Hey,
I wanted to run a new experiment and I suddenly got this error message
2025-07-01 13:15:52,296 DEBUG: command: /home/fuchsfa/align/.venv/bin/dvc exp run -v
2025-07-01 13:15:53,949 ERROR: unexpected error - corrupted TREE extension in index
Traceback (most recent call last):
File "/home/fuchsfa/align/.venv/lib/python3.12/site-packages/dvc/cli/__init__.py", line 211, in main
ret = cmd.do_run()
^^^^^^^^^^^^
File "/home/fuchsfa/align/.venv/lib/python3.12/site-packages/dvc/cli/command.py", line 27, in do_run
return self.run()
^^^^^^^^^^
File "/home/fuchsfa/align/.venv/lib/python3.12/site-packages/dvc/commands/experiments/run.py", line 14, in run
self.repo.experiments.run(
File "/home/fuchsfa/align/.venv/lib/python3.12/site-packages/dvc/repo/experiments/__init__.py", line 354, in run
return run(self.repo, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fuchsfa/align/.venv/lib/python3.12/site-packages/dvc/repo/__init__.py", line 58, in wrapper
return f(repo, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fuchsfa/align/.venv/lib/python3.12/site-packages/dvc/repo/experiments/run.py", line 77, in run
return repo.experiments.reproduce_one(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fuchsfa/align/.venv/lib/python3.12/site-packages/dvc/repo/experiments/__init__.py", line 125, in reproduce_one
self.queue_one(exp_queue, **kwargs)
File "/home/fuchsfa/align/.venv/lib/python3.12/site-packages/dvc/repo/experiments/__init__.py", line 136, in queue_one
return self.new(queue, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fuchsfa/align/.venv/lib/python3.12/site-packages/dvc/repo/experiments/__init__.py", line 218, in new
return queue.put(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fuchsfa/align/.venv/lib/python3.12/site-packages/dvc/repo/experiments/queue/workspace.py", line 38, in put
return self._stash_exp(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fuchsfa/align/.venv/lib/python3.12/site-packages/dvc/repo/experiments/queue/base.py", line 309, in _stash_exp
with self.scm.stash_workspace(reinstate_index=True) as workspace:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fuchsfa/.local/share/uv/python/cpython-3.12.7-linux-x86_64-gnu/lib/python3.12/contextlib.py", line 137, in __enter__
return next(self.gen)
^^^^^^^^^^^^^^
File "/home/fuchsfa/align/.venv/lib/python3.12/site-packages/scmrepo/git/__init__.py", line 477, in stash_workspace
rev = self.stash.push(**kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fuchsfa/align/.venv/lib/python3.12/site-packages/scmrepo/git/stash.py", line 36, in push
rev, reset = self.scm._stash_push( # pylint: disable=protected-access
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fuchsfa/align/.venv/lib/python3.12/site-packages/scmrepo/git/__init__.py", line 307, in _backend_func
result = func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/home/fuchsfa/align/.venv/lib/python3.12/site-packages/scmrepo/git/backend/pygit2/__init__.py", line 762, in _stash_push
oid = self.repo.stash(
^^^^^^^^^^^^^^^^
File "/home/fuchsfa/align/.venv/lib/python3.12/site-packages/pygit2/repository.py", line 1159, in stash
check_error(err)
File "/home/fuchsfa/align/.venv/lib/python3.12/site-packages/pygit2/errors.py", line 66, in check_error
raise GitError(message)
_pygit2.GitError: corrupted TREE extension in index
2025-07-01 13:15:54,157 DEBUG: link type reflink is not available ([Errno 95] no more link types left to try out)
2025-07-01 13:15:54,157 DEBUG: Removing '/home/fuchsfa/.oX3xUDLPfYIgRCCJPI-eKw.tmp'
2025-07-01 13:15:54,159 DEBUG: Removing '/home/fuchsfa/.oX3xUDLPfYIgRCCJPI-eKw.tmp'
2025-07-01 13:15:54,161 DEBUG: Removing '/home/fuchsfa/.oX3xUDLPfYIgRCCJPI-eKw.tmp'
2025-07-01 13:15:54,163 DEBUG: Removing '/home/fuchsfa/align/.dvc/cache/files/md5/.8YnQ6J2XqsoNLtEngz99Aw.tmp'
2025-07-01 13:15:54,169 DEBUG: Version info for developers:
DVC version: 3.60.1 (pip)
-------------------------
Platform: Python 3.12.7 on Linux-5.15.0-142-generic-x86_64-with-glibc2.36
Subprojects:
dvc_data = 3.16.10
dvc_objects = 5.1.1
dvc_render = 1.0.2
dvc_task = 0.40.2
scmrepo = 3.3.11
Supports:
http (aiohttp = 3.12.13, aiohttp-retry = 2.9.1),
https (aiohttp = 3.12.13, aiohttp-retry = 2.9.1)
Config:
Global: /home/fuchsfa/.config/dvc
System: /etc/xdg/dvc
Cache types: hardlink, symlink
Cache directory: beegfs on beegfs_nodev
Caches: local
Remotes: local
Workspace directory: beegfs on beegfs_nodev
Repo: dvc, git
Repo.site_cache_dir: /var/tmp/dvc/repo/5bd8845c8855293b65c1034fca596b01
Normal git commands are still working. dvc repro is working as well.
I tried dvc exp clean as well but this changed nothing.
. seems I did not search enough beforehand 