[torqueusers] pbs on single machine

James A. Peltier jpeltier at cs.sfu.ca
Wed Jan 9 15:34:38 MST 2008


James J Coyle wrote:
> Jan,
> 
> Try 
> 
> /usr/local/bin/mpirun -np 8 ./test > ./test.log
> 
> instead of 
> 
> /usr/local/bin/mpirun ./test > ./test.log
> 
> 
> This is the same command you;d need if you ran interactively.
> 
> - James Coyle, PhD
>  SGI Origin, Alpha, Xeon and Opteron Cluster Manager
>  High Performance Computing Group     
>  235 Durham Center            
>  Iowa State Univ.           phone: (515)-294-2099
>  Ames, Iowa 50011           web: http://jjc.public.iastate.edu
> -----------------------------------------------Oo
> 
> Hi all,
> 
> I have one 8 core machine (2 quad core cpus) running linux (named
> "headnode"). I would like to use PBS to run MPI jobs in it. I set up PBS
> according to the mini howto. I told pbs that "headnode" is the server
> and also the one node in the system. In the nodes file I entered
> headnode np=8
> 
> Everything seems to work.
> Running pbsnodes -a gives me:
> headnode
>      state = free
>      np = 8
>      ntype = cluster
>      status = opsys=linux,uname=Linux
> and a bunch more system info. I created a default queue and I can submit
> jobs. The problem is, when I submit a jobscript like:
> 
> #PBS -l nodes=1:ppn=8
> #PBS -l walltime=96:00:00
> #PBS -j oe
> cd $PBS_O_WORKDIR
> echo $PBS_O_WORKDIR
> /usr/local/bin/mpirun ./test > ./test.log
> 
> Everything seems to work fine, but when I look at the processes running
> (e.g. with top), only one copy of "test" runs on the machine. "test" is
> an executable usimg fortran and MPI.
> 
> I am wondering if there is anything obvious I missed in the
> configuration. As far as I understand, I can set up a PBS system
> consisting of a single machine with 8 cores. Any insight would be
> greatly appreciated.
> 
> Thanks a lot, Jan
> 
> _______________________________________________
> torqueusers mailing list
> torqueusers at supercluster.org
> http://www.supercluster.org/mailman/listinfo/torqueusers

If you are using Open-MPI you can compile Open-MPI with the --with-tm 
option which will eliminate the need to specify -np # as it is read 
automatically from the $PBS_NODEFILE variable and started accordingly.

-- 
James A. Peltier
Technical Director, RHCE
SCIRF | GrUVi @ Simon Fraser University - Burnaby Campus
Phone   : 778-782-3610
Fax     : 778-782-3045
Mobile  : 778-840-6434
E-Mail  : jpeltier at cs.sfu.ca
Website : http://gruvi.cs.sfu.ca | http://scirf.cs.sfu.ca
MSN     : subatomic_spam at hotmail.com


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