stop using MissingH for MD5

Cryptonite is faster and allocates less, and I want to get rid of
MissingH use.

Note that the new dependency on memory is free; it's a dependency of
cryptonite.

This commit was supported by the NSF-funded DataLad project.

11 files changed, 97 insertions, 29 deletions

diff --git a/Annex/DirHashes.hs b/Annex/DirHashes.hs
index 82d751eee..f8438484d 100644
--- a/Annex/DirHashes.hs
+++ b/Annex/DirHashes.hs
@@ -1,6 +1,6 @@
 {- git-annex file locations
  -
- - Copyright 2010-2015 Joey Hess <id@joeyh.name>
+ - Copyright 2010-2017 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU GPL version 3 or higher.
  -}
@@ -19,14 +19,15 @@ module Annex.DirHashes (
 
 import Data.Bits
 import Data.Word
-import Data.Hash.MD5
 import Data.Default
+import qualified Data.ByteArray
 
 import Common
 import Key
 import Types.GitConfig
 import Types.Difference
 import Utility.FileSystemEncoding
+import Utility.Hash
 
 type Hasher = Key -> FilePath
 
@@ -62,15 +63,24 @@ hashDirs :: HashLevels -> Int -> String -> FilePath
 hashDirs (HashLevels 1) sz s = addTrailingPathSeparator $ take sz s
 hashDirs _ sz s = addTrailingPathSeparator $ take sz s </> drop sz s
 
+hashDirLower :: HashLevels -> Hasher
+hashDirLower n k = hashDirs n 3 $ take 6 $ show $ md5 $
+	encodeBS $ key2file $ nonChunkKey k
+
+{- This was originally using Data.Hash.MD5 from MissingH. This new version
+- is faster, but ugly as it has to replicate the 4 Word32's that produced. -}
 hashDirMixed :: HashLevels -> Hasher
-hashDirMixed n k = hashDirs n 2 $ take 4 $ display_32bits_as_dir =<< [a,b,c,d]
+hashDirMixed n k = hashDirs n 2 $ take 4 $ concatMap display_32bits_as_dir $
+	encodeWord32 $ map fromIntegral $ Data.ByteArray.unpack $
+		Utility.Hash.md5 $ encodeBS $ key2file $ nonChunkKey k
   where
-	ABCD (a,b,c,d) = md5 $ md5FilePath $ key2file $ nonChunkKey k
-
-hashDirLower :: HashLevels -> Hasher
-hashDirLower n k = hashDirs n 3 $ take 6 $ md5s $ md5FilePath $ key2file $ nonChunkKey k
+	encodeWord32 (b1:b2:b3:b4:rest) =
+		(shiftL b4 24 .|. shiftL b3 16 .|. shiftL b2 8 .|. b1)
+		: encodeWord32 rest
+	encodeWord32 _ = []
 
 {- modified version of display_32bits_as_hex from Data.Hash.MD5
+ - in MissingH
  -   Copyright (C) 2001 Ian Lynagh 
  -   License: Either BSD or GPL
  -}
diff --git a/Annex/Ssh.hs b/Annex/Ssh.hs
index c53802941..a9ff91751 100644
--- a/Annex/Ssh.hs
+++ b/Annex/Ssh.hs
@@ -33,6 +33,7 @@ import Config
 import Annex.Path
 import Utility.Env
 import Utility.FileSystemEncoding
+import Utility.Hash
 import Types.CleanupActions
 import Types.Concurrency
 import Git.Env
@@ -42,7 +43,6 @@ import Annex.Perms
 import Annex.LockPool
 #endif
 
-import Data.Hash.MD5
 import Control.Concurrent.STM
 
 {- Some ssh commands are fed stdin on a pipe and so should be allowed to
@@ -287,7 +287,7 @@ hostport2socket host Nothing = hostport2socket' host
 hostport2socket host (Just port) = hostport2socket' $ host ++ "!" ++ show port
 hostport2socket' :: String -> FilePath
 hostport2socket' s
-	| length s > lengthofmd5s = md5s (Str s)
+	| length s > lengthofmd5s = show $ md5 $ encodeBS s
 	| otherwise = s
   where
 	lengthofmd5s = 32
diff --git a/Annex/VariantFile.hs b/Annex/VariantFile.hs
index 17658a9c6..8365073d5 100644
--- a/Annex/VariantFile.hs
+++ b/Annex/VariantFile.hs
@@ -9,8 +9,7 @@ module Annex.VariantFile where
 
 import Annex.Common
 import Utility.FileSystemEncoding
-
-import Data.Hash.MD5
+import Utility.Hash
 
 variantMarker :: String
 variantMarker = ".variant-"
@@ -42,4 +41,4 @@ variantFile file key
 	doubleconflict = variantMarker `isInfixOf` file
 
 shortHash :: String -> String
-shortHash = take 4 . md5s . md5FilePath
+shortHash = take 4 . show . md5 . encodeBS
diff --git a/Backend/Utilities.hs b/Backend/Utilities.hs
index d1fb94f2a..1691fa2b2 100644
--- a/Backend/Utilities.hs
+++ b/Backend/Utilities.hs
@@ -7,10 +7,9 @@
 
 module Backend.Utilities where
 
-import Data.Hash.MD5
-
 import Annex.Common
 import Utility.FileSystemEncoding
+import Utility.Hash
 
