[gmx-users] Gromacs 4.0.7 on Blue Gene/P

Rongliang Wu rongliangwu at gmail.com
Sun Aug 7 00:19:22 CEST 2011

Dear all,

I have installed the gromacs 4.0.7 on the Blue Gene/P according to the
instructions on the gromacs webpage, but after submitting my testing
system of water box around 10 nm, I found the simulation went really
slow, or not running at all, output files are always 0 bytes. the md.log
file gets stuck at:

Linking all bonded interactions to atoms

The maximum number of communication pulses is: X 1 Y 1 Z 1
The minimum size for domain decomposition cells is 1.200 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.48 Y 0.60 Z 0.60

I have used the double precision and fftw 3.2.2, the configure scripts
are like this for mdrun

../configure --prefix=/home/users/wurl/software/gromacs4.0.7 --host=ppc
--build=ppc64 --enable-ppc-sqrt=1 --enable-bluegene --enable-mpi
--with-fft=fftw3 --without-x --program-suffix=-mpi-bgp   CC="mpixlc_r"
CFLAGS="-O3 -qarch=450d -qtune=450" MPICC="mpixlc_r" CXX="mpixlc_r"
CXXFLAGS="-O3 -qarch=450d -qtune=450" F77="mpixlf_r" FFLAGS="-O3
-qarch=auto -qtune=auto" LIBS="-lmass"
CPPFLAGS="-I/opt/fftw/3.2.2/include" LDFLAGS="-L/opt/fftw/3.2.2/lib"

I also asked the administrator to install for me, the results were the

Does anyone have similar experience?


Yours Sincerely,

Rongliang Wu
Postdoc in K.U.Leuven


Molecular and Nanomaterials Division
Department of Chemistry
Katholieke Universiteit Leuven

Celestijnenlaan 200f - bus 2404
3001 Heverlee, Belgium


rongliang.wu at chem.kuleuven.be


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