[torqueusers] confused by mpiexec/mpirun with PBS

Salvatore Di Nardo salvatore.dinardo at itb.cnr.it
Wed Feb 9 04:28:43 MST 2005


Hi all,
i have a little cluster with a master and 8 nodes ( master and nodes
have 2 AMDx64 procs). We use this cluster to run several standard tools
(non mpi) and mpiblast.

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.

There is any way to tell pbs to use ( as example) 8 procs on free nodes,
avoiding to specify directly what nodes are free? PBS is supposed to do
this work so i expect that lauching mpiblast ( using 8 processors) via
pbs mean that pbs will automatically schedule it on free nodes ( or at
least with 1 proc free) and not that i need to give a lamboot file ( for
mpirun ) or "machine list" to mpiexec that contains only free nodes. 

where i'm wrong?

Salvatore Di Nardo
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