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

Yorquant Wang wangykoo at gmail.com
Thu Apr 11 17:41:56 CEST 2013

     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
     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
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

      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!

*$cmake ../ \*

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


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

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


*-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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