 {- Generates a keyName from an input string. Takes care of sanitizing it.
  - If it's not too long, the full string is used as the keyName.
@@ -20,7 +19,8 @@ genKeyName :: String -> String
 genKeyName s
 	-- Avoid making keys longer than the length of a SHA256 checksum.
 	| bytelen > sha256len =
-		truncateFilePath (sha256len - md5len - 1) s' ++ "-" ++ md5s (Str s)
+		truncateFilePath (sha256len - md5len - 1) s' ++ "-" ++ 
+			show (md5 (encodeBS s))
 	| otherwise = s'
   where
 	s' = preSanitizeKeyName s
diff --git a/Utility/FileSystemEncoding.hs b/Utility/FileSystemEncoding.hs
index ae3bd35d7..785b078ef 100644
--- a/Utility/FileSystemEncoding.hs
+++ b/Utility/FileSystemEncoding.hs
@@ -12,7 +12,6 @@ module Utility.FileSystemEncoding (
 	useFileSystemEncoding,
 	fileEncoding,
 	withFilePath,
-	md5FilePath,
 	decodeBS,
 	encodeBS,
 	decodeW8,
@@ -27,7 +26,6 @@ import qualified GHC.IO.Encoding as Encoding
 import Foreign.C
 import System.IO
 import System.IO.Unsafe
-import qualified Data.Hash.MD5 as MD5
 import Data.Word
 import Data.Bits.Utils
 import Data.List
@@ -101,10 +99,6 @@ _encodeFilePath fp = unsafePerformIO $ do
 	GHC.withCString enc fp (GHC.peekCString Encoding.char8)
 		`catchNonAsync` (\_ -> return fp)
 
-{- Encodes a FilePath into a Md5.Str, applying the filesystem encoding. -}
-md5FilePath :: FilePath -> MD5.Str
-md5FilePath = MD5.Str . _encodeFilePath
-
 {- Decodes a ByteString into a FilePath, applying the filesystem encoding. -}
 decodeBS :: L.ByteString -> FilePath
 #ifndef mingw32_HOST_OS
diff --git a/Utility/Hash.hs b/Utility/Hash.hs
index b6bf996f8..70f826b7a 100644
--- a/Utility/Hash.hs
+++ b/Utility/Hash.hs
@@ -1,8 +1,4 @@
-{- Convenience wrapper around cryptohash/cryptonite.
- -
- - SHA3 hashes are currently only enabled when using cryptonite,
- - because of https://github.com/vincenthz/hs-cryptohash/issues/36
- -}
+{- Convenience wrapper around cryptonite's hashing. -}
 
 module Utility.Hash (
 	sha1,
diff --git a/Utility/LockFile/PidLock.hs b/Utility/LockFile/PidLock.hs
index 87c11c01c..23560fa57 100644
--- a/Utility/LockFile/PidLock.hs
+++ b/Utility/LockFile/PidLock.hs
@@ -25,6 +25,8 @@ import Utility.Path
 import Utility.FileMode
 import Utility.LockFile.LockStatus
 import Utility.ThreadScheduler
+import Utility.Hash
+import Utility.FileSystemEncoding
 import qualified Utility.LockFile.Posix as Posix
 
 import System.IO
@@ -33,7 +35,6 @@ import Data.Maybe
 import Data.List
 import Network.BSD
 import System.FilePath
-import Data.Hash.MD5
 import Control.Applicative
 import Prelude
 
