I've been plugging away at the new append-only storage engine for jSuneido. I have a decent proof of concept, but it's still a long way from production.
Recently I was working on btree iteration. Usually btree's link the leaf nodes to simplify iteration. But this linking is problematic with an append-only btree. So the iteration has to work a little differently. One of the problems is how to handle changes made during the iteration. Being in an immutable mindset, my immediate thought was to iterate through a "snapshot" of the btree. (Since snapshots are just a pointer in immutable persistent data structures.)
But then I realized I was only immutable on disk. In memory, within a transaction, I was using mutable data structures. So I jumped in and converted my btree's and the redirection hash trie map to fully immutable. After I'd pretty much finished this, I realized I should have looked closer before I leaped. But when you have a hammer, everything looks like a nail :-)
Iterating through a snapshot won't work. For example, if you update a record during iteration, the iteration would see an out of date version of the record, and might even try to update this "stale" data. Back to the drawing board.
On the positive side, I improved the code quite a bit. I've lost track of how many times I've refactored, reshuffled, rewritten this new storage engine code. It's not that big - currently about 2500 lines. You wouldn't think there'd be that many ways to arrange it!
Since I ended up not needing full immutability I changed it back to being immutable in memory (better performance). But I couldn't just revert the code because I wanted to keep some of the improvements I'd made.
About three days work on a dead end path. Oh well, if you're trying to come up with something new you have to expect a few dead ends. Not the first time, and I'm sure it won't be the last.
Wednesday, March 30, 2011
Interview with Uncle Bob
I enjoyed this podcast of an interview with Robert Martin aka Uncle Bob.
It's interesting to hear how he still likes to spend his time programming after 40 years (as opposed to getting sucked into management or other activities).
It's interesting to hear how he still likes to spend his time programming after 40 years (as opposed to getting sucked into management or other activities).
Sunday, March 27, 2011
More on Java assert
Java's assert is a mixed blessing.
It's nice syntactic sugar. I'd rather write:
assert x == 0 : "expected x = 0, got " + x;
than:
if (x != 0)
throw new AssertionError("expected x = 0, got " + x);
You could make your own assert so you could write:
verify(x == 0, "expected x = 0, got " + x);
But there is are subtle but important differences. With your own function, the error message is always constructed, whether the error is thrown or not. Whereas with assert, as with writing out the if, the error message will only be constructed if the assert fails. That doesn't matter if the message is just a literal string (or there's no message) but if the message requires, for example, calling toString on a complex object you could take a significant performance hit. There's also the lesser overhead of calling a function. It's possible that the JVM JIT optimizer will in-line the function so it becomes equivalent to writing out the "if" and therefore eliminate the overhead, but I'm not sure if it's "safe" to count on this.
The downside of assert is that you have to remember to enable it. (My blog post on this is one of my most visited. Google for "enable java assert" and it's currently the third result.) One way to avoid this is to write a test to confirm that asserts are enabled. I did this after I got burnt by disabled assertions a second time.
I just ran into another problem with this. We were looking at using NativeJ but it doesn't appear to have any way to pass the -ea option since it uses the java dll rather than the actual java executable.
I discovered that there is a way to enable assertions from within the code:
ClassLoader.getSystemClassLoader()
.setPackageAssertionStatus("suneido", true);
It only applies to classes loaded after this, but I have it as the first statement of my main method which should be the first class loaded.
Another wrinkle to assert is that the exception it throws is AssertionError which is an Error. The Java exception hierarchy is:
Throwable
Error
Exception
RuntimeException
Only RuntimeException's can be thrown without declaring them. "Normal" code is only supposed to catch Exception, not Error. But in Suneido, I don't want an assertion failure to "crash" the system, I want to be able to catch them. But to do that, I have to catch Throwable, which is not the recommended practice. I could use two catch's - one for Exception and one for AssertionError. But apart from the extra code, I wonder if there aren't other Error's that I would want to catch.
One way around the AssertionError issue would again be to write my own assert function so I could throw whatever exception I wanted (e.g. a RuntimeException). But as I explained above, there are issues with that.
Yet another option is to use a javac (the Java compiler) annotation processor (like fa.jar) that converts assert to if-throw. But that seems a little scary.
Of course, a lot of this is due to wanting to keep the assertions enabled, even in production. I'm a believer in this since so many problems don't show up till the software gets used for real. However, it does mean you have to be a little careful to make the asserts fast enough for production.
It's nice syntactic sugar. I'd rather write:
assert x == 0 : "expected x = 0, got " + x;
than:
if (x != 0)
throw new AssertionError("expected x = 0, got " + x);
You could make your own assert so you could write:
verify(x == 0, "expected x = 0, got " + x);
But there is are subtle but important differences. With your own function, the error message is always constructed, whether the error is thrown or not. Whereas with assert, as with writing out the if, the error message will only be constructed if the assert fails. That doesn't matter if the message is just a literal string (or there's no message) but if the message requires, for example, calling toString on a complex object you could take a significant performance hit. There's also the lesser overhead of calling a function. It's possible that the JVM JIT optimizer will in-line the function so it becomes equivalent to writing out the "if" and therefore eliminate the overhead, but I'm not sure if it's "safe" to count on this.
The downside of assert is that you have to remember to enable it. (My blog post on this is one of my most visited. Google for "enable java assert" and it's currently the third result.) One way to avoid this is to write a test to confirm that asserts are enabled. I did this after I got burnt by disabled assertions a second time.
I just ran into another problem with this. We were looking at using NativeJ but it doesn't appear to have any way to pass the -ea option since it uses the java dll rather than the actual java executable.
I discovered that there is a way to enable assertions from within the code:
ClassLoader.getSystemClassLoader()
.setPackageAssertionStatus("suneido", true);
It only applies to classes loaded after this, but I have it as the first statement of my main method which should be the first class loaded.
Another wrinkle to assert is that the exception it throws is AssertionError which is an Error. The Java exception hierarchy is:
Throwable
Error
Exception
RuntimeException
Only RuntimeException's can be thrown without declaring them. "Normal" code is only supposed to catch Exception, not Error. But in Suneido, I don't want an assertion failure to "crash" the system, I want to be able to catch them. But to do that, I have to catch Throwable, which is not the recommended practice. I could use two catch's - one for Exception and one for AssertionError. But apart from the extra code, I wonder if there aren't other Error's that I would want to catch.
One way around the AssertionError issue would again be to write my own assert function so I could throw whatever exception I wanted (e.g. a RuntimeException). But as I explained above, there are issues with that.
Yet another option is to use a javac (the Java compiler) annotation processor (like fa.jar) that converts assert to if-throw. But that seems a little scary.
Of course, a lot of this is due to wanting to keep the assertions enabled, even in production. I'm a believer in this since so many problems don't show up till the software gets used for real. However, it does mean you have to be a little careful to make the asserts fast enough for production.
