On Thu, Apr 11, 2013 at 5:41 PM, Yorquant Wang <wangy...@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@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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
