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Mavibot Transactions

by Emmanuel Lécharny


Posted on Monday Sep 18, 2017 at 02:45PM in Technology


So here is the blog post I promised 6 months ago... It took a bit of a time, due to a family expansion that sucked up pretty much all our free time :-) Let's start stating the obvious !

What is a transaction ?

It's simply 'a unit of work'. That means it's either fully completed, or it never happened. This is critical to database, as it makes certain the database is always in a consistent state. But it's more that that. A Transaction system must provide the following properties (aka ACID) :

Atomicity

You can't split any of the tasks in a transaction. The transaction is always seen as a whole.

Consistency

The database must be valid after the transaction as it was before. It's mainly about guarantying that implied updates (like triggers, constraints, etc) are done within the transaction

Isolation

Here, we are going to use a restricted version of 'isolation' : read committed. That means we guarantee a user will always be able to read consistent data at any time, and will not see 'dirty' data (ie, data being written during a transaction). However, when the transaction is written, then a user doing a second read may not see the same data he got with a previous read. This has some deep impact on the way the user should manage the results : there is no guarantee that a data one get with a read is still valid a few seconds later. We don't lock the database on reads.

Durability

This seems trivial : once committed, the transaction will let the database in a stable state, for ever. It's mainly about guaranteeing that the database survives a crash.

Mavibot transaction implementation

So far, we can assume that being a MVCC system, Mavibot already covers all those aspects :
  • Atomicity : Updates are either done or not, in any case, a new version is not seen until it's fully committed.
  • Consistency : You can't modify some existing version. An update does not change anything i the database, it just adds a new version
  • Isolation : A reader just sees a single version
  • Durability : Once a new version is added, it's visible by readers using it until the readers don't need anymore the data.
The only part we have to take care of is the way we make a new version available to readers : at some point, every new reader should use the new version. In order to make that possible, we just have to switch one single reference to the current version.

Mavibot B-trees

At this point, I have to come back to how B-trees are managed in Mavibot.

A B-tree consist of three separate elements :

  • B-tree info : this data structure stores all the characteristics of the B-tree (it's name, the serializers being used, etc). It's immutable.
  • B-tree header : the starting point from which the B-tree can be pulled from the disk. It points to the root page, and has some extra information about the B-tree (number of elements, revision, Page ID, etc)
  • B-tree root page : the top level page, this is where data are stored (and in all the children nodes and leaves)
Basically, we always use the B-tree header as a reference when reading or updating a B-tree.

Now, we have special B-trees that are used to manage Mavibot :

  • B-tree of B-trees (aka BoB) : This special B-tree contains a reference to all the existing B-trees in Mavibot. It's critical as we need to know about the managed B-trees when we start Mavibot. Every B-tree update will result in this B-tree to be updated.
  • Copied Pages B-tree (aka CPB) : This other special B-tree stores the list of pages ID that has been copied when a new update is injected. This is used by the Pages Reclaimer (which is a process that move old pages into the free-page list. Think of it as a Garbage Collector, because this is exactly what it is). It's updated after each update.
  • Free-Page list : it's a chained list of Pages that can be reused. The Pages Reclaimer will update this list, and the writer will pull pages from this list before fetching some new pages at the end of the file if there is no more free pages.
I won't go any further here, I just wanted to expose those management elements for a better understanding of what will follow.

So what's the point of transaction in Mavibot?

Well, we could live without them, but it would be very inefficient. There are two problems :
  • performance : Flushing the modified pages every time we update a B-tree means we also flush the management B-trees as many times.
  • cross B-tree transaction : This is the critical piece. Users may need to ensure ACID properties across multiple B-trees.
This is where adding a higher level of transaction is required and good to have. Let's see what that means more in detail.

Performance

The following two schema show what happens when we update one single tree 5 times (from the very beginning, with an empty B-tree, up to a point we have added 4 elements in it.

For the purpose of this demonstration, I'm using pages that can contain only 2 elements, but we would get the exact same result with bigger pages (except that it would be way more dreadful to draw :-)

In this schema, each page has a reference (its offset on disk), noted O where 'x' is a integer number.

one-op-per-txn.png

Pretty complicated...

What if we gather updates within a single transaction ?

Here is what we get if 3 of the previous updates are done within one single transaction :

N-op-per-txn.png

As we can see, we have way less pages being created, mainly in the BoB and CPB B-trees. For the record, we avoid flushing 15 pages (out of 36), a 40% improvement.

Cross-B-tree transaction

Is it realistic to gather many operations on many B-trees into a single transaction ? It feels like we may lose some data if the system crashes in the middle of a transaction...

