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Subject: Re: [OMPI users] orted unknown option "--daemonize"
From: TH Chew (teonghan_at_[hidden])
Date: 2010-07-16 05:53:43


Jeff,

An update of what I did. Apparently, one of my lab mates installed another
version of OpenMPI manually and it clashed with the OpenMPI I installed from
the Ubuntu repository. I manually identified the files installed and deleted
them. After I installed OpenMPI from Ubuntu repository, my "mpirun.openmpi"
works!

On Fri, Jul 16, 2010 at 4:41 PM, TH Chew <teonghan_at_[hidden]> wrote:

> 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/
>>
>>
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>
>
>
> --
> Regards,
> THChew
>

-- 
Regards,
THChew