The People Behind The Software
I like how this video is about the people and the emotions behind the software.
Labels:
video
Sunday, March 20, 2011
A JVM Does That?
Cliff Click's recent blog post led me to the slides for his talk "A JVM Does That" - interesting stuff.
A quote from his post:
A quote from his post:
Java appears to have plateaued (although Projects Lambda and Coin may give it a serious boost), but the JVM is on a roll. Where people used to target C as their “assembly” of choice years ago (to avoid having to do code-generation), they now target the JVM – which avoids the code-gen AND supplies a GC, AND a well-understood threading model, plus true type-safety.
Labels:
java
Wednesday, March 16, 2011
jSuneido Goes Live
Almost three years after starting the project, the Java version of Suneido is now live in production. Last night one of my programmers switched our in-house accounting and customer support system over to jSuneido (thanks Kim). We have about 40 fairly heavy users so it's a good test.
We had a few minor problems today but for the most part it went quite smoothly. When I brought it up with several people they said they didn't notice anything different, which is what I want to hear. Several people thought it was faster. My own impression was mostly that it felt "smoother" - no annoying pauses like we've been running into lately.
(Honestly, I'm amazed that cSuneido manages to handle as many users as it does. When I designed it I never thought it would. It's definitely benefited from Moore's law.)
Our current server is only a dual core machine with 6 gb of memory. It doesn't really have enough cores or memory for jSuneido to take advantage of. We're in the process of getting a new i7 server with 8 cores (counting hyperthreading) and 24 gb of memory (thanks Dorlan). That should be a better platform for jSuneido.
One of the main goals of jSuneido was to scale better to handle larger systems with more users. For smaller systems cSuneido uses less resources. But it can't take advantage of 64 bit systems with large amounts of memory and multiple cores. jSuneido can.
Three years of work to reach this point. Not full time, but close to half my time. That's a lot of hours. It feels good to reach this point. No doubt there will be issues to deal with, but that's to be expected. In many ways it's just a transition between phases of the project. With climbing, reaching the top is only half the battle, the other half is getting down. With software, writing it is only half the battle, the other half is running, fixing, maintaining, and improving it.
This kind of project definitely requires being able to handle deferred gratification. But just as important is to take pleasure in the work itself, as well as in the end result. If I didn't enjoy the day to day programming (most days anyway!) there's no way I would do it for the relatively small amount of final gratification. It's not like anyone really understands what you've done or what it took to get there. The external rewards just aren't enough to justify something like this. The process itself has to be sufficient reward. Any pats on the back at the end are just icing on the cake.
I'm deliberately making a point of marking this milestone. It's good to celebrate small victories along the way. Too often they slide by and with no punctuation it can seem like just one long slog. It must have been an even bigger milestone when the original version of Suneido first went into production, but I can't even remember it. I remember thinking that I would reward myself with one of the brand new flat screen monitors (that dates it!). But I never did, because it never seemed like I was "finished" - there was always as much road ahead of me as there was behind. Here's to the road ahead.
We had a few minor problems today but for the most part it went quite smoothly. When I brought it up with several people they said they didn't notice anything different, which is what I want to hear. Several people thought it was faster. My own impression was mostly that it felt "smoother" - no annoying pauses like we've been running into lately.
(Honestly, I'm amazed that cSuneido manages to handle as many users as it does. When I designed it I never thought it would. It's definitely benefited from Moore's law.)
Our current server is only a dual core machine with 6 gb of memory. It doesn't really have enough cores or memory for jSuneido to take advantage of. We're in the process of getting a new i7 server with 8 cores (counting hyperthreading) and 24 gb of memory (thanks Dorlan). That should be a better platform for jSuneido.
One of the main goals of jSuneido was to scale better to handle larger systems with more users. For smaller systems cSuneido uses less resources. But it can't take advantage of 64 bit systems with large amounts of memory and multiple cores. jSuneido can.
Three years of work to reach this point. Not full time, but close to half my time. That's a lot of hours. It feels good to reach this point. No doubt there will be issues to deal with, but that's to be expected. In many ways it's just a transition between phases of the project. With climbing, reaching the top is only half the battle, the other half is getting down. With software, writing it is only half the battle, the other half is running, fixing, maintaining, and improving it.
This kind of project definitely requires being able to handle deferred gratification. But just as important is to take pleasure in the work itself, as well as in the end result. If I didn't enjoy the day to day programming (most days anyway!) there's no way I would do it for the relatively small amount of final gratification. It's not like anyone really understands what you've done or what it took to get there. The external rewards just aren't enough to justify something like this. The process itself has to be sufficient reward. Any pats on the back at the end are just icing on the cake.
I'm deliberately making a point of marking this milestone. It's good to celebrate small victories along the way. Too often they slide by and with no punctuation it can seem like just one long slog. It must have been an even bigger milestone when the original version of Suneido first went into production, but I can't even remember it. I remember thinking that I would reward myself with one of the brand new flat screen monitors (that dates it!). But I never did, because it never seemed like I was "finished" - there was always as much road ahead of me as there was behind. Here's to the road ahead.
Wednesday, March 09, 2011
ThreadPoolExecutor
I've been working with ThreadPoolExecutor and it's a little confusing so I thought I'd share my experience.
Some background - Executor is a simple interface:
Without a queue and with a maximum number of threads, it's possible that tasks will need to be rejected. By specifying the CallerRunsPolicy rejected tasks will be executed by the calling thread. This is a simple feedback mechanism that will throttle requests since the caller won't be able to accept additional requests while it's busy executing a task.
I chose MAX_THREADS of 8 to be a bit bigger than the expected number of cpu cores (to allow for some threads being blocked). In our actual usage one or two threads seem to be sufficient.
There is a standard Executors.newCachedThreadPool but the documentation isn't specific about what its configuration is. From other sources it appears quite similar to my configuration - zero core threads and a SynchronousQueue. However, it has unlimited MAX_THREADS instead of CallerRunsPolicy. In my case, I wanted to limit the number of thread because each holds some limited resources.
I'm not an expert on this stuff, so suggestions or criticisms are welcome.
Some background - Executor is a simple interface:
An object that executes submitted Runnable tasks. This interface provides a way of decoupling task submission from the mechanics of how each task will be run, including details of thread use, scheduling, etc. An Executor is normally used instead of explicitly creating threads.A ThreadPoolExecutor uses a pool of threads to execute the tasks. The trick is in configuring it. I wanted:- no threads when it's idle
- a limited number of threads when it's busy
- a bounded queue
You have to read the documentation for ThreadPoolExecutor very carefully. Forget about your preconceptions of how it "probably" works.
You can specify "core pool size" and "max pool size". Normally "core" threads do not time out. You also specify the type of queue (bounded, unbounded, or synchronous), and the rejection policy.
There are a couple of gotcha's.
