[gmx-users] efficiency in HPC

[Prentice Bisbal]

Albert,

It looks like you are trying to compile for an IBM Power 7 system. What 
is the 'other machine' you are comparing it to, and did you use the same 
number of cores in each case?

Prentice


On 08/29/2013 03:54 PM, Albert wrote:
> Hello:
>
>  I compiled 4.6.3 in HPC with following steps:
>
>
> setenv OBJECT_MODE 64
> /opt/cmake/2.8.9_new/bin/cmake .. 
> -DCMAKE_INSTALL_PREFIX=/opt/gromacs/4.6.3 -DBUILD_SHARED_LIBS=OFF 
> -DCMAKE_BUILD_TYPE=Release -DGMX_SOFTWARE_INVSQRT=OFF -DGMX_GPU=OFF 
> -DGMX_MPI=ON -DGMX_THREAD_MPI
> =OFF -DGMX_X11=OFF -DGMX_FLOAT_FORMAT_IEEE754=1 
> -DGMX_IEEE754_BIG_ENDIAN_BYTE_ORDER=1 
> -DGMX_IEEE754_BIG_ENDIAN_WORD_ORDER=1 
> -DCMAKE_C_COMPILER="/usr/bin/mpcc_r" -DCMAKE_CXX_COMPILER="/usr/bin/mpCC_
> r" -DCMAKE_C_FLAGS_RELEASE="-O3 -qstrict -qsimd=auto -qmaxmem=-1 
> -qarch=pwr7 -qtune=pwr7" -DCMAKE_XX_FLAGS_RELEASE="-O3 -qstrict 
> -qsimd=auto -qmaxmem=-1 -qarch=pwr7 -qtune=pwr7" -DFFTWF_LIBRARY="/o
> pt/fftw/3.3.2/lib/libfftw3f.a" 
> -DFFTWF_INCLUDE_DIR="/opt/fftw/3.3.2/include" 
> -DCMAKE_LINKER="/usr/bin/mpcc_r"
> gmake -j 16
> gmake install
>
> when I do the test, I found that the performance is really bad. It 
> tooks more than one year for a job to be done while it only take 2 
> months in other machine. Does anybody have any idea where is the problem?
>
> thanks a lot
>
> Albert