Ayende @ Rahien

Oren Eini aka Ayende Rahien CEO of Hibernating Rhinos LTD, which develops RavenDB, a NoSQL Open Source Document Database.

You can reach me by:

oren@ravendb.net

+972 52-548-6969

, @ Q j

Posts: 6,865 | Comments: 49,203

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time to read 1 min | 189 words

MVCC stands for Multi Versioning Concurrency Control. This is how you can have both readers & writer at the same time and not have to arrange locks for the two. With LMDB, MVCC is implemented by always creating a new page, never modifying them in place. That also means that when we “free” a page, we need to make sure not to actually use it until all the transactions that could see it has completed.

To be honest, I can’t follow the code. It is somewhat related to me_pghead , but I just can’t follow what is going on. I think that this is related to the way it manage multiple transactions, but I am just unable to follow the code .Maybe it is just that I overloaded my senses with too much C code, I have been diving into this code, and sometimes it feels like this:

That said, I understand how it has to work, so that should be enough for now. Next, I want to see how to do it myself Smile.

time to read 6 min | 1063 words

Okay, so in my last post (and last night, from my perspective), I wrote about the process in which LMDB maintains the B-Tree when it grows. But what about when it shrinks? And how does LMDB handle things like reusing space?

For that matter, we need to discuss another thing. As I understand this right now, LMDB is going to write a page once and only once .And when that is done, that page is now immutable. Updates to this page will result in a new page, and the old one will be marked for reuse. So you don’t actually have to worry about updating the page while others may be reading it. In other words, I would expect this code to use a lot of pages:

image

Actually, I would expect it to use two pages all the time. Alternating between the two after every transaction.

Indeed, following the code, it is easy to see that this magic happens during mdb_page_touch. We find (somehow, not sure how yet) a free page (or create a new one), and we mark the old one for reuse. That means that when you actually write to the data, you aren’t really writing to the old page, you are creating a new one. This drastically reduces a lot of complexity. However, it does mean that the db will be using more space, since every write transaction will use a minimum of one new page (and probably more, considering that there is the B-Tree to maintain). in fact, on average size dbs, I would be surprised if a single transaction could write less than 3 – 4 pages as a minimum. I’ll test the min number of pages per transaction in a bit, right now I want to focus on the implications of that decision.

Well, to start with, concurrency is easier. We aren’t writing to old data, so we have MVCC. The only thing we need to ensure is that we aren’t reusing a page before all of its transactions are complete. But it also has other implications, I haven’t confirmed my suspicions about transaction commits, but because we are writing to new locations, not modifying existing ones, this means that a crash midway would simply restore us to the previous state, and will not corrupt any data.

Since we don’t modify pages, it means that free pages aren’t just things that happen when we delete data, they happen all the time, so it would be interesting to see how LMDB handles them. Here is the relevant piece of the code:

image

So either find me a free page, or allocate a new one. Then add the existing page to the free list for the current transaction. A bit lower in the code we copy the data in the old page to the new one, and we are ready to go.

So, when we make updates, at least in this scenario, we are cycling between two pages, always allocating one and freeing the other, and on the next transaction we go the other way. This is really quite interesting, from the perspective of comparing that to other storage engines. CouchDB work in pretty much the same way, B-Tree with all the associated benefits. But CouchDB model is based on append only, and it cannot reuse the space in the file, which require compactions. LMDB model is much nicer in that regard. Since in both cases, in place updates are not allowed, there is a lot of wasted space that goes just for those updates. In LMDB’s case, that wasted space is a lot bigger, because it works in page sizes, and can reuse them. In CouchDB’s case, it doesn’t reuse space, so it doesn’t use pages (more space efficient this way).

Side note: C’s lack of native data structures beyond array is really annoying. You realize that in C, a Stack is a design pattern?!

