[gmx-users] efficiency in HPC

Mark Abraham mark.j.abraham at gmail.com
Fri Aug 30 10:19:42 CEST 2013

On Thu, Aug 29, 2013 at 9:54 PM, Albert <mailmd2011 at gmail.com> wrote:
> Hello:
>  I compiled 4.6.3 in HPC with following steps:
> setenv OBJECT_MODE 64
> /opt/cmake/2.8.9_new/bin/cmake .. -DCMAKE_INSTALL_PREFIX=/opt/gromacs/4.6.3

AFAICR there is no need or value in setting these three (and GROMACS
will do its own detection and over-write them anyway).

> -DCMAKE_C_COMPILER="/usr/bin/mpcc_r" -DCMAKE_CXX_COMPILER="/usr/bin/mpCC_
> r" -DCMAKE_C_FLAGS_RELEASE="-O3 -qstrict -qsimd=auto -qmaxmem=-1 -qarch=pwr7
> -qtune=pwr7" -DCMAKE_XX_FLAGS_RELEASE="-O3 -qstrict -qsimd=auto -qmaxmem=-1
> -qarch=pwr7 -qtune=pwr7" -DFFTWF_LIBRARY="/o
> pt/fftw/3.3.2/lib/libfftw3f.a" -DFFTWF_INCLUDE_DIR="/opt/fftw/3.3.2/include"
> -DCMAKE_LINKER="/usr/bin/mpcc_r"
> gmake -j 16
> gmake install
> when I do the test, I found that the performance is really bad. It tooks
> more than one year for a job to be done while it only take 2 months in other
> machine. Does anybody have any idea where is the problem?

The AMD platform has SIMD kernels targeted for it. There are none in
4.6 for Power7 because none of the developers uses such a system.

Historically, we also offered Fortran kernels from the days when
certain vendor's Fortran compilers were better than their C compilers.
We've stopped offering Fortran support because we don't use it.

You should be sure to read up on how to best use the SIMT capability
of each core (guessing wildly, 1 OpenMP thread each), and that all the
physical cores are being used. And balance the PME load. Despite the
higher Power7 clock speed, your results are not too surprising (but
even without touching the code, getting the most out of Power7 might
take more effort than you have expended so far).


> thanks a lot
> Albert
> --
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