OpenJDK 7 does not benefit from using an inflate stride on the input
array. The implementation of java.util.zip.Inflater supplies the
entire input byte[] to libz, with no regards for the bounds supplied.
Slicing at 512 byte increments in DfsBlock no longer has any benefit.

In OpenJDK 6 the native portion of Inflater used GetByteArrayRegion
to obtain a copy of the input buffer for libz. In this use case
supplying a small stride made sense, it avoided allocating space
for and copying data past the end of the object's compressed stream.

In OpenJDK 7 the native code uses GetPrimitiveArrayCritical,
which tries to avoid copying by freezing Java garbage collection
and accessing the byte[] contents in place. On OpenJDK 7 derived
JVMs it is likely more efficient to supply the entire DfsBlock.

Since OpenJDK 5 and 6 are deprecated and replaced by OpenJDK 7
it is reasonable to suggest any consumers running JGit with DFS
support use an OpenJDK 7 derived JVM. However, JGit still targets
local filesystem support on Java 5, so it is still not reasonble to
apply this same simplification to the internal.storage.file package.

See: JDK-6751338 (http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6751338)
Change-Id: Ib248b6d383da5c8aa887d9c355a0df6f3e2247a5

PackWriter generally chooses the order for objects when it builds the
object lists.  This ordering already depends on history information to
guide placing more recent objects first and historical objects last.

Allow PackWriter to make the basic ordering decisions, instead of
trying to override them.  The old approach of sorting the list caused
DfsReader to override any ordering change PackWriter might have tried
to make when repacking a repository.

This now better matches with WindowCursor's implementation, where
PackWriter solely determines the object ordering.

Change-Id: Ic17ab5631ec539f0758b962966c3a1823735b814

This implementation has been proven to deadlock in production server
loads. Google has been running with it disabled for a quite a while,
as the bugs have been difficult to identify and fix.

Instead of suggesting it works and is useful, drop the code. JGit
should not advertise support for functionality that is known to
be broken.

In a few of the places where read-ahead was enabled by DfsReader
there is more information about what blocks should be loaded when.
During object representation selection, or size lookup, or sending
object as-is to a PackWriter, or sending an entire pack as-is the
reader knows exactly which blocks are required in the cache, and it
also can compute when those will be needed. The broken read-ahead
code was stupid and just read a fixed amount ahead of the current
offset, which can waste IOs if more precise data was available.

DFS systems are usually slow to respond so read-ahead is still
a desired feature, but it needs to be rebuilt from scratch and
make better use of the offset information.

Change-Id: Ibaed8288ec3340cf93eb269dc0f1f23ab5ab1aea

Rewrite this complicated logic to examine each pack file exactly
once. This reduces thrashing when there are many large pack files
present and the reader needs to locate each object's header.

The intermediate temporary list is now smaller, it is bounded to
the same length as the input object list. In the prior version of
this code the list contained one entry for every representation of
every object being packed.

Only one representation object is allocated, reducing the overall
memory footprint to be approximately one reference per object found
in the current pack file (the pointer in the BlockList). This saves
considerable working set memory compared to the prior version that
made and held onto a new representation for every ObjectToPack.

Change-Id: I2c1f18cd6755643ac4c2cf1f23b5464ca9d91b22

This breaks all existing callers once. Applications are not supposed
to build against the internal storage API unless they can accept API
churn and make necessary updates as versions change.

Change-Id: I2ab1327c202ef2003565e1b0770a583970e432e9

The bitmap code in PackWriter knows exactly when to use a pack as
a "cached pack". It enables cached pack usage only when the pack
has a bitmap and its entire closure of objects needs to be sent.
This is a much simpler code path to maintain, and JGit actually
has a way to write the necessary index.

Change-Id: I2645d482f8733fdf0c4120cc59ba9aa4d4ba6881

Clients send a bunch of unknown objects to UploadPack on each round
of negotiation. Many of these are not known to the server, which
leads the implementation to be looking at indexes for garbage packs.

Disable examining the index of a garbage pack, allowing servers to
avoid reading them from disk during negotiation.

The effect of this change is the server will only ACK a have line
if the object was reachable during the last garbage collection,
or was recently added to the repository. For most repositories
there is no impact in this behavior change.

If a repository rewinds a branch, runs GC, and then resets the
branch back to where it was before, the now current tip is going to
be skipped by this change. A client that has the commit may wind up
getting a slightly larger data transfer from the server as an older
common ancestor will be chosen during negotiation. This is fixable
on the server side by running GC again to correct the layout of
objects in pack files.

Change-Id: Icd550359ef70fc7b701980f9b13d923fd13c744b

There is no reason for these to differ in name. Match the
shorter name used by PackFile.