And about the minimum number of pages per transaction, let us see what is going on about that. So I wrote the following code:

image

This should generate a deep enough B-Tree to show what I want. And indeed, the action happens here:

image

Both the root node and the data node are modified, because of the cursor stack. It isn’t really a big deal, to be honest, since usually you would only need to update H pages (where H is the height of the tree) and H is very small for B-Trees.

But this leads to me to consider something else. Usually when talking about on disk structures, one of the more important things that you want to keep in mind is reducing seeks. But the B-Tree model that we have here would result in having pages pretty much all over the file. Now, in something like CouchDB, it doesn’t actually matter, because the file is append only, so you always end up scanning from the end of the file backward. But because LMDB is reusing pages, it is entirely possible for a root page to be in the middle of the file, the next level to be in the start and the actual data in the end.

Now, I am guessing that this isn’t actually an issue, because LMDB relies on the OS page cache to handle this, and that would take care of that. In practice, I expect, the branches of the tree are always going to be in memory, since they were the last written and the most accessed.

And that is enough for now. Next, I want to figure out how we return free pages to the system. In order to do that, I think that I’ll need to look at how we transactions are committed.

time to read 3 min | 567 words

Okay, so I have a pretty good idea about how things works now, we have transactions, which contains the dirty pages (and a transaction can store up to 128K of pages, so there is a max about 512MB of changes in a single transaction). While inside the transaction, you are using the local dirty pages to get consistent view of the data, and keep track of the freed pages. But how do we actually get it committed, and how does it works with ensuring the DB is ACID?

A transaction would go to disk in one of two cases, either it has some dirty pages that it needs to flush, or it has to update the db flags (which aren’t really interesting for us right now).

The first thing that happen in the transaction commit is that we save the freed pages using mdb_freelist_save. Now, the interesting about this is that we save the freed pages in the file… in the file. This leads to some really interesting code, in which you are trying to write to the B-Tree about free pages, and during the write, you are freeing pages, so you need to record that too.

The data about free pages is stored in the FREE_DBI, and it is stored there with the transaction id as the key, and the list of freed pages as the value. There is also a bunch of code there that refers to overflow pages, but I am going to skip that for now.

And now, this is probably the most important part:

image

mdb_page_flush() will write all the data to disk. If using writable mmap, by just updating the memory and clearing the dirty flag, or by doing file I/O. The next part, mdb_env_sync basically just call fsync() on the newly written data.

But that just make sure that the data is on disk, it doesn’t commit it yet. This is done via mdb_env_write. Since this is the most essential part of the commit, it is interesting to see how LMDB ensure that this is safe. If you remember, when we created the file we saved the first two pages as copies of the environment metadata. At the time, I wasn’t sure why that was the case. It brought to mind the CouchDB’s method of writing the start of the B-Tree in the start of the file twice, to ensure safety. But I think that the LMDB method is better, what it does, the first time, it create a duplicate entry.

After that, however, it works by alternating between the two. One transaction will flush the data to the first page and the next to the second one. When starting up, LMDB will read the two entries and select the most recent of them. It is a really nice way of handling this. But I think that I would be happy with a better way to handle corruptions. For example, a CRC32 or something like that, to make sure that this isn’t actually a failed write that got midway through.

Next up, I need to figure out how this applies with regards to selecting a free page with respect to the oldest running transaction… But that is a topic for the next post.

time to read 2 min | 386 words

I thought that I would stop a bit from focusing on what the LMDB code is doing in favor to some observations about the code itself. Going into this codebase it like getting hit in the face with a shovel. Now, this might be my personal experience, as someone who has done a lot of managed code work in the past. But I used to be a pretty horrible C/C++ guy (the fact that I say C/C++ should tell you exactly what my level was).

But I don’t think that it was just that. Even beyond the fact that the code is C, and not C++ (which I am much more used to), there is a problem that only become clear to me well after I read the code for the millionth time. It grew. Looking at the way the code is structured, it looks like it was about as nice a C codebase as you can get (don’t get excited, that isn’t saying much). But overtime, features were added, but the general structure of the codebase wasn’t adjusted to account for that.

