[ale] high performance computing

[Jeff Layton]

  On 07/27/2012 04:07 PM, John Heim wrote:
> From: "Jeff Layton" <laytonjb at att.net>
> To: "Atlanta Linux Enthusiasts" <ale at ale.org>
>>
>> The follow-up question is whether the FFT's are done locally
>> or if they are using an MPI based FFT?
>>
>> However, I think as a starting point, you'll want compute nodes
>> that have reasonably fast processors, lots of cache (as Jim
>> pointed out) but you also needs tons of memory BW per core.
>> FFT's love memory BW!!
>>
>> If the FFT's themselves are parallelized, then you will definitely
>> need InfiniBand. FFT's each networks for breakfast (in fact there
>> was a proposal from John Gustafson at Intel to make a 3D MPI
>> FFT the new benchmark for HPC since it pushed systems so
>> hard).
>
> I sent the PI your questions.  Here are his answers (somewhat 
> abbreviated and w/o personal info).
>
> 1. 2D FFT's? 3D FFT's?
>
> Both.  Probably 3D more often then 2D.  But I am working on code right
> now that would always be 2code (never 3D).
>
> 2. Is the code parallelized via MPI or OpenMP or both?
>
> We have never bothered to explicitly parallelize our code.  We have 
> been using the built-in parallelization in  calls to FFTW.
>
> 3. Is the code written with CUDA?
>
> No.
>
> 4. How many cores or processes are used per run?
>
> We need to have the capability to use at least 64 cores per run, maybe 
> 128 or 256 if possible within our budget.
I'm not exactly sure if they have written the main part of the code as a 
serial application and then use fftw routines for the parallel portion 
or not. To me it sounds like they have written the application so that 
it is serial and then they build fftw either threaded 
(http://www.fftw.org/fftw3_doc/Multi_002dthreaded-FFTW.html#Multi_002dthreaded-FFTW) 
or with MPI 
(http://www.fftw.org/fftw3_doc/Distributed_002dmemory-FFTW-with-MPI.html#Distributed_002dmemory-FFTW-with-MPI).

Can you ask which routines they are using?

Thanks!

Jeff