Troubleshooting the “fatal error in commit_refs” Error in Git

Understanding Git Reference Files

Git stores information about commits, branches, tags, and other metadata in plain text reference files inside the .git/ directory. Some key reference files include:

• .git/HEAD – Points to the currently checked out commit
• .git/refs/heads/<branch> – Points to the most recent commit on a branch
• .git/refs/tags/<tag> – Points to the commit for a tag object
• .git/logs/HEAD – Stores previous values of HEAD

When you make a commit, Git needs to update these files to point to the new commit. If these files become corrupted or unwritable, Git will be unable to make the commit and you’ll see the “fatal error in commit_refs” message.

Potential Causes

Here are some common reasons why you might encounter this error:

Corrupted .git directory

The .git/ directory contains all of Git’s internal data including the reference files. If this directory becomes corrupted due to a system crash, hardware issue, or incorrect manual modification, it can lead to errors updating the reference files on commit.

Symptoms of a corrupted .git/ directory include missing files, strange file contents, and “Invalid gitfile format” errors.

Permissions errors

The user running the Git commands needs write permission to the .git/ directory and its contents. If the permissions are restricted, such as in shared repository scenarios, Git may fail to update reference files due to insufficient permissions.

Symptoms of permissions errors include “Access denied” messages when committing and checking out different branches.

Out of disk space

Git needs available disk space to update reference files and write new commit objects. If the file system containing your Git repository runs out of available space, Git will be unable to update reference files and you’ll see errors like “fatal error in commit_refs” on commit.

Symptoms include low disk space warnings from the OS and “No space left on device” error messages in Git.

Host file system issues

On networked or shared file systems like NFS, CIFS, or VFAT, file locking and concurrent write capabilities may be limited. Git requires exclusive locks on reference files when committing, so limitations in your host file system can cause “fatal error in commit_refs” errors.

Symptoms can include seemingly random commit failures, especially when committing from multiple systems against the same repository.

Diagnosing the Issue

To further diagnose the specific cause of the error, check the following:

• File system type – If on a network share, try reproducing the issue on a local ext4 or NTFS file system
• Disk space – Check for low space warnings from the OS or “No space left” errors in Git
• Permissions – Try committing as a privileged user like root or admin
• .git folder – Inspect the .git/ folder for corrupted files or incorrect permissions

Running git fsck can also help identify issues with the Git repository like corrupted objects that may be related to the underlying issue.

The output from git fsck --full along with the file system type and any disk space or permission errors can help narrow down the root cause.

Fixing “fatal: fatal error in commit_refs”

Here are some potential ways to fix the “fatal error in commit_refs” error based on the most common causes:

Fix corrupted .git directory

If .git/ appears corrupted, you can attempt to rebuild the corrupted files.

First, make a backup copy of the .git/ folder. Then try recreating any missing files and fixing corrupted files with these commands:

# Recreate lost HEAD file
git symbolic-ref HEAD refs/heads/main

# Recreate lost refs with 
git update-ref refs/heads/main <commit-hash>
git update-ref refs/tags/<tag-name> <commit-hash> 

# Fix corrupted packed-refs file
git reflog --walk-reflogs refs/heads/main | cut -d" " -f1 | git pack-refs --all

Alternatively, you can try removing and re-cloning the repository or using Git’s replace command to reassemble commit data.

Fix permissions errors

Make sure the user running Git has full read/write permissions to the entire .git/ folder. If permissions are restricted, modify them to allow access:

sudo chown -R $(whoami) <repo>/.git
sudo chmod -R u+rwX <repo>/.git

If hosted on a shared system, check the shared repository’s documentation for recommended permissions.

Free up disk space

Free up space on the file system containing the Git repository. Prune excess Git data, delete unneeded files in the working tree, or expand the storage capacity.

As a workaround, you can temporarily set receive.fsckObjects to 0 in the Git config to disable the disk space check during commits. However, this is not recommended as a permanent solution.

Use a local file system

For repositories hosted on remote shares, try cloning to a local file system like ext4 instead. Local file systems have better reliability for handling file lock contention and concurrent writes.

Or investigate replacing the network file system with one that handles atomic file updates better.

Manually rebuild references

As a last resort, you may be able to manually recreate the lost references by reading commit hashes from reflog history and resetting the HEAD and branch refs manually:

# Checkout previous HEAD from reflog 
git reflog show HEAD@{1} - find old HEAD
git checkout <old-commit-hash>

# Manually reset HEAD and branch refs
git update-ref HEAD <old-commit-hash>
git update-ref refs/heads/main <old-commit-hash>

# Reset any other missing references
git update-ref refs/tags/<tag-name> <commit-hash>

This will attempt to manually restore the references to a valid state. However, other repository corruption may still remain that requires cleanup.

Preventing Future Errors

To help avoid “fatal: fatal error in commit_refs” errors in the future:

• Maintain plenty of available disk space for your repository
• Use a suitable file system like ext4 for storing repositories
• Carefully manage file permissions on shared systems
• Consider hosting Git repos in a transactional file system
• Frequently gc and prune Git repositories to clean up loose objects
• Avoid excessive file system operations during commits like background antivirus scans

Also be extremely careful when manually editing or removing any files in the .git/ directory, as this can easily corrupt the repository.

Summary

The “fatal: fatal error in commit_refs” Git error indicates corrupted reference files and an inability to update refs on commit. Potential solutions include:

• Rebuilding damaged .git/ files with git update-ref
• Fixing permissions errors on .git/
• Freeing up disk space on the file system
• Moving the repository to a reliable local file system
• Manually restoring references from reflog history

Carefully diagnosing the issue can help narrow down the specific causes like file system limitations vs. corrupted Git data. Addressing the underlying file system or disk space concerns is key to reliably fixing and preventing these errors long-term.