I am talking about things like this:

image

image

image

There are actually 22 (!) ‘if(IS_LEAF(mp))’ references in the codebase.

Or what about this?

image

image

It looks like certain features (duplicate keys support, for example) was added that had a lot of implication on the code, but it wasn’t refactored accordingly. It make it very hard to go through.

time to read 4 min | 787 words

image

I don’t know if you noticed,  but the LMDB codebase is giving me serious headache issues. The bloody thing is a very dense piece of code, but at the same time, it is also quite interesting. In particular, B-Trees are pretty much The Answer for a lot of on disk data structures, but they tend to be quite hard to handle properly. So I am looking forward to this piece of code, in which I am going to figure out if I can figure out this code. Just to note mdb_page_split is also another 400 lines method with goto sprinkled all over.

In order to do that, I wrote the following code (in a single transaction):

image

And then I spent another few minutes trying to get it to compile. Mostly because I started out with “for (int i=0; …” and C doesn’t allow that (blah!).

Anyway, I got the page to split, and now I want to see how it actually behaves. I am currently at the first part where we take the root (currently leaf) page and turn it into a branch. This is an interesting case of a root split.

We start with:

image

And the first thing we do is to go to this mode:

image

We add an empty implicit pointer to the previous root. But this is really just the beginning, now we need to divide the entries that used to be in the root between the left & right sides. This is made complex by the fact that you might have it setup so it has a few large & small values, so just cutting them in the middle would produce a result that would be too big. At least, that is what a comment says. I am not sure how that can be. We are going from one page to two pages, so I don’t see how you can get into a situation where that would happen. I guess it is time to slot into more code.

Okay, I got it, the issue is that we do a page split because we need to add a new item. So that is the reason we have to jump through those hops. Because we add a new item (that is already too big for the original page, since that is why we are actually splitting that).

Another complex issue with page splits is that they might be recursive. If we need to split a page, we need to add an entry to the parent page, which might cause that page to split, etc…

An interesting observation on the sizes involved, a LMDB page has 4084 bytes available for storage. The data for the page number is 8 bytes long (it uses pointer size page number) and assuming keys that are 16 bytes keys in size (and including about 8 bytes for node header), we get about 128 keys per branch page. Even considering that B-Tree are specifically designed to make themselves efficient in the presence of memory hierarchies, it is  quite impressive.

Consider, assuming a full tree, if we hold just the root and the first level in memory, we would consume about 512kb. And that would give us just one seek to get any of ~2 million items. As an aside, one reason that I like reading this code is that for once, this is a B-Tree implementation that isn’t covered in locking code, which is how this is usually works in RDBMS.

Another aspect that is quite interesting is that this code really shows important aspects for working with relational databases. It is all about keeping things inside the same page, with spill over to overflow pages slowing things down because you need to do another seek. Or a really obvious explanation why page splits are such a bad thing, and a lot of other details that you learn when you go a bit deep into relational databases but (at least for me) have never been real before I started dealing with building databases myself.

time to read 7 min | 1203 words

As mentioned, the data in LMDB is actually stored in page. And I am currently tracking through the process in which we add a new item to the database. The first thing that happen is that we allocate a leaf page. I think that I’ll have to go over how pages are allocated now, which should explain a lot about how LMDB reuses disk space.

A new page is allocated by first finding the oldest transaction that is still active. This is how LMDB implements MVCC. Basically, any free page that is older than any existing transaction is eligible for reuse. The first db (although a better term would be to call it btree, or maybe a table) contains the free pages, and at first we search there for an available page. If we can’t find such a page, we use the end of the file for that. This happens in mdb_page_alloc.

An very interesting aspect is the fact that LMDB allows direct memory writes (with the additional risk of corrupting the db if you messed the data), interestingly, this is done in the following code:

image

If the options allows directly memory writes, you get a point to the mmap file. Otherwise, LMDB will allocate a page (or re-use one that has already been allocated).

