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

Vasilii Artyukhov darth.vasya at gmail.com
Fri Sep 18 07:08:48 CEST 2009


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

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!

Best regards,
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