Dear Rolf,

Thanks for your reply.
I've created another PE and changed the submission script, explicitly specify the hostname with "--host".
However the result is the same.

# qconf -sp orte
pe_name            orte
slots              8
user_lists         NONE
xuser_lists        NONE
start_proc_args    /bin/true
stop_proc_args     /bin/true
allocation_rule    $fill_up
control_slaves     TRUE
job_is_first_task  FALSE
urgency_slots      min
accounting_summary TRUE

$ cat hpl-8cpu-test.sge
#!/bin/bash
#
#$ -N HPL_8cpu_GB
#$ -pe orte 8
#$ -cwd
#$ -j y
#$ -S /bin/bash
#$ -V
#
cd /home/admin/hpl-2.0
/opt/openmpi-gcc/bin/mpirun -v -np $NSLOTS --host node0001,node0001,node0001,node0001,node0002,node0002,node0002,node0002 ./bin/goto-openmpi-gcc/xhpl


# pdsh -a ps ax --width=200|grep hpl
node0002: 18901 ?        S      0:00 /opt/openmpi-gcc/bin/mpirun -v -np 8 --host node0001,node0001,node0001,node0001,node0002,node0002,node0002,node0002 ./bin/goto-openmpi-gcc/xhpl
node0002: 18902 ?        RLl    0:29 ./bin/goto-openmpi-gcc/xhpl
node0002: 18903 ?        RLl    0:29 ./bin/goto-openmpi-gcc/xhpl
node0002: 18904 ?        RLl    0:28 ./bin/goto-openmpi-gcc/xhpl
node0002: 18905 ?        RLl    0:28 ./bin/goto-openmpi-gcc/xhpl
node0002: 18906 ?        RLl    0:29 ./bin/goto-openmpi-gcc/xhpl
node0002: 18907 ?        RLl    0:28 ./bin/goto-openmpi-gcc/xhpl
node0002: 18908 ?        RLl    0:28 ./bin/goto-openmpi-gcc/xhpl
node0002: 18909 ?        RLl    0:28 ./bin/goto-openmpi-gcc/xhpl

Any hint to debug this situation?

Also, if I have 2 IB ports in each node, which IB bonding was done, will Open MPI automatically benefit from the double bandwidth?

Thanks a lot.

Best Regards,
PN

2009/4/1 Rolf Vandevaart <Rolf.Vandevaart@sun.com>
On 03/31/09 11:43, PN wrote:
Dear all,

I'm using Open MPI 1.3.1 and SGE 6.2u2 on CentOS 5.2
I have 2 compute nodes for testing, each node has a single quad core CPU.

Here is my submission script and PE config:
$ cat hpl-8cpu.sge
#!/bin/bash
#
#$ -N HPL_8cpu_IB
#$ -pe mpi-fu 8
#$ -cwd
#$ -j y
#$ -S /bin/bash
#$ -V
#
cd /home/admin/hpl-2.0
# For IB
/opt/openmpi-gcc/bin/mpirun -v -np $NSLOTS -machinefile $TMPDIR/machines ./bin/goto-openmpi-gcc/xhpl

I've tested the mpirun command can be run correctly in command line.

$ qconf -sp mpi-fu
pe_name            mpi-fu
slots              8
user_lists         NONE
xuser_lists        NONE
start_proc_args    /opt/sge/mpi/startmpi.sh -catch_rsh $pe_hostfile
stop_proc_args     /opt/sge/mpi/stopmpi.sh
allocation_rule    $fill_up
control_slaves     TRUE
job_is_first_task  FALSE
urgency_slots      min
accounting_summary TRUE


I've checked the $TMPDIR/machines after submit, it was correct.
node0002
node0002
node0002
node0002
node0001
node0001
node0001
node0001

However, I found that if I explicitly specify the "-machinefile $TMPDIR/machines", all 8 mpi processes were spawned within a single node, i.e. node0002.

However, if I omit "-machinefile $TMPDIR/machines" in the line mpirun, i.e.
/opt/openmpi-gcc/bin/mpirun -v -np $NSLOTS ./bin/goto-openmpi-gcc/xhpl

The mpi processes can start correctly, 4 processes in node0001 and 4 processes in node0002.

Is this normal behaviour of Open MPI?

I just tried it both ways and I got the same result both times.  The processes are split between the nodes.  Perhaps to be extra sure, you can just run hostname?  And for what it is worth, as you have seen, you do not need to specify a machines file.  Open MPI will use the ones that were allocated by SGE.  You can also change your parallel queue to not run any scripts.  Like this:

start_proc_args    /bin/true
stop_proc_args     /bin/true



Also, I wondered if I have IB interface, for example, the hostname of IB become node0001-clust and node0002-clust, will Open MPI automatically use the IB interface?
Yes, it should use the IB interface.

How about if I have 2 IB ports in each node, which IB bonding was done, will Open MPI automatically benefit from the double bandwidth?

Thanks a lot.

Best Regards,
PN


------------------------------------------------------------------------

_______________________________________________
users mailing list
users@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users


--

=========================
rolf.vandevaart@sun.com
781-442-3043
=========================
_______________________________________________
users mailing list
users@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users