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
change:
-lmkl
to
-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?
Thanks,
Steve
______________________________________________________________________
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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