Hello,
I got a weird problem by running Gromacs 4.0.7 on a BG/P machine ("Intrepid" at
Argonne national lab).
The simulated system is a box of SPC water with 648,000 atoms and all MD
simulations were performed on 256 CPU cores with MPI. The compiling environment
was Linux with IBM compiler and libs.
I first compile the code with flags suggested on the Wiki, such as:
./configure --prefix=$PREFIX \
--host=ppc \
--build=ppc64 \
--disable-software-sqrt \
--enable-ppc-sqrt=1 \
--enable-ppc-altivec \
--enable-bluegene \
--disable-fortran \
--enable-mpi \
--with-fft=fftpack \
--without-x \
CC="mpixlc_r" \
CFLAGS="-O3 -qarch=450d -qtune=450" \
MPICC="mpixlc_r"
CXX="mpixlcxx_r"
CXXFLAGS="-O3 -qarch=450 -qtune=450"
F77="mpixlf77_r"
FFLAGS="-O3 -qarch=450 -qtune=450"
LIBS="-lmass"
Here I used fftpack to ensure that the problem is not due to the fftw lib. I
got the water system running will with Cut-off for electrostatics. However, the
systems always crashed after a few ( ~100) steps if I used PME. The same system
with same PME option runs fine on other non-blue gene clusters I tested.
The error message I got was sth like
t = 0.100 ps: Water molecule starting at atom 403468 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates.
and
2 particles communicated to PME node 63 are more than a cell length out of the
domain decomposition cell of their charge group
>From .log file, the kinetic energy is increasing and turned to be "nan". So
>the system is exploding.
I found if I turned off the blue gene optimizations during configure, the water
system could be run without problem. For example, I used
--enable-software-sqrt \
--disable-ppc-sqrt \
--disable-bluegene \
and everything else was the same.
I suspect there was an issue regarding the blue gene specific code and PME.
Could anyone give any comments?
Thanks a lot.
Lanyuan Lu
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