Optimizing database access in Django: A patchwork story

tl;dr: I made Patchwork a lot faster by looking at what database queries were being generated and optimizing them either by making Django produce better queries or by adding better indexes.

Introduction to Patchwork

One of the key bits of infrastructure a bunch of maintainers of Open Source Software use is a tool called Patchwork. We use it for a bunch of OpenPOWER firmware development, several Linux subsystems use it as well as freedesktop.org.

The purpose of Patchwork is to supplement the patches-to-a-mailing-list development work flow. It allows a maintainer to see all the patches that have been posted on the list, How many Acked-by/Reviewed-by/Tested-by replies they have, delegate responsibility for the patch to a co-maintainer, track (and change) the state of the patch (e.g. to “Under Review”, “Changes Requested”, or “Accepted”), and create bundles of patches to help in review and testing.

Since patchwork is an open source project itself, there’s several instances of it out there in common use. One of the main instances is https://patchwork.ozlabs.org/ which is (funnily enough) used by a bunch of people connected to OzLabs for projects that are somewhat connected to OzLabs. e.g. the linuxppc-dev project and the skiboot and petitboot projects. There’s also a kernel.org instance, which is used by some kernel subsystems.

Recent versions of Patchwork have added some pretty cool features such as the ability to integrate with CI systems such as Snowpatch which helps maintainers see if patches submitted are likely to break things.

Unfortunately, there’s also been some complaints that recent version of patchwork have gotten slower than previous ones. This may well be the case, or it could just be that the volume of patches is much higher and there’s load on the database. Anyway, after asking a few questions about what the size and scope was of the patchwork database on ozlabs.org, I went “hrm… this sounds like it shouldn’t really be a problem… perhaps I should look into this”.

Attacking the problem…

Every so often it is revealed that I know a little bit about databases.

Getting a development environment up for Patchwork is amazingly easy thanks to Docker and the great work of the Patchwork maintainers. The only thing you need to load in is an example dataset. I started by importing mail from a few mailing lists I’m subscribed to, which was Good Enough(TM) for an initial look.

Due to how Django forces us to design a database schema though, the suggested method of getting a sample data set will not mirror what occurs in a production system with multiple lists. It’s for this reason that I ended up using a copy of a live dataset for much of my work rather than constructing an artificial one.

Patchwork supports both a MySQL and PostgreSQL database backend. Since the one on ozlabs.org is backed by PostgreSQL, I ended up loading a large dataset into PostgreSQL for most of my work, although I also did some testing with MySQL.

The current patchwork.ozlabs.org instance has a database of around 13GB in side, with about a million patches. You may think this is big, my database brain goes “no, this is actually quite small and everything should be a lot faster than it is even on quite limited hardware”

The problem with ORMs

It turns out that Patchwork is written in Django, an ORM (Object-Relational Mapping) framework in Python – and thus something that pretty effectively obfuscates application code from the SQL being run.

There is one thing that Django misses that could be a pretty big general performance boost to many applications: it doesn’t support composite primary keys. For some databases (e.g. MySQL’s InnoDB engine) the PRIMARY KEY is a clustered index – that is, the physical layout of the rows on disk reflect primary key order. You can use this feature to your advantage and have much higher cache hits of your database pages.

Unfortunately though, we cannot do that with Django, so we lose a bunch of possible performance because of it (especially for queries that are going to have to bring in data from disk). In fact, we’re forced to use an ID field that’ll scatter our rows all over the place rather than do something efficient. You can somewhat get back some of the performance by creating covering indexes, but this costs in terms of index maintenance and disk space.

It should be noted that PostgreSQL doesn’t have a similar concept, although there is a (locking) CLUSTER statement that can (as an offline operation for the table) re-arrange existing rows to be in index order. In my testing, this can give a bit of a boost to performance of some of the Patchwork queries.

With MySQL, you’d look at a bunch of statistics on what pages are being brought in and paged out of the InnoDB buffer pool. With PostgreSQL it’s a bit more complex as it relies heavily on the OS page cache.

My main experience is with MySQL like environment, so I’ve had to re-learn a bunch of PostgreSQL things in this work which was kind of fun. It may be “because of my upbringing” but it seems as if there’s a lot more resources and documentation out in the wild about optimizing MySQL environments than PostgreSQL ones, especially when it comes to documentation around a bunch of things inside the database server. A lot of credit should go to the MySQL Documentation team – I wish the PostgreSQL documentation was up to the same standard.

Another issue is that fetching BLOBs is generally an expensive operation that you want to avoid unless you’re going to use them. Thus, fetching the whole “object” at once isn’t always optimal. The Django query generation appears to be somewhat buggy when it comes to “hey, don’t fetch these columns, I don’t need them”, so you do have to watch what query is produced not just what query you expect to be produced. For example, [01/11] Improve patch listing performance (~3x).

