Hi Bob,
Thanks very much for your prompt response. That is just what I want to know.
Have a nice day.
----------
Jeffrey
>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.dicp.ac.cn>
>To: "amber" <amber.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
>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber.scripps.edu
>> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>>
>
>
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber.scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Apr 18 2008 - 21:19:07 PDT
