The benchmark shows that the database access is quite fast indeed!
And, it scales linearly to the number of keys, with one exception,
getAssociatedKey.
Based on this benchmark, I don't think I need worry about optimising
for cases where all files are locked and the database is mostly empty.
In those cases, database access will be misses, and according to this
benchmark, should add only 50 milliseconds to runtime.
(NB: There may be some overhead to getting the database opened and locking
the handle that this benchmark doesn't see.)
joey@darkstar:~/src/git-annex>./git-annex benchmark
setting up database with 1000
setting up database with 10000
benchmarking keys database/getAssociatedFiles from 1000 (hit)
time 62.77 μs (62.70 μs .. 62.85 μs)
1.000 R² (1.000 R² .. 1.000 R²)
mean 62.81 μs (62.76 μs .. 62.88 μs)
std dev 201.6 ns (157.5 ns .. 259.5 ns)
benchmarking keys database/getAssociatedFiles from 1000 (miss)
time 50.02 μs (49.97 μs .. 50.07 μs)
1.000 R² (1.000 R² .. 1.000 R²)
mean 50.09 μs (50.04 μs .. 50.17 μs)
std dev 206.7 ns (133.8 ns .. 295.3 ns)
benchmarking keys database/getAssociatedKey from 1000 (hit)
time 211.2 μs (210.5 μs .. 212.3 μs)
1.000 R² (0.999 R² .. 1.000 R²)
mean 211.0 μs (210.7 μs .. 212.0 μs)
std dev 1.685 μs (334.4 ns .. 3.517 μs)
benchmarking keys database/getAssociatedKey from 1000 (miss)
time 173.5 μs (172.7 μs .. 174.2 μs)
1.000 R² (0.999 R² .. 1.000 R²)
mean 173.7 μs (173.0 μs .. 175.5 μs)
std dev 3.833 μs (1.858 μs .. 6.617 μs)
variance introduced by outliers: 16% (moderately inflated)
benchmarking keys database/getAssociatedFiles from 10000 (hit)
time 64.01 μs (63.84 μs .. 64.18 μs)
1.000 R² (1.000 R² .. 1.000 R²)
mean 64.85 μs (64.34 μs .. 66.02 μs)
std dev 2.433 μs (547.6 ns .. 4.652 μs)
variance introduced by outliers: 40% (moderately inflated)
benchmarking keys database/getAssociatedFiles from 10000 (miss)
time 50.33 μs (50.28 μs .. 50.39 μs)
1.000 R² (1.000 R² .. 1.000 R²)
mean 50.32 μs (50.26 μs .. 50.38 μs)
std dev 202.7 ns (167.6 ns .. 252.0 ns)
benchmarking keys database/getAssociatedKey from 10000 (hit)
time 1.142 ms (1.139 ms .. 1.146 ms)
1.000 R² (1.000 R² .. 1.000 R²)
mean 1.142 ms (1.140 ms .. 1.144 ms)
std dev 7.142 μs (4.994 μs .. 10.98 μs)
benchmarking keys database/getAssociatedKey from 10000 (miss)
time 1.094 ms (1.092 ms .. 1.096 ms)
1.000 R² (1.000 R² .. 1.000 R²)
mean 1.095 ms (1.095 ms .. 1.097 ms)
std dev 4.277 μs (2.591 μs .. 7.228 μs)
Linking the file to the tmp dir was not necessary in the clean
filter, and it caused the ctime to change, which caused git to think
the file was changed. This caused git status to get slow as it kept
re-cleaning unchanged files.
03cb2c8ece put a cat-file into the fast
bloomfilter generation path. Instead, add another bloom filter which diffs
from the work tree to the index.
Also, pull the sha of the changed object out of the diffs, and cat that
object directly, rather than indirecting through the filename.
Finally, removed some hacks that are unncessary thanks to the worktree to
index diff.
So, we need to look at both the file on disk to see if it's a annex link,
and the file in the index too. lookupFile doesn't look in the index if the file
is not present on disk.
In v5, that was not possible, but it is in v6, and so the test was failing.