Another issue with Django is how you go from your Python code to an actual SQL query, especially when the produced SQL query is needlessly complex or inefficient. I’ve seen Django always produce an ORDER BY for one table, even when not needed, I’ve also seen it always join tables even when you’re getting no columns from one of them and there’s no way you’re asking for it. In fact, I had to revert to raw SQL for one of my performance improvements as I just couldn’t beat it into submission: [10/11] Be sensible computing project patch counts.

An ORM can be great for getting apps out quickly, or programming in a familiar way. But like many things, an understanding of what is going on underneath is key for extracting maximum performance.

Also, if you ever hear something like “ORM $x doesn’t scale” then maybe that person just hasn’t looked at how to use the ORM better. The same goes for if they say “database $y doesn’t scale”- especially if it’s a long existing relational database such as MySQL or PostgreSQL.

Speeding up listing current patches for a project

17 SQL queries in 4477ms
More than 4 seconds in the database
does not make page load time great.

Fortunately though, the Django development environment lets you really easily dive into what queries are being generated and (at least roughly) where they’re being generated from. There’s a sidebar in your browser that shows how many SQL queries were needed to generate the page and how long they took. The key to making your application go faster is to run fewer queries in less time.

I was incredibly impressed with how easy it was to see what queries were run, where they were run from, and the EXPLAIN output for them.

By clicking on that SQL button on the right side of your browser, you get this wonderful chart of what queries were executed, when, and how long they took. From this, it is incredibly obvious which query is the most problematic: the one that took more than four seconds!

In the dim dark days of web development, you’d have to turn on a Slow Query Log on the database server and then grep through your source code or some other miserable activity. I am so glad I didn’t have to do that.

More than four seconds for a single database query does not make for a nice UX.

This particular query was a real hairy one, the EXPLAIN output from PostgreSQL (and MySQL) was certainly long and involved and would most certainly not feature in the first half of an “Introduction to query optimization” day long workshop. If you haven’t brushed up on various bits of documentation on understanding EXPLAIN, you should! The MySQL EXPLAIN FORMAT=JSON is especially fantastic for getting deep details as to what’s going on with query execution.

The big performance gain here was to have the database be able to execute the query in a much more efficient way by creating two covering indexes for part of the query. To work out what indexes to create, one has to look at the EXPLAIN output and work out why the database is choosing to do either a sequential scan of a large table, or use an index that doesn’t exclude that many rows. In this case, I tweaked the code to slightly change the query that was generated as well as adding a covering index. What we ended up with is something that is dramatically faster.

The main query is ~350x faster than before

You’ll notice that it appears that the first query there takes a lot more time but it doesn’t, it just takes a lot more time relative to the main query.

In fact, this particular page is one that people have mentioned at being really, really slow to load. With the main query now about 350 times faster than it was originally, it shouldn’t be a problem anymore.

A future improvement would be to cache the COUNT() for the common case, as it’s pretty easily computed when new patches come in or states change.

The patches that help this particular page have been submitted upstream here:

Making viewing a patch with comments faster

Now that we can list patches faster, can we make other pages that Patchwork has quicker?

One such page is viewing a patch (or cover letter) that has a lot of comments on it. One feature of Patchwork is that it will display all the email replies to a patch or cover letter in the Web UI. But… this seemed slow

On one of the most commented patches I could find, we ended up executing one hundred and seventy seven SQL queries to view it! If we dove into it, a bunch of the queries looked really really similar…

I’ve got 99 queries where I only need 1.

The problem here is that the Patchwork UI is wanting to find out the name of each person who submitted a comment, and is doing that by querying the ID from a table. What it should be doing instead is a SQL JOIN on the original query and just fetching all that information in one go: make the database server do the work, it’s really good at it.

My patch [02/11] 4x performance improvement for viewing patch with many comments   does just that by using the select_related() method correctly, as well as being explicit about what information we want to retrieve.

We’re now only a few milliseconds to grab all the comments

With that patch, we’re down to a constant number of queries and around a 3x-7x faster time executing them depending if we have a warm cache or not.

The one time I had to use raw SQL

When viewing a project page (such as https://patchwork.ozlabs.org/project/qemu-devel/ ) it displays the number of patches (archived and not archived) for the project. By looking at what SQL queries are executed to collect these numbers, you’ll notice two things. First, here are the queries:

COUNT() queries can be expensive

First thing you’ll notice is that they took a loooooong time to execute (more than a second each). The second thing, if you look closer, is that they contain a join which is completely unneeded.

I spent a good long while trying to make Django behave, and I just could not. I believe it’s due to the model having some inheritance in it. Writing the query by hand ended up being the best solution, and it gave a significant performance improvement:

Unfortunately, only 4x faster.