- Even if activity is very low and one thread could handle it, the full number of core threads will be created.
- Even if activity is high and all the core threads are busy, additional threads will not be created until the queue is full.
Both of these are because it's very hard to know if a thread is idle.
They combine to lead to a common mistake - setting core size to 0 because you want all the threads to time out, and using an unbounded queue, which will never be full. Using a large queue is almost as bad because additional threads won't be created until that many requests are queued up - ouch!
Here's what I ended up with:
private static final int CORE_THREADS = 0;
private static final int MAX_THREADS = 8;
private static final int KEEP_ALIVE = 1;
private static final ThreadPoolExecutor executor =
new ThreadPoolExecutor(CORE_THREADS, MAX_THREADS,
KEEP_ALIVE, TimeUnit.MINUTES,
new SynchronousQueue<Runnable>(),
threadFactory,
new ThreadPoolExecutor.CallerRunsPolicy());
A SynchronousQueue is a zero size queue, it hands off items directly. Because its remainingCapacity is always zero, it is always "full", so up to MAX_THREADS will be created as needed.Without a queue and with a maximum number of threads, it's possible that tasks will need to be rejected. By specifying the CallerRunsPolicy rejected tasks will be executed by the calling thread. This is a simple feedback mechanism that will throttle requests since the caller won't be able to accept additional requests while it's busy executing a task.
I chose MAX_THREADS of 8 to be a bit bigger than the expected number of cpu cores (to allow for some threads being blocked). In our actual usage one or two threads seem to be sufficient.
There is a standard Executors.newCachedThreadPool but the documentation isn't specific about what its configuration is. From other sources it appears quite similar to my configuration - zero core threads and a SynchronousQueue. However, it has unlimited MAX_THREADS instead of CallerRunsPolicy. In my case, I wanted to limit the number of thread because each holds some limited resources.
I'm not an expert on this stuff, so suggestions or criticisms are welcome.
Labels:
concurrency,
java,
suneido
Thursday, March 03, 2011
Mockito
Anyway, I decided I should try to clean up my act a little. I wanted to try using a mocking library. I did a few minutes of research and looked at a comparison between EasyMock and jMock. Then I ran across Mockito and it looked simple and easy to use.
I added the jar to my project and wrote my first test with it. No problems and very easy to use.
But it's never that easy. I ran my build, which uses Proguard, and got a ton of errors and warnings :-(
I probably could have fixed them, but I took the easy way out and just configured my build to exclude the tests. I only ever run them from Eclipse anyway. It's not the ideal solution but it'll do for now.
In the process I cleaned up my Ant build file. When I first created it I was even more ignorant about Ant and Java and Proguard than I am now.
I've revised a few more tests to use Mockito and I'm quite happy with it. If you're programming in Java and aren't using a mocking library, give it a try.
Saturday, January 15, 2011
Management
A few days ago I fired one of my programmers. It's one of the parts of my "job" that I could do without. Thankfully, I've only had to do it a few times. He's been with us quite a while, and although I was never quite happy with his work, there were alway extenuating circumstances and I kept hoping things would turn around. Eventually, I had to admit that it probably wasn't going to get any better.
It went about as well as these things can. No arguments, no tears. He actually admitted he really hadn't been very interested in the work. I hope he can find work that does motivate him. We all spend too much of our lives at work to waste it doing stuff we don't enjoy.
Despite being a partner in a small business with 40 employees I'm not much of a "business man" or manager. I've learnt enough to get by and I do as little as I can responsibly get away with. If it starts to take too much of my time I get unhappy. I'm still a programmer at heart, and if I spend a day at the office without writing a line of code I get grouchy. And no, answering coding questions and reviewing code doesn't count!
I'm lucky to have a partner who's happy (or at least willing) to look after the business and marketing and sales side. And lucky to have programmers (and a customer support team) who do a great job without a great manager.
It went about as well as these things can. No arguments, no tears. He actually admitted he really hadn't been very interested in the work. I hope he can find work that does motivate him. We all spend too much of our lives at work to waste it doing stuff we don't enjoy.
Despite being a partner in a small business with 40 employees I'm not much of a "business man" or manager. I've learnt enough to get by and I do as little as I can responsibly get away with. If it starts to take too much of my time I get unhappy. I'm still a programmer at heart, and if I spend a day at the office without writing a line of code I get grouchy. And no, answering coding questions and reviewing code doesn't count!
I'm lucky to have a partner who's happy (or at least willing) to look after the business and marketing and sales side. And lucky to have programmers (and a customer support team) who do a great job without a great manager.
Labels:
management
Sunday, January 09, 2011
I Give Up
I spoke too soon with my Hamcrest post. I was getting a clean compile and build, but when I ran the tests I got a security exception!
Based on what I found on the internet, this is because the hamcrest-core supplied by Eclipse is signed, but the hamcrest-library I downloaded separately isn't.
The suggested solutions is to make sure the unsigned one is first on the Eclipse build path. But mine was already first. I tried playing around with the order but it didn't help.
So I gave up and removed hamcrest-library. I'll just live with the matchers in the hamcrest-core supplied by Eclipse. I've wasted enough time and mental energy already.
Sometimes this stuff is just not as easy as it should be :-(
It's a good reminder of how much using Suneido simplifies life for my developers. (Not that they would agree that their life is simple!) The downside is that we don't have access to all these third party tools and libraries. But the huge upside is that we don't have to fight to integrate all those disparate pieces.
Based on what I found on the internet, this is because the hamcrest-core supplied by Eclipse is signed, but the hamcrest-library I downloaded separately isn't.
The suggested solutions is to make sure the unsigned one is first on the Eclipse build path. But mine was already first. I tried playing around with the order but it didn't help.
So I gave up and removed hamcrest-library. I'll just live with the matchers in the hamcrest-core supplied by Eclipse. I've wasted enough time and mental energy already.
Sometimes this stuff is just not as easy as it should be :-(
It's a good reminder of how much using Suneido simplifies life for my developers. (Not that they would agree that their life is simple!) The downside is that we don't have access to all these third party tools and libraries. But the huge upside is that we don't have to fight to integrate all those disparate pieces.
Saturday, January 08, 2011
Eclipse Hamcrest Runaround
I started reading Growing Object-Oriented Software and it talked about using the Hamcrest matchers with jUnit. It sounded like a good idea so the next time I was writing a test I tried using them.
The first problem is where to import assertThat from. That turned out to be easy, it's in org.junit.Assert along with the normal assertEquals etc.
The next question is where to import the matchers like equalTo. I found that in org.hamcrest.Matchers.
Next I wanted a lessThan matcher but I couldn't find it.
It turns out jUnit only includes Hamcrest core which doesn't have lessThan. I searched on the internet and didn't find a lot of help. I found a question on StackOverflow that suggested replacing the Eclipse supplied junit and hamcrest-core with junit-dep and hamcrest-all
I tried this and at first it seemed to work ok. But then I went to build my jars and Proguard gave all kinds of errors about missing dependencies.
