[gmx-users] Gromacs using MKL with Intel 11.1 compilers
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 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"
./configure --prefix=/usr/local/gromacs-4-mkl-noopts --without-x
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
time gmxtest.pl all
This may or may not be useful as they are just serial results with the
small test programs:
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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