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On Tue, 2005-02-15 at 12:23, Salvatore Di Nardo wrote:
<BLOCKQUOTE TYPE=CITE>
<FONT COLOR="#737373"><I>trying that did not work.<BR>
It "almost" worked this way:<BR>
</FONT><BR>
<FONT COLOR="#737373" SIZE="2">===========================================================<BR>
#!/bin/sh<BR>
#PBS -S /bin/sh<BR>
#PBS -m e<BR>
#PBS -l cput=500:00:00<BR>
#PBS -l nodes=3:ppn=2<BR>
echo "Ora del lancio: $DATE"<BR>
echo "E' stato sottoposto dalla macchina: "; hostname;<BR>
cd /home/salvator<BR>
time mpiexec -boot -v -n 6 mpiblast -p blastx -d nr -i frag.0 -o frag.0.out6p_pbs<BR>
===========================================================</FONT><BR>
<FONT COLOR="#737373"><BR>
i needed to set:<BR>
<BR>
<B>-boot</B> else i get "no lamd running"<BR>
<BR>
<B>-n 6</B> else i get "mpirun must use at least 3 processors"<BR>
<BR>
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 ?<BR>
<BR>
below my working queue:<BR>
</FONT><BR>
<FONT COLOR="#737373" SIZE="2">====================================================<BR>
create queue workq<BR>
set queue workq queue_type = Execution<BR>
set queue workq resources_max.cput = 10000:00:00<BR>
set queue workq resources_max.ncpus = 8<BR>
set queue workq resources_max.nodect = 4<BR>
set queue workq resources_max.walltime = 10000:00:00<BR>
set queue workq resources_min.cput = 00:00:01<BR>
set queue workq resources_min.ncpus = 1<BR>
set queue workq resources_min.nodect = 1<BR>
set queue workq resources_min.walltime = 00:00:01<BR>
set queue workq resources_default.cput = 10000:00:00<BR>
set queue workq resources_default.ncpus = 1<BR>
set queue workq resources_default.walltime = 10000:00:00<BR>
set queue workq resources_available.nodect = 4<BR>
set queue workq max_user_run = 8<BR>
set queue workq enabled = True<BR>
set queue workq started = True<BR>
====================================================</FONT><BR>
<FONT COLOR="#737373"><BR>
Any suggestion?<BR>
<BR>
<BR>
p.s) my OS if FC2, and pbs and lam comes with OSCAR4.<BR>
p.p.s) mpiblast work correctly ouside pbs using lamboot + hostfile<BR>
<BR>
<BR>
<BR>
<BR>
On Fri, 2005-02-11 at 11:10, Ake wrote:
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<PRE>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.</PRE>
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<BR>
<BR>
<BR>
<BR>
<BR>
Hemm... boys, <BR>
nobody can solve me this?
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