Change-Id: I2d3a299069acc5ce276b1b5439ff2258903c6ff3

Update the PackWriter to support writing out pack bitmap indexes,
a parallel ".bitmap" file to the ".pack" file.
Bitmaps are selected at commits every 1 to 5,000 commits for
each unique path from the start. The most recent 100 commits are
all bitmapped. The next 19,000 commits have a bitmaps every 100
commits. The remaining commits have a bitmap every 5,000 commits.
Commits with more than 1 parent are prefered over ones
with 1 or less. Furthermore, previously computed bitmaps are reused,
if the previous entry had the reuse flag set, which is set when the
bitmap was placed at the max allowed distance.

Bitmaps are used to speed up the counting phase when packing, for
requests that are not shallow. The PackWriterBitmapWalker uses
a RevFilter to proactively mark commits with RevFlag.SEEN, when
they appear in a bitmap. The walker produces the full closure
of reachable ObjectIds, given the collection of starting ObjectIds.

For fetch request, two ObjectWalks are executed to compute the
ObjectIds reachable from the haves and from the wants. The
ObjectIds needed to be written are determined by taking all the
resulting wants AND NOT the haves.

For clone requests, we get cached pack support for "free" since
it is possible to determine if all of the ObjectIds in a pack file
are included in the resulting list of ObjectIds to write.

On my machine, the best times for clones and fetches of the linux
kernel repository (with about 2.6M objects and 300K commits) are
tabulated below:

Operation                   Index V2               Index VE003
Clone                       37530ms (524.06 MiB)     82ms (524.06 MiB)
Fetch (1 commit back)          75ms                 107ms
Fetch (10 commits back)       456ms (269.51 KiB)    341ms (265.19 KiB)
Fetch (100 commits back)      449ms (269.91 KiB)    337ms (267.28 KiB)
Fetch (1000 commits back)    2229ms ( 14.75 MiB)    189ms ( 14.42 MiB)
Fetch (10000 commits back)   2177ms ( 16.30 MiB)    254ms ( 15.88 MiB)
Fetch (100000 commits back) 14340ms (185.83 MiB)   1655ms (189.39 MiB)

Change-Id: Icdb0cdd66ff168917fb9ef17b96093990cc6a98d

A pack bitmap index is an additional index of compressed
bitmaps of the object graph. Furthermore, a logical API of the index
functionality is included, as it is expected to be used by the
PackWriter.

Compressed bitmaps are created using the javaewah library, which is a
word-aligned compressed variant of the Java bitset class based on
run-length encoding. The library only works with positive integer
values. Thus, the maximum number of ObjectIds in a pack file that
this index can currently support is limited to Integer.MAX_VALUE.

Every ObjectId is given an integer mapping. The integer is the
position of the ObjectId in the complete ObjectId list, sorted
by offset, for the pack file. That integer is what the bitmaps
use to reference the ObjectId. Currently, the new index format can
only be used with pack files that contain a complete closure of the
object graph e.g. the result of a garbage collection.

The index file includes four bitmaps for the Git object types i.e.
commits, trees, blobs, and tags. In addition, a collection of
bitmaps keyed by an ObjectId is also included. The bitmap for each entry
in the collection represents the full closure of ObjectIds reachable
from the keyed ObjectId (including the keyed ObjectId itself). The
bitmaps are further compressed by XORing the current bitmaps against
prior bitmaps in the index, and selecting the smallest representation.
The XOR'd bitmap and offset from the current entry to the position
of the bitmap to XOR against is the actual representation of the entry
in the index file. Each entry contains one byte, which is currently
used to note whether the bitmap should be blindly reused.

Change-Id: Id328724bf6b4c8366a088233098c18643edcf40f

Update the ObjectReuseAsIs API to support creating new
ObjectToPack with only the AnyObjectId and Git object type. This is
needed to support the future pack index bitmaps, which only contain
this information and do not want the overhead of creating a temporary
object for every ObjectId.

Change-Id: I906360b471412688bf429ecef74fd988f47875dc

PackConstants previously contained string values for the pack and pack
index extension. Change PackConstant to be PackExt, a typed wrapper
around the string pack file extension.

Change-Id: I86ac4db6da8f33aa42d6f37cfcc119e819444318

Previously, the DfsObjDatabase had a hardcoded getPackFile() and
getPackIndex() methods which opens a .pack and .idx file, respectively.
A future change to add a bitmap index will need to be stored in a
parallel .bitmap file. Update the DfsObjDatabase to support opening and
writing of files for any pack extension.

Change-Id: I7c403b501e242096a2d435f6865d6025a9f86108

StartGenerator now processes .git/shallow to have the
RevWalk stop for shallow commits.

See RevWalkShallowTest for tests.

