Git
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Background

The index is one of the most important data structures in Git. It represents a virtual working tree state by recording list of paths and their object names and serves as a staging area to write out the next tree object to be committed. The state is "virtual" in the sense that it does not necessarily have to, and often does not, match the files in the working tree.

There are cases Git needs to examine the differences between the virtual working tree state in the index and the files in the working tree. The most obvious case is when the user asks git diff (or its low level implementation, git diff-files) or git-ls-files --modified. In addition, Git internally checks if the files in the working tree are different from what are recorded in the index to avoid stomping on local changes in them during patch application, switching branches, and merging.

In order to speed up this comparison between the files in the working tree and the index entries, the index entries record the information obtained from the filesystem via lstat(2) system call when they were last updated. When checking if they differ, Git first runs lstat(2) on the files and compares the result with this information (this is what was originally done by the ce_match_stat() function, but the current code does it in ce_match_stat_basic() function). If some of these "cached stat information" fields do not match, Git can tell that the files are modified without even looking at their contents.

Note: not all members in struct stat obtained via lstat(2) are used for this comparison. For example, st_atime obviously is not useful. Currently, Git compares the file type (regular files vs symbolic links) and executable bits (only for regular files) from st_mode member, st_mtime and st_ctime timestamps, st_uid, st_gid, st_ino, and st_size members. With a USE_STDEV compile-time option, st_dev is also compared, but this is not enabled by default because this member is not stable on network filesystems. With USE_NSEC compile-time option, st_mtim.tv_nsec and st_ctim.tv_nsec members are also compared. On Linux, this is not enabled by default because in-core timestamps can have finer granularity than on-disk timestamps, resulting in meaningless changes when an inode is evicted from the inode cache. See commit 8ce13b0 of git://git.kernel.org/pub/scm/linux/kernel/git/tglx/history.git ([PATCH] Sync in core time granularity with filesystems, 2005-01-04). This patch is included in kernel 2.6.11 and newer, but only fixes the issue for file systems with exactly 1 ns or 1 s resolution. Other file systems are still broken in current Linux kernels (e.g. CEPH, CIFS, NTFS, UDF), see https://lore.kernel.org/lkml/5577240D.7020309@gmail.com/

Racy Git

There is one slight problem with the optimization based on the cached stat information. Consider this sequence:

: modify 'foo'
$ git update-index 'foo'
: modify 'foo' again, in-place, without changing its size

The first update-index computes the object name of the contents of file foo and updates the index entry for foo along with the struct stat information. If the modification that follows it happens very fast so that the file’s st_mtime timestamp does not change, after this sequence, the cached stat information the index entry records still exactly match what you would see in the filesystem, even though the file foo is now different. This way, Git can incorrectly think files in the working tree are unmodified even though they actually are. This is called the "racy Git" problem (discovered by Pasky), and the entries that appear clean when they may not be because of this problem are called "racily clean".

To avoid this problem, Git does two things:

  1. When the cached stat information says the file has not been modified, and the st_mtime is the same as (or newer than) the timestamp of the index file itself (which is the time git update-index foo finished running in the above example), it also compares the contents with the object registered in the index entry to make sure they match.

  2. When the index file is updated that contains racily clean entries, cached st_size information is truncated to zero before writing a new version of the index file.

Because the index file itself is written after collecting all the stat information from updated paths, st_mtime timestamp of it is usually the same as or newer than any of the paths the index contains. And no matter how quick the modification that follows git update-index foo finishes, the resulting st_mtime timestamp on foo cannot get a value earlier than the index file. Therefore, index entries that can be racily clean are limited to the ones that have the same timestamp as the index file itself.

The callers that want to check if an index entry matches the corresponding file in the working tree continue to call ce_match_stat(), but with this change, ce_match_stat() uses ce_modified_check_fs() to see if racily clean ones are actually clean after comparing the cached stat information using ce_match_stat_basic().

The problem the latter solves is this sequence:

$ git update-index 'foo'
: modify 'foo' in-place without changing its size
: wait for enough time
$ git update-index 'bar'

Without the latter, the timestamp of the index file gets a newer value, and falsely clean entry foo would not be caught by the timestamp comparison check done with the former logic anymore. The latter makes sure that the cached stat information for foo would never match with the file in the working tree, so later checks by ce_match_stat_basic() would report that the index entry does not match the file and Git does not have to fall back on more expensive ce_modified_check_fs().

Runtime penalty

The runtime penalty of falling back to ce_modified_check_fs() from ce_match_stat() can be very expensive when there are many racily clean entries. An obvious way to artificially create this situation is to give the same timestamp to all the files in the working tree in a large project, run git update-index on them, and give the same timestamp to the index file:

$ date >.datestamp
$ git ls-files | xargs touch -r .datestamp
$ git ls-files | git update-index --stdin
$ touch -r .datestamp .git/index

This will make all index entries racily clean. The linux project, for example, there are over 20,000 files in the working tree. On my Athlon 64 X2 3800+, after the above:

$ /usr/bin/time git diff-files
1.68user 0.54system 0:02.22elapsed 100%CPU (0avgtext+0avgdata 0maxresident)k
0inputs+0outputs (0major+67111minor)pagefaults 0swaps
$ git update-index MAINTAINERS
$ /usr/bin/time git diff-files
0.02user 0.12system 0:00.14elapsed 100%CPU (0avgtext+0avgdata 0maxresident)k
0inputs+0outputs (0major+935minor)pagefaults 0swaps

Running git update-index in the middle checked the racily clean entries, and left the cached st_mtime for all the paths intact because they were actually clean (so this step took about the same amount of time as the first git diff-files). After that, they are not racily clean anymore but are truly clean, so the second invocation of git diff-files fully took advantage of the cached stat information.

Avoiding runtime penalty

In order to avoid the above runtime penalty, post 1.4.2 Git used to have a code that made sure the index file got timestamp newer than the youngest files in the index when there are many young files with the same timestamp as the resulting index file would otherwise would have by waiting before finishing writing the index file out.

I suspected that in practice the situation where many paths in the index are all racily clean was quite rare. The only code paths that can record recent timestamp for large number of paths are:

  1. Initial git add . of a large project.

  2. git checkout of a large project from an empty index into an unpopulated working tree.

Note: switching branches with git checkout keeps the cached stat information of existing working tree files that are the same between the current branch and the new branch, which are all older than the resulting index file, and they will not become racily clean. Only the files that are actually checked out can become racily clean.

In a large project where raciness avoidance cost really matters, however, the initial computation of all object names in the index takes more than one second, and the index file is written out after all that happens. Therefore the timestamp of the index file will be more than one seconds later than the youngest file in the working tree. This means that in these cases there actually will not be any racily clean entry in the resulting index.

Based on this discussion, the current code does not use the "workaround" to avoid the runtime penalty that does not exist in practice anymore. This was done with commit 0fc82cff on Aug 15, 2006.