Actually, this is badly needed : it's quite rare that we update only one B-tree. Typically, when using Mavibot in ApacheDS, we want to commit a transaction only when the full LDAP update is completed, and that involves many B-trees :

  • Master table
  • Rdn table (potentially many times, as many as we have RDNs in the DN)
  • Present index
  • ObjectClass index
  • entryCSN index
  • Alias index
  • One-Alias index
  • Sub-Alias index
  • AdministrativeRole index
  • Add all the user defined indexes...
We do want all these index to be updated all at once, otherwise if we have a crash when only a sub-set of them are cmmitted on disk, and teh rest aren't, then we end up with an inconsistent database.

So we want a transaction that covers all those B-trees, and the side benefit is that if any of those B-trees get updated more than once (like the RDN index), we save some disk access. We also save a lot of disk access as the BoB and CPB B-tress get updated at the very end, saving some more disk access.

Side benefits

We can move forward, and let the user decide that transaction should be committed only after a certain amount of updates being applied. This is typically something you want when pushing a lot of modifications in a batch.

The drawback is that you may lose everything from the point you started the transaction if your system crashes at some point before the commit, and it eats some memory as we have to keep the pending modification in memory until the moment the transaction is committed.

It's a balance : speed vs safety.

How it all works

As soon as we start a transaction, we create a copy of the existing B-trees (well, not all of them, just the parts that are to be protected !) so that the existing readers aren't impacted by the on going modifications.

Now, for every modification done in a B-tree, we will copy the modified pages in memory, and update them. If a page has already been copied - and is in memory -, we simply reuse the copy. We have a map of all the in-memory pages for that purpose, and every new copy is put into this map.

When we are done with the modifications, we just have to flush all the pages in this map on the disk : we are done.

Well, not completely... We also have to update the BoB and the CPB B-trees, as usual. The point is that those updates can be done at the very end. Last, not least, we can move the unused pages into the free-pages list.

That is the theory, the implementation is a bit complex, and I won't expose it here...

At this point, a bit of code sample could help :

    // Create the Mavibot database
    RecordManager recordManager = new RecordManager( "MyData.bin" );

    // Create a B-tree : we need to start a transaction...
    try ( WriteTransaction transaction = recordManager.beginWriteTransaction() )
    {
        btree = recordManager.addBTree( transaction, "test", LongSerializer.INSTANCE, StringSerializer.INSTANCE, true );
    }

    // Add some data in the created B-tree.
    try ( WriteTransaction writeTxn = recordManager.beginWriteTransaction() )
    {
        BTree btree = writeTxn.getBTree( "test" );

        btree.insert( writeTxn, 1L, "1" );
        btree.insert( writeTxn, 4L, "4" );
        btree.insert( writeTxn, 2L, "2" );
    }

    // Now, read the B-tree
    try ( Transaction readTxn = recordManager.beginReadTransaction() )
    {
        BTree btree = readTxn.getBTree( "test" );
        TupleCursor cursor = btree.browse( readTxn );

        while ( cursor.hasNext() )
        {
            System.out.println( cursor.next() );
        }
    }
...

This will print "<1,1>", "<2,2>" and "<4,4>".

A few remarks :

  • Transactions are implementing Closeable, which makes it possible to use them in try-with-resource statements. The automatically called close() method will call the transaction commit() method
  • W can see we have two transaction flavors : read and write. The Read transaction just get a context in which it applies, and this context is simply the latest committed version. The idea is that the reads won't be impacted by any forthcoming updates, as it works in its own context.
  • In any case, you have to pull the B-tree you want to update or read from the RecordManager, which manages the whole system

Conclusion

This is just a 10 feet high description of the transaction system we use in Mavibot, it does not go into details, nor it gives all the keys to be able to use Mavibot. The whole idea is to give a sense of what we are working on, and why we need transactions in Mavibot.

We may changes a thing here and there, typically some method names (so don't expect the code to be perfectly representative of what will be the released version). Anyway, it's going to be pretty close !

In the next blog post, I'll talk more in details about the management B-trees (BoB, CPB) and the free-pages management (ie, the Pages Reclaimer). There are quite interesting aspects to discuss when it comes to reclaiming pages :-)


Apache Mavibot history

by Emmanuel Lécharny


Posted on Friday Feb 17, 2017 at 12:23AM in Technology


Introduction

First of all, let me introduce Apache Mavibot: it's a MVCC B+ tree library in Java under an AL 2.0 license (MVCC stands for Multi-Version Concurrency Control). The whole idea is to have a B-tree implementation that never crashes, and does not use locks to protect the data against concurrent access (well … while reading).

The B+ tree is a variant of a B-tree, where values are only stored in the leaves, not in internal nodes.

Ok. Good. You don't know much about Mavibot after this introduction, so I'll dig a bit deeper in this post. Let's start with the original idea.

