The Derecho scratch file system is a Lustre-based Cray ClusterStor E1000 product configured as shown in the table below. An open-source, parallel system, Lustre will be familiar to users of similar POSIX-compliant file systems. This documentation provides a high-level overview of important Lustre concepts and terminology to help users achieve optimal performance.
Total capacity of the system is 40 TB of metadata and 60 PB of data.
|Metadata servers (MDS)||
|Each MDS has two 200 GbE CX6 Cassini network interfaces configured in an active/passive failover pair.|
|Metadata targets (MDT)||
Each metadata server has a single 12 TB MDT composed of 11 drives in a RAID-10 configuration formatted with ldiskfs (~40 TB usable metadata across the entire file system).
Object storage servers (OSS)
|24||Each OSS has a single 200 GbE CX6 Cassini network interface.|
|Object storage targets (OST)||96||
Each OSS has four 582 TB OSTs. Each OST is composed of 53 drives in a GridRAID configuration formatted with ldiskfs (~60PB usable data across the entire file system).
The notion of file metadata and data as related but separable entities is important to understanding Lustre because it is fundamental to the system's parallelization strategy. In a POSIX file system, the metadata describes information about a file (name, permissions, access controls, timestamps, and so on), and the data contains the contents of the file itself.
Lustre employs one or more metadata servers (MDS) to store the metadata and data layout of each file, and several object storage servers (OSS) to hold the file contents.
Each MDS has one or more metadata targets (MDT), which are storage devices attached to the MDS. Similarly, each OSS has one or more object storage target (OST) storage devices. Typically, the MDTs and OSTs are accessible from two different servers, providing fault tolerance and failover capabilities. A typical Lustre file system is shown in Figure 1 below.
Figure 1: Sample Lustre file system: 4 metadata servers (MDS), 4 object storage servers (OSS). Credit: Introduction to Lustre Wiki.
A file system may employ several metadata servers for scalability and load balancing, and several object storage servers for capacity and performance scalability. When a user creates a file on a Lustre file system, it communicates with an MDS that is responsible for managing the metadata of the file. The MDS also holds the file's striping layout, which is a template used to map file contents (conceptually, data blocks) onto one or more OSTs.
This is important to understand because when users are interacting with a Lustre file, they are really interfacing with several storage servers. Different file operations require different server communication requirements. For example, querying a file's modification time is a metadata-only operation and thus requires communication only with the MDS, whereas querying a file's size involves each OSS over which the file is striped.
File striping is a key feature of Lustre file systems. A file is said to be striped when its sequence of bytes is separated into small chunks, or stripes, so that read and write operations can involve multiple OSTs concurrently. This process is illustrated in Figures 2 and 3. In Figure 2, the sample file is split into five stripes: the first four are the same size while the fifth is smaller and contains the "remainder" of the file. This introduces an important striping concept: the stripe size.
Figure 2: Logical view of a file, broken into five "stripe" segments. The first four are the same size while the fifth is smaller and contains the "remainder" of the file. Credit: Lustre User Guide.
Figure 3 shows how the stripes can be mapped onto several OSTs as defined by the stripe count. In this example, the stripe count is four and the stripe segments are assigned in a round-robin fashion.
Figure 3: Physical view of a file broken into five stripes across four OST devices. Credit: Lustre User Guide.
Striping has important benefits as well as some drawbacks. Striping over more OSTs allows for more bandwidth. In general, as more OSTs are used, more servers are involved, so more network and disk subsystem bandwidth is available. Striping also allows for files larger than any single OST. The primary drawback of striping is overhead: as more OSTs are employed to store a file, more network overhead is required to orchestrate the components.
The preceding discussion is focused on striping the blocks of a given file. When multiple MDTs are present in the file system, as is the case with Derecho, metadata striping is also typically employed and the contents of directories are spread across the available MDSs in the system.
The configurable stripe size and stripe count parameters were at one time the only modifiable parameters available to govern striping behavior, which made it difficult to implement a one-size-fits-all default configuration on large systems with varied use cases. The introduction of progressive file layouts (PFLs) in modern Lustre versions, however, extended the striping concept to multiple, progressive segments of files, as shown in Figure 4.
Figure 4: Sample progressive file layout with three components of different stripe patterns. Credit: PFL Prototype High Level Design.
In Figure 4, a single file is mapped to three separate components, each with a different striping layout. The first component has a stripe size of 1 MB with a stripe count of 1, and is 2 MB in total extent. This means the first 2 MB of the file will be striped over only one OST, in two 1-MB chunks.
The second component begins beyond this 2 MB threshold up to 256 MB size. It employs a stripe size of 1 MB but increases the stripe count to four.
Finally, the third and final component begins when the file size exceeds 256 MB. The stripe size increases to 4 MB and the stripe count to 32 OSTs.
PFLs are useful because they define a template that is much more general than a single stripe size/count pair. They allow small files to be striped over a small number of OSTs and only incur the overhead of additional OST stripes when the file is sufficiently large to benefit from increased bandwidth.
When a file system is constructed, the underlying storage device blocks are segregated into two components: data blocks and inodes.
