[gmx-users] Gromacs using MKL with Intel 11.1 compilers

Steve Cousins cousins at umit.maine.edu
Fri Sep 18 16:33:41 CEST 2009

On Fri, 18 Sep 2009, Vasilii Artyukhov wrote:

> Hi,
> Anybody have any real-world comparisons of using MKL vs. FFTW3?
> [ http://www.quantumespresso.org/user_guide/node16.html ]http://www.quantumespresso.org/user_guide/node16.html says:
> Axel Kohlmeyer suggests the following (April 2008): "(I've) found that Intel is now turning on multithreading without any warning and that is for example why their FFT seems faster than FFTW. For serial and OpenMP based runs this makes no difference
> (in fact the multi-threaded FFT helps), but if you run MPI locally, you actually lose performance. Also if you use the 'numactl' tool on linux to bind a job to a specific cpu core, MKL will still try to use all available cores (and slow down badly).
> The cleanest way of avoiding this mess is to either link with
> -lmkl_intel_lp64 -lmkl_sequential -lmkl_core (on 64-bit: x86_64, ia64)
> -lmkl_intel -lmkl_sequential -lmkl_core (on 32-bit, i.e. ia32 )
> or edit the libmkl_'platform'.a file (I'm using now a file libmkl10.a with:
>  GROUP (libmkl_intel_lp64.a libmkl_sequential.a libmkl_core.a)
> It works like a charm".
> So, this might contribute to your problem. Please tell us if Axel's suggestion works for you!

Hi Vasilii,

Thanks for the suggestion. You read my mind! I was wondering about turning 
threads off in MKL and here it is!

And here are the results: MKL without threads:

real    1m23.235s
user    1m6.928s
sys     0m9.836s

and MKL with threads:

real    1m34.731s
user    3m33.024s
sys     0m15.280s

As with FFTW3:

real    1m17.889s
user    1m4.660s
sys     0m8.672s

Even with the big improvement, since Mark says that only a fraction of the 
tests use FFTW, the 5.3 seconds of difference between FFTW3 and MKL 
without threads is a bigger difference than it appears.

I'll take Berk's advice and just use FFTW3. Thanks for setting me 
straight. It's good to have confirmation that I don't need to spend any 
more time on this! I just didn't want to use it blindly and then have 
someone down the road ask "Why didn't you use MKL? It gives you twice the 
performance!" or something like that.

Thanks all,


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