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
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