Storage and file management
This is not a complete article: This is a draft, a work in progress that is intended to be published into an article, which may or may not be ready for inclusion in the main wiki. It should not necessarily be considered factual or authoritative.
Overview
Compute Canada provides a wide range of storage options to cover the needs of our very diverse users. These storage solutions range from high-speed temporary local storage to different kinds of long-term storage, so you can choose the storage medium that best corresponds to your needs and usage patterns. In most cases the filesystems on Compute Canada systems are a shared resource and for this reason should be used responsibly - unwise behaviour can negatively affect dozens or hundreds of other users. These filesystems are also designed to store a limited number of very large files, typically binary rather than text files, i.e. they are not directly human-readable. You should therefore avoid storing thousands of small files, where small means less than a few megabytes, particularly in the same directory. A better approach is to use commands like tar or zip to convert a directory containing many small files into a single very large archive file.
It is also your responsibility to manage the age of your stored data: most of the filesystems are not intended to provide an indefinite archiving service so when a given file or directory is no longer needed, you need to move it to a more appropriate filesystem which may well mean your personal workstation or some other storage system under your control. Moving significant amounts of data between your workstation and a Compute Canada system or between two Compute Canada systems should generally be done using Globus.
Note that Compute Canada storage systems are not for personal use and should only be used to store research data.
Storage Types
Unlike your personal computer, a Compute Canada system will typically have several storage spaces or filesystems and you should ensure that you are using the right space for the right task. In this section we will discuss the principal filesystems available on most Compute Canada systems and the intended use of each one along with its characteristics. Storage options are distinguished by the available hardware, access mode and write system. Typically, most Compute Canada systems offer the following storage types:
- Network Filesystem (NFS)
- This type of storage is generally equally visible on both login and compute nodes. This is the appropriate place to put small but important files that are regularly used: source code, programs, job scripts and parameter files. This type of storage offers performance comparable to a conventional hard disk.
- Parallel Filesystem (Lustre, GPFS)
- This type of storage is generally equally visible on both login and compute nodes. Combining multiple disk arrays and fast servers, it offers excellent performance for large files and large input/output operations. Often two types of storage are distinguished on such systems: long term storage and temporary storage (scratch). Performance is subject to variations caused by other users.
- Local Filesystem
- This type of storage consists of a local hard drive attached to each compute node. Its advantage is that its performance is high because it is very rarely shared --- typically, only one user will access a local drive at a time. However, you must copy your files back to another storage medium like the scratch space or project space before your job ends because everything will be cleaned after each job.
- RAM (memory) Filesystem
- This is a filesystem that exists within a compute node's RAM, so its use reduces available memory for computations. Such file systems are very fast for small files and particularly faster than other systems when file access is random. A RAM disk is always cleaned at the end of a job.
The following table summarizes the properties of these storage types.
| Storage Type | Accessibility | Throughput (large operations, > 1 MB per operation) | Latency (small operations) | Longevity |
|---|---|---|---|---|
| Network Filesystem (NFS) | All nodes | Poor | High | Long term |
| Long-Term Parallel Filesystem | All nodes | Fair | High | Long term |
| Short-Term Parallel Filesystem | All nodes | Fair | High | Short term (periodically cleaned) |
| Local Filesystem | Local to the node | Fair | Medium | Very short term |
| Memory (RAM) Filesystem | Local to the node | Good | Very low | Very short term, cleaned after every job |
Best practices
- Only use text format for files that are smaller than a few megabytes.
- As far as possible, use local storage for temporary files.
- If your program must search within a file, it is fastest to do it by first reading it completely before searching, or to use a RAM disk.
- Regularly clean up your data in the scratch and project spaces, because those filesystems are used for huge data collections.
- If you no longer use certain files but they must be retained, archive and compress them, and if possible copy them elsewhere.
- If your needs are not well served by the available storage options please contact us by sending an e-mail to Compute Canada support.
Filesystem Quotas and Policies
In order to ensure that there is adequate space for all Compute Canada users, there are a variety of quotas and policy restrictions concerning back-ups and automatic purging of certain filesystems. Every user has access to the home and scratch spaces by default as well as a certain amount of project space. To have access to the full 10 TB quota of project space users must submit a request while the nearline space is allocated using the annual RAC (resource allocation) process, which can also have the effect of increasing a group's quote for the project and scratch spaces.
| Filesystem | Quotas | Backed up? | Purged? | Available by Default? | Mounted on Compute Nodes? |
|---|---|---|---|---|---|
| Home Space | 50 GB, 500K files | Yes | No | Yes | Yes |
| Scratch Space | 20 TB and 1000K files per user, 100 TB and 10M files per group | No | Yes, all files older than a certain number of days | Yes | Yes |
| Project Space | Up to 10 TB and 5M files per group, 500K files per user | Yes | No | Yes | Yes |
| Nearline Space | 5 TB per group | No | No | No | No |