Investigating, it turns out that locking was copying the pointer file
content to the annex object despite the content not being present. So,
add a check to prevent that.
Fixes several bugs with updates of pointer files. When eg, running
git annex drop --from localremote
it was updating the pointer file in the local repository, not the remote.
Also, fixes drop ../foo when run in a subdir, and probably lots of other
problems. Test suite drops from ~30 to 11 failures now.
TopFilePath is used to force thinking about what the filepath is relative
to.
The data stored in the sqlite db is still just a plain string, and
TopFilePath is a newtype, so there's no overhead involved in using it in
DataBase.Keys.
The smudge filter does need to be run, because if the key is in the local
annex already (due to renaming, or a copy of a file added, or a new file
added and its content has already arrived), git merge smudges the file and
this should provide its content.
This does probably mean that in merge conflict resolution, git smudges the
existing file, re-copying all its content to it, and then the file is
deleted. So, not efficient.
Several tricky parts:
* When the conflict is just between the same key being locked and unlocked,
the unlocked version wins, and the file is not renamed in this case.
* Need to update associated file map when conflict resolution renames
an unlocked file.
* git merge runs the smudge filter on the conflicting file, and actually
overwrites the file with the same content it had before, and so
invalidates its inode cache. This makes it difficult to know when it's
safe to remove such files as conflict cruft, without going so far as to
compare their entire contents.
Dealt with this by preventing the smudge filter from populating the file
when a merge is run. However, that also prevents the smudge filter being
run for non-conflicting files, so eg moving a file won't put its new
content into place.
* Ideally, if a merge or a merge conflict resolution renames an unlocked
file, the file in the work tree can just be moved, rather than copying
the content to a new worktree file.
This is attempted to be done in merge conflict resolution, but
due to git merge's behavior of running smudge filters, what actually
seems to happen is the old worktree file with the content is deleted and
rewritten as a pointer file, so doesn't get reused.
So, this is probably not as efficient as it optimally could be.
If that becomes a problem, could look into running the merge in a separate
worktree and updating the real worktree more efficiently, similarly to the
direct mode merge. However, the direct mode merge had a lot of bugs, and
I'd rather not use that more error-prone method unless really needed.
Decided it's too scary to make v6 unlocked files have 1 copy by default,
but that should be available to those who need it. This is consistent with
git-annex not dropping unused content without --force, etc.
* Added annex.thin setting, which makes unlocked files in v6 repositories
be hard linked to their content, instead of a copy. This saves disk
space but means any modification of an unlocked file will lose the local
(and possibly only) copy of the old version.
* Enable annex.thin by default on upgrade from direct mode to v6, since
direct mode made the same tradeoff.
* fix: Adjusts unlocked files as configured by annex.thin.
The direct flag is also set when sending unlocked content, to support old
versions of git-annex-shell. At some point, the direct flag will be
removed, and only the unlocked flag will be used.
This fixes a race where the modified file ended up in annex/objects, and
the InodeCache stored in the database was for the modified version, so
git-annex didn't know it had gotten modified.
The race could occur when the smudge filter was running; now it gets the
InodeCache before generating the Key, which avoids the race.
The annex object for it may have been modified due to hard link, and
that should be cleaned up when the new version is added. If another
associated file has the old key's content, that's linked into the annex
object. Otherwise, update location log to reflect that content has been
lost.
1. git add file
2. git commit
3. modify file
4. git commit
5. git reset HEAD^
Before this fix, that resulted in git saying the file was modified. And
indeed, it didn't have the content it should in the just checked out ref,
because step 3 modified the object file for the old key.
This only adds 1 stat to each file fscked for locked files, so
added overhead is minimal.
For unlocked files it has to access the database to see if a file
is modified.
If multiple files point to the same annex object, the user may want to
modify them independently, so don't use a hard link.
Also, check diskreserve when copying.
Note that the implementation uses replaceFile, so that the actual
replacement of the work tree file is atomic. This seems a good property to
have!