Arguably, a better way would be to precompute the count for the archived/non-archived patches and just display them. I (or someone else who knows more about Django) may want to look at that for a future improvement.

Conclusion and final thoughts

There’s a few more places where there could be some optimizations, but currently I cannot get any single page to take more than between 40-400ms in the database when running on my laptop – and that’s Good Enough(TM) for now.

The next steps are getting these patches through a round or two of review, and then getting them into a Patchwork release and deployed out on patchwork.ozlabs.org and see if people can find any new ways to make things slow.

If you’re interested, the full patchset with cover letter is here: [00/11] Performance for ALL THE THINGS!

The diffstat is interesting, as most of the added code is auto-generated by Django for database migrations (adding of indexes).

 .../migrations/0027_add_comment_date_index.py | 23 +++++++++++++++++
 .../0028_add_list_covering_index.py           | 19 ++++++++++++++
 .../0029_add_submission_covering_index.py     | 19 ++++++++++++++
 patchwork/models.py                           | 21 ++++++++++++++--
 patchwork/templates/patchwork/submission.html | 16 ++++++------
 patchwork/views/__init__.py                   |  8 +++++-
 patchwork/views/cover.py                      |  5 ++++
 patchwork/views/patch.py                      |  7 ++++++
 patchwork/views/project.py                    | 25 ++++++++++++++++---
 9 files changed, 128 insertions(+), 15 deletions(-)
 create mode 100644 patchwork/migrations/0027_add_comment_date_index.py
 create mode 100644 patchwork/migrations/0028_add_list_covering_index.py
 create mode 100644 patchwork/migrations/0029_add_submission_covering_index.py

I think the lesson is that making dramatic improvements to performance of your Django based app does not mean you have to write a lot of code or revert to raw SQL or abandon your ORM. In fact, use it properly and you can get a looong way. It’s just that to use it properly, you’re going to have to understand the layer below the ORM, and not just treat the database as a magic black box.

POWER8 Accelerated CRC32 merged in MariaDB 10.1

Earlier on in benchmarking MySQL and MariaDB on POWER8, we noticed that on write workloads (or read workloads involving a lot of IO) we were spending a bunch of time computing InnoDB page checksums. This is a relatively well known MySQL problem and has existed for many years and Percona even added innodb_fast_checksum to Percona Server to help alleviate the problem.

In MySQL 5.6, we got the ability to use CRC32 checksums, which are great in that they’re a lot faster to compute than tho old InnoDB “new” checksum. There’s code inside InnoDB to use the x86 SSE2 crc32q instruction to accelerate performing the checksum on compatible x86 CPUs (although oddly enough, the CRC32 checksum in the binlog does not use this acceleration).

However, on POWER, we’d end up using the software implementation of CRC32, which used a lot more CPU than we’d like. Luckily, CRC32 is really common code and for POWER8, we got some handy instructions to help computing it. Unfortunately, this required brushing up on vector polynomial math in order to understand how to do it all quickly. The end result was Anton coming up with crc32-vpmsum code that we could drop into projects that embed a copy of crc32 that was about 41 times faster than the best non-vpmsum implementation.

Recently, Daniel Black took the patch that had passed through both Daniel Axten‘s and my hands and worked on upstreaming it into MariaDB and MySQL. We did some pretty solid benchmarking on the improvement you’d get, and we pretty much cannot notice the difference between innodb_checksum=off and having it use the POWER8 accelerated CRC32 checksum, which frees up maybe 30% of CPU time to be used for things like query execution! My original benchmark showed a 30% improvement in sysbench read/write workloads.

The excellent news? Two days ago, MariaDB merged POWER8 accelerated crc32! This means that IO heavy workloads on MariaDB on POWER8 will get much faster in the next release.

MySQL bug 74776 is open, with patch attached, so hopefully MySQL will merge this soon too (hint hint).

Preliminary MySQL Cluster benchmark results on POWER8

Yesterday, I got the basics going for MySQL Cluster on POWER. Today, I finished up a couple more patches to improve performance and ran some benchmarks.

This is on a 3.7Ghz POWER8 machine with non-balanced memory (only 2 of the 4 NUMA nodes have memory, so we have less total memory bandwidth than we could have, plus I’m going to bind ndbmtd to the CPUs in these NUMA nodes)

With a setup of a single replica and two data nodes on the one machine (each bound to a specific NUMA node), running the flexAsync benchmark on MySQL Cluster 7.3.7, I could get around:

  • 3.2 million reads/sec
  • 2.6 million deletes/sec
  • 2.4 million updates/sec
  • 2.4 million inserts/sec.

So, that’s at least in the right ballpark for a first go.

(I’m running this on a big endian host kernel, some random kernel I booted on the box and built with gcc 4.8 with whatever build options the MySQL Cluster cmake foo chooses by default)

MySQL 5.6 Performance on POWER8

The following sentence is brought to you by IBM Legal: The postings on this site are my own and don’t necessarily represent IBM’s positions, strategies or opinions.

