george.
On Nov 6, 2008, at 3:07 PM, Ralph Castain wrote:
I have no idea what "oar" is, but it looks to me like the rsh launcher is getting confused about the remote shell it will use - I don't believe that the "set" cmd shown below is proper bash syntax, and that is the error that is causing the launch to fail.What remote shell should it fine? I know we don't have any "oar" shell-specific code in the system, but maybe it looks like something else?On Nov 6, 2008, at 12:55 PM, Andrea Pellegrini wrote:Hi all,I'm trying to run an openmpi application on a oar cluster. I think the cluster is configured correctly but I still have problems when I run mpirun:apellegr@m45-037:~$ mpirun -prefix /n/poolfs/z/home/apellegr/ openmpi -machinefile $OAR_FILE_NODES -mca pls_rsh_agent "oarsh" -np 10 /n/poolfs/z/home/apellegr/mpi_test/hello_world.x86 bash: -c: line 0: syntax error near unexpected token `(' bash: -c: line 0: ` set path = ( /n/poolfs/z/home/apellegr/openmpi/ bin $path ) ; if ( $?LD_LIBRARY_PATH == 1 ) set OMPI_have_llp ; if ( $?LD_LIBRARY_PATH == 0 ) setenv LD_LIBRARY_PATH /n/poolfs/z/home/ apellegr/openmpi/lib ; if ( $?OMPI_have_llp == 1 ) setenv LD_LIBRARY_PATH /n/poolfs/z/home/apellegr/openmpi/lib: $LD_LIBRARY_PATH ; /n/poolfs/z/home/apellegr/openmpi/bin/orted -- bootproxy 1 --name 0.0.4 --num_procs 5 --vpid_start 0 --nodename m45-040.pool --universe apell...@m45-037.pool:default- universe-29482 --nsreplica "0.0.0;tcp://10.11.45.37:36790" -- gprreplica "0.0.0;tcp://10.11.45.37:36790"'bash: -c: line 0: syntax error near unexpected token `('bash: -c: line 0: ` set path = ( /n/poolfs/z/home/apellegr/openmpi/ bin $path ) ; if ( $?LD_LIBRARY_PATH == 1 ) set OMPI_have_llp ; if ( $?LD_LIBRARY_PATH == 0 ) setenv LD_LIBRARY_PATH /n/poolfs/z/home/ apellegr/openmpi/lib ; if ( $?OMPI_have_llp == 1 ) setenv LD_LIBRARY_PATH /n/poolfs/z/home/apellegr/openmpi/lib: $LD_LIBRARY_PATH ; /n/poolfs/z/home/apellegr/openmpi/bin/orted -- bootproxy 1 --name 0.0.2 --num_procs 5 --vpid_start 0 --nodename m45-038.pool --universe apell...@m45-037.pool:default- universe-29482 --nsreplica "0.0.0;tcp://10.11.45.37:36790" -- gprreplica "0.0.0;tcp://10.11.45.37:36790"' [m45-037.pool:29482] ERROR: A daemon on node m45-038.pool failed to start as expected. [m45-037.pool:29482] ERROR: There may be more information available from[m45-037.pool:29482] ERROR: the remote shell (see above).[m45-037.pool:29482] ERROR: The daemon exited unexpectedly with status 2.bash: -c: line 0: syntax error near unexpected token `('bash: -c: line 0: ` set path = ( /n/poolfs/z/home/apellegr/openmpi/ bin $path ) ; if ( $?LD_LIBRARY_PATH == 1 ) set OMPI_have_llp ; if ( $?LD_LIBRARY_PATH == 0 ) setenv LD_LIBRARY_PATH /n/poolfs/z/home/ apellegr/openmpi/lib ; if ( $?OMPI_have_llp == 1 ) setenv LD_LIBRARY_PATH /n/poolfs/z/home/apellegr/openmpi/lib: $LD_LIBRARY_PATH ; /n/poolfs/z/home/apellegr/openmpi/bin/orted -- bootproxy 1 --name 0.0.3 --num_procs 5 --vpid_start 0 --nodename m45-039.pool --universe apell...