avoid double work in git-annex init

reconcileStaged was doing a redundant scan to scannAnnexedFiles.

It would probably make sense to move the body of scannAnnexedFiles
into reconcileStaged, the separation does not really serve any purpose.

Sponsored-by: Dartmouth College's Datalad project

Annex/WorkTree.hs

@@ -70,27 +70,29 @@ ifAnnexed file yes no = maybe no yes =<< lookupKey file
 
 {- Find all annexed files and update the keys database for them.
  - 
- - This is expensive, and so normally the associated files are updated
- - incrementally when changes are noticed. So, this only needs to be done
- - when initializing/upgrading a repository.
- -
  - Also, the content for an unlocked file may already be present as
  - an annex object. If so, populate the pointer file with it.
  - But if worktree file does not have a pointer file's content, it is left
  - as-is.
+ -
+ - Normally the keys database is updated incrementally when changes are
+ - noticed. For an initial scan, this is faster than that incremental
+ - update.
  -}
 scanAnnexedFiles :: Annex ()
-scanAnnexedFiles = whenM (inRepo Git.Ref.headExists <&&> not <$> isBareRepo) $ do
-	g <- Annex.gitRepo
-	Database.Keys.runWriter $
-		liftIO . Database.Keys.SQL.dropAllAssociatedFiles
-	(l, cleanup) <- inRepo $ Git.LsTree.lsTree
-		Git.LsTree.LsTreeRecursive
-		(Git.LsTree.LsTreeLong True)
-		Git.Ref.headRef
-	catObjectStreamLsTree l want g go
-	liftIO $ void cleanup
+scanAnnexedFiles = whenM (inRepo Git.Ref.headExists <&&> not <$> isBareRepo) $
+	Database.Keys.runWriter' (Just reconciler) (const noop)
   where
+	reconciler dbh = do
+		g <- Annex.gitRepo
+		liftIO $ Database.Keys.SQL.dropAllAssociatedFiles dbh
+		(l, cleanup) <- inRepo $ Git.LsTree.lsTree
+			Git.LsTree.LsTreeRecursive
+			(Git.LsTree.LsTreeLong True)
+			Git.Ref.headRef
+		catObjectStreamLsTree l want g (go dbh)
+		liftIO $ void cleanup
+	
 	-- Want to process symlinks, and regular files.
 	want i = case Git.Types.toTreeItemType (Git.LsTree.mode i) of
 		Just Git.Types.TreeSymlink -> Just (i, False)
@@ -103,17 +105,16 @@ scanAnnexedFiles = whenM (inRepo Git.Ref.headExists <&&> not <$> isBareRepo) $ d
 		Just n | n < maxPointerSz -> Just (i, True)
 		_ -> Nothing
 	
-	go getnext = liftIO getnext >>= \case
+	go dbh getnext = liftIO getnext >>= \case
 		Just ((i, isregfile), Just c) -> do
-			maybe noop (add i isregfile)
+			maybe noop (add i isregfile dbh)
 				(parseLinkTargetOrPointer (L.toStrict c))
-			go getnext
+			go dbh getnext
 		_ -> return ()
 	
-	add i isregfile k = do
+	add i isregfile dbh k = do
 		let tf = Git.LsTree.file i
-		Database.Keys.runWriter $
-			liftIO . Database.Keys.SQL.addAssociatedFileFast k tf
+		liftIO $ Database.Keys.SQL.addAssociatedFileFast k tf dbh
 		whenM (pure isregfile <&&> inAnnex k) $ do
 			f <- fromRepo $ fromTopFilePath tf
 			liftIO (isPointerFile f) >>= \case

Database/Keys.hs

@@ -23,6 +23,7 @@ module Database.Keys (
 	removeInodeCache,
 	isInodeKnown,
 	runWriter,
+	runWriter',
 ) where
 
 import qualified Database.Keys.SQL as SQL
@@ -73,7 +74,7 @@ runReader a = do
 		v <- a (SQL.ReadHandle qh)
 		return (v, st)
 	go DbClosed = do
-		st' <- openDb True DbClosed
+		st' <- openDb True Nothing DbClosed
 		v <- case st' of
 			(DbOpen qh) -> a (SQL.ReadHandle qh)
 			_ -> return mempty
@@ -87,7 +88,15 @@ runReaderIO a = runReader (liftIO . a)
  -
  - The database is created if it doesn't exist yet. -}
 runWriter :: (SQL.WriteHandle -> Annex ()) -> Annex ()
-runWriter a = do
+runWriter = runWriter' Nothing
+
+runWriterIO :: (SQL.WriteHandle -> IO ()) -> Annex ()
+runWriterIO a = runWriter (liftIO . a)
+
+{- When a reconcile action is passed, it is run by reconcileStaged instead
+ - of its usual scan, and must update the database in the same way. -}
+runWriter' :: Maybe (SQL.WriteHandle -> Annex ()) -> (SQL.WriteHandle -> Annex ()) -> Annex ()
+runWriter' reconciler a = do
 	h <- Annex.getRead Annex.keysdbhandle
 	withDbState h go
   where
@@ -95,15 +104,12 @@ runWriter a = do
 		v <- a (SQL.WriteHandle qh)
 		return (v, st)
 	go st = do
-		st' <- openDb False st
+		st' <- openDb False reconciler st
 		v <- case st' of
 			DbOpen qh -> a (SQL.WriteHandle qh)
 			_ -> error "internal"
 		return (v, st')
 
