Possibility to run borg check for specific segment(s)

[jensb]

Have you checked borgbackup docs, FAQ, and open GitHub issues?

Yes

Is this a BUG / ISSUE report or a QUESTION?

Question

System information. For client/server mode post info for both machines.

Your borg version (borg -V).

v1.2.0 (Ubuntu package)
and
v1.2.7 (fat binary for ARM on Synology)

Operating system (distribution) and version.

Ubuntu 22.04 on x64, and Synology OS on ARM.

Hardware / network configuration, and filesystems used.

ext4

How much data is handled by borg?

~400 GB

Full borg commandline that lead to the problem (leave away excludes and passwords)

borg check, borg delete, borg create - doesn't matter

Describe the problem you're observing.

I canceled a running backup operation (using Ctrl-C), which was backing up to a SMB mount onto a Synology NAS.
After this action I was left with a checkpoint snapshot which apparently has missing archives:

• "data/17/17896" is missing.

borg check on this archive would take over 8 hours (extrapolated) and was canceled twice because of network issues, so I'd like to avoid running it if possible. Deleting the broken snapshot would be OK, however borg delete ::linuxkiste-2024-01-29T20:13:27.checkpoint throws the same exception, so I cannot even delete the snapshot which has this problem (not even with --force).

Would borg check --repair fix this error?
If so, can I run borg check just for this single segment, and/or somehow force-delete the last checkpoint snapshot?
I know I can use --max-duration, but this too starts at the beginning and (probably needlessly) scans >17000 512MB files.

Fetching and building archive index for linuxkiste-2024-01-29T20:13:27.checkpoint ...
Local Exception
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/borg/repository.py", line 1432, in get_fd
    ts, fd = self.fds[segment]
  File "/usr/lib/python3/dist-packages/borg/lrucache.py", line 21, in __getitem__
    value = self._cache[key]  # raise KeyError if not found
KeyError: 17896

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/borg/archiver.py", line 5089, in main
    exit_code = archiver.run(args)
  File "/usr/lib/python3/dist-packages/borg/archiver.py", line 5020, in run
    return set_ec(func(args))
  File "/usr/lib/python3/dist-packages/borg/archiver.py", line 183, in wrapper
    return method(self, args, repository=repository, **kwargs)
  File "/usr/lib/python3/dist-packages/borg/archiver.py", line 1165, in do_delete
    return self._delete_archives(args, repository)
  File "/usr/lib/python3/dist-packages/borg/archiver.py", line 1213, in _delete_archives
    with Cache(repository, key, manifest, progress=args.progress, lock_wait=self.lock_wait) as cache:
  File "/usr/lib/python3/dist-packages/borg/cache.py", line 383, in __new__
    return local()
  File "/usr/lib/python3/dist-packages/borg/cache.py", line 374, in local
    return LocalCache(repository=repository, key=key, manifest=manifest, path=path, sync=sync,
  File "/usr/lib/python3/dist-packages/borg/cache.py", line 493, in __init__
    self.sync()
  File "/usr/lib/python3/dist-packages/borg/cache.py", line 899, in sync
    self.chunks = create_master_idx(self.chunks)
  File "/usr/lib/python3/dist-packages/borg/cache.py", line 853, in create_master_idx
    fetch_and_build_idx(archive_id, decrypted_repository, archive_chunk_idx)
  File "/usr/lib/python3/dist-packages/borg/cache.py", line 752, in fetch_and_build_idx
    csize, data = decrypted_repository.get(archive_id)
  File "/usr/lib/python3/dist-packages/borg/remote.py", line 1087, in get
    return next(self.get_many([key], cache=False))
  File "/usr/lib/python3/dist-packages/borg/remote.py", line 1090, in get_many
    for key, data in zip(keys, self.repository.get_many(keys)):
  File "/usr/lib/python3/dist-packages/borg/repository.py", line 1188, in get_many
    yield self.get(id_)
  File "/usr/lib/python3/dist-packages/borg/repository.py", line 1182, in get
    return self.io.read(segment, offset, id)
  File "/usr/lib/python3/dist-packages/borg/repository.py", line 1548, in read
    fd = self.get_fd(segment)
  File "/usr/lib/python3/dist-packages/borg/repository.py", line 1434, in get_fd
    fd = open_fd()
  File "/usr/lib/python3/dist-packages/borg/repository.py", line 1415, in open_fd
    fd = open(self.segment_filename(segment), 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/....../Backups/Linuxkiste_18.04_Borg/data/17/17896'

Platform: Linux linuxkiste 6.5.0-14-generic #14~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Mon Nov 20 18:15:30 UTC 2 x86_64
Linux: Unknown Linux  
Borg: 1.2.0  Python: CPython 3.10.12 msgpack: 1.0.3 fuse: pyfuse3 3.2.0 [pyfuse3,llfuse]
PID: 54340  CWD: /home/jens
sys.argv: ['/usr/bin/borg', 'delete', '--debug', '::linuxkiste-2024-01-29T20:13:27.checkpoint']
SSH_ORIGINAL_COMMAND: None

Can you reproduce the problem? If so, describe how. If not, describe troubleshooting steps you took before opening the issue.

Yes, every time.

[ThomasWaldmann]

Can you post the output of borg check -v --repair ..., please?

[ThomasWaldmann]

BTW, I can't explain how Ctrl-C would ever lead to that state (a missing, but referenced segment file) in a repository.

So there might be some unidentified additional problem: "why does the repo lose files"?

Maybe consider a fsck on the repo filesystem, smartctl -t long on the repo disk, some sort of memtest on the server and client machine.

[ThomasWaldmann]

Besides the stuff you already noted, there is only borg check --repair --repository-only that uses less time to check/repair a repo, but that only does the low-level checks.

As there is known damage in your repo and we do not really know whether it is just that single segment file, it would be better to run a full check --repair (including the high level archives part).