@m45-037.pool:default- universe-29482 --nsreplica "0.0.0;tcp://10.11.45.37:36790" -- gprreplica "0.0.0;tcp://10.11.45.37:36790"' [m45-037.pool:29482] ERROR: A daemon on node m45-039.pool failed to start as expected. [m45-037.pool:29482] ERROR: There may be more information available from[m45-037.pool:29482] ERROR: the remote shell (see above).[m45-037.pool:29482] ERROR: The daemon exited unexpectedly with status 2. [m45-037.pool:29482] [0,0,0] ORTE_ERROR_LOG: Timeout in file ../../../../orte/mca/pls/base/pls_base_orted_cmds.c at line 275 [m45-037.pool:29482] [0,0,0] ORTE_ERROR_LOG: Timeout in file ../../../../../orte/mca/pls/rsh/pls_rsh_module.c at line 1158 [m45-037.pool:29482] [0,0,0] ORTE_ERROR_LOG: Timeout in file ../../../../../orte/mca/errmgr/hnp/errmgr_hnp.c at line 90 [m45-037.pool:29482] ERROR: A daemon on node m45-040.pool failed to start as expected. [m45-037.pool:29482] ERROR: There may be more information available from[m45-037.pool:29482] ERROR: the remote shell (see above).[m45-037.pool:29482] ERROR: The daemon exited unexpectedly with status 2. [m45-037.pool:29482] [0,0,0] ORTE_ERROR_LOG: Timeout in file ../../../../orte/mca/pls/base/pls_base_orted_cmds.c at line 188 [m45-037.pool:29482] [0,0,0] ORTE_ERROR_LOG: Timeout in file ../../../../../orte/mca/pls/rsh/pls_rsh_module.c at line 1190--------------------------------------------------------------------------mpirun was unable to cleanly terminate the daemons for this job. Returned value Timeout instead of ORTE_SUCCESS.-------------------------------------------------------------------------- apellegr@m45-037:~$ If I run it with the option "-mca pls_rsh_debug 1" I get:apellegr@m45-037:~$ mpirun -prefix /n/poolfs/z/home/apellegr/ openmpi -machinefile $OAR_FILE_NODES -mca pls_rsh_debug 1 -mca pls_rsh_agent "oarsh" -np 10 /n/poolfs/z/home/apellegr/mpi_test/ hello_world.x86[m45-037.pool:29473] pls:rsh: local shell: 2 (tcsh)[m45-037.pool:29473] pls:rsh: assuming same remote shell as local shell[m45-037.pool:29473] pls:rsh: remote shell: 2 (tcsh) [m45-037.pool:29473] pls:rsh: final template argv:[m45-037.pool:29473] pls:rsh: /usr/bin/oarsh <template> orted -- bootproxy 1 --name <template> --num_procs 5 --vpid_start 0 -- nodename <template> --universe apell...