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

Steve Cousins cousins at umit.maine.edu
Thu Sep 17 23:52:46 CEST 2009

I just thought I'd mention some troubles and fixes I had with trying to 
get Gromacs 4.0.5 to configure with --with-fft=mkl on a SGI Altix 3700 
BX2 system.  I did:

export CC=icc
export F77=ifort
export CFLAGS="-O3 -ip -ftz"
export FFLAGS="-O3 -ip -ftz"
export LDFLAGS="-O3 -ip -ftz -L/opt/intel/Compiler/11.1/046/mkl/lib/64 -L/usr/lib"
export CPPFLAGS="-I/opt/intel/Compiler/11.1/046/mkl/include/fftw -I/usr/include"

and then:

./configure --prefix=/usr/local/gromacs-4-mkl-noopts --without-x 
--enable-fortran --with-fft=mkl

However, this gave messages saying that it couldn't find the mkl 
libraries. This is because MKL doesn't include a library called libmkl.so 
anymore. To get this to work I had to edit the configure script and 



 	-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lguide -lpthread

In the end, I found that using MKL is about 20% slower than using fftw3 
when running:

 	time gmxtest.pl all

This may or may not be useful as they are just serial results with the 
small test programs:

With fftw3:

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

With MKL:

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

Maybe the overhead of starting up the threads for such small jobs is what 
is causing the slow-down in MKL.

Anybody have any real-world comparisons of using MKL vs. FFTW3?


  Steve Cousins - Supercomputer Engineer/Administrator - Univ of Maine
  Marine Sciences, 452 Aubert Hall       Target Tech, 20 Godfrey Drive
  Orono, ME 04469    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~     Orono, ME 04473
  (207) 581-4302     ~ cousins at umit.maine.edu ~      (207) 866-6552

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