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@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@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 <jsquy...@cisco.com> 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@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 > > us...@open-mpi.org > > http://www.open-mpi.org/mailman/listinfo.cgi/users > > > -- > Jeff Squyres > jsquy...@cisco.com > For corporate legal information go to: > http://www.cisco.com/web/about/doing_business/legal/cri/ > > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users > -- Regards, THChew
