Moving from MySQL to DuckDB

I mentioned earlier that I’ve been doing some work on the old Bookworm project as I see that there’s nothing else that occupies quite the same spot in the world of public- facing, nonconsumptive text tools.

That codebase is old–pieces of it date back to this blog post from a decade ago. Parts of that old architecture (e.g., perl) got quickly jettisoned (for Python). But others persist. In re-examining the technical stack behind Bookworm, I’ve realized that it’s finally possible to jettison one of the biggest pain points–MySQL–for something that better matches the workflows here.

People often ask about Postgres, but I’m moving to something a little bit more unexpected–the 2-year-old program DuckDB. This might seem like an odd choice! The core data architecture challenge of Bookworm is managing some enormous tables for storing a sparse matrix– the term-document matrix–for a large number of long documents. The HathiTrust bookworm has about 2 trillion words in 17 million books–I haven’t looked at the core tables recently, but I’d guess they have tens of billions of rows.

DuckDB, on the other hand, is manifestly targeted at a much smaller size–it borrows intensely in footprint from SQLlite by using the SQLlite shell, existing only as an embedded process in running program (i.e., no daemon), and putting each file into a single moveable file. I never seriously considered SQLlite as a Bookworm backing, because it’s too lightweight to handle enormous tables, because at the time of the original design I only knew how to write single-startup CGI scripts, and because MySQL gives intense options for tweaking performance on the margins. (Back in 2010-11 I got very used to using 3-byte unsigned integers, which can store values up to about 16 million, for ids, since they’re actually a convenient size; it took me a while to realize that 3-byte integers are an extraordinarily unusual thing.)

Column stores

But DuckDB has some major advantages. For one thing, it uses column-oriented stores, which means rather than store rows of interspersed data types, like MySQL, it groups primarily by the values–so you get all the counts as a series of integers, all the wordids as a series of integers, etc. For performance, Bookworm has always encoded words to integers under the hood; there are a variety of performance advantages to this form of storage. The costs mostly tend to be things that don’t matter in analytics (like it being harder to update a single customer record in a table with their latest purchase.) That’s why DuckDB exists– as something that will work better for analytics from Python or R than SQLlite. And the basic design seems to be probably better conceived than SQLlite because it’s starting from the ground up; it uses the Postgres parser and supports modern SQL reasonably well. For the large joins that accompany a typical Bookworm query (in which you declare which 1 million out of 10 million teacher evaluations you want to look at), this works well.

Here’s a dumb analogy for column stores. Imagine your data as being a bunch of different cookies. Addresses are Oreos, dates are chocolate chips, whatever. And you’ve got different types of values in there–some people live at doublestuff lane, some with those weird mint green oreos. The point of a column store is to keep all the oreos in line with each other because they’re the same shape.

Yum

Each sleeve is clear, so you can get an idea what’s inside it, but it’s also nicely shaped, so you can quickly pass it along to the next person. Imagine you’ve got a state-champion 400m relay race running around track passing cookies to each other. Every team will to better if, instead of passing a motley arrangement of cookies to the next team, they can just hand off a single baton of oreos in a sleeve. That’s what a column store does.

Indexing

While the relational queries against catalog tables are important, the most difficult part of any bookworm query is accessing the individual word counts– those 50 billion row tables of the term-document matrix. What MySQL did for us there was to allow the creation of fast b-tree indices that put related rows together on disk. This was often the most time-consuming task, because MySQL index creation could take a week on a really huge table; and it left the indices far larger than the actual tables themselves. (In fact, the design of the database was such that the original table is never used–queries only ever read from the index.) The default MySQL settings made it very difficult to create these indices as well.

DuckDB uses mostly block range indexes, which tell you roughly what part of the file any given dataset might be in, and don’t sort the underlying data. This is faster, but wouldn’t allow for quick lookup in a big table–you’d end up scanning almost everything.

But there’s a trick here, which is to sort the data first before putting it into DuckDB. If the term-document matrix is sorted by wordid, all of the occurrences for each word will be right next to each other, just as with the MySQL index. It’s probably not quite as fast for retrieval, but the column-oriented structure that comes out can race ahead on the subsequent joins. Pre-sorting isn’t trivial, since we’re talking about far more data than fits in memory. But pyarrow exposes some strikingly fast pivot methods for partially sorting arrays, which makes it possible to shuffle things around without fully sorting. This matters, because conventional merge sorts involving entirely sorting each subarray before merging–that can be extremely time-consuming for little benefit in a column-oriented situation where a record is not contiguous to itself.

In ignorance of the best way to handle this, I’ve coded up a new routine that does sorts in three passes:

  1. Splits each input batch in 16 pieces;
  2. Sorts those batches, and then continuously finds the least sorted 16 contiguous batches, combines them into a new table, and then breaks them into 16 new non-overlapping batches.
  3. Once the order is barely stable enough to ensure that a single merge pass will work, traverse in order for a merge sort.

This algorithm seems pretty neat to me, but I have no idea if it’s especially good or even if it’s guaranteed to converge on a sorted array. In any case, it’s much, much faster than the old MySQL index creation was and has a much smaller memory footprint.

Once the table is sorted, it’s just a matter of loading it into duckdb. The final write happens to a massive parquet file, which can be written out of memory; then duckdb can ingest it straight into its database format.

DuckDB doesn’t yet support compression or a stable on-disk format, but the pace of development is fast enough and impressive enough that I’m willing to take a bet on it. Especially because we never used compression in MySQL, either.

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Ben Schmidt
Director of Digital Humanities and Clinical Associate Professor of History

I am a digital historian and Director of Digital Humanities at NYU.