Tuesday, May 19, 2015

Stonebraker on Databases

I recently listened to a podcast on Software Engineering Radio with database expert Michael Stonebraker. (at the recommendation of a friend - thanks Larry) It's a few years old, but still quite relevant.

As usual, I relate much of what I read and hear about to Suneido. In this case it was interesting to see how Suneido's database held up to Stonebraker's criticism of current conventional relational databases.

He talks about profiling a database and finding that 90% of the time was spent on "overhead". The time consisted of four main areas:

buffer pool management
Keeping a cache of database pages, page replacement tracking, and converting from external (disk) record format to internal (in-memory) format. Since most transactional (OLTP) databases now fit in main memory, this work is even more wasteful.

record locking
Most conventional relational databases use pessimistic row level read and write locks to ensure that transactions are atomic, consistent, and isolated (i.e. ACID). Managing locks and waiting to acquire locks can be slow.

thread locking
Most databases are multi-threaded which, in most cases, means they use locking to protect shared data structures. Locking limits parallelism.

crash recovery write-ahead logs
For durability (the last part of ACID) databases commonly use a write-ahead log where changes are written (and in theory flushed to disk) prior to updating the actual database. In case of a crash, the log can be used for recovery. But writing the log is slow.

So how does Suneido do in these areas?

Instead of a buffer pool, the database is memory mapped. This handles databases that fit into memory as well as ones that don't. When they don't the page replacement is handled by the operating system which is in a good position to do this efficiently. Modern operating systems and hardware already have so many layers of caching and buffering that it seems crazy to add yet another layer of your own!

Suneido also does as much work as possible using the external format of records, only converting to internal format when necessary. For example, most database "wheres" are done in external format. The encoding of values into external format maintains ordering, so sorting can also be done while still in external format.

Rather than pessimistic record locking, Suneido uses optimistic multi-version concurrency control in conjunction with an append-only "immutable" database. This means that read transactions do not require any locking and do not interact with update transactions. Write transactions only require locking for the actual commit.

Suneido's database server  is multi-threaded with requests handled by a pool of threads. But most of the internal data is in immutable persistent data structures, which require minimal locking. And the database itself is an immutable persistent data structure requiring minimal locking. (I minimized the locking as much to avoid bugs as for performance.)

Finally, Suneido doesn't use a write-ahead log. Instead, its immutable append-only design makes it a type of log structured database, where the database itself can act as the log.

NOTE: This is based on the newer Java implementation of Suneido which has a different database engine than the older C++ version.

I haven't benchmarked Suneido's database against other systems so I can't make any claims about speed. But in terms of avoiding most of the overheads that Stonebraker identifies, Suneido seems to hold up pretty well.

Saturday, May 16, 2015

Beautiful Code for Parsing

I've recently been reading up on JavaScript. One of the books I was re-reading was JavaScript: The Good Parts by Douglas Crockford. In there he mentioned the chapter he wrote in Beautiful Code. (Of which, there are mixed reviews.) It's been a while since I read that book and I didn't remember his chapter. So I pulled out my copy (old enough that it's an actual paper copy). I didn't want to carry the (large) book around so I took advantage of how O'Reilly lets you register your paper books and then buy the ebook for $5. Of course, after I did that I found Crockford's chapter is available on his web site. That's ok, I wouldn't mind re-reading the whole book.

The chapter was on parsing based on Top Down Operator Precedence by Vaughn Pratt. I thought I'd start by reading Pratt's original paper. Crockford's link takes you to the ACM citation which wants to charge you to read the paper (even though it's from 1973), but a quick web search found a public version. I found the paper a little hard to follow.

Crockford's article is an example of a parser for a subset of JavaScript written in that subset. It still took some effort to understand but I found it easier to follow than the original paper.

Suneido's hand written top down recursive descent parser is ok, but it has a lot of methods to parse expressions. It always seemed like there should be a better way. At some point I looked at the Go parser and it manages with a lot less methods by using precedence. I'd be quite interested to see what a Suneido parser would look like using Pratt's approach. Although, because Suneido's syntax grew ad hoc, it has some parts that are a little ugly to parse.

I love coming across elegant new algorithms and ideas. You can tell how much of a geek I am by the fact that I get as much pleasure out of a new algorithm as most people would from a bowl of ice cream :-) Which might help explain why I'm so skinny - not many calories in a delicious algorithm.

Thursday, April 23, 2015

When is a PriorityQueue Not Ordered?

aka When does a final field change?


jSuneido limits how long a database update transaction can be active. This is because active update transactions consume resources.

Read-only transactions consume little resources and are not limited. (This is a benefit of the append-only database structure.)

There are two parts to the limiting. If an update transaction commits and it was active more than a certain amount of time (currently 5 seconds) then a warning is logged but otherwise the transaction completes normally.

A separate process runs periodically (currently once per second) and any update transactions that have been active for too long (default 10 seconds) are aborted. A PriorityQueue is used for this so that only the longest running update transaction needs to be looked at.