Bug: 394543
CQ: 6908
Change-Id: Ia5af1dab3fe9c7888f44eeecab1e1bcf2e8e48fe
Signed-off-by: Chris Aniszczyk <zx@twitter.com>

Expose class DfsReader and method DfsPackFile.hasObject() as public.
Applications may want to be able to inquire about some details of
the storage of a repository. Make this possible by exposing some
simple accessor methods.

Expose method DfsObjDatabase.clearCache() as protected, allowing
implementing subclasses to dump the cache if necessary, and force
it to reload on a future request.

Change-Id: Ic592c82d45ace9f2fa5f8d7e4bacfdce96dea969

Change-Id: I763590a45d75f00a09097ab6f89581a3bbd3c797

Change-Id: Ie22ac47e315bff76f224214bc042fc483eb01550
Signed-off-by: Robin Rosenberg <robin.rosenberg@dewire.com>

The DfsReader must offer every representation of an object that
exists on the local repository when PackWriter asks for them. This
is necessary to identify objects in the thin pack part that are also
in the cached pack that will be appended onto the end of the stream.

Without looking at all alternatives, PackWriter may pack the same
object twice (once in the thin section, again in the cached base
pack). This may cause the command line C version to go into an
infinite loop when repacking the resulting repository, as it may see
a delta chain cycle with one of those duplicate copies of the object.

Previously the DfsReader tried to avoid looking at packs that it
might not care about, but this is insufficient, as all versions
must be considered during pack generation.

Change-Id: Ibf4a3e8ea5c42aef16404ffc42a5781edd97b18e

Make the code more clear with a simple refactoring of the boolean
logic into a method that describes the condition we are looking
for on each pack file. A cached pack is possible if there exists
a tips collection, and the collection is non-empty.

Change-Id: I4ac42b0622b39d159a0f4f223e291c35c71f672c

Change-Id: I64577f8fd19ee0d2d407479cc70e521adc367f37
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

In practice the DHT storage layer has not been performing as well as
large scale server environments want to see from a Git server.

The performance of the DHT schema degrades rapidly as small changes
are pushed into the repository due to the chunk size being less than
1/3 of the pushed pack size.  Small chunks cause poor prefetch
performance during reading, and require significantly longer prefetch
lists inside of the chunk meta field to work around the small size.

The DHT code is very complex (>17,000 lines of code) and is very
sensitive to the underlying database round-trip time, as well as the
way objects were written into the pack stream that was chunked and
stored on the database.  A poor pack layout (from any version of C Git
prior to Junio reworking it) can cause the DHT code to be unable to
enumerate the objects of the linux-2.6 repository in a completable
time scale.

Performing a clone from a DHT stored repository of 2 million objects
takes 2 million row lookups in the DHT to locate the OBJECT_INDEX row
for each object being cloned. This is very difficult for some DHTs to
scale, even at 5000 rows/second the lookup stage alone takes 6 minutes
(on local filesystem, this is almost too fast to bother measuring).
Some servers like Apache Cassandra just fall over and cannot complete
the 2 million lookups in rapid fire.

On a ~400 MiB repository, the DHT schema has an extra 25 MiB of
redundant data that gets downloaded to the JGit process, and that is
before you consider the cost of the OBJECT_INDEX table also being
fully loaded, which is at least 223 MiB of data for the linux kernel
repository.  In the DHT schema answering a `git clone` of the ~400 MiB
linux kernel needs to load 248 MiB of "index" data from the DHT, in
addition to the ~400 MiB of pack data that gets sent to the client.
This is 193 MiB more data to be accessed than the native filesystem
format, but it needs to come over a much smaller pipe (local Ethernet
typically) than the local SATA disk drive.

I also never got around to writing the "repack" support for the DHT
schema, as it turns out to be fairly complex to safely repack data in
the repository while also trying to minimize the amount of changes
made to the database, due to very common limitations on database
mutation rates..

This new DFS storage layer fixes a lot of those issues by taking the
simple approach for storing relatively standard Git pack and index
files on an abstract filesystem. Packs are accessed by an in-process
buffer cache, similar to the WindowCache used by the local filesystem
storage layer. Unlike the local file IO, there are some assumptions
that the storage system has relatively high latency and no concept of
"file handles". Instead it looks at the file more like HTTP byte range
requests, where a read channel is a simply a thunk to trigger a read
request over the network.

The DFS code in this change is still abstract, it does not store on
any particular filesystem, but is fairly well suited to the Amazon S3
or Apache Hadoop HDFS. Storing packs directly on HDFS rather than
HBase removes a layer of abstraction, as most HBase row reads turn
into an HDFS read.

Most of the DFS code in this change was blatently copied from the
local filesystem code. Most parts should be refactored to be shared
between the two storage systems, but right now I am hesistent to do
this due to how well tuned the local filesystem code currently is.

Change-Id: Iec524abdf172e9ec5485d6c88ca6512cd8a6eafb