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Subject: Re: [OMPI users] Elementary question on openMPI application location when using PBS submission
From: Gus Correa (gus_at_[hidden])
Date: 2009-12-01 13:50:57


Hi Belaid MOA

See this FAQ:
http://www.open-mpi.org/faq/?category=running#do-i-need-a-common-filesystem
http://www.open-mpi.org/faq/?category=building#where-to-install
http://www.open-mpi.org/faq/?category=tm#tm-obtain-host

Your executable needs to be on a directory that is accessible
by all nodes in your node pool.
An easy way to achieve this is to put it in a directory that
is NFS mounted on all nodes, and launch your pbs script from there.

A less convenient alternative, if no NFS directory is available,
is to copy the executable over to the nodes.

I also find it easier to write a PBS script instead of putting
all the PBS directives in the command line.
In this case you can put the lines below in your PBS script,
to ensure all nodes will be on your work directory (cd $PBS_O_WORKDIR):

########

#PBS ... (PBS directives)
...
cd $PBS_O_WORKDIR
mpiexec -n ....

########

IIRR, by default Torque/PBS puts you in your home directory on
the nodes, which may or may not be the location of your executable.

I hope this helps,
Gus Correa
---------------------------------------------------------------------
Gustavo Correa
Lamont-Doherty Earth Observatory - Columbia University
Palisades, NY, 10964-8000 - USA
---------------------------------------------------------------------

Belaid MOA wrote:
> Hello everyone,
> I am new to this list and I have a very elementary question: suppose we
> have three machines, HN (Head Node hosting the pbs server), WN1 (A
> worker node) and WN (another worker node). The PBS nodefile has WN1 and
> WN2 in it (DOES NOT HAVE HN).
> My openMPI program (hello) and PBS script(my_script.sh) reside on the
> HN. When I submit my PBS script using qsub -l nodes=2 my_script.sh, I
> get the following error:
>
> --------------------------------------------------------------------------
> mpirun was unable to launch the specified application as it could not
> find an executable:
>
> Executable: hello
> Node: WN2
>
> while attempting to start process rank 0.
> --------------------------------------------------------------------------
>
> How come my hello program is not copied automatically to the worker
> nodes? This leads to my elementary question:
> where the application should be when using a PBS submission?
>
> Note that when I run mpirun from HN with machinefile containing WN1 and
> WN2, I get the right output.
>
> Any help on this is very appreciated.
>
> ~Belaid.
>
>
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