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Tom Clegg, 04/12/2013 05:32 PM


Keep

Keep is a distributed content-addressable storage system designed for high performance in I/O-bound cluster environments.

Notable design goals and features include:

  • High scalability
  • Node-level redundancy
  • Maximum overall throughput in a busy cluster environment
  • Maximum data bandwidth from client to disk
  • Minimum transaction overhead
  • Elimination of disk thrashing (commonly caused by multiple simultaneous readers)
  • Client-controlled redundancy

Design

The above goals are accomplished by the following design features.

  • Data are transferred directly between the client and the physical node where the disk is connected.
  • Data collections are encoded in large (≤64 MiB) blocks to minimize short read/write operations.
  • Each disk accepts only one block-read/write operation at a time. This prevents disk thrashing and maximizes total throughput when many clients compete for a disk.
  • Storage redundancy is directly controlled, and can be easily verified, by the client simply by reading or writing a block of data on multiple nodes.
  • Data block distribution is computed based on a cryptographic digest of the data block being stored or retrieved. This eliminates the need for a central or synchronized database of block storage locations.

Components

The Keep storage system consists of data block read/write services, SDKs, and management agents.

The responsibilities of the Keep service are:

  • Write data blocks
  • When writing: ensure data integrity by comparing client-supplied cryptographic digest and data
  • Read data blocks (subject to permission, which is determined by the system/metadata DB)
  • Send read/write/error event logs to management agents

The responsibilities of the SDK are:

  • When writing: split data into ≤64 MiB chunks
  • When writing: encode directory trees as manifests
  • When writing: write data to the desired number of nodes to achieve storage redundancy
  • After writing: register a collection with Arvados
  • When reading: parse manifests
  • When reading: verify data integrity by comparing locator to MD5 digest of retrieved data

The responsibilities of management agents are:

  • Verify validity of permission tokens
  • Determine which blocks have higher or lower redundancy than required
  • Monitor disk space and move or delete blocks as needed
  • Collect per-user, per-group, per-node, and per-disk usage statistics

Benefits

Keep offers a variety of major benefits over POSIX file systems and other object file storage systems. This is a summary of some of those benefits:

  • Elimination of Duplication — One of the major storage management problems today is the duplication of data. Often researchers will make copies of data for backup or to re-organize files for different projects. Content addressing automatically eliminates unnecessary duplication: if a program saves a file when an identical file has already been stored, Keep simply reports success without having to write a second copy.
  • Canonical Records — Content addressing creates clear and verifiable canonical records for files. By combining Keep with the computation system in Arvados, it becomes trivial to verify the exact file that was used for a computation. By using a collection to define an entire data set (which could be 100s of terabytes or petabytes), you maintain a permanent and verifiable record of which data were used for each computation. The file that defines a collection is very small relative to the underlying data, so you can make as many as you need.
  • Provenance — The combination of Keep and the computation system make it possible to maintain clear provenance for all the data in the system. This has a number of benefits including making it easy to ascertain how data were derived at any point in time.
  • Easy Management of Temporary Data — One benefit of systematic provenance tracking is that Arvados can automatically manage temporary and intermediate data. If you know how a data set or file is was created, you can decide whether it is worthwhile to keep a copy on disk. Knowing what pipeline was run on which input data, how long it took, etc., makes it possible to automate such decisions.
  • Flexible Organization — In Arvados, files are grouped in collections and can be easily tagged with metadata. Different researcher and research teams can manage independent sets of metadata. This makes it possible for researchers to organize files in a variety of different ways without duplicating or physically moving the data. A collection is represented by a text file, which lists the filenames and data blocks comprising the collection, and is itself stored in Keep. As a result, the same underlying data can be referenced by many different collections, without ever copying or moving the data itself.
  • High Reliability — By combining content addressing with an object file store, Keep is fault tolerant across drive and even node failures. The Data Manager monitors the replication level of each data collection. Storage redundancy can thus be adjusted according to the relative importance of individual datasets in addition to default site policy.
  • Easier Tiering of Storage — The Data Manager in Arvados manages the distribution of files to storage systems such as a NAS or cloud back up service. The files are all content addressed and tracked in the metadata database: when a pipeline uses data which is not on the cluster, Arvados can automatically move the necessary data onto the cluster before starting the job. This makes tiered storage feasible without imposing an undue burden on end users.
  • Security and Access Control — Keep can encrypt files on disk and this storage architecture makes the implementation of very fine grained access control significantly easier than traditional POSIX file systems.
  • POSIX Interface — Keep can be mounted as a POSIX filesystems in a virtual machine in order to access data with tools that expect a POSIX interface. Because collections are so flexible, one can easily create many different virtual directory structures for the same underlying files without copying or even reading the underlying data. Combining the native Arvados tools with UNIX pipes provides better performance, but the POSIX mount option is more convenient in some situations.
  • Data Sharing — Keep makes it much easier to share data between clusters in different data centers and organizations. Keep content addresses include information about which cluster data is stored on. With federated clusters, collections of data can reside on multiple clusters, and distribution of computations across clusters can eliminate slow, costly data transfers.