@m45-037.pool:default- universe-29473 --nsreplica "0.0.0;tcp://10.11.45.37:55477" -- gprreplica "0.0.0;tcp://10.11.45.37:55477"[m45-037.pool:29473] pls:rsh: launching on node m45-037.pool [m45-037.pool:29473] pls:rsh: m45-037.pool is a LOCAL node[m45-037.pool:29473] pls:rsh: reset PATH: /n/poolfs/z/home/apellegr/ openmpi/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/ sbin:/bin:/usr/X11R6/bin:/n/poolfs/z/home/apellegr/openmpi/bin:/n/ poolfs/z/home/apellegr/openssl/bin [m45-037.pool:29473] pls:rsh: reset LD_LIBRARY_PATH: /n/poolfs/z/ home/apellegr/openmpi/lib[m45-037.pool:29473] pls:rsh: changing to directory /home/apellegr[m45-037.pool:29473] pls:rsh: executing: (/n/poolfs/z/home/apellegr/ openmpi/bin/orted) orted --bootproxy 1 --name 0.0.1 --num_procs 5 -- vpid_start 0 --nodename m45-037.pool --universe apell...@m45-037.pool:default-universe-29473 --nsreplica "0.0.0;tcp://10.11.45.37:55477" --gprreplica "0.0.0;tcp:// 10.11.45.37:55477" --set-sid [OAR_JOBID=597856 HOST=m45-037.pool TERM=xterm SHELL=/bin/tcsh OAR_WORKING_DIRECTORY=/home/apellegr SSH_CLIENT=10.11.0.4 50481 6667 OAR_USER=apellegr GROUP=csestudents USER=apellegr SUDO_USER=oar OAR_WORKDIR=/home/apellegr SUDO_UID=30143 HOSTTYPE=i486-linux USERNAME=apellegr OAR_JOB_NAME= OAR_NODE_FILE=/var/lib/oar/597856 OAR_RESOURCE_PROPERTIES_FILE=/var/ lib/oar/597856_resources MAIL=/var/mail/oar PATH=/n/poolfs/z/home/ apellegr/openmpi/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/ bin:/sbin:/bin:/usr/X11R6/bin:/n/poolfs/z/home/apellegr/openmpi/ bin:/n/poolfs/z/home/apellegr/openssl/bin OAR_PROJECT_NAME=default OAR_JOB_WALLTIME_SECONDS=7200 PWD=/home/apellegr HOME=/home/ apellegr SUDO_COMMAND=OAR SHLVL=2 OAR_FILE_NODES=/var/lib/oar/ 597856 OSTYPE=linux VENDOR=intel OAR_JOB_WALLTIME=2:0:0 MACHTYPE=i486 LOGNAME=apellegr OAR_NODEFILE=/var/lib/oar/597856 OAR_RESOURCE_FILE=/var/lib/oar/597856 SUDO_GID=390 OAR_JOB_ID=597856 OAR_O_WORKDIR=/home/apellegr _=/n/poolfs/z/home/ apellegr/openmpi/bin/mpirun OLDPWD=/home/apellegr/openmpi OMPI_MCA_rds_hostfile_path=/var/lib/oar/597856 OMPI_MCA_pls_rsh_debug=1 OMPI_MCA_pls_rsh_agent=oarsh LD_LIBRARY_PATH=/n/poolfs/z/home/apellegr/openmpi/lib OMPI_MCA_seed=0][m45-037.pool:29473] pls:rsh: launching on node m45-038.pool [m45-037.pool:29473] pls:rsh: m45-038.pool is a REMOTE node[m45-037.pool:29473] pls:rsh: executing: (//usr/bin/oarsh) /usr/bin/ oarsh m45-038.pool set path = ( /n/poolfs/z/home/apellegr/openmpi/ bin $path ) ; if ( $?LD_LIBRARY_PATH == 1 ) set OMPI_have_llp ; if ( $?LD_LIBRARY_PATH == 0 ) setenv LD_LIBRARY_PATH /n/poolfs/z/home/ apellegr/openmpi/lib ; if ( $?OMPI_have_llp == 1 ) setenv LD_LIBRARY_PATH /n/poolfs/z/home/apellegr/openmpi/lib: $LD_LIBRARY_PATH ; /n/poolfs/z/home/apellegr/openmpi/bin/orted -- bootproxy 1 --name 0.0.2 --num_procs 5 --vpid_start 0 --nodename m45-038.pool --universe apell...