[torqueusers] confused by mpiexec/mpirun with PBS

Salvatore Di Nardo salvatore.dinardo at itb.cnr.it
Fri Feb 18 02:33:33 MST 2005


On Tue, 2005-02-15 at 12:23, Salvatore Di Nardo wrote:

> 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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> 
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Hemm... boys, 
nobody can solve me this?
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