Faster garbage collection in S3

When there is a large number of unneeded blocks stored in an S3 bucket, particularly when using PrefixLength: 0, the speed of garbage collection can be severely limited by AWS API rate limits and Arvados’s multi-step trash/delete process.

The multi-step trash/delete process can be short-circuited by setting BlobTrashLifetime to zero and enabling UnsafeDelete on S3-backed volumes. However, on an actively used cluster such a configuration can result in data loss in the rare case where a given block is trashed and then rewritten soon afterward, and S3 processes the write and delete requests in the opposite order.

The following steps can be used to temporarily disable writes on an S3 bucket to enable faster garbage collection without data loss or service interruption. Note that garbage collection on other S3 volumes will be temporarily disabled during this procedure.

  1. Create a new S3 bucket and configure it as an additional volume (this step may be skipped if the configuration already has enough writable volumes that clients will still be able to write blocks while the target volume is read-only). We recommend using PrefixLength: 3 for the new volume because this results in a much higher rate limit for I/O and garbage collection operations compared to the default PrefixLength: 0. If the target volume configuration specifies StorageClasses, use the same values for the new volume.
  2. Shut down the keep-balance service.
  3. Update your configuration as follows:
        BlobTrashLifetime: 0
        BalancePullLimit: 0
          ReadOnly: true
          AllowTrashWhenReadOnly: true
            UnsafeDelete: true
    Note that BlobTrashLifetime: 0 instructs keepstore to delete unneeded blocks outright (bypassing the recoverable trash phase); however, in this mode it will normally not trash any blocks at all on an S3 volume due to the safety issue mentioned above, unless the volume is configured with UnsafeDelete: true.
  4. Restart all keepstore services with the updated configuration.
  5. Start the keep-balance service.
  6. Objects will be deleted immediately instead of being first copied to trash on the S3 volume, which should significantly speed up cleanup of trashed objects. Monitor progress by watching keep-balance logs and metrics. When garbage collection is complete, keep-balance logs will show an empty changeset:
    zzzzz-bi6l4-0123456789abcdef (, disk): ChangeSet{Pulls:0, Trashes:0}
  7. Remove the UnsafeDelete configuration entry on the target volume.
  8. Remove the BlobTrashLifetime configuration entry (or restore it to its previous value).
  9. If the target volume has PrefixLength: 0 and the new volume has PrefixLength: 3, skip the next two steps: new data will be stored on the new volume, some existing data will be moved automatically to other volumes, and some will be left on the target volume as long as it’s needed.
  10. If you want to resume writing new data to the target volume, revert to ReadOnly: false and AllowTrashWhenReadOnly: false on the target volume.
  11. If you want to stop writing new data to the newly created volume, set ReadOnly: true and AllowTrashWhenReadOnly: true on the new volume.
  12. Remove the BalancePullLimit configuration entry (or restore its previous value), and restart keep-balance.
  13. Restart all keepstore services with the updated configuration.

Previous: Measuring deduplication Next: Using Preemptible instances

The content of this documentation is licensed under the Creative Commons Attribution-Share Alike 3.0 United States licence.
Code samples in this documentation are licensed under the Apache License, Version 2.0.