Introducing irmin-pack

by Clément Pascutto on Sep 1st, 2020

irmin-pack is an Irmin storage backend that we developed over the last year specifically to meet the Tezos use-case. Tezos nodes were initially using an LMDB-based backend for their storage, which after only a year of activity led to 250 GB disk space usage, with a monthly growth of 25 GB. Our goal was to dramatically reduce this disk space usage.

Part of the Irmin.2.0.0 release and still under active development, it has been successfully integrated as the storage layer of Tezos nodes and has been running in production for the last ten months with great results. It reduces disk usage by a factor of 10, while still ensuring similar performance and consistency guarantees in a memory-constrained and concurrent environment.

irmin-pack was presented along with Irmin v2 at the OCaml workshop 2020; you can watch the presentation here:

General structure

irmin-pack exposes functors that allow the user to provide arbitrary low-level modules for handling I/O, and provides a fast key-value store interface composed of three components:

  • The pack is used to store the data contained in the Irmin store, as blobs.
  • The dict stores the paths where these blobs should live.
  • The index keeps track of the blobs that are present in the repository by containing location information in the pack.

Each of these use both on-disk storage for persistence and concurrence and various in-memory caches for speed.

Storing the data in the pack file

The pack contains most of the data stored in this Irmin backend. It is an append-only file containing the serialized data stored in the Irmin repository. All three Irmin stores (see our architecture page in the tutorial to learn more) are contained in this single file.

Content and Commit serialization is straightforward through Irmin.Type. They are written along with their length (to allow correct reading) and hash (to enable integrity checks). The hash is used to resolve internal links inside the pack when nodes are written.

The `pack` file

Optimizing large nodes

Serializing nodes is not as simple as contents. In fact, nodes might contain an arbitrarily large number of children, and serializing them as a long list of references might harm performance, as that means loading and writing a large amount of data for each modification, no matter how small this modification might be. Similarly, browsing the tree means reading large blocks of data, even though only one child is needed.

For this reason, we implemented a Patricia Tree representation of internal nodes that allows us to split the child list into smaller parts that can be accessed and modified independently, while still being quickly available when needed. This reduces duplication of tree data in the Irmin store and improves disk access times.

Of course, we provide a custom hashing mechanism, so that hashing the nodes using this partitioning is still backwards-compatible for users who rely on hash information regardless of whether the node is split or not.

Optimizing internal references

In the Git model, all data are content-addressable (i.e. data are always referenced by their hash). This naturally lends to indexing data by hashes on the disk itself (i.e. the links from commits to nodes and from nodes to nodes or contents are realized by hash).

We did not comply to this approach in irmin-pack, for at least two reasons:

  • Referencing by hash does not allow fast recovery of the children, since there is no way to find the relevant blob directly in the pack by providing the hash. We will go into the details of this later in this post.
  • While hashes are being used as simple objects, their size is not negligible. The default hashing function in Irmin is BLAKE2B, which provides 64-byte digests.

Instead, our internal links in the pack file are concretized by the offsets – int64 integers – of the children instead of their hash. Provided that the trees are always written bottom-up (so that children already exist in the pack when their parents are written), this solves both issues above. The data handled by the backend is always immutable, and the file is append-only, ensuring that the links can never be broken.

Of course, that encoding does not break the content-addressable property: one can always retrieve an arbitrary piece of data through its hash, but it allows internal links to avoid that indirection.

Deduplicating the path names through the dict

In fact, the most common operations when using irmin-pack consist of modifying the tree's leaves rather then its shape. This is similar to the way most of us use Git: modifying the contents of files is very frequent, while renaming or adding new files is rather rare. Even still, when writing a node in a new commit, that node must contain the path names of its children, which end up being duplicated a large number of times.

The dict is used for deduplication of path names so that the pack file can uniquely reference them using shorter identifiers. It is composed of an in-memory bidirectional hash table, allowing to query from path to identifier when serializing and referencing, and from identifier to path when deserializing and dereferencing.

To ensure persistence of the data across multiple runs and in case of crashes, the small size of the dict – less than 15 Mb in the Tezos use-case – allows us to write the bindings to a write-only, append-only file that is fully read and loaded on start-up.