Data blocks are the most familiar; storing a 1 GB file simply requires a sufficient number of data blocks to hold its contents.
Inodes, by contrast, are index nodes that hold the metadata associated with a file or directory: ownership, time stamps, striping information, and so on. The number of inodes available in a file system is generally fixed and provides a strict limit on the number of files and directories the file system can hold.
This is especially important in a Lustre file system. Its capacity is limited by the size and quantity of OSTs, and its file count capacity is also limited by the number of inodes available on the MDTs. In an extreme example, it is possible to exhaust the available inodes in a file system before its storage capacity by creating many tiny files, so it is important to manage both the overall file system data volume and the file count.
Users have quotas for both data volume and file count on the Derecho Lustre file system. The gladequota utility is preferred for reporting comprehensive storage usage across all GLADE file spaces, including Lustre scratch spaces. Additionally, the lfs quota command can be used to query Lustre-specific quota information.
Many simulation codes produce large quantities of small, diagnostic output files that are useful for diagnosing problems but not often referenced for successful production runs. Consider removing or tarring such files incrementally in your workflow to manage overall file count.
From the background provided above, it is clear not all metadata access requests are equal. Querying a file's timestamps is a cheap operation requiring communication with the appropriate MDT, whereas querying a file's size requires communication with each and every OST holding data stripes. Therefore, it is a best practice to be aware of these performance implications and request only the metadata needed for a given operation.
For example, especially when in a large directory with hundreds of files, avoid typing ls -l if a simple ls will do. The former will communicate with every MDS and OSS in the file system in order to determine the current file size, while the latter is simply an MDS communication. Unnecessary communication can make the file system feel slower to you and other users. When file size is required, limit the request to the file(s) of interest when practical.
Finally, Lustre provides the notion of a "lazy" file size that can be useful in circumstances where approximation is appropriate, for example finding the largest or smallest files in a directory tree. See examples below.
Similarly, avoid excessive file status calls when possible. When repeatedly checking a file's status in a script – inside a loop for example – consider adding a sleep command as a preventive measure. This will prevent flooding the MDS with status requests when your loop executes very quickly.
Lustre's lfs find is an optimized implementation of the familiar find command. It will request only the data required to perform the specified action, and so should be preferred whenever possible. See the examples and use cases below.
Use the familiar df utility to query overall file system capacity. For example, df -h shows the data size of a file system in a human-readable format:
Use df -ih to get the corresponding metadata information:
In the example, the file system overall capacity is 1.2 PB, of which 35 TB is used. The file system has 1.2 billion inodes, 19 million of which are used, providing an additional limit on the total number of files and directories that can be stored.
Running lfs df provides similar information but at the Lustre-aware component level. For example, lfs df -h shows the data size broken down by MDS and OST components:
This sample file system is composed of two MDTs and two OSTs, and lfs df shows the data size of each component. Administrators typically monitor this information to ensure overall file system health, but it can provide useful user diagnostics as well. If one or more of the OSTs is temporarily unavailable due to a storage server issue, for example, lfs df will hang at the affected component, indicating the file system is not healthy. Using lfs dh -ih works similarly, showing the per-component inode usage. Because Lustre file systems typically have a smaller number of MDTs than OSTs, the per-MDT inode usage is an important bound on the overall file system file/directory count capacity.
Tools such as chown, chgrp, and chmod provide a recursive option to allow easy application to all the contents of a given directory. Best practice is to avoid such features and invoke the desired action through lfs find instead.
For example, if you want to change the group ownership of an entire directory tree, you might run a command similar to chgrp -R <newgroup> <dirname>. However, you can do it more efficiently – albeit more verbosely – with lfs find as follows:
To be UNIX-specific about the preceding command, it first asks lfs find to list all the contents of a directory and print them separated with a NULL character ('\0'). This list is then sent to the command xargs, which is told to expect a NULL-separated list with the -0 flag. Then xargs will run the command chgrp <newgroup> on batches of files and split what could be a long list of files into small enough chunks to comply with UNIX's maximum command line argument restrictions. See man lfs-find and man xargs for additional details and examples.
This example shows how to create a tar archive file from a specified directory tree efficiently:
First, lfs find will list all contents of the directory, NULL separated. Then tar will operate on the list of files and subdirectories. Its behavior is modified by the following flags:
The process creates several tar files but does not modify the original source tree directory. One consequence is that storage volume increases during this process until the user removes the directory. An alternative to consider carefully is to also use the --remove-files option. It will remove each source file after it is successfully added to the tar archive, so the overall storage requirements should remain flat. This is just one example of many possibilities with this approach. See man lfs-find and man tar for more ideas.
Determining the precise size of a file on a Lustre system is generally an expensive operation in that it requires communication with every object storage server that stores segments of the file. In some cases, knowing the approximate file size may be sufficient, and it can be obtained solely from the metadata server(s). For example, to locate all files in a directory modified seven or more days ago that are approximately 10 MB or larger, run:
The --lazy flag requests the approximate file size instead of requiring the precise size and the associated communication overhead. That approach can be useful for quickly locating files to clean up and recover quota space. It could also be combined with xargs and rm to remove the files, similar to the chgrp example.