Perhaps I'm missing it, but it seems to me that the real problem lies in the
interaction between SGE and OMPI during OMPI's two-phase launch. The verbose
output shows that SGE dutifully allocated the requested number of cores on
each node. However, OMPI launches only one process on each node (the ORTE
daemon), which SGE "binds" to a single core since that is what it was told
Since SGE never sees the local MPI procs spawned by ORTE, it can't assign
bindings to them. The ORTE daemon senses its local binding (i.e., to a
single core in the allocation), and subsequently binds all its local procs
to that core.
I believe all you need to do is tell SGE to:
1. allocate a specified number of cores on each node to your job
2. have SGE bind procs it launches to -all- of those cores. I believe SGE
does this automatically to constrain the procs to running on only those
3. tell OMPI to --bind-to-core.
In other words, tell SGE to allocate a certain number of cores on each node,
but to bind each proc to all of them (i.e., don't bind a proc to a specific
core). I'm pretty sure that is a standard SGE option today (at least, I know
it used to be). I don't believe any patch or devel work is required (to
either SGE or OMPI).
On Tue, Nov 16, 2010 at 4:07 AM, Reuti <reuti_at_[hidden]> wrote:
> Am 16.11.2010 um 10:26 schrieb Chris Jewell:
> > Hi all,
> >> On 11/15/2010 02:11 PM, Reuti wrote:
> >>> Just to give my understanding of the problem:
> >>>>>> Sorry, I am still trying to grok all your email as what the problem
> >>>>>> are trying to solve. So is the issue is trying to have two jobs
> >>>>>> processes on the same node be able to bind there processes on
> >>>>>> resources. Like core 1 for the first job and core 2 and 3 for the
> 2nd job?
> >>>>>> --td
> >> You can't get 2 slots on a machine, as it's limited by the core count to
> one here, so such a slot allocation shouldn't occur at all.
> > So to clarify, the current -binding <binding_strategy>:<binding_amount>
> allocates binding_amount cores to each sge_shepherd process associated with
> a job_id. There appears to be only one sge_shepherd process per job_id per
> execution node, so all child processes run on these allocated cores. This
> is irrespective of the number of slots allocated to the node.
> > I agree with Reuti that the binding_amount parameter should be a maximum
> number of bound cores per node, with the actual number determined by the
> number of slots allocated per node. FWIW, an alternative approach might be
> to have another binding_type ('slot', say) that automatically allocated one
> core per slot.
> > Of course, a complex situation might arise if a user submits a combined
> MPI/multithreaded job, but then I guess we're into the realm of setting
> IIRC there was a discussion on the [GE users] list about it, to get an
> uniform distribution on all slave nodes for such jobs, as also e.g.
> $OMP_NUM_THREADS will be set to the same value for all slave nodes for
> hybrid jobs. Otherwise it would be necessary to adjust SGE to set this value
> in the "-builtin-" startup method automatically on all nodes to the local
> granted slots value. For now a fixed allocation rule of 1,2,4 or whatever
> must be used and you have to submit by reqeusting a wildcard PE to get any
> of these defined PEs for an even distribution and you don't care whether
> it's two times two slots, one time four slots, or four times one slot.
> In my understanding, any type of parallel job should always request and get
> the total number of slots equal to the cores it needs to execute.
> Independent whether these are threads, forks or any hybrid type of jobs.
> Otherwise any resource planing and reservation will most likely fail.
> Nevertheless, there might exist rare cases where you submit an exclusive
> serial job but create threads/forks in the end. But such a setup should be
> an exception, not the default.
> > Is it going to be worth looking at creating a patch for this?
> > I don't know much of the internals of SGE -- would it be hard work to
> do? I've not that much time to dedicate towards it, but I could put some
> effort in if necessary...
> I don't know about the exact coding for it, but when it's for now a plain
> "copy" of the binding list, then it should become a loop to create a list of
> cores from the original specification until all granted slots got a core
> -- Reuti
> > Chris
> > --
> > Dr Chris Jewell
> > Department of Statistics
> > University of Warwick
> > Coventry
> > CV4 7AL
> > UK
> > Tel: +44 (0)24 7615 0778
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