[gmx-users] fftw vs cmkl

Dallas B. Warren Dallas.Warren at pharm.monash.edu.au
Fri Dec 11 02:55:49 CET 2009

3D-FFT under both situations is 21.4% and PME mesh down as 54% (figures taken from the second last and last tables in the .log file, respectively).

Catch ya,

Dr Dallas Warren
Pharmacy and Pharmaceutical Sciences
Monash University

A polar bear is a Cartesian bear that has undergone a polar transformation

-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of Mark Abraham
Sent: Fri 12/11/2009 11:33 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] fftw vs cmkl
Dallas B. Warren wrote:
> Thanks Mark.
> My stats on this, GROMACS 4.0.7 compiled with gcc, run on two quad-core Xeon processors with 16GB of RAM, 100,000 atoms, PME, 200,000 steps
> fftw 3.2.1 - 20,027 seconds
> Intel cmkl - 19,792 seconds
> So about 1.2% faster.

IIRC icc does a better job on mkl than gcc. Of course you need to make 
sure the PME job is being dominated by the FFT part to be sure you're 
measuring a relevant speed difference. The output at the end of the log 
file reveals this.

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