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Subject: Re: [OMPI users] orted unknown option "--daemonize"
From: TH Chew (teonghan_at_[hidden])
Date: 2010-07-16 04:41:17


Jeff,

Thanks for the suggestion. Been looking into it and although, I installed
the same OpenMPI version. But somehow, another software (Discovery Studio)
was installed on birg-desktop-10, causing the mpirun to be messed up (since
Discovery Studio also install some kind of mpirun/mpiexec). I type
"mpirun.openmpi --version" on birg-desktop-10, the output is:

####################################################
birg_at_birg-desktop-10:~$ mpirun.openmpi --version
mpirun.openmpi: symbol lookup error: mpirun.openmpi: undefined symbol:
orted_cmd_line
####################################################

and when I type on other machine

####################################################
birg_at_birg-frontnode:~/Desktop/nfs_shared$ mpirun.openmpi --version
mpirun.openmpi (OpenRTE) 1.4.1

Report bugs to http://www.open-mpi.org/community/help/
####################################################

I am now uninstalling Discovery Studio and see whether it works or not.

Thanks again.

On Thu, Jul 15, 2010 at 7:15 PM, Jeff Squyres <jsquyres_at_[hidden]> wrote:

> This usually means that you have mis-matched versions of Open MPI across
> your machines. Double check that you have the same version of Open MPI
> installed on all the machines that you'll be running (e.g., perhaps
> birg-desktop-10 has a different version?).
>
>
> On Jul 15, 2010, at 5:18 AM, TH Chew wrote:
>
> > Hi all,
> >
> > I am setting up a 7+1 nodes cluster for MD simulation, specifically using
> GROMACS. I am using Ubuntu Lucid 64-bit on all machines. Installed gromacs,
> gromacs-openmpi, and gromacs-mpich from the repository. MPICH version of
> gromacs runs fine without any error. However, when I ran OpenMPI version of
> gromacs by
> >
> >
> ###########################################################################
> > mpirun.openmpi -np 8 -wdir /home/birg/Desktop/nfs/ -hostfile
> ~/Desktop/mpi_settings/hostfile mdrun_mpi.openmpi -v
> >
> ###########################################################################
> >
> > an error occur, something like this
> >
> >
> ###########################################################################
> > [birg-desktop-10:02101] Error: unknown option "--daemonize"
> > Usage: orted [OPTION]...
> > Start an Open RTE Daemon
> >
> > --bootproxy <arg0> Run as boot proxy for <job-id>
> > -d|--debug Debug the OpenRTE
> > -d|--spin Have the orted spin until we can connect a
> debugger
> > to it
> > --debug-daemons Enable debugging of OpenRTE daemons
> > --debug-daemons-file Enable debugging of OpenRTE daemons, storing
> output
> > in files
> > --gprreplica <arg0> Registry contact information.
> > -h|--help This help message
> > --mpi-call-yield <arg0>
> > Have MPI (or similar) applications call yield
> when
> > idle
> > --name <arg0> Set the orte process name
> > --no-daemonize Don't daemonize into the background
> > --nodename <arg0> Node name as specified by host/resource
> > description.
> > --ns-nds <arg0> set sds/nds component to use for daemon
> (normally
> > not needed)
> > --nsreplica <arg0> Name service contact information.
> > --num_procs <arg0> Set the number of process in this job
> > --persistent Remain alive after the application process
> > completes
> > --report-uri <arg0> Report this process' uri on indicated pipe
> > --scope <arg0> Set restrictions on who can connect to this
> > universe
> > --seed Host replicas for the core universe services
> > --set-sid Direct the orted to separate from the current
> > session
> > --tmpdir <arg0> Set the root for the session directory tree
> > --universe <arg0> Set the universe name as
> > username_at_hostname:universe_name for this
> > application
> > --vpid_start <arg0> Set the starting vpid for this job
> >
> --------------------------------------------------------------------------
> > A daemon (pid 5598) died unexpectedly with status 251 while attempting
> > to launch so we are aborting.
> >
> > There may be more information reported by the environment (see above).
> >
> > This may be because the daemon was unable to find all the needed shared
> > libraries on the remote node. You may set your LD_LIBRARY_PATH to have
> the
> > location of the shared libraries on the remote nodes and this will
> > automatically be forwarded to the remote nodes.
> >
> --------------------------------------------------------------------------
> >
> --------------------------------------------------------------------------
> > mpirun.openmpi noticed that the job aborted, but has no info as to the
> process
> > that caused that situation.
> >
> --------------------------------------------------------------------------
> >
> --------------------------------------------------------------------------
> > mpirun.openmpi was unable to cleanly terminate the daemons on the nodes
> shown
> > below. Additional manual cleanup may be required - please refer to
> > the "orte-clean" tool for assistance.
> >
> --------------------------------------------------------------------------
> > birg-desktop-04 - daemon did not report back when launched
> > birg-desktop-07 - daemon did not report back when launched
> > birg-desktop-10 - daemon did not report back when launched
> >
> ###########################################################################
> >
> > It is strange that it only happen on one of the compute node
> (birg-desktop-10). If I remove birg-desktop-10 from the hostfile, I can run
> OpenMPI gromacs successfully. Any idea?
> >
> > Thanks.
> >
> > --
> > Regards,
> > THChew
> > _______________________________________________
> > users mailing list
> > users_at_[hidden]
> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>
> --
> Jeff Squyres
> jsquyres_at_[hidden]
> For corporate legal information go to:
> http://www.cisco.com/web/about/doing_business/legal/cri/
>
>
> _______________________________________________
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> http://www.open-mpi.org/mailman/listinfo.cgi/users
>

-- 
Regards,
THChew