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
The filesystems on Compute Canada systems are with just a few exceptions 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.
Filesystem Layout
Unlike your personal computer, a Compute Canada system will typically have several filesystems and you should ensure that you are using the right filesystem 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 and restrictions.
When you login to a Compute Canada system you will normally begin in your home directory ($HOME) and which is intended to store relatively small text files such as job submission scripts, parameter files and source code.
Quotas
The home directory ($HOME) is restricted to 50 GB of space and 500,000 files per user. It is mainly intended for the storage of source code, parameter files, job submission scripts and so forth. Research groups which require significant amounts of persistent storage may also request space in the project directory ($PROJECT), which offers 10 TB of disk space and 5 million files per research group with a further limitation of 500,000 files per user. The scratch filesystem ($SCRATCH) is as the name suggests intended for temporary storage of intermediate results, checkpoint files and so on. It offers 20 TB of space per user, up to 100 TB for a research group, with 1 million files per user and 10 million per research group.
Backup
The home and project directories are backed up.
Permissions
Like most modern filesystems, those used on the servers of Compute Canada include the idea of permissions to read, write and execute files and directories. When you attempt to read, modify or delete file or descend into a directory the Linux kernel first verifies that you have the right to do this and if not, you'll see the error message "Permission denied". For every given filesystem object, there are three classes of users: the object's owner (normally the user who created the file or directory), the owner's group and finally everyone else. Each of these different user classes can have the right to read, write or execute a filesystem object, so that all told there are nine permissions associated with each such object.
You can see what the current permissions are for a filesystem object with the command
[name@server ~]$ ls -l name_of_object
which will print out the permissions for the owner, the group and everyone else, for example -rw-r--r-- for a file that the owner can read and write but not execute and for which everyone else can only read. You'll also see printed out the name of the object's owner and the group. It's common for people to use "octal notation" when referring to Unix filesystem permissions. In this case, we use three bits to represent the permissions for each category of user, with these three bits then interpreted as a number from 0 to 7 using the formula (read_bit)*2^2 + (write_bit)*2^1 + (execute_bit)*2^0. The file permissions given in the above example would have the octal representation 1*2^2 + 1*2^1 + 0*2^0 = 6 for the owner and 1*2^2 + 0*2^1 + 0*2^0 = 4 for the group and everyone else, so 644 overall. Note that to be able to exercise your rights on a file, you also need to be able to access the directory in which it resides, which means having both read and execute permission (or "5" in octal notation) on the directory in question.
You can alter these permissions using the command chmod in conjunction with the octal notation discussed above, so for example
[name@server ~]$ chmod 777 name_of_file
means that everyone on the machine now has the right to read, write and execute this file. Naturally you can only modify the permissions of a file or directory you own and you can also alter the owner and group by means of the commands chown and chgrp respectively.
The file permissions discussed above have been available in Unix-like operating systems for decades now but they are very coarse-grained since the whole set of users is divided into just three categories: the owner, a group and everyone else. What if I want to allow a single user who isn't in my group to read a file? Do I really need to make the file readable by everyone in that case? Fortunately, the machines at Compute Canada offer what are called "access control lists" (ACLs) to enable extended permissions that are much more fine-grained and can be set on a user-by-user basis if desired. The two commands needed to manipulate these extended permissions are getfacl and setfacl to see and alter the ACL permissions respectively. If I want to allow a single person with username smithj to have read and execute permission on the file my_script.py I can achieve this with the command
[name@server ~]$ setfacl -m u:smithj:rx my_script.py
File Ageing
The scratch filesystem is subjected to periodic purging and any file older than three months (90 days) is a candidate for purging.