I've run out of storage space

There are two tracked resources in the NeSI filesystem, disk space and inodes (number of files) .

Trying to write to a filesystem over it's inode or disk quota will cause an error (and probably kill your job).

Current file-count and disk space can be found using nn_storage_quota.

Filesystem         Available      Used     Use%     Inodes     IUsed     IUse%
home_user123 20G 1.957G 9.79% 92160 21052 22.84%
project_nesi99999 2T 798G 38.96% 100000 66951 66.95%
nobackup_nesi99999 6.833T 10000000 2691383 26.91%

Note

There is a delay between making changes to a filesystem and seeing the change in nn_storage_quota, immediate file count and disk space can be found using the commands du --inodes and du -h respectively.

There are a few ways to deal with file count problems

  • Use /nesi/nobackup/<projectcode>
    The nobackup directory has a significantly higher inode count and no disk space limits. Files here are not backed up, so best used for intermediary or replaceable data.
  • Delete unnecessary files
    Some applications will generate a large number of files during runtime, using the command du --inodes -d 1 | sort -hr (for inodes) or du -h -d 1 | sort -hr for disk space.  You can then drill down into the directories with the largest file count deleting files as viable.
  • SquashFS archive (recommended)
    Many files can be compressed into a single SquashFS archive. We have written a utility, nn_archive_files, to help with this process. This utility can be run on Māui or Mahuika, but not, as yet, on Māui-ancil; and it can submit the work as a Slurm job, which is preferred. nn_archive_files can take, as trailing options, the same options as mksquashfs, including choice of compression algorithm; see man mksquashfs for more details.
    nn_archive_files -p <project-code> -n <num-processors> -t <time-limit> --verify -- /path/containing/files /path2/containing/files destination.squash
    Then when files need to be accessed again they can be extracted using,
    /usr/sbin/unsquashfs destination.squash
    You can do many other things with SquashFS archives, like quickly list the files in the archive, extract some but not all of the contents, and so on. See man unsquashfs for more details.
  • Tarball (usable, but SquashFS is recommended)
    Many files can be compressed into a single 'tarball' 
    tar -czf name.tar /path/containing/files/
    Then when files need to be accessed again they can be un-tarred using,
    tar -xzf tarname.tar
  • Contact Support
    If you are following the recommendations here yet are still concerned about inodes or disk space, open a support ticket and we can raise the limit for you.
Labels: disk quota exceeded
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