I am not really sure what is going on with the insert yet. This is a function pointer (delegate for C#). And it select which behavior will happen later on. I am just not sure what those two different function do yet.

I think I got it, the key is here:

image

You can see that we use the insert method to add the mid variable to the dirty list. So if we give you a direct pointer, we append it to the list. But if we give you allocate a page, we need to add it in order.

The mdb_mid2l_insert will add an item to the list in the appropriate location to ensure sorting. I think that this is done so when we actually write the dirty page to disk, if we do that using file I/O, we will do that in ascending file order, so we can get good seek times from the disk. A new page has 4,084 bytes available for it (12 bytes are taken by header data).

A database is actually created the first time data is written to it. The root page is allocated and recorded. And then the data is added to the page.

As you might recall, data inside a page is kept in a sorted list. But remember that the data is also stored on the page, and there is the whole notion of overflow pages, so I think that I am going to have to draw a picture to figure out what is going on.

image

This is more or less how it works. But I don’t think that I really get it. Note that there are two collections here. First is the positions of nodes in the page, and the second is the node themselves. The reason we have this complexity is that we need to maintain both of them in an efficient manner. And we need to do that without too much copying. Therefor, the list of nodes in the page is in the beginning, growing downward, and the actual nodes are in the end, growing upward. The page is full when you can’t fit anything between those two lists.

A node, by the way, is the LMDB internal name for a key (and maybe data). But I think that I might have an error here, because I don’t see the code here to actually add nodes to the page in a sorted fashion, so it might be doing linear search on the content of a node. I am not tracking through the code for adding a second value into a database. And I think that I have to be wrong about linear node search. The code I was looking at was invoked at the the new db creation section, so it might be taking shortcuts that aren’t generally available.

At any rate, the logic for adding an item goes like this… first we need to find the appropriate page. And we do this by starting from the root and asking for the actual page. Which gets us to mdb_page_get, where we have the following:

image

The really interesting part here is that each transaction have a dirty list of pages, so if you modified a page, you’ll get your own version, even before the data was committed. Otherwise, we will just hand you the current version. This is quite nice.

And then we get to the already familiar mdb_page_search_root function, and I can confirm that the nodes in a page are actually sorted, which only make sense. I am not sure where that happens yet, but I have got the feeling that I am going to see that in a bit.

Okay, I am going to go on a bit of a rant here, mostly against C, to be honest.

image

Take a look at this code. mdb_page_search does something, but what it does it mutate the state for the cursor (mc), and you are then going to access the mc->mc_pg[mc->mc_top] to get the actual result you wanted. To make things more interesting, the is also a mc->mc_ki, which is the index of the node inside the node. And it drove me crazy, because I just couldn’t see the association between those three values, especially because I am so not used to this type of code that I never even considered this as a possibility.

At any rate, now I know how it gets to insert things in the right order. When doing mdb_page_search, it calls to mdb_node_search, which does the appropriate setup to tell the next call where it need to actually do the insert to get things in a sorted fashion. I am currently in the mdb_cursor_put, which is trice cursed and really hard to follow. A 400+ lines method with gotos galore.

But I am in the section where we are actually going to be writing a new value. (new_sub: goto header, if you care). And the code is pretty straight forward from there.

Next up, I want to see how it handles a page split, but that is a subject to another post.

time to read 4 min | 624 words

Okay, I know that I have been critical about the LMDB codebase so far. But one thing that I really want to point out for it is that it was pretty easy to actually get things working on Windows. It wasn’t smooth, in the sense that I had to muck around with the source a bit (hack endianess, remove a bunch of unix specific header files, etc). But that took less than an hour, and it was pretty much it. Since I am by no means an experienced C developer, I consider this a major win. Compare that to leveldb, which flat out won’t run on Windows no matter how much time I spent trying, and it is a pleasure.

