel version of pmemd with fftw, must the fftw
> be compiled in parallel version first? Can I compile the parallel pmemd
> with serial fftw?
> 3. Should I use the same mpi library to compile the amber, pmemd and fftw?
> 4. In fftw3.1.2 and fftw3.0.1, I can't find an option for mpi(e.g. mpich)
> in "configure" file. In that case, how do I compile pmemd with parallel
> fftw?
>
>
> Any suggestion is greatly appreciated.
> Thanks in advance.
> Have a nice day.
>
> -------
> Jeffrey
>
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