I've been meaning to look into Maven and it's supposed to handle dependencies, so I thought I'd give it a try. Since I'm using Eclipse I looked for an Eclipse add-on for Maven. I found one and installed it. Big mistake. Not only did it not help with the dependency problems (at least I couldn't figure out how) but it also messed up my project. No problem, I thought, I'll just uninstall it. Except it left a mess behind. I ended up restoring my Eclipse install, but I still had problems. I kept getting errors referencing maven but I couldn't find any references to maven in my project. Eventually I found that the launch configurations for your project are stored in the workspace, not in the project. (That doesn't make much sense to me, but I'm sure there's some good reason.) After I deleted those (easier than trying to fix them) things were back to before the Maven detour.
It said I was missing jMock and EasyMock so I went and found those jars and added them. But it still wanted some kind of Ant jar. That seemed like a little much.
I saw there were various other jars for Hamcrest but frustratingly, no explanation of them. (I did find someone had filed an issue that there should be an explanation, but no one had responded.) I downloaded the complete package and it contained a readme that gave some explanation. It looked like I wanted hamcrest-core and hamcrest-library rather than hamcrest-all.
That eliminated the dependencies on jMock and EasyMock and Ant. But I still got an error that junit was referencing something that was missing from hamcrest. I thought maybe it was a version issue, so I tried multiple versions of junit and multiple versions of hamcrest but no luck.
Then I realized that the junit supplied by Eclipse includes hamcrest-core. So maybe all I needed to do was go back to that, and then add hamcrest-library. Sure enough, that did the trick.
No doubt the junit and hamcrest and eclipse folks would say, of course, it's obvious. But it sure wasn't obvious to me.
The first problem is where to import assertThat from. That turned out to be easy, it's in org.junit.Assert along with the normal assertEquals etc.
The next question is where to import the matchers like equalTo. I found that in org.hamcrest.Matchers.
Next I wanted a lessThan matcher but I couldn't find it.
It turns out jUnit only includes Hamcrest core which doesn't have lessThan. I searched on the internet and didn't find a lot of help. I found a question on StackOverflow that suggested replacing the Eclipse supplied junit and hamcrest-core with junit-dep and hamcrest-all
I tried this and at first it seemed to work ok. But then I went to build my jars and Proguard gave all kinds of errors about missing dependencies.
I've been meaning to look into Maven and it's supposed to handle dependencies, so I thought I'd give it a try. Since I'm using Eclipse I looked for an Eclipse add-on for Maven. I found one and installed it. Big mistake. Not only did it not help with the dependency problems (at least I couldn't figure out how) but it also messed up my project. No problem, I thought, I'll just uninstall it. Except it left a mess behind. I ended up restoring my Eclipse install, but I still had problems. I kept getting errors referencing maven but I couldn't find any references to maven in my project. Eventually I found that the launch configurations for your project are stored in the workspace, not in the project. (That doesn't make much sense to me, but I'm sure there's some good reason.) After I deleted those (easier than trying to fix them) things were back to before the Maven detour.
It said I was missing jMock and EasyMock so I went and found those jars and added them. But it still wanted some kind of Ant jar. That seemed like a little much.
I saw there were various other jars for Hamcrest but frustratingly, no explanation of them. (I did find someone had filed an issue that there should be an explanation, but no one had responded.) I downloaded the complete package and it contained a readme that gave some explanation. It looked like I wanted hamcrest-core and hamcrest-library rather than hamcrest-all.
That eliminated the dependencies on jMock and EasyMock and Ant. But I still got an error that junit was referencing something that was missing from hamcrest. I thought maybe it was a version issue, so I tried multiple versions of junit and multiple versions of hamcrest but no luck.
Then I realized that the junit supplied by Eclipse includes hamcrest-core. So maybe all I needed to do was go back to that, and then add hamcrest-library. Sure enough, that did the trick.
No doubt the junit and hamcrest and eclipse folks would say, of course, it's obvious. But it sure wasn't obvious to me.
jSuneido Immutable Database
I've made a good start on rewriting the jSuneido database as an immutable persistent data structure.
It's hard to know what to call it. Overall, it's not immutable, since you can add, update, and delete like any database. The "immutable" part is that once data is written to the database file it's never updated.
You could call it "append only" because you only ever append to the database file, never update. But again, that sounds like you can't update or delete, which you can.
I started bottom up, writing a persistent hash trie to store the redirections. This is similar to my persistent hash map but designed to be stored in the database file. I also rewrote my memory mapped file access, simplifying it a lot. Now I'm working on the btree code.
The code seems a lot cleaner this time. Of course, it always does at the beginning of a rewrite because you haven't handled all the details yet. But I'm still optimistic.
As usual I'm struggling with how much to optimize. The conventional wisdom is that you write the code and then if it's too slow you profile it and optimize the problem areas. But what is "too slow" in a language or a database? You always want as much speed as you can get (without sacrificing robustness and maintainability). And that wisdom assumes that speed problems will be localized. But if the slowness is spread diffusely through the code, then it's not so easy to optimize after the fact. It's a bit like saying you can add good design after the fact.
A big part of performance is the right algorithms. Another part is implementing those algorithms efficiently on your platform. If I can "cut with the grain" of Java I think I can do more with less.
I have a lot better handle on Java and the JVM than I did when I did the first implementation. And at that point I was simply trying to port the cSuneido code, not redesign it. Now that I have a working implementation I have the freedom to explore alternatives. And I'll have something to compare performance to.
It won't be till I get to the transaction code that I'll really see how this redesign will work out. I'm hoping that the immutability of the database will simplify transaction handling. We'll see.
It's hard to know what to call it. Overall, it's not immutable, since you can add, update, and delete like any database. The "immutable" part is that once data is written to the database file it's never updated.
You could call it "append only" because you only ever append to the database file, never update. But again, that sounds like you can't update or delete, which you can.
I started bottom up, writing a persistent hash trie to store the redirections. This is similar to my persistent hash map but designed to be stored in the database file. I also rewrote my memory mapped file access, simplifying it a lot. Now I'm working on the btree code.
The code seems a lot cleaner this time. Of course, it always does at the beginning of a rewrite because you haven't handled all the details yet. But I'm still optimistic.
As usual I'm struggling with how much to optimize. The conventional wisdom is that you write the code and then if it's too slow you profile it and optimize the problem areas. But what is "too slow" in a language or a database? You always want as much speed as you can get (without sacrificing robustness and maintainability). And that wisdom assumes that speed problems will be localized. But if the slowness is spread diffusely through the code, then it's not so easy to optimize after the fact. It's a bit like saying you can add good design after the fact.
A big part of performance is the right algorithms. Another part is implementing those algorithms efficiently on your platform. If I can "cut with the grain" of Java I think I can do more with less.
