[gmx-users] replica exchange
Mark.Abraham at anu.edu.au
Thu Jan 12 16:44:30 CET 2006
Marc F. Lensink wrote:
> congratulations to the gmx developers for their implementation of the
> replica exchange algorithm.
> however, i noticed that the use of remd requires low-latency network
> communication, because when using simple ethernet no communication can
> be established.
I don't believe you are really observing gromacs REMD running on a
low-latency network and not on a higher latency network. If you can
install LAM MPI on a system, parallel gromacs (and thus gromacs REMD)
will run on it. Probably you are observing a problem with your MPI
installation, or gromacs doesn't like your MPI installation.
> i do not understand why this is. replica's only need to talk to their
> neighbours, and only then every so many simulation steps. for that,
> communication by phone should be enough!
> i'm talking about 16-20 replica's ie cpu's (8-10 nodes). using mpich,
> not lam.
MPICH is not supported/recommended. LAM is. Please read the
documentation on the gromacs webpage.
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