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Subject: Re: [OMPI users] Error when using OpenMPI with SGE multiple hosts
From: Reuti (reuti_at_[hidden])
Date: 2010-11-16 10:59:33

Am 16.11.2010 um 15:26 schrieb Terry Dontje:

>>> <snip>
>>> 1. allocate a specified number of cores on each node to your job
>> this is currently the bug in the "slot <=> core" relation in SGE, which has to be removed, updated or clarified. For now slot and core count are out of sync AFAICS.
> Technically this isn't a bug but a gap in the allocation rule. I think the solution is a new allocation rule.

Yes, you can phrase it this way. But what do you mean by "new allocation rule"? The slot allocation should follow the specified cores?

>>> 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 cores.
>> This is another "bug/feature" in SGE: it's a matter of discussion, whether the shepherd should get exactly one core (in case you use more than one `qrsh`per node) for each call, or *all* cores assigned (which we need right now, as the processes in Open MPI will be forks of orte daemon). About such a situtation I filled an issue a long time ago and "limit_to_one_qrsh_per_host yes/no" in the PE definition would do (this setting should then also change the core allocation of the master process):
> Isn't it almost required to have the shepherd bind to all the cores so that the orted inherits that binding?

Yes, for orted. But if you want to have any other (legacy) application which using N times `qrsh` to an exechost when you got N slots thereon, then only one core should be bound to each of the started shepherds.

>>> 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).
>> When you use a fixed allocation_rule and a matching -binding request it will work today. But any other case won't be distributed in the correct way.
> Ok, so what is the "correct" way and we sure it isn't distributed correctly?

You posted the two cases yesterday. Do we agree that both cases aren't correct, or do you think it's a correct allocation for both cases? Even if it could be "repaired" in Open MPI, it would be better to fix the generated 'pe' PE hostfile and 'set' allocation, i.e. the "slot <=> cores" relation.

> In the original case of 7 nodes and processes if we do -binding pe linear:2, and add the -bind-to-core to mpirun I'd actually expect 6 of the nodes processes bind to one core and the 7th node with 2 processes to have each of those processes bound to different cores on the same machine.

Yes, possibly it could be repaired this way (for now I have no free machines to play with). But then the "reserved" cores by the "-binding pe linear:2" are lost for other processes on these 6 nodes, and the slot count gets out of sync with slots.

> Can we get a full output of such a run with -report-bindings turned on. I think we should find out that things actually are happening correctly except for the fact that the 6 of the nodes have 2 cores allocated but only one is being bound to by a process.

You mean, to accept the current behavior as being the intended one, as finally for having only one job running on these machines we get what we asked for - despite the fact that cores are lost for other processes?

-- Reuti