I have a lot better handle on Java and the JVM than I did when I did the first implementation. And at that point I was simply trying to port the cSuneido code, not redesign it. Now that I have a working implementation I have the freedom to explore alternatives. And I'll have something to compare performance to.
It won't be till I get to the transaction code that I'll really see how this redesign will work out. I'm hoping that the immutability of the database will simplify transaction handling. We'll see.
Tuesday, December 28, 2010
The Joy of Programming
It's ridiculous how good I can feel after accomplishing a decent programming task smoothly. I almost feel a bit foolish getting pleasure from something so ... geeky. But it's a bit like a good run. It feels like you've done something worthwhile, even if it only benefits you.
Last evening, with the new MacBook Air on my lap, I cleaned up one of the last parts of the jSuneido compiler that I was uncomfortable with. I had already figured out what I wanted to do, and for once I didn't run into any unexpected problems, finishing tidily in the amount of time I had.
Previously, I'd been building a list of constants (other than strings and int's that Java handles) and then stuffing this list into the instance of the compiled class. Then, to speed things up in the generated code, I loaded an array of the constants into a local variable. It worked ok, but a lot of functions didn't need any constants. Unfortunately, I had to generate the load before I knew if there would be any. And it would be tricky to determine ahead of time if there would be any. Plus, ideally, constants should be static final so the optimizer would know they were constant.
With the new changes, I create a static final field for each constant, and then generate a class initializer that initialized them. Accesses to the constants are simple GETSTATIC instructions. The only trick was how to get the list of constants from the compiler to the class initializer. I ended up using a static field (basically a global variable). A bit ugly, but I couldn't come up with a better way. To handle multi-threading I used a ThreadLocal. (My first thought was a ConcurrentHashMap keyed by ClassLoader, but ThreadLocal was simpler.)
I don't know how much difference this will make to performance, but I really wanted to generate code that was clean and similar to compiled Java. I think I'm pretty much there. (Apart from boxed integers and the extra layer of method/call dispatch.)
Damn! Reviewing the code as I write this I realize I missed something. (I use that list of constants in the instance for a couple of other minor things.) Oh well, can't take away how good I felt when I thought it had all gone smoothly! Good thing I'm not superstitious or I'd think I'd jinxed myself talking about how well it had gone :-) Hopefully it won't be too hard to handle.
Last evening, with the new MacBook Air on my lap, I cleaned up one of the last parts of the jSuneido compiler that I was uncomfortable with. I had already figured out what I wanted to do, and for once I didn't run into any unexpected problems, finishing tidily in the amount of time I had.
Previously, I'd been building a list of constants (other than strings and int's that Java handles) and then stuffing this list into the instance of the compiled class. Then, to speed things up in the generated code, I loaded an array of the constants into a local variable. It worked ok, but a lot of functions didn't need any constants. Unfortunately, I had to generate the load before I knew if there would be any. And it would be tricky to determine ahead of time if there would be any. Plus, ideally, constants should be static final so the optimizer would know they were constant.
With the new changes, I create a static final field for each constant, and then generate a
I don't know how much difference this will make to performance, but I really wanted to generate code that was clean and similar to compiled Java. I think I'm pretty much there. (Apart from boxed integers and the extra layer of method/call dispatch.)
Damn! Reviewing the code as I write this I realize I missed something. (I use that list of constants in the instance for a couple of other minor things.) Oh well, can't take away how good I felt when I thought it had all gone smoothly! Good thing I'm not superstitious or I'd think I'd jinxed myself talking about how well it had gone :-) Hopefully it won't be too hard to handle.
Monday, December 27, 2010
jSuneido Catching Up with cSuneido
It's been a while since I paid attention to the relative speed of jSuneido versus cSuneido. I just realized that with my recent optimizations, jSuneido now runs the standard library test suite in pretty much the same time as cSuneido.
In some ways that's not surprising, the JVM is a sophisticated platform - the garbage collector is very fast and multi-threaded, the JIT compiles to optimized machine code, etc.
On the other hand, Java forces a lot more overhead than C++. Integers have to be boxed, classes can only be nested by reference not embedding, you can't use pointers, you can't allocate objects on the stack, and so on. It's impressive that the JVM can overcome these "drawbacks".
It's nice to reach this point. And a nice confirmation that I wasn't totally out to lunch deciding to use Java and the JVM to re-implement Suneido.
Of course, the real advantage of jSuneido over cSuneido is that the server is multi-threaded and will scale to take advantage of multiple cores.
In some ways that's not surprising, the JVM is a sophisticated platform - the garbage collector is very fast and multi-threaded, the JIT compiles to optimized machine code, etc.
On the other hand, Java forces a lot more overhead than C++. Integers have to be boxed, classes can only be nested by reference not embedding, you can't use pointers, you can't allocate objects on the stack, and so on. It's impressive that the JVM can overcome these "drawbacks".
It's nice to reach this point. And a nice confirmation that I wasn't totally out to lunch deciding to use Java and the JVM to re-implement Suneido.
Of course, the real advantage of jSuneido over cSuneido is that the server is multi-threaded and will scale to take advantage of multiple cores.
Sunday, December 26, 2010
informIT eBooks
This is (as far as I know) almost impossible for mainstream books. But for computer books it's not too bad. Both Pragmatic Programmers and O'Reilly sell DRM free ebooks. And I've recently started buying ebooks from informIT (mostly Addison-Wesley ones).
The other issue with ebooks is format. The Kindle currently only handles mobi and pdf. And pdf's are generally painful to read on ebook readers because they have a fixed, usually large (e.g. 8.5 x 11) page size, with big margins. Because of this I bought one of the bigger 9.7" Kindle DX's, and it helps, but it's still not great.
The Kindle helpfully trims white margins on pdf's, but the problem is that the ebooks informIT is providing are images of the paper books so they have stuff like page numbers and titles in the top and bottom margins which prevent trimming from working properly. And worse, the stuff in the margins is not symmetrical so odd pages end up trimmed differently than even pages which means the zoom level keeps changing. Not the end of the world, but annoying.
Both Pragmatic and O'Reilly provide ebooks in epub, mobi, and pdf. But informIT only provides epub and pdf. At first I made do with the pdf's but eventually I got fed up and started looking for alternatives.
I took a look at the epub's from informIT and they seemed better, at least they were hyperlinked. So I looked for tools to convert epub to mobi. Stanza was one that was suggested and I already had it installed so I gave it a try. I like Stanza but it didn't do a very good job of converting these epubs to mobi.
The other tool that was suggested was Calibre. A plus for Calibre is that it's an open source project. The user interface is a little confusing but it did a great job of converting epub to mobi, including the cover image and hyperlinks. And it even recognized when I plugged in my Kindle and let me copy the books over. I downloaded the epub versions of all my informIT books and converted them - a big improvement.
