Slow News by Forest Gregg
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January 21, 2022 - Weeknotes

January 21, 2022

Dedupe

I did a lot of gardening of the dedupe library, and cut the 2.0.9 version of the library. The big enhancement in this release was refactoring the parallelization of scoring pairs.

Previously, worker processes pulled chunks of record pairs off a queue, scored them, and wrote the results to a memmapped numpy array. Each chunk got its own array backed by a separate file. Then, the worker would put the name of the file into a result queue.

A collector process would read those filenames from the result queue and open those files and copy the content into as single, big memmapped numpy array.

I got rid of that collector process and now the scoring workers write directly to the same memmapped numpy array. The workers need to know where in the array they should write, and they communicate that through a shared memory value, with a built-in locking mechanism.

Python’s parallezation paradigm is based on multiple processes. Inter-process can often be more expensive than the benefits of using multiple cores, and this change gets rid of two ponts of inter-process communication.

It also, in my opinion, makes it easier to follow what’s going on.

That said, it probably won’t change performance hugely, since we were just communicating filepaths before and those are quite small. But still, it’s a nice simplification.

Musing on even less communication

The real win in performance would be to have the workers produce the record pairs themselves. I’ve been thinking about that for a while, but have not found an elegant way to do it.

The key problem is how to get workers access to the data. By default, we represent the record set as python dictionary. This dictionary can be quite big, and so we don’t want to make a copy of each for process because that could take up too much memory.

For the scoring workers, this dictionary should be read-only. If we were creating processes through forks, then we could set up the workers so they all had access to the same dictionary (i.e. same object in memory).

However, forking is not available on Mac OS and Windows, so parent memory is not shared in this way.

So, if we can’t use shared memory, then the second best alternative is to hold the data in database that each process can access independently.

There’s a lot that’s attractive about making that move. We are already using sqlite extensively in the library.

In order to not radically change the API, we would need to be able to load the records from a data dictionary into sqlite tables. The problem is that right now the fields of a record can be of any type, and sqlite does not have very rich set of native types.

We have comparators for strings, integers, and floats fields. Sqlite has native support for those. We also have comparators for tuples and sets and allow people to create arbitrary compartors that could take arbitrary types.

The json1 extension might be a reasonable way of handling tuples and sets. I could also potentially handle this by normalizing these array-ish values into a separate table.

It might be acceptable to limit the types that custom comparators can handle to strings, integers, floats, and arrays of those types.

Hmm… maybe it wouldn’t be too bad.

If we took this step, it would open us up to moving some of the blocking and even record comparison into sqlite, which could be quite nice.

Remarkable 2

I asked twitter for recommendations for e-readers that handled pdfs of articles well. The resounding recommendation was for a Remarkable 2. I ordered one with my DataMade annual office-equipment stipend, and it came on Thursday. So far, I really like it. It’s a cool, in a McLuhan sense, piece of technology.