On 11/17/2010 10:48 AM, Ralph Castain wrote:
No problem at all. I confess that I am lost in all the sometimes disjointed emails in this thread. Frankly, now that I search, I can't find it either! :-(

I see one email that clearly shows the external binding report from mpirun, but not from any daemons. I see another email (after you asked if there was all the output) that states "yep", indicating that was all the output, and then proceeds to offer additional output that wasn't in the original email you asked about!

So I am now as thoroughly confused as you are...

That said, I am confident in the code in ORTE as it has worked correctly when I tested it against external bindings in other environments. So I really do believe this is an OGE issue where the orted isn't getting correctly bound against all allocated cores.

I am confused by your statement above because we don't even know what is being bound or not.  We know that in it looks like the hnp is bound to 2 cores which is what we asked for but we don't know what any of the processes themselves are bound to.   So I personally cannot point to ORTE or OGE as the culprit because I don't think we know whether there is an issue.

So, until we are able to get the -report-bindings output from the a.out code (note I did not say orted) it is kind of hard to claim there is even an issue.  Which brings me back to the output question.  After some thinking the --report-bindings output I am expecting is not from the orted itself but from the a.out before it executes the user code.   Which now makes me wonder if there is some odd OGE/OMPI integration issue which the -bind-to-code -report-bindings options are not being propagated/recognized/honored when qsub is given the -binding option.

Perhaps if someone could run this test again with --report-bindings --leave-session-attached and provide -all- output we could verify that analysis and clear up the confusion?

Yeah, however I bet you we still won't see output.

--td


On Wed, Nov 17, 2010 at 8:13 AM, Terry Dontje <terry.dontje@oracle.com> wrote:
On 11/17/2010 10:00 AM, Ralph Castain wrote:
--leave-session-attached is always required if you want to see output from the daemons. Otherwise, the launcher closes the ssh session (or qrsh session, in this case) as part of its normal operating procedure, thus terminating the stdout/err channel.


I believe you but isn't it weird that without the --binding option to qsub we saw -report-bindings output from the orteds?

Do you have the date of the email that has the info you talked about below.  I really am not trying to be an a-hole about this but there have been so much data and email flying around it would be nice to actually see the output you mention.

--td


On Wed, Nov 17, 2010 at 7:51 AM, Terry Dontje <terry.dontje@oracle.com> wrote:
On 11/17/2010 09:32 AM, Ralph Castain wrote:
Cris' output is coming solely from the HNP, which is correct given the way things were executed. My comment was from another email where he did what I asked, which was to include the flags:

--report-bindings --leave-session-attached

so we could see the output from each orted. In that email, it was clear that while mpirun was bound to multiple cores, the orteds are being bound to a -single- core.

Hence the problem.

Hmm, I see Ralph's comment on 11/15 but I don't see any output that shows what Ralph say's above.  The only report-bindings output I see is when he runs without OGE binding.   Can someone give me the date and time of Chris' email with the --report-bindings and --leave-session-attached.  Or a rerun of the below with the --leave-session-attached option would also help.

I find it confusing that --leave-session-attached is not required when the OGE binding argument is not given.

--td

HTH
Ralph


On Wed, Nov 17, 2010 at 6:57 AM, Terry Dontje <terry.dontje@oracle.com> wrote:
On 11/17/2010 07:41 AM, Chris Jewell wrote:
On 17 Nov 2010, at 11:56, Terry Dontje wrote:
You are absolutely correct, Terry, and the 1.4 release series does include the proper code. The point here, though, is that SGE binds the orted to a single core, even though other cores are also allocated. So the orted detects an external binding of one core, and binds all its children to that same core.
I do not think you are right here.  Chris sent the following which looks like OGE (fka SGE) actually did bind the hnp to multiple cores.  However that message I believe is not coming from the processes themselves and actually is only shown by the hnp.  I wonder if Chris adds a "-bind-to-core" option  we'll see more output from the a.out's before they exec unterm?
As requested using 

$ qsub -pe mpi 8 -binding linear:2 myScript.com'  

and 

'mpirun -mca ras_gridengine_verbose 100 --report-bindings -by-core -bind-to-core ./unterm'

[exec5:06671] System has detected external process binding to cores 0028
[exec5:06671] ras:gridengine: JOB_ID: 59434
[exec5:06671] ras:gridengine: PE_HOSTFILE: /usr/sge/default/spool/exec5/active_jobs/59434.1/pe_hostfile
[exec5:06671] ras:gridengine: exec5.cluster.stats.local: PE_HOSTFILE shows slots=2
[exec5:06671] ras:gridengine: exec1.cluster.stats.local: PE_HOSTFILE shows slots=2
[exec5:06671] ras:gridengine: exec4.cluster.stats.local: PE_HOSTFILE shows slots=1
[exec5:06671] ras:gridengine: exec3.cluster.stats.local: PE_HOSTFILE shows slots=1
[exec5:06671] ras:gridengine: exec2.cluster.stats.local: PE_HOSTFILE shows slots=1
[exec5:06671] ras:gridengine: exec7.cluster.stats.local: PE_HOSTFILE shows slots=1

No more info.  I note that the external binding is slightly different to what I had before, but our cluster is busier today :-)

I would have expected more output.

--td

Chris


--
Dr Chris Jewell
Department of Statistics
University of Warwick
Coventry
CV4 7AL
UK
Tel: +44 (0)24 7615 0778






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Terry D. Dontje | Principal Software Engineer
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Oracle - Performance Technologies
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Email terry.dontje@oracle.com




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Oracle - Performance Technologies
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Email terry.dontje@oracle.com




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Terry D. Dontje | Principal Software Engineer
Developer Tools Engineering | +1.781.442.2631
Oracle - Performance Technologies
95 Network Drive, Burlington, MA 01803
Email terry.dontje@oracle.com