Recently I noticed that some of our customers were getting the warning, but the duration given was well over the abort limit. That should have been impossible - the transactions should have been aborted before they reached that point. My first thought was that I had "broken" it with some recent change. But going back through the logs it looked like this had been happening for quite a while.

Searching the logs, I found that there were some transactions getting aborted due to duration, so that part of the code was working at least some of the time.

I added some debugging and found that the problem was that PriorityQueue peek was not returning the oldest transaction. That seemed impossible since by definition PriorityQueue peek returns the smallest element.

I checked my comparator but it was simple and seemed correct. I wrote some equivalent test code and it worked fine.

I started searching on the internet to see if anyone else had run into similar problems. Sure enough they had, but the reason was that they had been modifying the elements after inserting them. (Similar to problems if you modify elements after inserting into hash tables.)

But the field I was ordering by was final so it couldn't be modified.

Or could it? A final field still has to get set at some point. Sure enough, I was inserting the transactions into the queue in the super constructor, which ran before the field was initialized. So the queue insertion was always seeing a value of zero and the order was undefined. Argh!

(Java normally prevents this kind of problem, but I was casting to a derived class in code called by a base class constructor. Moral of the story - avoid tricky code!)

In case you're wondering, I had tested. But it worked when testing since I would only have a single active transaction, and the order was irrelevant.

It was an easy fix to reorganize the code slightly to ensure the queue insertion was done after the field was initialized. (Although that splits what used to be a single synchronized method into two, which makes me nervous about concurrency problems. I think it's ok, hopefully it won't be the subject of a future blog post!)

Monday, February 09, 2015

Gimme Structure

"I believe that it may happen that one will succeed, and one must not begin to despair, even though defeated here and there; and even though one sometimes feels a kind of decay, though things go differently from the expected, it is necessary to take heart again and new courage. For the great things are not done by impulse, but by a series of small things brought together. And great things are not something accidental, but must certainly be willed. What is drawing? How does one learn it? It is working through an invisible iron wall that seems to stand between what one feels and what one can do.”
-- Vincent Van Gogh

I used to think what I was looking for was good design. On more cynical days I'd settle for any design, or not even design, just some kind of structure.

I guess that's a bit like saying you want "quality". Would that be good quality or bad quality? Obviously, good structure is better than bad structure. But even bad structure is better than no structure.

I see, and work with, a lot of bad code, some of it written by my programmers, some of it (sadly) written by myself. The code seems to be split up into methods and classes more or less randomly. Names of variables and methods make no sense or are even outright misleading. It might work (most of the time) but it is difficult to understand, usually has duplication, commonly has logic errors, often old dead code, incorrect comments, etc. It will come as no surprise that it is hard to modify.

Part of the problem is incremental development. Even if there was some structure at some point, unless everyone modifying the code pays attention to maintaining that structure, it will degrade. And if it didn't have much structure to begin with it's even worse.

I don't think you can blame this on "evolution". Bad code is not very "fit". Natural selection would soon kill it off. Evolution is not intelligent design, but it comes up with lean, efficient solutions. It's not sloppy.

Much of the blame goes back to a common weakness in programmers - thinking that you are done when you have something that appears to work. Not going the extra distance to make sure it's readable, understandable, logically complete and correct. Often not even bothering to take care of the low hanging fruit like variable and method names.

And of course, once the code is a tangled mess no one wants to touch it to clean it up. Understandably, since it's a lot of work. And there's no doubt unobvious behavior in that code that you need to figure out and preserve. And there's a high risk of breaking things, and many programmers pay more attention to fear than to any desire for good code.

I have no silver bullets. Just a plea - please try to write code with some sort of comprehensible structure, for your own sake if nothing else.

Sunday, January 25, 2015

Effective Modern C++

I just finished reading Effective Modern C++ by Scott Meyers. Like his More Effective C++ and the original Effective C++ it's well written with good explanations and examples. This third book covers the latest C++ features in C++11 and 14.

It's been a long time since I read the first two books. Effective C++ was published in 1991! Back then I was writing fair amounts of C++ code. Nowadays the only C++ programming I do is maintaining the C++ implementation of Suneido.

I expected the new book to be similar to the previous ones - practical advice on how to effectively use modern C++. And there is lots of that. But it was also full of "gotchas" - things that won't compile (and give horrendous error messages), or compile but won't run, or compile and run but do the wrong thing.

C++ has always been a complex language and the new versions have only pushed that even further. If makes me appreciate the simplicity of the Go language which in some ways is a reaction to the complexity of C++.

Don't get me wrong, the new features of C++ are great, they improve the language in many ways. But my head is spinning with things like when perfect forwarding isn't perfect, when universal references aren't, and when uniform initialization isn't uniform.

Monday, January 05, 2015

Safety First

I recently fixed a long standing (many years) bug in the C++ implementation of Suneido. A friend remarked how you'd wish that after this long all the bugs would have been found. Of course, it doesn't take much code to provide room for bugs to lurk.

