re: BonsaiDb performance update: A deep-dive on file synchronization

Est. reading time: 10 min

I run into this fascinating blog post discussing the performance of BonsaiDb. To summarize the post, the author built a database and benchmarked it, but wasn’t actually calling fsync() to ensure durability. When they added the fsync() call at the right time, the performance didn’t degrade as expected. It turned out that they were running benchmarks on tmpfs, which is running in memory and where fsync() has no impact. Once they tested on a real system, there was a much higher cost, to the point where the author is questioning whether to continue writing the database library he has developed.

Forgetting to call fsync() is an understandable issue (they called the flush() method, but that didn’t translate to an fsync() call). I recall that at one point the C#’s API once had a bug where a Flush() would not call fsync() if you were making writes with 4KB alignment (that is… super bad).

After figuring out the issue, the author has out to figure exactly how to ensure durability. That is a journey that is fraught with peril, and he has some really interesting tidbits there. Including sync_file_range(), fdatasync() and how you cannot write a durable database for Mac or iOS.

From my perspective, you cannot really trust anything beyond O_DIRECT | O_DSYNC or fdatasync() for durability. Almost a decade ago I wrote about performance testing that I did for various databases. My code was the 2nd fastest around for the tested scenarios. It was able to achieve almost 23,000 writes, almost 25% of the next slowest database. However, the fastest database around was Esent, which clocked at 786,782 writes.

I dug deep into how this is done and I realized that there is a fundamental difference between how all other databases were working and how Esent was handling things. All other databases issued fsync() calls (or fdatasync()). While Esent skipped that altogether. Instead, it opened a file with FILE_FLAG_NO_BUFFERING | FILE_FLAG_WRITE_DIRECT (the Unix version is O_DIRECT | O_DSYNC). That change alone was responsible for a major performance difference. When using O_DIRECT | O_DSYNC, the write is sent directly to persistent medium, skipping all buffers. That means that you don’t have to flush anything else that is waiting to be written.

If you are interested, I wrote a whole chapter on the topic of durable writes. It is a big topic.

The other thing that has a huge impact on performance is whether you are doing transaction merging or not. If you have multiple operations running at roughly the same time, are you going to do a separate disk write for each one of them, or will you be able to do that in a single write. The best example that I can think of is the notion of taking the bus. If you send a whole bus for each passenger, you’ll waste a lot of time and fuel. If you pack the bus as much as possible, for almost the same cost, you’ll get a far better bang.

In other words, your design has to include a way for the database to coalesce such operations into a single write.

Yesterday there was an update to this task, which more or less followed that direction. The blog post covers quite a lot of ground and is going in the right direction, in my opinion. However, there are a few things there that I want to comment upon.

First, pre-allocation of disk space can make a huge impact on the overall performance of the system. Voron does that by allocating up to 1GB of disk space at a time, which dramatically reduces the amount of I/O work you have to do. Just to give some context, that turns a single disk write to multiple fsyncs that you have to do, on both your file and the parent directory, on each write. That is insanely expensive. The storage engine discussed here used append only mode, which makes this a bit of a problem, but not that much. You can still preallocate the disk space. You have to scan the file from the end on startup anyway, and the only risk here is the latency for reading the whole pre-allocation size on startup if we shut down immediately after the preallocation happened. It’s not ideal, but it is good enough.

Second, the way you manage writes shouldn’t rely on fsync and friends. That is why we have the log for, and you can get away with a lot by letting just the log handle the durability issue. The log is pre-allocated to a certain size (Voron uses dynamic sizes, with a max of 256MB) and written to using O_DIRECT | O_

O_DSYNC each time. But because this is expensive, we have something like this (Python code, no error handling, demo code, etc):

The idea is that you can call writeToLog() each time and you’ll get a future on the write to the log file. You can continue with your transaction when the log holds the data. Note that in this model, if you have concurrent writes, they will be merged into a single disk write. You can also benefit significantly from reduced amount we write to disk by applying compression.

Third, something that has been raised as an option here is a new storage format. I’m not sure that I 100% get what is the intention, but… what I understand I don’t like. I think that looking at how LMDB does things would help a lot here. It is a COW model (which the append only is very similar to). The key difference is that the new model is going to store every header twice. Probably with a CURRENT and NEXT model, where you can switch between the two configurations. That… works, but it is pretty complex. Given that you have a log involved, there is no need for any of this. You can just store the most recent changes in the log and use that to find what the current version is of the data is.

I don’t like append only models, since they require you to do compaction at some point. A better model is what LMDB does, where it re-used the same pages (with copy on write). It requires you to manage a free list of pages, of course, but that isn’t that big a task.

Woah, already finished? 🤯

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