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There are multiple filesystems mounted to each of Pawsey's supercomputers. Each of these filesystems are designed for particular use cases. This page provides a detailed description of these filesystems. |
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Apart from /home, all are Lustre distributed filesystems. Lustre is an open-source, high performance parallel file system optimised for high throughput.
The filesystems are different in many ways and are designed to facilitate different activities in supercomputing. The intended usage for each of them is explained below. Use outside of these purposes may cause poor performance for a particular activity as well as create detrimental impacts to other users.
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The /software filesystem is a Lustre file system with much higher throughput than /home. It is intended for software installations and Slurm batch script templates. Each project has an associated directory on the filesystem whose path is /software/projects/<project>. Within a project directory, each project member has his or her own directory whose full path, /software/projects/<project>/<username>, is contained in the MYSOFTWARE environment variable.
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File permissions and ownerships are also important to consider. The The default permissions of files created by a user on anhy any of the Setonix filesystems is the same, but the default ownerships are different. An example of default properties of a file in /home filesystem is as below:
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Recall that Linux file permissions are broken down into three groups of three:
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-rwx------...
The first set of permissions determines what actions can be performed by the owner of the file. In this case username is the owner, and is allowed to read (r), write (w), and execute the file (x).
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---r-----...
Note that there are 10 characters describing the permissions. The first character is not really a permission, but an indication of the type "file". So a "-" in the first character indicates that myscript.sh is indeed a file. (A "d" would indicate it is not a file but a directory, an "l" would indicate it is a link, etc.). The rest nine characters indicate the permissions of the file, and these permissions are broken down into three groups of three:
- | The - in the first character indicates this is a file. |
rwx | The first set of permissions determines what actions can be performed by other users who belong to the same group as the owner of the file. The group here is the primary or default group In this case |
r-- | The second set of permissions determines what actions can be performed by other users who belong to the same group as the file. The group here is the primary or default group of the file's owner, which is |
------- r-- | The final set of permissions apply to all other users. While the permissions are set to read, the top-level user directory is locked to just the user or project, so others are not able to read, write, or execute files in another group's directories. |
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other users. While the permissions are set to read, the top-level user directory is locked to just the user or project, so others are not able to read, write, or execute files in another group's directories. |
An example of default properties of a file in /software filesystem is as below:
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So, as said, default permissions are the same, but not the default ownerships (the next two words after the permissions).
The next two words after the permissions are, respectively, the owner-name and the group-name of the file. In the case of files created in /home, both the owner and the group are assigned to the username by default. And in the case of files created in /software and /scratch, the default for the group-name is the projectgroup for your project. This is important to note because the quota limits explained in the section above are really counted on the group-name of the files and not the owner-name. So you can consider that the quota limit of all the files with your username as the group-name (added among all our filesytems) is 10k files, which is very limited. This limitation has frequently hit the quota limit for users that do not follow our recommendations for installing software, because some installation tools/commands may override the default group-name of /scratch and software and assign it as username instead of projectgroup.
For the same reason, when transferring files between filesystems, we do not recommend the use of the mv (move) command, because this command preserves the original group-name. Instead, we recommend the use of the cp command (or other tools that allow the assingment of the default ownerships for the destination filesystem). When using cp, do not use the -a or -p flags. If you want to preserve timestamps, use cp --preserve=timestamps.
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Pawsey provides a tool that lets you fix file and directory permissions ownerships on /software. The fix.group.permission.sh script is available in the pawseytools module, which is loaded by default. To use it, enter the script name followed by your group name. For example, if your project ID is projectgroup you would enter this:
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