It would be possible for unlock in v6 mode to be run on files that do not
have their content present. However, that would be a behavior change from
before, and I don't see any immediate need to support it, so I didn't
implement it.
Before the smudge filter added a trailing newline, but other things that
wrote formatPointer to a file did not.
also some new pointer staging code to use later
The Keys database can hold multiple inode caches for a given key. One for
the annex object, and one for each pointer file, which may not be hard
linked to it.
Inode caches for a key are recorded when its content is added to the annex,
but only if it has known pointer files. This is to avoid the overhead of
maintaining the database when not needed.
When the smudge filter outputs a file's content, the inode cache is not
updated, because git's smudge interface doesn't let us write the file. So,
dropping will fall back to doing an expensive verification then. Ideally,
git's interface would be improved, and then the inode cache could be
updated then too.
Renamed the db to keys, since it is various info about a Keys.
Dropping a key will update its pointer files, as long as their content can
be verified to be unmodified. This falls back to checksum verification, but
I want it to use an InodeCache of the key, for speed. But, I have not made
anything populate that cache yet.
This removes ambiguity, because while someone might have "WORM--foo" in a
file that's not intended to be a git-annex pointer file,
"annex/objects/WORM--foo" is less likely.
Also, 664cc987e8 had a caveat about symlink
targets being parsed as pointer files, and now the same parser is used for
both.
I did not include any hash directories before the key in the pointer file,
as they're not needed. However, if they were included, the parser would
still work ok.
Backend.lookupFile is changed to always fall back to catKey when
operating on a file that's not a symlink.
catKey is changed to understand pointer files, as well as annex symlinks.
Before, catKey needed a file mode witness, to be sure it was looking at a
symlink. That was complicated stuff. Now, it doesn't actually care if a
file in git is a symlink or not; in either case asking git for the content
of the file will get the pointer to the key.
This does mean that git-annex will treat a link
foo -> WORM--bar as a git-annex file, and also treats
a regular file containing annex/objects/WORM--bar as a git-annex file.
Calling catKey could make git-annex commands need to do more work than
before. This would especially be the case if a repo contained many regular
files, and only a few annexed files, as now git-annex will need to ask
git about the contents of the regular files.
Since all places where a repo is used in direct mode need to have git-annex
upgraded before the repo can safely be converted to v6, the upgrade needs
to be manual for now.
I suppose that at some point I'll want to drop all the direct mode support
code. At that point, will stop supporting v5, and will need to auto-upgrade
any remaining v5 repos. If possible, I'd like to carry the direct mode
support for say, a year or so, to give people plenty of time to upgrade and
avoid disruption.
The git filter config can be used to map the single git-annex command to
the 2 actions, and this avoids "git annex clean" being used for this thing,
it might have a better use for that name later.
importfeed just calls addurl functions, so inherits this from it.
Note that addurl still generates a temp file, and uses that key to download
the file. It just adds it to the work tree at the end when the file is small.
Commands that want to use it have to run their seek action inside
allowConcurrentOutput. Which seems reasonable; perhaps some future command
will want to support the -J flag but not use regions.
The region state moved from Annex to MessageState. This makes sense
organizationally, and note that some uses of onLocal use a different Annex
state, but pass the MessageState into it, which is what is needed.
sideAction is for things not generally related to the current action being
performed. And, it adds a newline after the side action. This was not the
right thing to use for stuff like "checksum", where doing a checksum is
part of the git annex get process, and indeed we want it to display
"(checksum...) ok"
There should be no behavior changes in this commit, it just adds a more
expressive data type and adjusts code that had been passing around a [UUID]
or sometimes a Maybe Remote to instead use [VerifiedCopy].
Although, since some functions were taking two different [UUID] lists,
there's some potential for me to have gotten it horribly wrong.
Also, rename lockContent to lockContentExclusive
inAnnexSafe should perhaps be eliminated, and instead use
`lockContentShared inAnnex`. However, I'm waiting on that, as there are
only 2 call sites for inAnnexSafe and it's fiddly.
In c6632ee5c8, it actually only handled
uploading objects to a shared repository. To avoid verification when
downloading objects from a shared repository, was a lot harder.