I wish I'd got fed up sooner! I could have avoided a lot of painful pdf reading.
Although I'm happy to be able to get Addison-Wesley ebooks from informIT, I do have a minor complaint - their sleazy marketing. I got an email offering me a limited time 50% off deal. Sounded good to me so I found a few books I'd been planning to get. They came to something like $80. When I entered the 50% off code the price only dropped to around $70. That's a very strange 50%. Looking closer I found that you normally get 30% off, and over $55 it goes up to 35%. So the 50% deal was only 15% better than usual. I realize this is a common marketing scam, but it still annoys me. O'Reilly plays some similar games but not quite as bad.
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Friday, December 24, 2010
jSuneido Compiler Optimizations
For my own reference, and to justify my month of work, I thought I'd go over some of the optimizations I've done recently. The changes involve:
The downside is that every call had to allocate an argument array, and often re-allocate it to accommodate default arguments or local variables. And access to variables requires larger and presumably slower code. (ALOAD, ICONST, AALOAD/STORE instead of just ALOAD/STORE)
To keep the calling code smaller I was generating calls via helper functions (with variations for 1 to 9 arguments) that built the argument array. One drawback of this approach is that it added another level to the call stack. This can impede optimization since the Hotspot JVM only in-lines a limited depth.
The first step was to compile with Java arguments and locals for functions (and methods) that did not use blocks.
Then I realized that if a block didn't share any variables with its containing scope, it could be compiled as a standalone function. Which is nice because blocks require allocating a new instance of the block for each instantiation, whereas standalone functions don't since they are "static". And it meant that the outer function could then be compiled without the argument array. Determing if a function shares variables with blocks is a little tricky e.g. you have to ignore block parameters, except when you have nested blocks and an inner block references an outer blocks parameter. See AstSharesVars
Where I still needed the argument array I changed the calling code to build it in-line, without a helper function. This is what the Java compiler does with varargs calls. Generating code that is similar to what javac produces is a good idea because the JVM JIT compiler is tuned for that kind of code.
One of the complications of a dynamic language is that when you're compiling a call you don't know anything about what you'll end up calling.
On top of this, Suneido allows "fancier" argument passing and receiving than Java. This means there can be mismatches where a call is "simple" and the function is "fancy", or where the call is "fancy" and the function is simple. So there needs to be adapter functions to handle this. But you still want a "simple" call to a "simple" function to be direct.
Each Suneido function/method is compiled into a Java class that has Java methods for simple calls and fancy calls. If the Suneido function/method is simple, then it implements the simple method and the fancy method is an adapter (that pulls arguments out of a varargs array). (for example, see SuFunction2, the base class for two argument functions) If the Suneido function/method is fancy, then it implements the fancy method and the simple method is an adapter (that builds an argument array).
In cSuneido, all values derive from SuValue and you can simply call virtual methods. But jSuneido uses native types e.g. for strings and numbers. (To avoid the overhead of wrappers.) So you need something between calls and implementations that uses "companion" objects for methods on Java native types. For example, Ops.eval2 (simple method calls with two arguments) looks like:
For SuValue's (which have a lookup method) target simply returns x. For Java native types it returns a companion object (which has a lookup method). lookup then returns the method object.
One issue I ran into is that now I'm using actual Java locals, the code has to pass the Java verifier's checking for possibly uninitialized variables. I ran into a bunch of our Suneido code that wouldn't compile because of this. In some cases the code was correct - the variable would always be initialized, but the logic was too complex for the verifier to confirm it. In other cases the code was just plain wrong, but only in obscure cases that probably never got used. I could have generated code to initialize every variable to satisfy the verifier, but it was easier just to "fix" our Suneido code.
The "fast path" is now quite direct, and doesn't involve too deep a call stack so the JIT compiler should be able to in-line it.
The remaining slow down over Java comes from method lookup and from using "boxed" integers (i.e. Integer instead of int). The usual optimization for method lookup is call site caching. I could roll my own, but it probably makes more sense to wait for JSR 292 in Java 7. Currently, there's not much you can do about having to use boxed integers in a dynamic language. Within functions it would be possible to recognize that a variable was only ever an int and generate code based on that. I'm not sure it's worth it - Suneido code doesn't usually do a lot of integer calculations. It's much more likely to be limited by database speed.
- how functions/methods/blocks are compiled
- how calls are compiled
- the run-time support code e.g. in Ops, SuValue, SuClass, SuInstance, etc.
The downside is that every call had to allocate an argument array, and often re-allocate it to accommodate default arguments or local variables. And access to variables requires larger and presumably slower code. (ALOAD, ICONST, AALOAD/STORE instead of just ALOAD/STORE)
To keep the calling code smaller I was generating calls via helper functions (with variations for 1 to 9 arguments) that built the argument array. One drawback of this approach is that it added another level to the call stack. This can impede optimization since the Hotspot JVM only in-lines a limited depth.
The first step was to compile with Java arguments and locals for functions (and methods) that did not use blocks.
Then I realized that if a block didn't share any variables with its containing scope, it could be compiled as a standalone function. Which is nice because blocks require allocating a new instance of the block for each instantiation, whereas standalone functions don't since they are "static". And it meant that the outer function could then be compiled without the argument array. Determing if a function shares variables with blocks is a little tricky e.g. you have to ignore block parameters, except when you have nested blocks and an inner block references an outer blocks parameter. See AstSharesVars
Where I still needed the argument array I changed the calling code to build it in-line, without a helper function. This is what the Java compiler does with varargs calls. Generating code that is similar to what javac produces is a good idea because the JVM JIT compiler is tuned for that kind of code.
One of the complications of a dynamic language is that when you're compiling a call you don't know anything about what you'll end up calling.
On top of this, Suneido allows "fancier" argument passing and receiving than Java. This means there can be mismatches where a call is "simple" and the function is "fancy", or where the call is "fancy" and the function is simple. So there needs to be adapter functions to handle this. But you still want a "simple" call to a "simple" function to be direct.
Each Suneido function/method is compiled into a Java class that has Java methods for simple calls and fancy calls. If the Suneido function/method is simple, then it implements the simple method and the fancy method is an adapter (that pulls arguments out of a varargs array). (for example, see SuFunction2, the base class for two argument functions) If the Suneido function/method is fancy, then it implements the fancy method and the simple method is an adapter (that builds an argument array).
In cSuneido, all values derive from SuValue and you can simply call virtual methods. But jSuneido uses native types e.g. for strings and numbers. (To avoid the overhead of wrappers.) So you need something between calls and implementations that uses "companion" objects for methods on Java native types. For example, Ops.eval2 (simple method calls with two arguments) looks like:
Object eval2(Object x, Object method, Object arg1, Object arg2) {
return target(x).lookup(method).eval2(x, arg1, arg2);
}For SuValue's (which have a lookup method) target simply returns x. For Java native types it returns a companion object (which has a lookup method). lookup then returns the method object.