@m45-037.pool:default- universe-29473 --nsreplica "0.0.0;tcp://10.11.45.37:55477" -- gprreplica "0.0.0;tcp://10.11.45.37:55477" [OAR_JOBID=597856 HOST=m45-037.pool TERM=xterm SHELL=/bin/tcsh OAR_WORKING_DIRECTORY=/ home/apellegr SSH_CLIENT=10.11.0.4 50481 6667 OAR_USER=apellegr GROUP=csestudents USER=apellegr SUDO_USER=oar OAR_WORKDIR=/home/ apellegr SUDO_UID=30143 HOSTTYPE=i486-linux USERNAME=apellegr OAR_JOB_NAME= OAR_NODE_FILE=/var/lib/oar/597856 OAR_RESOURCE_PROPERTIES_FILE=/var/lib/oar/597856_resources MAIL=/ var/mail/oar PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/ bin:/sbin:/bin:/usr/X11R6/bin:/n/poolfs/z/home/apellegr/openmpi/ bin:/n/poolfs/z/home/apellegr/openssl/bin OAR_PROJECT_NAME=default OAR_JOB_WALLTIME_SECONDS=7200 PWD=/home/apellegr HOME=/home/ apellegr SUDO_COMMAND=OAR SHLVL=2 OAR_FILE_NODES=/var/lib/oar/ 597856 OSTYPE=linux VENDOR=intel OAR_JOB_WALLTIME=2:0:0 MACHTYPE=i486 LOGNAME=apellegr OAR_NODEFILE=/var/lib/oar/597856 OAR_RESOURCE_FILE=/var/lib/oar/597856 SUDO_GID=390 OAR_JOB_ID=597856 OAR_O_WORKDIR=/home/apellegr _=/n/poolfs/z/home/ apellegr/openmpi/bin/mpirun OLDPWD=/home/apellegr/openmpi OMPI_MCA_rds_hostfile_path=/var/lib/oar/597856 OMPI_MCA_pls_rsh_debug=1 OMPI_MCA_pls_rsh_agent=oarsh OMPI_MCA_seed=0]bash: -c: line 0: syntax error near unexpected token `('bash: -c: line 0: ` set path = ( /n/poolfs/z/home/apellegr/openmpi/ bin $path ) ; if ( $?LD_LIBRARY_PATH == 1 ) set OMPI_have_llp ; if ( $?LD_LIBRARY_PATH == 0 ) setenv LD_LIBRARY_PATH /n/poolfs/z/home/ apellegr/openmpi/lib ; if ( $?OMPI_have_llp == 1 ) setenv LD_LIBRARY_PATH /n/poolfs/z/home/apellegr/openmpi/lib: $LD_LIBRARY_PATH ; /n/poolfs/z/home/apellegr/openmpi/bin/orted -- bootproxy 1 --name 0.0.2 --num_procs 5 --vpid_start 0 --nodename m45-038.pool --universe apell...@m45-037.pool:default- universe-29473 --nsreplica "0.0.0;tcp://10.11.45.37:55477" -- gprreplica "0.0.0;tcp://10.11.45.37:55477"'[m45-037.pool:29473] pls:rsh: launching on node m45-039.pool[m45-037.pool:29473] ERROR: A daemon on node m45-038.pool failed to start as expected. [m45-037.pool:29473] ERROR: There may be more information available from[m45-037.pool:29473] ERROR: the remote shell (see above).[m45-037.pool:29473] ERROR: The daemon exited unexpectedly with status 2.[m45-037.pool:29473] pls:rsh: m45-039.pool is a REMOTE node[m45-037.pool:29473] pls:rsh: executing: (//usr/bin/oarsh) /usr/bin/ oarsh m45-039.pool set path = ( /n/poolfs/z/home/apellegr/openmpi/ bin $path ) ; if ( $?LD_LIBRARY_PATH == 1 ) set OMPI_have_llp ; if ( $?LD_LIBRARY_PATH == 0 ) setenv LD_LIBRARY_PATH /n/poolfs/z/home/ apellegr/openmpi/lib ; if ( $?OMPI_have_llp == 1 ) setenv LD_LIBRARY_PATH /n/poolfs/z/home/apellegr/openmpi/lib: $LD_LIBRARY_PATH ; /n/poolfs/z/home/apellegr/openmpi/bin/orted -- bootproxy 1 --name 0.0.3 --num_procs 5 --vpid_start 0 --nodename m45-039.pool --universe apell...