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

[Mark Abraham]

You omitted a space after the new option, like the message says.

Mark
On Apr 12, 2013 7:21 AM, "Yorquant Wang" <wangykoo at gmail.com> wrote:

>    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
> --
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