On the plus side, if the process of downloading a file from a remote
is able to verify its content on the side, the remote can indicate this
now, and avoid the extra post-download verification.
As of yet, I don't have any remotes (except Git) using this ability.
Some more work would be needed to support it in special remotes.
It would make sense for tahoe to implicitly verify things downloaded from it;
as long as you trust your tahoe server (which typically runs locally),
there's cryptographic integrity. OTOH, despite bup being based on shas,
a bup repo under an attacker's control could have the git ref used for an
object changed, and so a bup repo shouldn't implicitly verify. Indeed,
tahoe seems unique in being trustworthy enough to implicitly verify.
* When annex objects are received into git repositories, their checksums are
verified then too.
* To get the old, faster, behavior of not verifying checksums, set
annex.verify=false, or remote.<name>.annex-verify=false.
* setkey, rekey: These commands also now verify that the provided file
matches the key, unless annex.verify=false.
* reinject: Already verified content; this can now be disabled by
setting annex.verify=false.
recvkey and reinject already did verification, so removed now duplicate
code from them. fsck still does its own verification, which is ok since it
does not use getViaTmp, so verification doesn't happen twice when using fsck
--from.
Seems easy, but git ls-files can't list the right subset of files.
So, I wrote a whole new parser for git status output, and converted the
status command to use that.
There are a few other small behavior changes. The order changed. Unlocked
files show as T. In indirect mode, deleted files were not shown before, and
that's fixed. Regular files checked directly into git and modified
were not shown before, and are now.
Fix typo in commit 160d4b9 ("convert Unused, and remove some dead code
for old style option parsing", 2015-07-10), the "git-annex unused
--used-refspec" option was incorrectly changed to --unused-refspec.
Ben Boeckel had a patch, but..
Actually, that was not the only place that used ScheduleIncremental when
built w/o database. Since the data type doesn't need database stuff,
I've instead fixed this build problem by exposing the
ScheduleIncremental constructor to database-less builds.
Note that I had one in Annex.Action.startup too, but it resulted in a weird
message printed by ssh, "channel 2: bad ext data". I don't know why, but
it only happened when transferinfo was run, so I wonder
if 983a95f021 introduced a fragility somehow.
This was potentially a hole in the readonly mode armor even before my last
commit. If the user could push a git-annex branch to a repo, they could get
git-annex-shell to initialize the repo. After my last commit, the user
didn't even need to be allowed to push a branch to init the repo, so
this hole certianly needs to be closed now.
Now it suffices to run git remote add, followed by git-annex sync. Now the
remote is automatically initialized for use by git-annex, where before the
git-annex branch had to manually be pushed before using git-annex sync.
Note that this involved changes to git-annex-shell, so if the remote is
using an old version, the manual push is still needed.
Implementation required git-annex-shell be changed, so configlist can
autoinit a repository even when no git-annex branch has been pushed yet.
Unfortunate because we'll have to wait for it to get deployed to servers
before being able to rely on this change in the documentation.
Did consider making git-annex sync push the git-annex branch to repos that
didn't have a uuid, but this seemed difficult to do without complicating it
in messy ways.
It would be cleaner to split a command out from configlist to handle
the initialization. But this is difficult without sacrificing backwards
compatability, for users of old git-annex versions which would not use the
new command.
Git.Ref.headSha doesn't really work in direct mode as there's not a head,
so it was actually diffing against the empty tree and so not removing any
deleted files. Get the sha of the current branch instead, which is the same
thing Command.Sync does.
* proxy: Fix proxy git commit of non-annexed files in direct mode.
* proxy: If a non-proxied git command, such as git revert
would normally fail because of unstaged files in the work tree,
make the proxied command fail the same way.
* Perform a clean shutdown when --time-limit is reached.
This includes running queued git commands, and cleanup actions normally
run when a command is finished.
* fsck: Commit incremental fsck database when --time-limit is reached.
Previously, some of the last files fscked did not make it into the
database when using --time-limit.
