[gmx-users] gmx4.6.1 performance problem "CPU acceleration: NONE"

[Yorquant Wang]

   1. Hi Mark:

    As your suggestion, I reinstalled GMX4.6.1, when I run CMAKE using

*$**cmake ../ \*

*-DCMAKE_INSTALL_PREFIX=/public/software/gromacs-4.6_avx \*

*-DGMX_MPI=ON \*

*-DCMAKE_C_COMPILER=/public/software/mpi/openmpi-16-intel/bin/mpicc \*

*  -DCMAKE_CXX_COMPILER=/public/software/mpi/openmpi-16-intel/bin/mpicxx \*

* -DGMX_BINARY_SUFFIX=_mpi \*

*-DGMX_CPU_ACCELERATION=AVX_256\*

*-DFFTWF_INCLUDE_DIR=/public/software/mathlib/fftw332-float/include \*

***-DFFTWF_LIBRARY=/public/software/mathlib/fftw332-float/lib/libfftw3f.so*

I met an error:
-----------------------------------------------------
-- Performing Test _finite_compile_ok
-- Performing Test _finite_compile_ok - Failed
-- Checking for _finite - no
-- Checking for system XDR support
-- Checking for system XDR support - present
CMake Error at CMakeLists.txt:880 (MESSAGE):
  Unrecognized option for accelerated kernels:
  AVX_256-DFFTWF_INCLUDE_DIR=/PUBLIC/SOFTWARE/MATHLIB/FFTW332-FLOAT/INCLUDE.
  Pick one of None, SSE2, SSE4.1, AVX_128_FMA, AVX_256, IBM_QPX


-- Configuring incomplete, errors occurred!
-----------------------------------------------------
   Could you give me some advise?  Thank you very much!

Best,
Yukun


2013/4/12 Mark Abraham <mark.j.abraham at gmail.com>

> On Thu, Apr 11, 2013 at 5:41 PM, Yorquant Wang <wangykoo at gmail.com> wrote:
>
> > Hello:
> >      I have installed GMX4.6.1 and GMX4.5.5 on the same cluster. There
> are
> > 2 Xoen E5 2630CPU in one node on this cluster. I tested the performance
> of
> > those two versions of GMX, found GMX4.6.1 only had 0.62 performance of
> > GMX4.5.5.
> >      When I checked the .log file of GMX4.6.1, I found
> > ...
> > CPU acceleration:   NONE
> > FFT library:        FFTW 3.2 wrappers to MKL
> > Large file support: enabled
> > RDTSCP usage:       disabled
> > Built on:           Mon Apr  8 10:46:58 CST 2013
> > Built by:           root at node3 [CMAKE]
> > Build OS/arch:      Linux 2.6.18-274.el5 x86_64
> > Build CPU vendor:   Unknown, detect failed
> > Build CPU brand:    Unknown, detect failed
> >
>
> Whatever your build system is was too weird/new for the auto-detection
> system to cope with. And perhaps the assumption that your build CPU and
> your mdrun CPU are the same is not valid.
>
>
> > Build CPU family:   0   Model: 0   Stepping: 0
> > Build CPU features:
> > C compiler:         /public/software/mpi/openmpi-16-intel/bin/mpicc Intel
> > icc (ICC) 12.1.0 20111011
> > C compiler flags:     -std=gnu99 -Wall   -ip -funroll-all-loops  -O3
> > -DNDEBUG
> >
> >       So I think my installed GMX4.6.1 failed to use AVX_256 kenerl.  The
> > installed commend is below. Could someone give some suggestion how to
> solve
> > this problem? Thank you very much!
> >
>
> Since the detection is failing for unknown reasons, you will need to select
> an appropriate acceleration for your mdrun *execution* environment in your
> call to CMake, e.g. with -DGMX_CPU_ACCELERATION=AVX_256.
>
> Mark
>
>
> > *$cmake ../ \*
> >
> > *-DCMAKE_INSTALL_PREFIX=/public/software/gromacs-4.6 \*
> >
> > *-DGMX_MPI=ON \*
> >
> > *-DCMAKE_C_COMPILER=/public/software/mpi/openmpi-16-intel/bin/mpicc \*
> >
> > *-DCMAKE_CXX_COMPILER=/public/software/mpi/openmpi-16-intel/bin/mpicxx \*
> >
> > * -DGMX_BINARY_SUFFIX=_mpi \*
> >
> > *-DFFTWF_INCLUDE_DIR=/public/software/mathlib/fftw331-float/include \*
> >
> > *-DFFTWF_LIBRARY=/public/software/mathlib/fftw331-float/lib/libfftw3f.so
> *
> >
> > *$make –j 6*
> >
> > *$make install*
> >
> > Cheers up
> > --
> > Yukun Wang
> > PhD candidate
> > Institute of Natural Sciences && College of Life Science, Shanghai Jiao
> > Tong University
> > Cell phone: 13621806236.
> > China Shanghai
> > --
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-- 
Yukun Wang
PhD candidate
Institute of Natural Sciences && College of Life Science, Shanghai Jiao
Tong University
Cell phone: 13621806236.
China Shanghai