revindex: Export new APIs

Allow users to efficiently lookup consecutive entries that are expected
to be found on the same revindex by exporting `find_revindex_position`:
this function takes a pointer to revindex itself, instead of looking up
the proper revindex for a given packfile on each call.

Signed-off-by: Vicent Marti <tanoku@gmail.com>
pack-objects: Refactor the packing list

The hash table that stores the packing list for a given `pack-objects`
run was tightly coupled to the pack-objects code.

In this commit, we refactor the hash table and the underlying storage
array into a `packing_data` struct. The functionality for accessing and
adding entries to the packing list is hence accessible from other parts
of Git besides the `pack-objects` builtin.

This refactoring is a requirement for further patches in this series
that will require accessing the commit packing list from outside of
`pack-objects`.

The hash table implementation has been minimally altered: we now
use table sizes which are always a power of two, to ensure a uniform
index distribution in the array.

Signed-off-by: Vicent Marti <tanoku@gmail.com>
pack-objects: factor out name_hash

As the pack-objects system grows beyond the single
pack-objects.c file, more parts (like the soon-to-exist
bitmap code) will need to compute hashes for matching
deltas. Factor out name_hash to make it available to other
files.

Signed-off-by: Vicent Marti <tanoku@gmail.com>
revision: allow setting custom limiter function

This commit enables users of `struct rev_info` to peform custom limiting
during a revision walk (i.e. `get_revision`).

If the field `include_check` has been set to a callback, this callback
will be issued once for each commit before it is added to the "pending"
list of the revwalk. If the include check returns 0, the commit will be
marked as added but won't be pushed to the pending list, effectively
limiting the walk.

Signed-off-by: Vicent Marti <tanoku@gmail.com>
sha1_file: export `git_open_noatime`

The `git_open_noatime` helper can be of general interest for other
consumers of git's different on-disk formats.

Signed-off-by: Vicent Marti <tanoku@gmail.com>
compat: add endianness helpers

The POSIX standard doesn't currently define a `ntohll`/`htonll`
function pair to perform network-to-host and host-to-network
swaps of 64-bit data. These 64-bit swaps are necessary for the on-disk
storage of EWAH bitmaps if they are not in native byte order.

Many thanks to Ramsay Jones <ramsay@ramsay1.demon.co.uk> and
Torsten Bögershausen <tboegi@web.de> for cygwin/mingw/msvc
portability fixes.

Signed-off-by: Vicent Marti <tanoku@gmail.com>
ewah: compressed bitmap implementation

EWAH is a word-aligned compressed variant of a bitset (i.e. a data
structure that acts as a 0-indexed boolean array for many entries).

It uses a 64-bit run-length encoding (RLE) compression scheme,
trading some compression for better processing speed.

The goal of this word-aligned implementation is not to achieve
the best compression, but rather to improve query processing time.
As it stands right now, this EWAH implementation will always be more
efficient storage-wise than its uncompressed alternative.

EWAH arrays will be used as the on-disk format to store reachability
bitmaps for all objects in a repository while keeping reasonable sizes,
in the same way that JGit does.

This EWAH implementation is a mostly straightforward port of the
original `javaewah` library that JGit currently uses. The library is
self-contained and has been embedded whole (4 files) inside the `ewah`
folder to ease redistribution.

The library is re-licensed under the GPLv2 with the permission of Daniel
Lemire, the original author. The source code for the C version can
be found on GitHub:

	https://github.com/vmg/libewok

The original Java implementation can also be found on GitHub:

	https://github.com/lemire/javaewah

Signed-off-by: Vicent Marti <tanoku@gmail.com>
documentation: add documentation for the bitmap format

This is the technical documentation for the JGit-compatible Bitmap v1
on-disk format.

Signed-off-by: Vicent Marti <tanoku@gmail.com>
pack-bitmap: add support for bitmap indexes

A bitmap index is a `.bitmap` file that can be found inside
`$GIT_DIR/objects/pack/`, next to its corresponding packfile, and
contains precalculated reachability information for selected commits.
The full specification of the format for these bitmap indexes can be found
in `Documentation/technical/bitmap-format.txt`.

For a given commit SHA1, if it happens to be available in the bitmap
index, its bitmap will represent every single object that is reachable
from the commit itself. The nth bit in the bitmap is the nth object in
the packfile; if it's set to 1, the object is reachable.

By using the bitmaps available in the index, this commit implements
several new functions:

	- `prepare_bitmap_git`
	- `prepare_bitmap_walk`
	- `traverse_bitmap_commit_list`
	- `reuse_partial_packfile_from_bitmap`

The `prepare_bitmap_walk` function tries to build a bitmap of all the
objects that can be reached from the commit roots of a given `rev_info`
struct by using the following algorithm:

- If all the interesting commits for a revision walk are available in
the index, the resulting reachability bitmap is the bitwise OR of all
the individual bitmaps.

