> Date: Tue, 1 Dec 2009 14:55:53 -0500
> From: g...@ldeo.columbia.edu
> To: us...@open-mpi.org
> Subject: Re: [OMPI users] Elementary question on openMPI application
location when using PBS submission
>
> Hi Belaid Moa
>
> Belaid MOA wrote:
> > Thank you very very much Gus. Does this mean that OpenMPI does not
copy
> > the executable from the master node to the worker nodes?
>
> Not that I know.
> Making the executable available on the nodes, and any
> input files the program may need, is the user's responsibility,
> not of mpiexec.
>
> On the other hand,
> Torque/PBS has a "stage_in/stage_out" feature that is supposed to
> copy files over to the nodes, if you want to give it a shot.
> See "man qsub" and look into the (numerous) "-W" option under
> the "stage[in,out]=file_list" sub-options.
> This is a relic from the old days where everything had to be on
> local disks on the nodes, and NFS ran over Ethernet 10/100,
> but it is still used by people that
> run MPI programs with heavy I/O, to avoid pounding on NFS or
> even on parallel file systems.
> I tried the stage_in/out feature a loooong time ago,
> (old PBS before Torque), but it had issues.
> It probably works now with the newer/better
> versions of Torque.
>
> However, the easy way to get this right is just to use an NFS mounted
> directory.
>
> > If that's case, I will go ahead and NFS mount my working directory.
> >
>
> This would make your life much easier.
>
> My $0.02.
> Gus Correa
> ---------------------------------------------------------------------
> Gustavo Correa
> Lamont-Doherty Earth Observatory - Columbia University
> Palisades, NY, 10964-8000 - USA
> ---------------------------------------------------------------------
>
>
>
>
> > ~Belaid.
> >
> >
> > > Date: Tue, 1 Dec 2009 13:50:57 -0500
> > > From: g...@ldeo.columbia.edu
> > > To: us...@open-mpi.org
> > > Subject: Re: [OMPI users] Elementary question on openMPI application
> > location when using PBS submission
> > >
> > > 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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