-runWriterIO :: (SQL.WriteHandle -> IO ()) -> Annex ()
-runWriterIO a = runWriter (liftIO . a)
-
 {- Opens the database, creating it if it doesn't exist yet.
  -
  - Multiple readers and writers can have the database open at the same
@@ -112,10 +118,10 @@ runWriterIO a = runWriter (liftIO . a)
  - the database doesn't exist yet, one caller wins the lock and
  - can create it undisturbed.
  -}
-openDb :: Bool -> DbState -> Annex DbState
-openDb _ st@(DbOpen _) = return st
-openDb False DbUnavailable = return DbUnavailable
-openDb forwrite _ = catchPermissionDenied permerr $ withExclusiveLock gitAnnexKeysDbLock $ do
+openDb :: Bool -> (Maybe (SQL.WriteHandle -> Annex ())) -> DbState -> Annex DbState
+openDb _ _ st@(DbOpen _) = return st
+openDb False _ DbUnavailable = return DbUnavailable
+openDb forwrite reconciler _ = catchPermissionDenied permerr $ withExclusiveLock gitAnnexKeysDbLock $ do
 	dbdir <- fromRepo gitAnnexKeysDb
 	let db = dbdir P.</> "db"
 	dbexists <- liftIO $ R.doesPathExist db
@@ -133,7 +139,7 @@ openDb forwrite _ = catchPermissionDenied permerr $ withExclusiveLock gitAnnexKe
 	
 	open db = do
 		qh <- liftIO $ H.openDbQueue H.MultiWriter db SQL.containedTable
-		reconcileStaged qh
+		reconcileStaged qh reconciler
 		return $ DbOpen qh
 
 {- Closes the database if it was open. Any writes will be flushed to it.
@@ -223,8 +229,8 @@ isInodeKnown i s = or <$> runReaderIO ((:[]) <$$> SQL.isInodeKnown i s)
  - So when using getAssociatedFiles, have to make sure the file still
  - is an associated file.
  -}
-reconcileStaged :: H.DbQueue -> Annex ()
-reconcileStaged qh = do
+reconcileStaged :: H.DbQueue -> Maybe (SQL.WriteHandle -> Annex ()) -> Annex ()
+reconcileStaged qh mreconciler = do
 	gitindex <- inRepo currentIndexFile
 	indexcache <- fromRawFilePath <$> fromRepo gitAnnexKeysDbIndexCache
 	withTSDelta (liftIO . genInodeCache gitindex) >>= \case
@@ -246,12 +252,21 @@ reconcileStaged qh = do
 	go cur indexcache (Just newtree) = do
 		oldtree <- getoldtree
 		when (oldtree /= newtree) $ do
+			case mreconciler of
+				Just reconciler ->
+					reconciler (SQL.WriteHandle qh)
+				Nothing -> noop
 			g <- Annex.gitRepo
-			void $ catstream $ \mdfeeder -> 
-				void $ updatetodiff g
-					(Just (fromRef oldtree)) 
-					(fromRef newtree)
-					(procdiff mdfeeder)
+			void $ catstream $ \mdfeeder -> do
+				case mreconciler of
+					Nothing -> void $ updatetodiff g
+						(Just (fromRef oldtree)) 
+						(fromRef newtree)
+						(procdiff mdfeeder)
+					Just _ -> void $ updatetodiff g
+						Nothing "--staged"
+						(procdiff mdfeeder)
+
 			liftIO $ writeFile indexcache $ showInodeCache cur
 			-- Storing the tree in a ref makes sure it does not
 			-- get garbage collected, and is available to diff

doc/bugs/significant_performance_regression_impacting_datal/comment_4_85d1031d2b51c0fc1271c283d8ee7888._comment

@@ -0,0 +1,14 @@
+[[!comment format=mdwn
+ username="joey"
+ subject="""comment 4"""
+ date="2021-06-07T20:22:24Z"
+ content="""
+Turns out `git-annex init` got a lot slower than it had to, it was doing
+the same kind of scan twice. I think that probably explains much of the
+slowdown you saw. (Although it still needs to do somewhat more work than
+before, but also does it more efficiently than before.)
+
+Also I've optimised the update scan's use of git, around a 20% speedup,
+although I don't know if your test case speed was impacted much by that
+scan anyway.
+"""]]

doc/bugs/significant_performance_regression_impacting_datal/comment_5_b0f1e94e96cf8fe992425cf81f8d1105._comment

@@ -0,0 +1,9 @@
+[[!comment format=mdwn
+ username="joey"
+ subject="""comment 5"""
+ date="2021-06-07T20:42:34Z"
+ content="""
+Looking at the CI log, I don't see any past runs that took 1h 46min.
+A month ago they were taking 2h 6min. Let's see if the changes I'm pushing
+now drop it back to that.
+"""]]

doc/todo/Avoid_lengthy___34__Scanning_for_unlocked_files_...__34__/comment_20_e9a36e9600561201969c4d21499833af._comment

@@ -0,0 +1,16 @@
+[[!comment format=mdwn
+ username="joey"
+ subject="""comment 20"""
+ date="2021-06-07T19:22:03Z"
+ content="""
+Turns out git-annex init was running both scanAnnexedFiles and
+reconcileStaged, which after recent changes to the latter, both do
+close to the same scan when run in a fresh clone. So double work!
+
+Benchmarking with 100,000 files, git-annex init took 88 seconds.  
+Fixed not to use reconcileStaged it took 37 seconds.
+
+(Keeping reconcileStaged and removing scanAnnexedFiles it took 47 seconds.
+That makes sense; reconcileStaged is an incremental updater and is not
+able to use SQL as efficiently as scanAnnexedFiles.)
+"""]]