Also, stepping through the code I am starting to get a sense of how it works that is much different than the one I had when I just read the code. It is like one of those 3D images, you suddenly see something.

The first thing that became obvious is that I totally missed the significance of the lock file. LMDB actually create two files:

  • lock.mdb
  • data.mdb

Lock.mdb is used to synchronized data between different readers. It seems to mostly be there if you want to have multiple writers using different processes. That is a very interesting model for an embedded database, I’ve to admit. Not something that I think other embedded databases are offering. In order to do that, it create two named mutexes (one for read and one for write).

A side note on Windows support:

LMDB supports Windows, but it is very much a 2nd class citizen. You can see it in things like path not found error turning into a no such process error (because it try to use GetLastError() codes as C codes), or when it doesn’t create a directory even though not creating it would fail.

I am currently debugging through the code and fixing such issues as I go along (but no, I am doing heavy handed magic fixes, just to get past this stage to the next one, otherwise I would have sent a pull request).

Here is one such example. Here is the original code:

image

But ReadFile in Win32 will return false if the file is empty, so you actually need to write something like this to make the code work:

image

Past that hurdle, I think that I get a lot more about what is going on with the way LMDB works than before.

Let us start with the way data.mdb works. It is important to note that for pretty much everything in LMDB we use the system page size. By default, that is 4KB.

The data file starts with 2 pages allocated. Those page contain the following information:

image

Looking back at how CouchDB did things, I am pretty sure that those two pages are going to be pretty important. I am guess that they would always contain the root of the data in the file. There is also the last transaction on them, which is what I imagine determine how something gets committed. I don’t know yet, as I said, guessing based on how CouchDB works.

I’ll continue this review in another time. Next time, transactions…

time to read 5 min | 842 words

Okay, I now have a pretty rough idea about how the codebase actually works. I still think that the codebase is quite ugly. For example, take a look at this:image

The len parameter for CreateFile is whatever to open or create or just open (read only). But why is it in a parameter called len?

Probably because it was just there, and it would be a sin to create another local variable just for this, I guess (in a codebase where a method had > 18 local variables!).  To make things more interesting, in the rest of this method, this is actually a string len variable, sigh.

At any rate, let us actually dig deeper now. The following structure is holding data about a db.

image

This is actually somewhat misleading, at least with regards to how I would think about a db. This is the entry point for all the pages that belong to a specific db. But a db in LMDB is not really the same thing as a db in SQL Server or RavenDB. It all reside in the same file, and you always have at least two. The first one is the free db, which is used to track all the free pages. The second one is the main db. Then you have additional, named databases.

This is used here:

image

This define the metadata for the entire environment. Note that we have the two dbs there in mm_dbs. The mm_txnid denotes the last committed transaction id. This value is what gives LMDB its MVCC support.  The mm_last_pg value is the last used page, any transaction that wants to write will start writing at that value.

Let us see how we deal with pages here, shall we?

image

The first part find try to find a dirty page if we are in a read/write transaction and we haven’t specify that we can write directly to memory. This is done by doing a binary search on the list of dirty pages.

Otherwise, we can just hand the user the actual page by accessing it directly.

Next, let us look where this is actually used. Searching for a page with a specific key in it. This is done mostly in mdb_node_search.

image

This seems to be doing a binary search for the keys inside a specific page (in this case, the page that is at the top of the stack on the cursor). That leads to the conclusion that pages internally have data internally stored as sorted arrays.

And this leads me to another pet peeve with this code base. Take a look at this line:

image

Sure, this is a well known trick to cheaply divide  a number by half, but are you seriously telling me that the compiler isn’t going to optimize  (low + high) / 2 ? To my knowledge, no C compiler updated in the last 10 – 15 years managed to miss this optimization. So why write code that is going to be harder to read?

Okay, so now we know how we search for a specific key inside a page, but how do we get to the actual page that we want to search on? This happens on mdb_page_search_root. Let me see if I can take it apart.