Note that this changes Annex.addCleanup hooks, to run after --time-limit
expires. Fsck was using such a hook to clean up after a
--incremental-schedule, and that shouldn't run when --time-limit exipires
it. So, instead, moved that cleanup code to be run by cleanupIncremental.
Resulted in some data type juggling.
I've seen rss feeds that have no permalinks, only guids (which are
sometimes in the form of permalinks, argh/sigh).
I had previously avoided trusting guids to be globally unique, because my
survey of rss feeds that I subscribe to shows a lot of pretty bad
"guids" like "2 at http://serialpodcast.org" or even worse "oth20150401-hq".
Worry was that two podcasts that are generating guids so badly, that
there's no guarantee they're actually globally unique.
But, I'm seeing too many url changes that result in redundant files, so
let's try this. If feeds are so broken that guids overlap, they could just
as well incorrectly call them permalinks too.
This is a work in progress. It compiles and is able to do basic command
dispatch, including git autocorrection, while using optparse-applicative
for the core commandline parsing.
* Many commands are temporarily disabled before conversion.
* Options are not wired in yet.
* cmdnorepo actions don't work yet.
Also, removed the [Command] list, which was only used in one place.
The branch needs to be created when merging from the remote in sync,
since we diff between it and the remote's sync branch. But git annex merge
should not be creating sync branches.
This is needed because when preferred content matches on files,
the second pass would otherwise want to drop all keys. Using a bloom filter
avoids this, and in the case of a false positive, a key will be left
undropped that preferred content would allow dropping. Chances of that
happening are a mere 1 in 1 million.
This makes git annex unused use around 48 mb more memory than it did before,
but the massive increase in accuracy makes this worthwhile for all but the
smallest systems.
Also, I want to use the bloom filter for sync --all --content, to avoid
dropping files that the preferred content doesn't want, and 1/1000
false positives would be far too many in that use case, even if it were
acceptable for unused.
Actual memory use numbers:
1000: 21.06user 3.42system 0:26.40elapsed 92%CPU (0avgtext+0avgdata 501552maxresident)k
1000000: 21.41user 3.55system 0:26.84elapsed 93%CPU (0avgtext+0avgdata 549496maxresident)k
10000000: 21.84user 3.52system 0:27.89elapsed 90%CPU (0avgtext+0avgdata 549920maxresident)k
Based on these numbers, 10 million seemed a better pick than 1 million.
This removes a bit of complexity, and should make things faster
(avoids tokenizing Params string), and probably involve less garbage
collection.
In a few places, it was useful to use Params to avoid needing a list,
but that is easily avoided.
Problems noticed while doing this conversion:
* Some uses of Params "oneword" which was entirely unnecessary
overhead.
* A few places that built up a list of parameters with ++
and then used Params to split it!
Test suite passes.
This is especially useful because the caller doesn't need to generate valid
url keys, which involves some escaping of characters, and may involve
taking a md5sum of the url if it's too long.
Only the assistant uses these, and only the assistant cleans them up, so
make only git annex transferkeys write them,
There is one behavior change from this. If glacier is being used, and a
manual git annex get --from glacier fails because the file isn't available
yet, the assistant will no longer later see that failed transfer file and
retry the get. Hope no-one depended on that old behavior.
This potentially fixes a numcopies counting bug when dropping --from a
remote, and the local repository is trusted. The local repo would end up in
the list twice, so it would verify one less copy than it was supposed to.
This is a nearly free feature; it piggybacks on the location log lookups
done for the numcopies stats. So, the only extra overhead is updating
the map of repository sizes.
However, I had to switch to Data.Map.Strict, which needs containers 0.5.
If backporting to wheezy, will probably need to revert this commit.
This works, and seems fairly robust. Clean get of 20 files at -J3. At -J10,
there are some messages about ssh multiplexing, probably due to a race
spinning up the ssh connection cacher. But, it manages to get all the files
ok regardless.
The progress bars are a scrambled mess though, due to bugs in
ascii-progress, which I've already filed. Particularly this one:
https://github.com/yamadapc/haskell-ascii-progress/issues/8
