[torqueusers] confused by mpiexec/mpirun with PBS

Chris Samuel csamuel at vpac.org
Sun Feb 13 17:19:13 MST 2005

On Wed, 9 Feb 2005 10:28 pm, Salvatore Di Nardo wrote:

> Since now we ran mpiblast outside pbs ( using lamboot and mpirun ), but
> this have the issue that lambboot do not consider nodes already busy by
> pbs ( and vice-versa) so i tryed to run mpiblast subliting it with qsub,
> but i'm a bit confused.
> If i run mpiblast with mpirun i still to launch lamboot with hes own
> config file, and this mean that mpiblast will be ran on nodes already
> busy from other jobs.
> If i use mpiexec i must give a "machine list" where tu run it, so i must
> give free nodes.

It'd probably be much much easier to run this inside PBS, you should be able 
to build mpiblast against the latest LAM (v7.1.1 which apparently now has 
much better integration with PBS through the TM boot interface) and use its 
native understanding of how PBS works.

Look at building LAM with the:


to use the TM interface by default, rather than the rsh one.

This is doc'd in the install guide at:


NB: We don't use LAM here at present, so none of this is from experience! :-)

 Christopher Samuel - (03)9925 4751 - VPAC Systems & Network Admin
 Victorian Partnership for Advanced Computing http://www.vpac.org/
 Bldg 91, 110 Victoria Street, Carlton South, VIC 3053, Australia

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