Apache Directory, CouchDB, and some other databases...

Back in 2009, I was attending the Apache Conference in Oakland. I had been working on the Apache Directory project for a bit more than a 4 years and a half. Apache Directory is a LDAP server written in Java, and we chose to store data in B-trees. There was a very limited choice back then, and the library we used - and still use as of today - was JDBM , a java avatar of GDBM.

JDBM is written in Java, implements B+trees and has transactions support (experimental), but it has one big drawback: it's not a cross-B-trees transaction system. And that does not fit our requirement in LDAP.

An alternative could have been Berkeley DB &tm;, which released a Java edition of its database, but its license was incompatible with the AL 2.0 license. Moreover Berkeley DB was bought by Oracle in 2006, so it was simply not an option.

What’s wrong with using JDBM?

In LDAP, an update operation impacts one single entry but this entry uses many AttributeTypes, which can be indexed. In other words, an update will impact as many B-trees as we have indexes (and a bit more). In order to guarantee that an entry UPDATE is consistent, we must be sure that either all or none of the indexes have been flushed to disk: otherwise we might end with an inconsistent database, where some indexes are up to date when some other aren't.

indexeldap.png

Even worse, in the event of a crash, we might simply not be able to restart the server because the database gets corrupted (and sadly, we are experiencing this problem today...).

So in Oakland, I went to the Apache Couch-DB presentation (sadly, the slides are not anymore available), and was struck by the idea behind their database: MVCC. Crucially when you start to use the database at a given revision, you always see everything associated with this revision, up to the point you are done. Sounds like Git or Subversion … actually, it's pretty much the same mechanism.

Being able to process some read operations on a specific version of the database guarantees that no update will ever corrupt the data being processed. And every time we want to access the database, the very first thing it will do is to select the latest available version: this is all we will see during the operation processing. Perfect when you don't really care about having a fresh view of the stored data at any time, which is the case in LDAP.

But Apache CouchDB was written in Erlang :/ Anyway, the discussion we had with the Directory team was really about moving to a MVCC database.

Transactions

Transactions are another big missing feature in LDAP. This is not something that was in the air back then: it was specified only one year later. Of course, the original specifications said that every operation is atomic, but there is no requirement for multiple operations to be atomic (and we often need to update two entries in LDAP, and to guarantee that those two operations are either completed, or roll-backed). Think about user/group management...

Alex Karasulu always had in mind that we needed a transactional database in Apache Directory, too. And his point was proved correct when years later, we faced the first database corruptions. It's a bit sad that we ignored this aspect for so long :/

Anyway, we needed (a) transactions and (b) a rock solid database that could resist any type of crash.

Locks

For some time, we tried to mitigate the consistency problems we had by adding tons of locks. As we weren't able to protect the database against concurrent reads and writes we made them exclusive (i.e. when some write is processed, no read can be processed). This was slightly better, but it came at a huge cost: a major slowdown when writes were done. Also it was not good enough: long-lasting searches were just killing us, as there were no solution to guarantee that an entry for which we had a reference would still be present in the database when we needed to fetch it. In such cases, we simply ended up by discarding the entry.  Last, not least, a crash in the middle of an update operation would leave the database in a potential inconsistent state, which would make it impossible to start again (this was somehow mitigated by adding a 'repair' mode lately, but this is just an horrible hack).

Mavibot first steps

So we needed something better, which turned out to be Mavibot. We started working on Mavibot in June 2012 (Jun 13 00:04:10 2012, exactly).

The funny thing is that OpenLDAP started to work on the exact same kind of database 1 year before (LMDB) - even if the discussion about the need for such a database started in 2009. Parallel discussions, parallel developments, we have always shared a lot!

The very first released version of Mavibot was out one year later, in June 2013, followed by 7 other versions (all of them milestones). At some point, we added a MVBT partition in ApacheDS, in 2.0.0-M13 (and it was using a SNAPSHOT!!! Mavibot 1.0.0-M1 was used in ApacheDS 2.0.0-M15). This was 'good enough' to have the LDAPJDBM, too ;-), but it didn't offer all we wanted to add: typically, we didn't have transaction support.

So why isn’t Mavibot the Apache Directory Server backend of choice today?

Well, we don't have cross B-tree transactions, so we are pretty much in the same situation as with JDBM (except that it's faster, and we also have a bulk-loader for Mavibot). Adding cross-B-trees transaction is not a piece of cake, and it requires some thinking. Sadly, it arrived at a moment where the team had less time to work on it (new jobs, family, you name it).

So in 2017, the effort has been rebooted, and we do expect to have a working version soon enough!

I'll blog later on about various technical aspects on Apache Mavibot, so keep tuned !