@@ -99,7 +100,9 @@ sideLockFile lockfile = do
 	f <- absPath lockfile
 	let base = intercalate "_" (splitDirectories (makeRelative "/" f))
 	let shortbase = reverse $ take 32 $ reverse base
-	let md5sum = if base == shortbase then "" else md5s (Str base)
+	let md5sum = if base == shortbase
+		then ""
+		else show (md5 (encodeBS base))
 	dir <- ifM (doesDirectoryExist "/dev/shm")
 		( return "/dev/shm"
 		, return "/tmp"
diff --git a/Utility/Tuple.hs b/Utility/Tuple.hs
new file mode 100644
index 000000000..78dd5d0c9
--- /dev/null
+++ b/Utility/Tuple.hs
@@ -0,0 +1,15 @@
+{- tuple utility functions
+ -
+ - Copyright 2017 Joey Hess <id@joeyh.name>
+ -
+ - License: BSD-2-clause
+ -}
+
+fst3 :: (a,b,c) -> a
+fst3 (a,b,c) = a
+
+snd3 :: (a,b,c) -> b
+snd3 (a,b,c) = b
+
+thd3 :: (a,b,c) -> c
+thd3 (a,b,c) = c
diff --git a/debian/control b/debian/control
index fa68c87fe..1d012cea0 100644
--- a/debian/control
+++ b/debian/control
@@ -11,6 +11,7 @@ Build-Depends:
 	libghc-hslogger-dev,
 	libghc-pcre-light-dev,
 	libghc-cryptonite-dev,
+	libghc-memory-dev,
 	libghc-sandi-dev,
 	libghc-utf8-string-dev,
 	libghc-aws-dev (>= 0.9.2-2~),
diff --git a/doc/todo/make_copy_--fast__faster/comment_11_1ca8d9765e6e3a18ae09df74bc390a00._comment b/doc/todo/make_copy_--fast__faster/comment_11_1ca8d9765e6e3a18ae09df74bc390a00._comment
new file mode 100644
index 000000000..619351d4c
--- /dev/null
+++ b/doc/todo/make_copy_--fast__faster/comment_11_1ca8d9765e6e3a18ae09df74bc390a00._comment
@@ -0,0 +1,49 @@
+[[!comment format=mdwn
+ username="joey"
+ subject="""comment 11"""
+ date="2017-05-15T21:56:52Z"
+ content="""
+Switched from MissingH to cryptonite for md5. It did move md5 out of the top CPU spot but
+the overall runtime didn't change much. Memory allocations did go down by a
+good amount.
+
+Updated profiles:
+
+	           git-annex +RTS -p -RTS find
+	
+	        total time  =        1.63 secs   (1629 ticks @ 1000 us, 1 processor)
+	        total alloc = 1,496,336,496 bytes  (excludes profiling overheads)
+	
+	COST CENTRE              MODULE                     SRC                                             %time %alloc
+	
+	catchIO                  Utility.Exception          Utility/Exception.hs:79:1-17                     14.1   15.1
+	inAnnex'.checkindirect   Annex.Content              Annex/Content.hs:(108,9)-(119,39)                10.6    4.8
+	catches                  Control.Monad.Catch        src/Control/Monad/Catch.hs:(432,1)-(436,76)       8.6    6.9
+	spanList                 Data.List.Utils            src/Data/List/Utils.hs:(150,1)-(155,36)           6.7   11.1
+	isAnnexLink              Annex.Link                 Annex/Link.hs:35:1-85                             5.0   10.2
+	keyFile                  Annex.Locations            Annex/Locations.hs:(456,1)-(462,19)               5.0    7.0
+	readish                  Utility.PartialPrelude     Utility/PartialPrelude.hs:(48,1)-(50,20)          3.8    2.0
+	startswith               Data.List.Utils            src/Data/List/Utils.hs:103:1-23                   3.6    2.3
+	splitc                   Utility.Misc               Utility/Misc.hs:(52,1)-(54,25)                    3.4    6.5
+	s2w8                     Data.Bits.Utils            src/Data/Bits/Utils.hs:65:1-15                    2.6    6.4
+	keyPath                  Annex.Locations            Annex/Locations.hs:(492,1)-(494,23)               2.5    4.4
+	fileKey.unesc            Annex.Locations            Annex/Locations.hs:(469,9)-(474,39)               2.0    3.5
+	copyAndFreeze            Data.ByteArray.Methods     Data/ByteArray/Methods.hs:(224,1)-(227,21)        1.8    0.5
+
+	           git-annex +RTS -p -RTS find --not --in web
+	
+	        total time  =        5.33 secs   (5327 ticks @ 1000 us, 1 processor)
+	        total alloc = 2,908,489,000 bytes  (excludes profiling overheads)
+	
+	COST CENTRE          MODULE                     SRC                                             %time %alloc
+	
+	catObjectDetails.\   Git.CatFile                Git/CatFile.hs:(80,72)-(88,97)                    7.8    2.8
+	catchIO              Utility.Exception          Utility/Exception.hs:79:1-17                      7.6    8.3
+	spanList             Data.List.Utils            src/Data/List/Utils.hs:(150,1)-(155,36)           5.8    9.1
+	readish              Utility.PartialPrelude     Utility/PartialPrelude.hs:(48,1)-(50,20)          4.5    4.0
+	parseResp            Git.CatFile                Git/CatFile.hs:(113,1)-(124,28)                   4.4    2.9
+	readFileStrict       Utility.Misc               Utility/Misc.hs:33:1-59                           3.7    1.6
+	catches              Control.Monad.Catch        src/Control/Monad/Catch.hs:(432,1)-(436,76)       3.1    3.6
+	encodeW8             Utility.FileSystemEncoding Utility/FileSystemEncoding.hs:(131,1)-(133,70)    3.1    2.3
+	
+"""]]
diff --git a/git-annex.cabal b/git-annex.cabal
index 545fab3f7..8d8255027 100644
--- a/git-annex.cabal
+++ b/git-annex.cabal
@@ -361,7 +361,8 @@ Executable git-annex
    stm-chans,
    securemem,
    crypto-api,
-   cryptonite
+   cryptonite,
+   memory
   CC-Options: -Wall
   GHC-Options: -Wall -fno-warn-tabs
   Extensions: PackageImports