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Subject: Re: [OMPI users] Error when using OpenMPI with SGE multiple hosts
From: Ralph Castain (rhc_at_[hidden])
Date: 2010-11-17 10:00:32


--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.

On Wed, Nov 17, 2010 at 7:51 AM, Terry Dontje <terry.dontje_at_[hidden]>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_at_[hidden]>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
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> users mailing listusers_at_[hidden]http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>>
>>
>> --
>> [image: Oracle]
>> 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_at_[hidden]
>>
>>
>>
>>
>> _______________________________________________
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>> users_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>
>
> _______________________________________________
> users mailing listusers_at_[hidden]http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>
>
> --
> [image: Oracle]
> 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_at_[hidden]
>
>
>
>
> _______________________________________________
> users mailing list
> users_at_[hidden]
> http://www.open-mpi.org/mailman/listinfo.cgi/users
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