We guarantee that the dict memory usage is bounded by providing a capacity parameter. Adding a binding is guarded by this capacity, and will be inlined in the pack file in case this limit has been reached. This scenario does not happen during normal use of irmin-pack, but prevents attacks that would make the memory grow in an unbounded way.

The `dict`

Retrieve the data in the pack by indexing

Since the pack file is append-only, naively reading its data would require a linear search through the whole file for each lookup. Instead, we provide an index that maps hashes of data blocks to their location in the pack file, along with their length. This module allows quick recovery of the values queried by hash.

It provides a simple key-value interface, that actually hides the most complex part of irmin-pack.

type t
val v : readonly:bool -> path:string -> t

val find    : t -> Key.t -> Value.t
val replace : t -> Key.t -> Value.t -> unit
(* ... *)

It has lead most of our efforts in the development of irmin-pack and is now available as a separate library, wisely named index, that you can checkout on GitHub under mirage/index and via opam as the index and index-unix packages.

When index is used inside irmin-pack, the keys are the hashes of the data stored in the backend, and the values are the (offset, length) pair that indicates the location in the pack file. From now on in this post, we will stick to the index abstraction: key and value will refer to the keys and values as viewed by the index.

Our index is split into two major parts. The log is relatively small, and most importantly, bounded; it contains the recently-added bindings. The data is much larger, and contains older bindings.

The log part consists of a hash table associating keys to values. In order to ensure concurrent access, and to be able to recover on a crash, we also maintain a write-only, append-only file with the same contents, such that both always contain exactly the same data at any time.

When a new key-value binding is added index, the value is simply serialized along with its key and added to the log.

An obvious caveat of this approach is that the in-memory representation of the log (the hashtable) is unbounded. It also grows a lot, as the Tezos node stores more that 400 million objects. Our memory constraint obviously does not allow such unbounded structures. This is where the data part comes in.

When the log size reaches a – customizable – threshold, its bindings are flushed into a data component, that may already contain flushed data from former log overloads. We call this operation a merge.

Merging the index

The important invariant maintained by the merge operation is that the data file must remain sorted by the hash of the bindings. This will enable a fast recovery of the data.

During this operation, both the log and the former data are read in sorted order – data is already sorted, and log is small thus easy to sort in memory – and merged into a merging_data file. This file is atomically renamed at the end of the operation to replace the older data while still ensuring correct concurrent accesses.

This operation obviously needs to re-write the whole index, so its execution is very expensive. For this reason, it is performed by a separate thread in the background to still allow regular use of the index and be transparent to the user.

In the meantime, a log_async – similar to log, with a file and a hash table – is used to hold new bindings and ensure the data being merged and the new data are correctly separated. At the end of the merge, the log_async becomes the new log and is cleared to be ready for the next merge.

Recovering the data

This design allows us a fast lookup of the data present in the index. Whenever find or mem is called, we first look into the log, which is simply a call to the corresponding Hashtbl function, since this data is contained in memory. If the data is not found in the log, the data file will be browsed. This means access to recent values is generally faster, because it does not require any access to the disk.

Searching in the data file is made efficient by the invariant that we kept during the merge: the file is sorted by hash. The search algorithm consists in an interpolation search, which is permitted by the even distribution of the hashes that we store. The theoretical complexity of the interpolation search is O(log (log n)), which is generally better than a binary search, provided that the computation of the interpolant is cheaper than reads, which is the case here.

This approach allows us to find the data using approximately 5-6 reading steps in the file, which is good, but still a source of slowdowns. For this reason, we use a fan-out module on top of the interpolation search, able to tell us the exact page in which a given key is located, in constant time, for an additional space cost of ~100 Mb. We use this to find the correct page of the disk, then run the interpolation search in that page only. That approach allows us to find the correct value with a single read in the data file.

Conclusion

This new backend is now used byt the Tezos nodes in production, and manages to reduce the storage size from 250 Gb down to 25 Gb, with a monthly growth rate of 2 Gb , achieving a tenfold reduction.

In the meantime, it provides and single writer, multiple readers access pattern that enables bakers and clients to connect to the same storage while it is operated.

On the memory side, all our components are memory bounded, and the bound is generally customizable, the largest source of memory usage being the log part of the index. While it can be reduced to fit in 1 Gb of memory and run on small VPS or Raspberry Pi, one can easily set a higher memory limit on a more powerful machine, and achieve even better time performance.