@m45-037.pool:default- universe-29473 --nsreplica "0.0.0;tcp://10.11.45.37:55477" -- gprreplica "0.0.0;tcp://10.11.45.37:55477" [OAR_JOBID=597856 HOST=m45-037.pool TERM=xterm SHELL=/bin/tcsh OAR_WORKING_DIRECTORY=/ home/apellegr SSH_CLIENT=10.11.0.4 50481 6667 OAR_USER=apellegr GROUP=csestudents USER=apellegr SUDO_USER=oar OAR_WORKDIR=/home/ apellegr SUDO_UID=30143 HOSTTYPE=i486-linux USERNAME=apellegr OAR_JOB_NAME= OAR_NODE_FILE=/var/lib/oar/597856 OAR_RESOURCE_PROPERTIES_FILE=/var/lib/oar/597856_resources MAIL=/ var/mail/oar PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/ bin:/sbin:/bin:/usr/X11R6/bin:/n/poolfs/z/home/apellegr/openmpi/ bin:/n/poolfs/z/home/apellegr/openssl/bin OAR_PROJECT_NAME=default OAR_JOB_WALLTIME_SECONDS=7200 PWD=/home/apellegr HOME=/home/ apellegr SUDO_COMMAND=OAR SHLVL=2 OAR_FILE_NODES=/var/lib/oar/ 597856 OSTYPE=linux VENDOR=intel OAR_JOB_WALLTIME=2:0:0 MACHTYPE=i486 LOGNAME=apellegr OAR_NODEFILE=/var/lib/oar/597856 OAR_RESOURCE_FILE=/var/lib/oar/597856 SUDO_GID=390 OAR_JOB_ID=597856 OAR_O_WORKDIR=/home/apellegr _=/n/poolfs/z/home/ apellegr/openmpi/bin/mpirun OLDPWD=/home/apellegr/openmpi OMPI_MCA_rds_hostfile_path=/var/lib/oar/597856 OMPI_MCA_pls_rsh_debug=1 OMPI_MCA_pls_rsh_agent=oarsh OMPI_MCA_seed=0]bash: -c: line 0: syntax error near unexpected token `('bash: -c: line 0: ` set path = ( /n/poolfs/z/home/apellegr/openmpi/ bin $path ) ; if ( $?LD_LIBRARY_PATH == 1 ) set OMPI_have_llp ; if ( $?LD_LIBRARY_PATH == 0 ) setenv LD_LIBRARY_PATH /n/poolfs/z/home/ apellegr/openmpi/lib ; if ( $?OMPI_have_llp == 1 ) setenv LD_LIBRARY_PATH /n/poolfs/z/home/apellegr/openmpi/lib: $LD_LIBRARY_PATH ; /n/poolfs/z/home/apellegr/openmpi/bin/orted -- bootproxy 1 --name 0.0.3 --num_procs 5 --vpid_start 0 --nodename m45-039.pool --universe apell...@m45-037.pool:default- universe-29473 --nsreplica "0.0.0;tcp://10.11.45.37:55477" -- gprreplica "0.0.0;tcp://10.11.45.37:55477"'[m45-037.pool:29473] pls:rsh: launching on node m45-040.pool[m45-037.pool:29473] ERROR: A daemon on node m45-039.pool failed to start as expected. [m45-037.pool:29473] ERROR: There may be more information available from[m45-037.pool:29473] ERROR: the remote shell (see above).[m45-037.pool:29473] ERROR: The daemon exited unexpectedly with status 2.[m45-037.pool:29473] pls:rsh: m45-040.pool is a REMOTE node[m45-037.pool:29473] pls:rsh: executing: (//usr/bin/oarsh) /usr/bin/ oarsh m45-040.pool set path = ( /n/poolfs/z/home/apellegr/openmpi/ bin $path ) ; if ( $?LD_LIBRARY_PATH == 1 ) set OMPI_have_llp ; if ( $?LD_LIBRARY_PATH == 0 ) setenv LD_LIBRARY_PATH /n/poolfs/z/home/ apellegr/openmpi/lib ; if ( $?OMPI_have_llp == 1 ) setenv LD_LIBRARY_PATH /n/poolfs/z/home/apellegr/openmpi/lib: $LD_LIBRARY_PATH ; /n/poolfs/z/home/apellegr/openmpi/bin/orted -- bootproxy 1 --name 0.0.4 --num_procs 5 --vpid_start 0 --nodename m45-040.pool --universe apell...