[gmx-users] secure gromacs lam setup?

[Anton Feenstra]

Jack Howarth wrote:

>     I have built and installed both the gromacs and gromacs-mpi rpms
> on a dual Xenon Fedora Core 2 Linux workstation. The standard gromacs
> works fine however it seems to only use one of the two cpus despite
> using threaded code. Thus I am interested in setting up lam-mpi to
> run on this box allowing gromacs to fully utilize both cpu's. However
> I am very concerned about the security implications and have the
> following questions....

In short, hoping it may help, most MPI implementations, including Lam,
have SMP specific communication routines that bypass the NIC completely
on multi-cpu nodes. Whether this also circumvents the use of rsh for
slave process spawning, I am not sure, but it would seem likely that
a mechanism is present in the MPI package that doen't need rsh to start
multiple processes of a parallel job on the same host.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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