Steve Cousins wrote:
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
... or put LIBS="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lguide
-lpthread" on the configure command line.
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.
Plausible, but even if FFT threads were not available, only a fraction
of these tests were using FFT and some of those were probably I/O
dominated. So the relative speed is still unknown. These tests are
designed to assess correct implementation and compilation, and not as
benchmarks or real-world examples. There was a benchmark set years ago
for the last major GROMACS release, which will probably still serve your
purpose http://oldwww.gromacs.org/content/view/24/37/. Lys/PME is the
relevant test. Bear in mind that grompp no longer accepts -np, -sort or
-shuffle arguments, and these should be deleted as necessary. Your speed
should probably beat any of those reported there.
Anybody have any real-world comparisons of using MKL vs. FFTW3?
No, but in the meantime build both, and if your users are actually using
PME (the main algorithm that uses FFT), they can do a simple speed tests
once they have a full-sized system set up.
Mark
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