@m45-037.pool:default- universe-29473 --nsreplica "0.0.0;tcp://10.11.45.37:55477" -- gprreplica "0.0.0;tcp://10.11.45.37:55477" [OAR_JOBID=597856 HOST=m45-037.pool TERM=xterm SHELL=/bin/tcsh OAR_WORKING_DIRECTORY=/ home/apellegr SSH_CLIENT=10.11.0.4 50481 6667 OAR_USER=apellegr GROUP=csestudents USER=apellegr SUDO_USER=oar OAR_WORKDIR=/home/ apellegr SUDO_UID=30143 HOSTTYPE=i486-linux USERNAME=apellegr OAR_JOB_NAME= OAR_NODE_FILE=/var/lib/oar/597856 OAR_RESOURCE_PROPERTIES_FILE=/var/lib/oar/597856_resources MAIL=/ var/mail/oar PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/ bin:/sbin:/bin:/usr/X11R6/bin:/n/poolfs/z/home/apellegr/openmpi/ bin:/n/poolfs/z/home/apellegr/openssl/bin OAR_PROJECT_NAME=default OAR_JOB_WALLTIME_SECONDS=7200 PWD=/home/apellegr HOME=/home/ apellegr SUDO_COMMAND=OAR SHLVL=2 OAR_FILE_NODES=/var/lib/oar/ 597856 OSTYPE=linux VENDOR=intel OAR_JOB_WALLTIME=2:0:0 MACHTYPE=i486 LOGNAME=apellegr OAR_NODEFILE=/var/lib/oar/597856 OAR_RESOURCE_FILE=/var/lib/oar/597856 SUDO_GID=390 OAR_JOB_ID=597856 OAR_O_WORKDIR=/home/apellegr _=/n/poolfs/z/home/ apellegr/openmpi/bin/mpirun OLDPWD=/home/apellegr/openmpi OMPI_MCA_rds_hostfile_path=/var/lib/oar/597856 OMPI_MCA_pls_rsh_debug=1 OMPI_MCA_pls_rsh_agent=oarsh OMPI_MCA_seed=0]bash: -c: line 0: syntax error near unexpected token `('bash: -c: line 0: ` set path = ( /n/poolfs/z/home/apellegr/openmpi/ bin $path ) ; if ( $?LD_LIBRARY_PATH == 1 ) set OMPI_have_llp ; if ( $?LD_LIBRARY_PATH == 0 ) setenv LD_LIBRARY_PATH /n/poolfs/z/home/ apellegr/openmpi/lib ; if ( $?OMPI_have_llp == 1 ) setenv LD_LIBRARY_PATH /n/poolfs/z/home/apellegr/openmpi/lib: $LD_LIBRARY_PATH ; /n/poolfs/z/home/apellegr/openmpi/bin/orted -- bootproxy 1 --name 0.0.4 --num_procs 5 --vpid_start 0 --nodename m45-040.pool --universe apell...@m45-037.pool:default- universe-29473 --nsreplica "0.0.0;tcp://10.11.45.37:55477" -- gprreplica "0.0.0;tcp://10.11.45.37:55477"' [m45-037.pool:29473] ERROR: A daemon on node m45-040.pool failed to start as expected. [m45-037.pool:29473] ERROR: There may be more information available from[m45-037.pool:29473] ERROR: the remote shell (see above).[m45-037.pool:29473] ERROR: The daemon exited unexpectedly with status 2. [m45-037.pool:29473] [0,0,0] ORTE_ERROR_LOG: Timeout in file ../../../../orte/mca/pls/base/pls_base_orted_cmds.c at line 188 [m45-037.pool:29473] [0,0,0] ORTE_ERROR_LOG: Timeout in file ../../../../../orte/mca/pls/rsh/pls_rsh_module.c at line 1190--------------------------------------------------------------------------mpirun was unable to cleanly terminate the daemons for this job. Returned value Timeout instead of ORTE_SUCCESS.-------------------------------------------------------------------------- apellegr@m45-037:~$ Can anybody help me? Thanks, ~Andrea _______________________________________________ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users_______________________________________________ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users
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