[gmx-users] PME problem on BG/P cluster

LuLanyuan lulanyuan at msn.com
Tue Jun 8 18:09:46 CEST 2010

Dear Mark,
When I set NOASSEMBLYLOOPS to 1, the simulation could be finished without any problem. So I guess it's related to the assembly loops for BG.

From: mark.abraham at anu.edu.au
To: gmx-users at gromacs.org
Date: Sat, 5 Jun 2010 03:31:33 +1000
Subject: Re: [gmx-users] PME problem on BG/P cluster

----- Original Message -----
From: LuLanyuan <lulanyuan at msn.com>
Date: Saturday, June 5, 2010 2:01
Subject: [gmx-users] PME problem on BG/P cluster
To: gmx-users at gromacs.org

   >  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 \
>         &n  bsp;          --enable-ppc-altivec \

The wiki doesn't suggest this, and it's for another architecture entirely. I don't know if it's causing a problem, but you should see what kernels the .log file reports it is trying to use.

>                    --enable-bluegene \
>                    --disable-fortran \
>                    --enable-mpi \
>                    --with-fft=fftpack \

This is a waste of a good BlueGene :-) Use FFTW, which has been optimized for BlueGene. [Edit: ah I see why you tried this]

>                    --without-x \
>                    CC="mpixlc_r" \
>                    CFLAGS="-O3 -qarc  h=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?

First, try without --enable-ppc-altivec in case that's confusing things. Then try setting the enviroment variable NOASSEMBLYLOOPS to 1 before mdrun to see whether the issue really is specific to the BlueGene-kernel. (Consult mpirun documentation about how to set env vars suitably) You might also try compiling with lower optimization levels, to see if its a compiler/optimization issue. Depending what you find above, there are other things to try.


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