When this method is called, the cursor is setup so the first page on the pages stack is the root page. 

And… that is enough for me. Up until now, I have been trying to just read the code. Not execute it, not debug through it, nothing .Just go over the code one line at a time and figure out what is going on. I actually think that I have a really good grasp about what is going on in there, but I think that this is pretty much all I can do at that point from just reading the code. So I am going to stop now and setup an debug environment so I can work with it, and report my finding from stepping through the code.

time to read 2 min | 371 words

I decided to resume my attempt to figure out the LMDB codebase. Okay, I did some more figuring out and I think that I know where I went wrong. The codebase appears to be trying small enough to fit into the CPU caches, in order to do that, they decided to make it hard enough to make sure it won’t fit into my cache. But I’m trying to work through that.

One of the things that I figured out was that I made a mistake, I kept thinking about databases in the same way you’ll see in RavenDB or SQL Server, as complete separate items. Instead, LMDB does something quite different. It basically uses a single file for everything. This is called the environment, and that can contains named dbs. If you have multiple databases, all of them are going to reside in the same file. The way it works, it creates a file and then map it into memory. On Windows, it actually allocate the space for the file upfront (which doesn’t appears to be necessary).

But the basic idea is that you need to specify upfront the size of the file you want, and that is the maximum data size you have. This can change, but only if you close the environment and start it up again with a higher value. This also explains why you have to specify the number of databases you want to have per environment.  Once you created the environment, everything else become an issue of just managing the pages. In particular, because LMDB only allows a single writer, it doesn’t really have to worry about concurrency issues. It has mapped all the data into memory, and then it is just a matter of creating the appropriate data structure.

A lot of the code is dedicated to managing pages of data, and now that I have gone through enough of the codebase to be sure that I sort of have a vague idea about what is going on I can still say that I think that this is way denser than it should. And I shudder to think what it would take to make any sort of change to this codebase.

time to read 4 min | 659 words

I decided to resume my attempt to figure out the LMDB codebase. The previous attempt ended when my eyes started bleeding a little, but I think that I can get a bit further now.

One thing that I figured out already is that because this is C code, memory management is really painful. I noted previous how good it was from leveldb to use std::string for most allocations, since it frees both caller and lib from having to worry about the memory. LMDB only shows how important that was. Take a look at the following method:

image

Quick, what do you think it does. As it turn out, what is does is update the key to point to the key that the cursor is currently pointing at. The reason for that is that the library doesn’t want to own the memory for key (since then it would have to provide a way to free it).

Now, to be fair, this appears to be an internal method, only used by the lib itself, but such things are pretty pervasive in the codebase, and it is really annoying that the code is all in one spot, with no real structure, since I am still trying to figure out some sort of hierarchy for the code so I could get a grip on what is actually going on.

I decided to just go to the start and figure out how it opens a database:

image

It is interesting that you need a transaction to open the database. However, the opened database survives the transaction closing, and from the docs, if you open a db in a transaction, that is the only thing you can do in that transaction.

I think that I just figured out something, the code in mdb.c is actually written in reverse depth order. So the closer to the end of the file a function is, the more visible it is.

Okay, it appears that there is the notion of multiple dbs, but there is also the notion of the main db. It looks like the main db is also used for tracking things for child dbs. In particular, when opening a named db, we have the following:image

We search for the db information in the main db. As you can see, mdb_cursor_set is actually setting the data on the cursor to the value we passed in. More interesting is what happens if the db is not there. It appears to merely create the db data and set it in the main db. Okay, looking at this function docs, it appears that this is just about allocating a database handle, not about opening the actual database.

I am not really sure that I understand the reasoning behind it, but a new database is actually created in mdb_cursor_put. So only after the first time you create a value, will the db actually be created.

image

I guess that explains why this function goes on for over 400 lines of code and has no less than 10 goto(!) and 7 goto sections!

image

I get that this is C, but come on, seriously!

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