Support multiprocessing of operations on cubes through decomposition and recombination

[wjbenfold]

✨ Feature Request

Iris could offer a clear, tested, robust method for multiprocessing cubes by splitting them into pieces, multiprocessing the pieces and then stitching them back together.

Motivation

Working with a team who use Iris on their code aimed at doing exactly this, it didn't feel like a use case specific to their problems but something more general.

Additional context

Requirements:

• Allow the user to specify how the splitting will happen (number of pieces, max data size and/or other sensible ways).
• Handle halos (where calculations in a given tile relies on original data from neighbouring tiles) with user specification of how much of this is necessary.
• Multiprocess in a fashion that respects constraints on the number of CPUs that the process can claim, without an explosion of threads/processes from each process.

Ideas:

• We could offer a context manager that could be used to wrap operations applied to a cube
• Temporary saving to disk might help for rechunking and passing files between processes.

[zklaus]

It seems most of the goals here would best be achieved by better supporting the dask.distributed scheduler. This would not only allow for parallelism on one node, as multiprocessing does, but even across nodes. This is already possible to considerable extent, with a better I/O layer being the main stumbling block.

[pp-mo]

@zklaus most of the goals here would best be achieved by better supporting the dask.distributed scheduler.

I think that is not really the point of this ticket.. The point here is, simply, that we need to assist the provision of some complex operations on cubes, where it is already possible to do the relevant on calculations on arrays via Dask.

So, we'd like a generic operation that can take a cube function and parallelise the operation as stated.

Simple element-wise cube calculations can be achieved using 'map_blocks', and plenty of users have already used that themselves. As it's not very tricky, we haven't yet moved to provide any generic facility to convert a cube function in that way. But we now identified a need for overlap processing, as done in Dask with 'map_overlap', which is a rather trickier to manage, so now seems like a good time to develop a special facility.

( IMHO : the possible saving of intermediate results to disk, and even the 'splitting' (like a rechunk) are maybe separable operations, and not really core to the main task here. )

[zklaus]

Perhaps I was thrown off by the use of multiprocessing. So to be clear, you don't mean multiprocessing?

[pp-mo]

you don't mean multiprocessing?

I don't think so. @wjbenfold ??

[wjbenfold]

I meant "multiprocessing" in the sense of "having work done by multiple processes", with no intention of implying a specific library

[pp-mo]

Another point :

It seems logical to me that this is best provided as a "wrapper" to Dask.map_overlap. Since that provides a lot of detailed controls, it makes very good sense to simply borrow, thinly wrap and/or pass-through those keys -- and totally lean on the Dask terminology + documentation.

So, that approach could be very capable, but totally Dask-specific. That would make a bit of a break with previous practice in core Iris, where we have tried to provide for an abstracted "lazy" data handling, via our own APIs, rather than simply declaring "cube content may be a Dask array". ( whether that was a good idea is another debate ! ... )

From offline discussion with @bjlittle, rather than just cave in and say "Iris lazy is really just Dask", we might instead choose to have this facility live somewhere else, i.e. not in "core Iris". That should be ok, since I don't foresee this needing to use a lot of private Cube API.

( Actually there is also special-case benefit, since the expected partners here would rather run this with a release-version Iris )

[zklaus]

I'll be interested to see what you come up with. From my personal experience, it seems that almost any non-trivial application will require direct dask programming for the core array parts, while the metadata part would benefit from not being split up since the individual parts will usually have the same units etc.

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[pp-mo]

Just re-reviewing this in context of discussion with @hdyson et al ... @trexfeathers can you suggest what kind of priority you think this might get ?

Personally, I think this idea only flies if we can provide a generalised operation that is easier for the user than just "pull out the arrays and use Dask yourself". It certainly feels to me like we will struggle to support the "interesting" cases --i.e. those with block overlaps-- while still shielding the user from the underlying complexities of the Dask implementation (i.e. Dask map_blocks or blockwise).
In my experience of such problems, it's really only possible to assess or optimise performance for a specific usecase, and it requires an understanding of how Dask will "see" that problem, and how it could be adjusted.

So I don't think we can realistically hope to just "solve" that problem... but we might be able to provide a "potted" solution to help some computations work without blowing memory. Probably we can specialise the operation to horizontal data dimensions, which is a typically obvious simplification which Dask itself would not be aware of. I am imagining a simplified API providing a first stab at problems of that sort, with perhaps keywords to control the size or number of divisions and overlaps in X and Y. The user would need to provide a function of cubes --> cube, along with the relative sizes and alignments of its inputs and outputs.

[trexfeathers]

Discussed offline with @trexfeathers @pp-mo @hdyson. Something to make clear publicly - our prioritisation is currently driven by:

• https://github.com/SciTools/iris/issues/4631
• Significant problems we are aware of
• Items escalated to @tkknight and @bjlittle

With the resource we have available, there are inevitably plenty of perfectly valid issues that just can't be addressed within a reasonable time frame, hence the https://github.com/SciTools/iris/labels/Stale label. Always open to discuss.