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 <teong...@gmail.com> 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@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 > -- Regards, THChew