One issue I ran into is that now I'm using actual Java locals, the code has to pass the Java verifier's checking for possibly uninitialized variables. I ran into a bunch of our Suneido code that wouldn't compile because of this. In some cases the code was correct - the variable would always be initialized, but the logic was too complex for the verifier to confirm it. In other cases the code was just plain wrong, but only in obscure cases that probably never got used. I could have generated code to initialize every variable to satisfy the verifier, but it was easier just to "fix" our Suneido code.
The "fast path" is now quite direct, and doesn't involve too deep a call stack so the JIT compiler should be able to in-line it.
The remaining slow down over Java comes from method lookup and from using "boxed" integers (i.e. Integer instead of int). The usual optimization for method lookup is call site caching. I could roll my own, but it probably makes more sense to wait for JSR 292 in Java 7. Currently, there's not much you can do about having to use boxed integers in a dynamic language. Within functions it would be possible to recognize that a variable was only ever an int and generate code based on that. I'm not sure it's worth it - Suneido code doesn't usually do a lot of integer calculations. It's much more likely to be limited by database speed.
This Developer's Life
This Developer's Life - Stories About Developers and Their Lives
I just came across this podcast and started listening to it. So far I'm really enjoying it. It's nice to hear more of the human, personal side to "the software life". And I enjoy the music interspersed. Check it out.
I also listen to Scott's Hanselminutes but it's a totally different podcast, much more technical and Microsoft focused. (I use it to keep up on Microsoft technology, which I feel I should be aware of even if I tend to avoid it.)
Wednesday, December 22, 2010
Optimizing jSuneido Argument Passing - part 2
I think I've finished optimizing jSuneido's argument passing and function calling. The "few days" I optimistically estimated in my last post turned into almost a month. I can't believe it's taken me that long! But I can't argue with the calendar.
I gained about 10% in speed. (running the stdlib tests) That might not seem like much, but that means function call overhead was previously more than 10%, presumably quite a bit more since I didn't improve it that much. Considering that's a percentage of total time, including database access, that's quite an improvement.
When I was "finished", I wanted to check that it was actually doing what I thought it was, mostly in terms of which call paths were being used the most.
I could insert some counters, but I figured a profiler would be the best approach. The obvious choice with Eclipse is their Test and Performance Tools Platform. It was easy to install, but when I tried to use it I discovered it's not supported on OS X. It's funny - the better open source tools get, the higher our expectations are. I'm quite annoyed when what I want isn't available!
NetBeans has a profiler built in so I thought I'd try that. I installed the latest copy and imported my Eclipse project. I had some annoying errors because NetBeans assumes that your application code won't reference your test code. But include the tests as part of the application so they can be run outside the development environment. I assume there's some way to re-configure this, but I took the shortcut of simply commenting out the offending code.
I finally got the profiler working, but it was incredibly slow, and crashed with "out of memory". I messed around a bit but didn't want to waste too much time on it.
I went back to manually inserting counters, the profiling equivalent of debugging with print statements. I got mostly the results I expected, except that one of the slow call paths was being executed way more often than I thought it should be.
So I was back to needing a profiler to track down the problem. I'd previously had a trial version of YourKit, so this time I downloaded a trial version of JProfiler. It ran much faster than the NetBeans profiler and gave good results. But unfortunately, it didn't help me find my problem. (Probably just due to my lack of familiarity.)
I resorted to using a breakpoint in the debugger and hitting continue over and over again checking the the call stack each time. I soon spotted the problem. I hadn't bothered optimizing one case in the compiler because I assumed it was rare. And indeed, when I added counters, it was very rare, only occurring a handful of times. The problem was, those handful of occurrences were executed a huge number of times. I needed to be optimizing the cases that occurred a lot dynamically, not statically.
Although I only optimize common, simple cases, they account for about 98% of the calls, which explains why my optimizations made a significant difference.
One of my other questions was how many arguments I needed to optimize for. I started out with handling up to 9 arguments, but based on what I saw, the number of calls dropped off rapidly over 3 or 4 arguments, so I went with optimizing up to 4.
I can't decide whether it's worth buying YourKit or JProfiler. It doesn't seem like I want a profiler often enough to justify buying one. Of course, if I had one, and learnt how it worked, maybe I'd use it more often.
I gained about 10% in speed. (running the stdlib tests) That might not seem like much, but that means function call overhead was previously more than 10%, presumably quite a bit more since I didn't improve it that much. Considering that's a percentage of total time, including database access, that's quite an improvement.
When I was "finished", I wanted to check that it was actually doing what I thought it was, mostly in terms of which call paths were being used the most.
I could insert some counters, but I figured a profiler would be the best approach. The obvious choice with Eclipse is their Test and Performance Tools Platform. It was easy to install, but when I tried to use it I discovered it's not supported on OS X. It's funny - the better open source tools get, the higher our expectations are. I'm quite annoyed when what I want isn't available!
NetBeans has a profiler built in so I thought I'd try that. I installed the latest copy and imported my Eclipse project. I had some annoying errors because NetBeans assumes that your application code won't reference your test code. But include the tests as part of the application so they can be run outside the development environment. I assume there's some way to re-configure this, but I took the shortcut of simply commenting out the offending code.
I finally got the profiler working, but it was incredibly slow, and crashed with "out of memory". I messed around a bit but didn't want to waste too much time on it.
I went back to manually inserting counters, the profiling equivalent of debugging with print statements. I got mostly the results I expected, except that one of the slow call paths was being executed way more often than I thought it should be.
So I was back to needing a profiler to track down the problem. I'd previously had a trial version of YourKit, so this time I downloaded a trial version of JProfiler. It ran much faster than the NetBeans profiler and gave good results. But unfortunately, it didn't help me find my problem. (Probably just due to my lack of familiarity.)
I resorted to using a breakpoint in the debugger and hitting continue over and over again checking the the call stack each time. I soon spotted the problem. I hadn't bothered optimizing one case in the compiler because I assumed it was rare. And indeed, when I added counters, it was very rare, only occurring a handful of times. The problem was, those handful of occurrences were executed a huge number of times. I needed to be optimizing the cases that occurred a lot dynamically, not statically.
Although I only optimize common, simple cases, they account for about 98% of the calls, which explains why my optimizations made a significant difference.
One of my other questions was how many arguments I needed to optimize for. I started out with handling up to 9 arguments, but based on what I saw, the number of calls dropped off rapidly over 3 or 4 arguments, so I went with optimizing up to 4.
I can't decide whether it's worth buying YourKit or JProfiler. It doesn't seem like I want a profiler often enough to justify buying one. Of course, if I had one, and learnt how it worked, maybe I'd use it more often.
Monday, December 20, 2010
Append Only Databases
The more I think about the redirection idea from RethinkDB the more I like it.