My previous post covered the work needed to get MySQL 5.6.17 running reliably on modern POWER systems. The patch to MySQL 5.6.17 that’s needed is available here.

For those who don’t know, POWER8 is the latest Power Architecture processors from IBM (my employer). These chips will be available in systems from IBM in June 2014 (i.e. Real Soon Now(TM)). There’s some fairly impressive specs and numbers (see Wikipedia and elsewhere) – but what could this mean for actual applications?

Well, it turns out that MySQL is a pretty big thing in some target markets for POWER8, and inspired by Dimitri’s impressive benchmark numbers, I thought we should have a go on POWER8.

Firstly, I focused on MySQL 5.6 as it is the current stable release. MySQL 5.7 will be the subject of a future blog post.

The first step was to ensure that MySQL 5.6 worked correctly on POWER. My previous blog post covered the few bugs I ran into and filed (often  with patches). This wasn’t too hard and I’m fairly confident the bug fixes are simple enough to get into MySQL 5.6 – I can’t comment on what would be/could be “officially supported”, that’s a business discussion :)

In order to ensure that my patch was not only correct but performing well, I needed a benchmark. For my initial benchmark. I chose sysbench point selects (i.e. read only key lookups), which should show the theoretical maximum queries per second you could pump through the MySQL Server as well as really stressing the mutex code, helping ensure it was not only correct, but performing well.

A simple comparison of my early patch that used heavyweight memory barriers versus Yasufumi’s patch that used more lightweight ones showed that using heavyweight barriers could be as much as a 50% performance hit – so getting this code right is important.

To add to the fun, the POWER8 processor has a few parameters you can tweak. There is the SMT mode, which dictates how many threads per core there are. This can be changed at runtime. You can be in SMT=off, SMT=2, SMT=4 or SMT=8. Typically, only some workloads can benefit from SMT8 rather than SMT4. There is also DSCR, which is data prefetching. For sysbench point selects, I’ve found we do slightly better (around 10%) when DSCR is set to 1 rather than zero – but YMMV on other benchmarks.

In my experiments, I’ve found that SMT4 or SMT8 seems to be the best bang for buck for MySQL workloads on POWER8. With SMT=2 rather than off, I’ve seen a ~50% performance boost in sysbench point select results. With SMT=4 I’ve seen another 50% boost (i.e. roughly double SMT=off performance). The benefit of SMT8 for MySQL 5.6 (and the 5.6 part is crucial here) may be minimal, especially for this benchmark. This is mostly due to hitting heavy mutex contention inside the MySQL server rather than anything else.

POWER8 systems come in either single or dual socket, with the number of cores being a total of 4, 6, 8, 10, 12, 16, 20 or 24 depending on configuration of the system (go check IBM web site for specifics of what’s available in what model). This means with SMT8, a dual socket, 24 core POWER8 system has 192 hardware threads – the system I was using for these benchmarks.With this number of cores and hardware threads, those familiar with MySQL on multi core systems may already have an inkling that using the full capacity of such a system may be hard for MySQL.

Certainly for old versions of MySQL (such as 5.0 or 5.1) you’re going to get nowhere near full system utilization on POWER8. For MySQL 5.6 (and in the future, 5.7) you have a much better hope.

Before anyone asks, yes, I used jemalloc for most of my benchmarks and it helps by giving a single digit percent performance increase (around 3-4%).

The bottlenecks inside MySQL 5.6 for sysbench point select workload are fairly well documented, so at best we may be striving to equal the performance of other CPU architectures rather than get too much higher simply due to hitting mutex contention in creating read views inside InnoDB. So the maximum performance will be a function of individual core CPU speed and the speed at which a lock can be acquired (i.e. related to how quick you can bounce a cacheline with a lock between cores).

This is exactly what I found on POWER8 with MySQL 5.6 – you hit the same bottleneck on POWER8 as you do everywhere else – creating read views in InnoDB.

That being said, my maximum sysbench point select results on POWER8 was 344kQPS. This not only matches but exceeds the previous record holder by quite a decent amount.

This number was across 8 tables with mysqld bound to a single NUMA node (6 cores) and sysbench bound to another NUMA node (6 cores) on the same socket. For this benchmark, due to the mutex contention, bringing the second socket into play didn’t improve performance. For other benchmarks, (e.g. standard sysbench read only) it seems to scale with more CPU cores much better (no doubt the subject of a future blog post).

Single table sysbench point select was also impressive at 335kQPS – you only got an additional 10kQPS by going to 8 tables! All of these results were with SMT4 and DSCR=1, which seems to be the best configuration for this type of workload.

Up next: MySQL 5.7 on POWER8.