Thank you, Ralph.
I have read the wiki and the man pages. But I am still not sure I
understand what is going on in my example. I cannot filter the slots
allocated by SGE. I also think that there is a deviation from the
behavior described on the wiki (precisely example 5 from the top in
section "NOW RUNNING FROM THE INTERACTIVE SHELL").
So, below, I am copy-pasting my session, and I am asking if you could
please follow my line of thought and correct me where I am mistaken?
Here I request an interactive session with 16 slots on 4 four-core nodes
like so:
$ qrsh -cwd -V -pe ompi* 16 -l h_rt=10:00:00,h_vmem=2G bash
Now, I show that all 16 slots are available and everything is working as
expected with both OMPI 1.2.9 and OMPI 1.4.1:
graphics01 $ ~/openmpi/gnu141/bin/mpirun hostname
[graphics01:24837] ras:gridengine: JOB_ID: 89052
graphics01
graphics01
graphics01
graphics01
graphics04
graphics04
graphics02
graphics02
graphics04
graphics02
graphics04
graphics02
graphics03
graphics03
graphics03
graphics03
graphics01 $ ~/openmpi/gnu129/bin/mpirun hostname
[graphics01:24849] ras:gridengine: JOB_ID: 89052
graphics01
graphics04
graphics02
graphics03
graphics01
graphics04
graphics02
graphics03
graphics01
graphics03
graphics01
graphics04
graphics03
graphics04
graphics02
graphics02
Now, I want to filter the list of 16 slots by using the host file. I
want to run 1 process per node.
graphics01 $ cat hosts
graphics01 slots=1
graphics02 slots=1
graphics03 slots=1
graphics04 slots=1
And I try to use it with OMPI 1.2.9 and 1.4.1
graphics01 $ ~/openmpi/gnu129/bin/mpirun -hostfile hosts hostname
graphics04
graphics01
graphics03
graphics02
graphics01 $ ~/openmpi/gnu141/bin/mpirun -hostfile hosts hostname
[graphics01:24903] ras:gridengine: JOB_ID: 89052
graphics01
So, as you can see OMPI1.4.1 did not recognize any hosts except the
current shepherd host.
Moreover, similarly to the example down below on
https://svn.open-mpi.org/trac/ompi/wiki/HostFilePlan,
I create two other host files:
graphics01 $ cat hosts1
graphics02
graphics02
graphics01 $ cat hosts2
graphics02 slots=2
And then try to use them with both versions of Open MPI:
It works properly with OMPI 1.2.9 (the same way as showed on the wiki!),
but does NOT with 1.4.1
graphics01 $ ~/openmpi/gnu129/bin/mpirun -hostfile hosts1 hostname
graphics02
graphics02
graphics01 $ ~/openmpi/gnu129/bin/mpirun -hostfile hosts2 hostname
graphics02
graphics02
graphics01 $ ~/openmpi/gnu141/bin/mpirun -hostfile hosts1 hostname
[graphics01:25756] ras:gridengine: JOB_ID: 89055
--------------------------------------------------------------------------
There are no allocated resources for the application
hostname
that match the requested mapping:
hosts1
Verify that you have mapped the allocated resources properly using the
--host or --hostfile specification.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
A daemon (pid unknown) died unexpectedly on signal 1 while
attempting to
launch so we are aborting.
= Serge
Ralph Castain wrote:
I should have read your original note more closely and I would have spotted the
issue. How a hostfile is used changed between OMPI 1.2 and the 1.3 (and above)
releases per user requests. It was actually the SGE side of the community that
led the change :-)
You can get a full description of how OMPI uses hostfiles in two ways:
* from the man pages: man orte_hosts
* from the wiki: https://svn.open-mpi.org/trac/ompi/wiki/HostFilePlan
As far as I can tell, OMPI 1.4.x is behaving per that specification. You get
four slots on your submission script because that is what SGE allocated to you.
The hostfile filters that when launching, using the provided info to tell it
how many slots on each node within the allocation to use for that application.
I suggest reading the above documentation to see how OMPI uses hostfiles, and
then let us know if you have any questions, concerns, or see a deviation from
the described behavior.
HTH
Ralph
On Apr 7, 2010, at 5:36 AM, Serge wrote:
If you run your cmd with the hostfile option and add
--display-allocation, what does it say?
Thank you, Ralph.
This is the command I used inside my submission script:
mpirun --display-allocation -np 4 -hostfile hosts ./program
And this is the output I got.
Data for node: Name: node03 Num slots: 4 Max slots: 0
Data for node: Name: node02 Num slots: 4 Max slots: 0
Data for node: Name: node04 Num slots: 4 Max slots: 0
Data for node: Name: node01 Num slots: 4 Max slots: 0
If I run the same mpirun command on the cluster head node "clhead" then this is
what I get:
Data for node: Name: clhead Num slots: 0 Max slots: 0
Data for node: Name: node01 Num slots: 1 Max slots: 0
Data for node: Name: node02 Num slots: 1 Max slots: 0
Data for node: Name: node03 Num slots: 1 Max slots: 0
Data for node: Name: node04 Num slots: 1 Max slots: 0
The content of the 'hosts' file:
node01 slots=1
node02 slots=1
node03 slots=1
node04 slots=1
= Serge
On Apr 6, 2010, at 12:18 PM, Serge wrote:
Hi,
OpenMPI integrates with Sun Grid Engine really well, and one does not need to specify any parameters for the
mpirun command to launch the processes on the compute nodes, that is having in the submission script
"mpirun ./program" is enough; there is no need for "-np XX" or "-hostfile
file_name".
However, there are cases when being able to specify the hostfile is important
(hybrid jobs, users with MPICH jobs, etc.). For example, with Grid Engine I can
request four 4-core nodes, that is total of 16 slots. But I also want to
specify how to distribute processes on the nodes, so I create the file 'hosts'
node01 slots=1
node02 slots=1
node03 slots=1
node04 slots=1
and modify the line in the submission script to:
mpirun -hostfile hosts ./program
With Open MPI 1.2.x everything worked properly, meaning that Open MPI could
count the number of slots specified in the 'hosts' file - 4 (i.e. effectively
supplying the mpirun command with the -np parameter), as well as properly
distribute processes on the compute nodes (one process per host).
It's different with Open MPI 1.4.1. It cannot process the 'hosts' file properly
at all. All the processes get launched on just one node -- the shepherd host.
The format of the 'hosts' file does not matter. It can be, say
node01
node01
node02
node02
meaning 2 slots on each node. Open MPI 1.2.x would handle that with no problem,
however Open MPI 1.4.x would not.
The problem appears with OMPI 1.4.1, SGE 6.1u6. It was also tested with OMPI
1.3.4 and SGE 6.2u4.
It's important to notice that if the mpirun command is run interactively, not
from inside the Grid Engine script, then it interprets the content of the host
file just fine.
I am wondering what changed from OMPI 1.2.x to OMPI 1.4.x that prevents
expected behavior, and is it possible to get it from OMPI 1.4.x by, say, tuning
some parameters?
= Serge
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