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Pablo Sánchez edited this page Mar 26, 2025 · 3 revisions

File system

The /home filesystem

Marbits relies on a parallel filesystem (see Lustre below) to store all your data. Hence, the /home filesystem is very small (about 150 GB for all users) and your ~/ directory has to be small too. When activating your user account, a soft link is created such as /home/your-user-name that points to your personal directory in the Lustre filesystem. Please keep your home as lightweight as possible, with configuration files and not much more. Also, feel free to make as many soft links to the Lustre filesystem as you want.

Quota on the /home filesystem

Your /home directory has a quota so that no one can take too much space by mistake and degrade the performance of the master node. Currently, there is a soft quota that will allow you to exceed its value during a grace period of 7 days. After that period, you won't be able to write any more files to your home volume. There's also a hard quota that can never be exceeded.

  • soft quota: 2.5 GB
  • hard quota: 3 GB

Lustre filesystem

Marbits mounts two Lustre parallel filesystems (/mnt/lustre and /mnt/smart) that are shared among several HPC clusters and services within the CMIMA. It allows parallel access to data, providing high speeds, and also distributes data among several servers and the redundancy also protects them.

🚨NOTICE🚨: /mnt/lustre is not reliable at the moment. Please use /mnt/smart for computation, but remove your things as soon as possible to leave space for others!

The Lustre filesystems are not administered by Marbits, as it is a common resource for several CMIMA services. Please use them in a sensible way by following these guidelines:

  • Make your jobs write their output to /mnt/lustre/scratch. When the job has finished, move everything that you want to keep to your Lustre user directory (~/your-user-name. It is a soft link to /mnt/lustre/bio/users/your-user-name). Failing to do so may degrade the backup service, and your jobs could be killed by the monitor of the filesystem. Moving files from one location to another within the same filesystem is immediate, so there's no excuse not to do it! NOTE: Files in /mnt/lustre/scratch older than 3 months will be automatically deleted by the system
  • Try to discard anything that you won't really need. Storage space is expensive, and we are not alone anymore.
  • Compress all the files you can. Many programs accept *.gz files as input...

Quota on the Lustre filesystem

Currently, the "Classic" Lustre filesystem has ~800 TB of storage, the "Smart" lustre has 220 TB. Storage use by the users will be closely monitored by the Lustre administrators. Please adhere to the previously detailed guidelines.

Additional Filesystems

In addition to the Lustre filesystem, Marbits also provides:

  • /mnt/biostore: An NFS-mounted storage for data archival. This filesystem is not optimized for computation, so avoid running jobs from it.
  • /mnt/cold02: Another NFS-mounted storage for long-term data retention. As with /mnt/biostore, this is meant for data storage only, not for computational tasks.

Users should ensure they select the appropriate filesystem based on their needs. For computation, use Lustre (/mnt/lustre, /mnt/smart). For long-term storage, use NFS-mounted filesystems (/mnt/biostore, /mnt/cold02).

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