The problem that was reported was that if you created one thread inside another that cSuneido would crash. It seemed to happen quite consistently and predictably. That was from the IDE. If you ran the same code without the IDE it worked fine. Or if you played around a bit in the IDE first, it would also work fine.

cSuneido "threads" aren't real threads. They are Windows "fibers" - more like coroutines. They don't actually run concurrently, but they allow cooperative multi-tasking. The big advantage is that since you control when the task switching happens and can do it at "safe" points in the code, you don't have to worry about low level concurrency issues. The downside is that you can't take advantage of multiple cpu's. But this was implemented at a time when no one had multiple cpu's and Moore's Law was still happily improving single cpu performance.

Suneido's C++ fiber code had a std::vector of fibers. It also had a main fiber, separate from the vector. The current fiber was a reference (pointer) to either the main fiber or an element of the vector.

Even from that minimal description you could probably guess the problem. Vector implementations normally grow by allocating a new larger array, copying over the data, and throwing out the smaller old array. So adding an element to a vector invalidates any references to its content. So the current fiber reference would be pointing to stale data. (It wouldn't actually be a dangling pointer because cSuneido uses garbage collection.) The reference to stale data could cause an "impossible" situation that would lead to a fatal error. (So the problem was nothing to do with creating one fiber inside another, it was simply that creating two fibers in that sequence happened to be one way to expose the bug.)

The problem was rare because it required a specific sequence of events. First, the vector had to grow. Which is why if you played around first (and expanded the vector) it wouldn't happen. Second, the stale reference had to be used in such a way that it caused a problem. Since the data would normally be identical the stale reference wouldn't matter. And the next fiber switch would update it to a valid value so the stale reference wouldn't hang around.

Actually, I think there was at least one more potential problem scenario. When fibers ended they were removed from the vector. This probably wouldn't cause a reallocation (many implementations never shrink the array) but it would invalidate any references after that item. You'd either end up with a reference to the wrong item or past the end of the array.

I'm a little embarrassed to discover such a long standing blatant mistake, and a newbie mistake at that. All the times I've looked at that code and I never picked up on it. Ouch.

But to me the real moral of the story is "don't use unsafe languages". Interestingly, this bug was not a memory management issue since cSuneido (unlike almost all C++ programs) uses garbage collection. It's just a result of C++ allowing unsafe raw pointers/references.

C++ fans would tell you that modern C++ has plenty of high level features that are "safe". But the point is that it still has lots of unsafe features. (And AFAIK there is no way to enforce use of a "safe" subset. And C++ continues to resist "real" garbage collection.) I would much rather work in a language like Java or Go (or others) that just don't allow unsafe code of this nature, and eliminate a whole class of problems. Figuring out my high level issues is challenging enough without worrying about unsafe low level issues.

Thursday, January 01, 2015

Go Editors

Up till recently I've been using Sublime Text with GoSublime to write Go code. It works pretty well. Sublime is a good editor and GoSublime integrates with the Go tools fairly well. But coming back to it after being away I found it quite annoying that compile errors are only shown in the output pane, not marked on the source code. And you can't even click on the error to go to that line. I'm not a big fan of using line numbers but with Sublime I was pretty much forced to display line numbers and use them manually. (There's probably some way to get clicking on errors to go to the line but nothing obvious.)

I'm not sure where Sublime is at. Sublime 3 has been in beta for a long time. GoSublime has some activity but doesn't seem to be doing too much either.

So I've been on the lookout for alternatives. And I needed something that was available on both Mac and Windows.

I came across something about Github's Atom editor and the go-plus extension. I had some difficulties getting it working on Windows, easier on Mac. It has better integration between Go and the editor, showing lines with errors and letting you click on the errors. But it doesn't seem to have much support for things like running tests. I realize that's outside the scope of just an editor, and I can always run the tests outside the editor. But I'd still prefer to have it. (Again, there may be some way to do it, but if so it wasn't obvious.)

Both Eclipse and IntelliJ have facilities for Go but they seem like very heavy weight tools for a "lightweight" language like Go.

The other recommendation I'd seen was LiteIDE. It's somewhere in between a full IDE like Eclipse, and an editor like Atom. It was easier to install than either Sublime or Atom since it's a single package, no add ons to worry about. I haven't used it a lot yet but it seems like it might be a good option. The editor is decent and it doesn't force me to use line numbers. I can run tests. The only weakness I've found so far is that it doesn't support column select or multiple select. I can probably live without that, if need be I can always use another editor for the odd time I need it. And it looks like the Kate editor that LiteIDE uses does support this so I'd guess it might be added at some point.

The project seems quite active. I found a bug where some keyboard shortcuts didn't work when you had multiple windows open. I couldn't find any mention of this problem so I entered a bug for it. Within hours I got a notification of a fix committed. It looked like an easy fix, and I haven't tried to build from source to test it, but it's still impressive that the issue was addressed so quickly.