The usual way to implement a persistent immutable tree data structure is "copy on write". i.e. when you need to update a node, you copy it and update the copy. The trick is that other nodes that point to this one then also need to be updated (to point to the new node) so they have to be copied as well, and this continues up to the root of the tree. The new root becomes the way to access the new version of the tree. Old roots provide access to old versions of the tree. In memory, this works well since copying nodes is fast and old nodes that are no longer referenced will be garbage collected. But when you're writing to disk, instead of just updating one node, now you have to write every node up the tree to the root. Even if the tree is shallow, as btrees usually are, it's still a lot of extra writing. And on top of the speed issues, it also means your database grows much faster.
The redirection idea replaces creating new copies of all the parent nodes with just adding a "redirection" specifying that accesses to the old version of the leaf node should be redirected to the new leaf node. A new version of the tree now consists of a set of redirections, rather than a new root. And you only need a single redirection for the updated leaf node, regardless of the depth of the tree. There is added overhead checking for redirection as you access the tree, but this is minimal, assuming the redirections are in memory (they're small).
One catch is that redirections will accumulate over time. Although, if you update the same node multiple times (which is fairly common) you will just be "replacing" the same redirection. (Both will exist on disk, but in memory you only need the most recent.)
At first I didn't see the big advantage of redirection. I could get similar performance improvements by lazily writing index nodes.
But the weakness of delayed writes is that if you crash you can't count on the indexes being intact. Any delayed writes that hadn't happened yet would be lost.
The current Suneido database has a similar weakness. Although it doesn't delay writes, it updates index nodes, and if the computer or OS crashes, you don't know if those writes succeeded.
The current solution is that crash recovery simply rebuilds indexes. This is simple and works well for small databases. But for big databases, it can take a significant amount of time, during which the customer's system is down. Crashes are supposed to be rare, but it's amazing how often it happens. (bad hardware, bad power, human factors)
Of course, you don't need the redirection trick to make an append only index. But without it you do a lot more writing to disk and performance suffers.
Even with an append only database, you still don't know for sure that all your data got physically written to disk, especially with memory mapped access, and writes being re-ordered. But the advantage is that you only have to worry about the end of the file, and you can easily use checksums to verify what was written.
On top of the crash recovery benefits, there are a number of other interesting benefits from an append only database. Backups become trivial, even while the database is running - you just copy the file, ignoring any partial writes at the end. Replication is similarly easy - you just copy the new parts as they're added to the database.
Concurrency also benefits, as it usually does with immutable data structures. Read transactions do not require any locking, and so should scale well. Commits need to be appended to the end of the database one at a time, obviously, but writing to a memory mapped file is fast.
Another nice side benefit is that the redirections can also be viewed as a list of the changed nodes. That makes comparing and merging changes a lot easier than tree compares and merges. (When a transaction commits, it needs to merge its changes, which it has been making on top of the state of the database when it started, with the current state of the database, which may have been modified by commits that happened since it started.)
Ironically, I was already using a similar sort of redirection internally to handle updated nodes that hadn't been committed (written) yet. But I never made the connection to tree updating.
I love having a tricky design problem to chew on. Other people might like to do puzzles or play computer games, I like to work on software design problems. I like to get absorbed enough that when I half wake up in the night and stagger to the bathroom, my brain picks up where it left off and I start puzzling over some thorny issue, even though I'm half asleep.
The usual way to implement a persistent immutable tree data structure is "copy on write". i.e. when you need to update a node, you copy it and update the copy. The trick is that other nodes that point to this one then also need to be updated (to point to the new node) so they have to be copied as well, and this continues up to the root of the tree. The new root becomes the way to access the new version of the tree. Old roots provide access to old versions of the tree. In memory, this works well since copying nodes is fast and old nodes that are no longer referenced will be garbage collected. But when you're writing to disk, instead of just updating one node, now you have to write every node up the tree to the root. Even if the tree is shallow, as btrees usually are, it's still a lot of extra writing. And on top of the speed issues, it also means your database grows much faster.
The redirection idea replaces creating new copies of all the parent nodes with just adding a "redirection" specifying that accesses to the old version of the leaf node should be redirected to the new leaf node. A new version of the tree now consists of a set of redirections, rather than a new root. And you only need a single redirection for the updated leaf node, regardless of the depth of the tree. There is added overhead checking for redirection as you access the tree, but this is minimal, assuming the redirections are in memory (they're small).
One catch is that redirections will accumulate over time. Although, if you update the same node multiple times (which is fairly common) you will just be "replacing" the same redirection. (Both will exist on disk, but in memory you only need the most recent.)
At first I didn't see the big advantage of redirection. I could get similar performance improvements by lazily writing index nodes.
But the weakness of delayed writes is that if you crash you can't count on the indexes being intact. Any delayed writes that hadn't happened yet would be lost.
The current Suneido database has a similar weakness. Although it doesn't delay writes, it updates index nodes, and if the computer or OS crashes, you don't know if those writes succeeded.
The current solution is that crash recovery simply rebuilds indexes. This is simple and works well for small databases. But for big databases, it can take a significant amount of time, during which the customer's system is down. Crashes are supposed to be rare, but it's amazing how often it happens. (bad hardware, bad power, human factors)
Of course, you don't need the redirection trick to make an append only index. But without it you do a lot more writing to disk and performance suffers.
Even with an append only database, you still don't know for sure that all your data got physically written to disk, especially with memory mapped access, and writes being re-ordered. But the advantage is that you only have to worry about the end of the file, and you can easily use checksums to verify what was written.
On top of the crash recovery benefits, there are a number of other interesting benefits from an append only database. Backups become trivial, even while the database is running - you just copy the file, ignoring any partial writes at the end. Replication is similarly easy - you just copy the new parts as they're added to the database.
Concurrency also benefits, as it usually does with immutable data structures. Read transactions do not require any locking, and so should scale well. Commits need to be appended to the end of the database one at a time, obviously, but writing to a memory mapped file is fast.
Another nice side benefit is that the redirections can also be viewed as a list of the changed nodes. That makes comparing and merging changes a lot easier than tree compares and merges. (When a transaction commits, it needs to merge its changes, which it has been making on top of the state of the database when it started, with the current state of the database, which may have been modified by commits that happened since it started.)
Ironically, I was already using a similar sort of redirection internally to handle updated nodes that hadn't been committed (written) yet. But I never made the connection to tree updating.
I love having a tricky design problem to chew on. Other people might like to do puzzles or play computer games, I like to work on software design problems. I like to get absorbed enough that when I half wake up in the night and stagger to the bathroom, my brain picks up where it left off and I start puzzling over some thorny issue, even though I'm half asleep.
Sunday, December 05, 2010
The Deep Threat
"It was an illuminating moment: the deep threat isn’t losing my job, it’s working on something for which I lack passion."
- John Nack
- John Nack
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