[gmx-users] Re: GROMACS + MOSIX (fwd)

Alan Wilter Sousa da Silva alan at biof.ufrj.br
Wed Apr 17 16:04:03 CEST 2002


	From my experience (we have a Mosix cluster here):

1- Unfortunately you can *cheat* LAM-MPI (or MPICH).
2- MOSIX and LAM-MPI (or MPICH) can co-exist in the same cluster.

	If run a parallel job with MPI, MOSIX gets knowing and so it try
balance the load although it can migrate MPI procs, so it just avoid that
procs that MPI is requiring.

	Anyway, it's still *amazing* (thanks Mosix!).

On Wed, 17 Apr 2002, David van der Spoel wrote:

> >Dear Sir,
> >   I have a 16 node beowulf cluster configured using
> >MOSIX. I want to run MD simulation using GROMACS.
> >Instead of using LAM to transfer processes to another
> >node is it possible to make mdrun spawn several
> >processes on the same node and let MOSIX balance the
> >load.

> Mosix can not handle processes that access sockets, i.e. the mechanism to
> transport data between unix machines, that is it can not move suche
> processes to other nodes. Having said that, it may be able to handle
> processes that use shared memory. Since LAM can use shared memory within a
> node, maybe you can fool LAM into running all the processes through shared
> memory on one node, and then let MOSIX handle the process scheduling. In
> effect this would come down to having one large virtual shared memory
> machine, composed out of many normal PCs.
> This is hypothetical, check www.openmosix.org for more information. If it
> doesn't work, you can either run a lot of single machine jobs or remove

Alan Wilter S. da Silva
 Laboratório de Física Biológica
  Instituto de Biofísica Carlos Chagas Filho
   Universidade do Brasil/UFRJ
    Rio de Janeiro, Brasil

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