[gmx-users] PME problem on BG/P cluster
lulanyuan at msn.com
Fri Jun 4 17:49:24 CEST 2010
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 \
CFLAGS="-O3 -qarch=450d -qtune=450" \
CXXFLAGS="-O3 -qarch=450 -qtune=450"
FFLAGS="-O3 -qarch=450 -qtune=450"
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.
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
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.
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