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From: Vittorio Zaccaria (zaccaria_at_[hidden])
Date: 2007-10-17 12:49:05


Hello,

  I am just trying to run a very simple application using mpirun in
an SGE 6 environment.
The job is called 'example' and it is submitted to the SGE
environment with the
following command:

> qsub -pe parallel 2 example

where 'parallel' is a working parallel environment.
'example' is a very simple script which executes the command
'hostname' on two MPI nodes (I enabled some debug options):

mpirun --debug-daemons --mca pls_gridengine_debug 1 --mca
pls_rsh_agent ssh --prefix /home/dei/931277/openmpi/build/image --mca
pls_gridengine_verbose 1 -np 2 hostname

The job fails with the following output:

[compute-1-16:11144] pls:gridengine: final template argv:
[compute-1-16:11144] pls:gridengine: qrsh -inherit -noshell -
nostdin -V -verbose <template> orted --no-daemonize --debug-daemons --
bootprox
y 1 --name <template> --num_procs 3 --vpid_start 0 --nodename
<template> --universe 931277_at_compute-1-16:default-universe-11144 --
nsreplica "0.0
.0;tcp://192.168.1.116:33076;tcp://172.16.1.116:33076" --gprreplica
"0.0.0;tcp://192.168.1.116:33076;tcp://172.16.1.116:33076"
[compute-1-16:11144] pls:gridengine: reset PATH: /home/dei/931277/
openmpi/build/image/bin:/home/dei/931277/openmpi/build/image/bin:/
home/dei/93
1277/gsl/build/image/bin:/home/dei/931277/openmpi/build/image/bin:/
home/dei/931277/openmpi/build/image/bin:/home/dei/931277/gsl/build/
image/bin
:/apps/sge6/bin/lx24-amd64:/usr/kerberos/bin:/scratch/11780.1.all.q:/
usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:/apps/local/bin:/opt/
intel_fc_8
0/bin:/apps/pgi/linux86/5.1/bin:/home/dei/931277/bin:/home/dei/931277/
bin:/home/dei/931277/bin
[compute-1-16:11144] pls:gridengine: reset LD_LIBRARY_PATH: /home/dei/
931277/openmpi/build/image/lib:/home/dei/931277/openmpi/build/image/
lib:/
home/dei/931277/gsl/build/image/lib:/home/dei/931277/readline/build/
image/lib
[compute-1-16:11144] pls:gridengine: launching on node
compute-1-16.hpc.polimi.it
[compute-1-16:11144] pls:gridengine: parent
[compute-1-16:11144] pls:gridengine: launching on node
compute-1-8.hpc.polimi.it
[compute-1-16:11144] pls:gridengine: parent
[compute-1-16:11144] pls:gridengine: exec_argv[0]=qrsh, exec_path=//
apps/sge6/bin/lx24-amd64/qrsh
[compute-1-16:11144] pls:gridengine: exec_argv[0]=qrsh, exec_path=//
apps/sge6/bin/lx24-amd64/qrsh
[compute-1-16:11144] pls:gridengine: orted_path=/home/dei/931277/
openmpi/build/image/bin/orted
[compute-1-16:11144] pls:gridengine: changing to directory /home/dei/
931277
[compute-1-16:11144] pls:gridengine: orted_path=/home/dei/931277/
openmpi/build/image/bin/orted
[compute-1-16:11144] pls:gridengine: changing to directory /home/dei/
931277
[compute-1-16:11144] pls:gridengine: executing: qrsh -inherit -
noshell -nostdin -V -verbose compute-1-16.hpc.polimi.it /home/dei/
931277/openmpi
/build/image/bin/orted --no-daemonize --debug-daemons --bootproxy 1 --
name 0.0.1 --num_procs 3 --vpid_start 0 --nodename
compute-1-16.hpc.polim
i.it --universe 931277_at_compute-1-16:default-universe-11144 --
nsreplica "0.0.0;tcp://192.168.1.116:33076;tcp://172.16.1.116:33076"
--gprreplica
"0.0.0;tcp://192.168.1.116:33076;tcp://172.16.1.116:33076"
[compute-1-16:11144] pls:gridengine: executing: qrsh -inherit -
noshell -nostdin -V -verbose compute-1-8.hpc.polimi.it /home/dei/
931277/openmpi/
build/image/bin/orted --no-daemonize --debug-daemons --bootproxy 1 --
name 0.0.2 --num_procs 3 --vpid_start 0 --nodename
compute-1-8.hpc.polimi.
it --universe 931277_at_compute-1-16:default-universe-11144 --nsreplica
"0.0.0;tcp://192.168.1.116:33076;tcp://172.16.1.116:33076" --
gprreplica "0
.0.0;tcp://192.168.1.116:33076;tcp://172.16.1.116:33076"
Starting server daemon at host "compute-1-8.hpc.polimi.it"
Starting server daemon at host "compute-1-16.hpc.polimi.it"
error: executing task of job 11780 failed:
error: executing task of job 11780 failed:
[compute-1-16:11144] ERROR: A daemon on node
compute-1-8.hpc.polimi.it failed to start as expected.
[compute-1-16:11144] ERROR: There may be more information available from
[compute-1-16:11144] ERROR: the 'qstat -t' command on the Grid Engine
tasks.
[compute-1-16:11144] ERROR: If the problem persists, please restart the
[compute-1-16:11144] ERROR: Grid Engine PE job
[compute-1-16:11144] ERROR: The daemon exited unexpectedly with
status 1.
[compute-1-16:11144] ERROR: A daemon on node
compute-1-16.hpc.polimi.it failed to start as expected.
[compute-1-16:11144] ERROR: There may be more information available from
[compute-1-16:11144] ERROR: the 'qstat -t' command on the Grid Engine
tasks.
[compute-1-16:11144] ERROR: If the problem persists, please restart the
[compute-1-16:11144] ERROR: Grid Engine PE job
[compute-1-16:11144] ERROR: The daemon exited unexpectedly with
status 1.

It seems that 'orted' daemons just fail to start due to some reason,
but no message
is given:

error: executing task of job 11780 failed:

Executing 'qstat -t' shows two pending jobs, one marked as MASTER,
the other marked as SLAVE.

Please note that if I run mpirun directly from the command line, it
just works fine.

Any suggestions?

Thanks,

Vittorio

--
Vittorio Zaccaria, Ph. D.
Politecnico di Milano
Dipartimento di Elettronica e Informazione
Via Giuseppe Ponzio 34/5 - 20133 Milano
E-mail: zaccaria_at_[hidden]