[torqueusers] confused by mpiexec/mpirun with PBS

Salvatore Di Nardo salvatore.dinardo at itb.cnr.it
Tue Feb 15 04:23:01 MST 2005


trying that did not work.
It "almost" worked this way:

===========================================================
#!/bin/sh
#PBS -S /bin/sh
#PBS -m e
#PBS -l cput=500:00:00
#PBS -l nodes=3:ppn=2
echo "Ora del lancio: $DATE"
echo "E' stato sottoposto dalla macchina: "; hostname;
cd /home/salvator
time mpiexec -boot -v -n 6 mpiblast -p blastx -d nr -i frag.0 -o
frag.0.out6p_pbs
===========================================================

i needed to set:

-boot else i get "no lamd running"

-n 6 else i get "mpirun must use at least 3 processors"

The problem is that all 6 processors run on the same node, and not
splitted in 3 nodes ( each of them have 2 cpus). Why that ?

below my working queue:

====================================================
create queue workq
set queue workq queue_type = Execution
set queue workq resources_max.cput = 10000:00:00
set queue workq resources_max.ncpus = 8
set queue workq resources_max.nodect = 4
set queue workq resources_max.walltime = 10000:00:00
set queue workq resources_min.cput = 00:00:01
set queue workq resources_min.ncpus = 1
set queue workq resources_min.nodect = 1
set queue workq resources_min.walltime = 00:00:01
set queue workq resources_default.cput = 10000:00:00
set queue workq resources_default.ncpus = 1
set queue workq resources_default.walltime = 10000:00:00
set queue workq resources_available.nodect = 4
set queue workq max_user_run = 8
set queue workq enabled = True
set queue workq started = True
====================================================

Any suggestion?


p.s) my OS if FC2, and pbs and lam comes with OSCAR4.
p.p.s) mpiblast work correctly ouside pbs using lamboot + hostfile




On Fri, 2005-02-11 at 11:10, Ake wrote: 

> On Fri, Feb 11, 2005 at 10:36:10AM +0100, Salvatore Di Nardo wrote:
> > > If i use mpiexec i must give a "machine list" where tu run it, so i
> > > must give free nodes.
> 
> Example of submitfile with mpiexec
> 
> #PBS -l nodes=5
> mpiexec ./my-code my-args1 my-args2
> 
> Thats all you need. Mpiexec takes the nodelist from the PBS environment.
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