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@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