You omitted a space after the new option, like the message says. Mark On Apr 12, 2013 7:21 AM, "Yorquant Wang" <wangy...@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.abra...@gmail.com> > > > 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 > > > > > > -- > 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? 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