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

[Mark Abraham]

----- Original Message -----
From: LuLanyuan <lulanyuan at msn.com>
Date: Saturday, June 5, 2010 5:04
Subject: RE: [gmx-users] PME problem on BG/P cluster
To: gmx-users at gromacs.org


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>  Hi, 
> Thanks for all the suggestions.
> Actually I also tried it without the ativec flag (using the same flags as those on the wiki) and the outcome was the same.
> I did test it with the fftw3 officially installed on the cluster, and got the same error. Because the problem is related to PME, my first guess is that it may due to fftw and then tried it with fftpack. However, I also did many tests with fftw-3 and got similar results.




OK, so what about my other suggestions?




Mark



> Thanks,
> Lanyuan Lu 
> 
> > Date: Fri, 4 Jun 2010 19:32:45 +0200
> > From: spoel at xray.bmc.uu.se
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] PME problem on BG/P cluster
> > 
> > On 2010-06-04 17.49, LuLanyuan wrote:
> > > 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 co  res 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 \
> > > --enable-bluegene \
> > > --disable-fortran \
> > > --enable-mpi \
> > > --with-fft=fftpack \
> > > --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 runni  ng 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 co  uld 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?
> > >
> > I would strongly suggest to use FFTW3.
> > All other FFT libraries are not so well tested.
> > 
> > -- 
> > David van der Spoel, Ph.D., Professor of Biology
> > Dept. of Cell & Molec. Biol., Uppsala University.
> > Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
> > spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> > -- 
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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