- When the full set of WANTs is not available in the index, we perform a
partial revision walk using the commits that don't have bitmaps as
roots, and limiting the revision walk as soon as we reach a commit that
has a corresponding bitmap. The earlier OR'ed bitmap with all the
indexed commits can now be completed as this walk progresses, so the end
result is the full reachability list.

- For revision walks with a HAVEs set (a set of commits that are deemed
uninteresting), first we perform the same method as for the WANTs, but
using our HAVEs as roots, in order to obtain a full reachability bitmap
of all the uninteresting commits. This bitmap then can be used to:

	a) limit the subsequent walk when building the WANTs bitmap
	b) finding the final set of interesting commits by performing an
	   AND-NOT of the WANTs and the HAVEs.

If `prepare_bitmap_walk` runs successfully, the resulting bitmap is
stored and the equivalent of a `traverse_commit_list` call can be
performed by using `traverse_bitmap_commit_list`; the bitmap version
of this call yields the objects straight from the packfile index
(without having to look them up or parse them) and hence is several
orders of magnitude faster.

As an extra optimization, when `prepare_bitmap_walk` succeeds, the
`reuse_partial_packfile_from_bitmap` call can be attempted: it will find
the amount of objects at the beginning of the on-disk packfile that can
be reused as-is, and return an offset into the packfile. The source
packfile can then be loaded and the bytes up to `offset` can be written
directly to the result without having to consider the entires inside the
packfile individually.

If the `prepare_bitmap_walk` call fails (e.g. because no bitmap files
are available), the `rev_info` struct is left untouched, and can be used
to perform a manual rev-walk using `traverse_commit_list`.

Hence, this new set of functions are a generic API that allows to
perform the equivalent of

	git rev-list --objects [roots...] [^uninteresting...]

for any set of commits, even if they don't have specific bitmaps
generated for them.

In further patches, we'll use this bitmap traversal optimization to
speed up the `pack-objects` and `rev-list` commands.

Signed-off-by: Vicent Marti <tanoku@gmail.com>
pack-objects: split add_object_entry

This function actually does three things:

  1. Check whether we've already added the object to our
     packing list.

  2. Check whether the object meets our criteria for adding.

  3. Actually add the object to our packing list.

It's a little hard to see these three phases, because they
happen linearly in the rather long function. Instead, this
patch breaks them up into three separate helper functions.

The result is a little easier to follow, though it
unfortunately suffers from some optimization
interdependencies between the stages (e.g., during step 3 we
use the packing list index from step 1 and the packfile
information from step 2).

More importantly, though, the various parts can be
composed differently, as they will be in the next patch.
pack-objects: use bitmaps when packing objects

In this patch, we use the bitmap API to perform the `Counting Objects`
phase in pack-objects, rather than a traditional walk through the object
graph. For a reasonably-packed large repo, the time to fetch and clone
is often dominated by the full-object revision walk during the Counting
Objects phase. Using bitmaps can reduce the CPU time required on the
server (and therefore start sending the actual pack data with less
delay).

For bitmaps to be used, the following must be true:

  1. We must be packing to stdout (as a normal `pack-objects` from
     `upload-pack` would do).

  2. There must be a .bitmap index containing at least one of the
     "have" objects that the client is asking for.

  3. Bitmaps must be enabled (they are enabled by default, but can be
     disabled by setting `pack.usebitmaps` to false, or by using
     `--no-use-bitmap-index` on the command-line).

If any of these is not true, we fall back to doing a normal walk of the
object graph.

Here are some sample timings from a full pack of `torvalds/linux` (i.e.
something very similar to what would be generated for a clone of the
repository) that show the speedup produced by various
methods:

    [existing graph traversal]
    $ time git pack-objects --all --stdout --no-use-bitmap-index \
			    </dev/null >/dev/null
    Counting objects: 3237103, done.
    Compressing objects: 100% (508752/508752), done.
    Total 3237103 (delta 2699584), reused 3237103 (delta 2699584)

    real    0m44.111s
    user    0m42.396s
    sys     0m3.544s

    [bitmaps only, without partial pack reuse; note that
     pack reuse is automatic, so timing this required a
     patch to disable it]
    $ time git pack-objects --all --stdout </dev/null >/dev/null
    Counting objects: 3237103, done.
    Compressing objects: 100% (508752/508752), done.
    Total 3237103 (delta 2699584), reused 3237103 (delta 2699584)

    real    0m5.413s
    user    0m5.604s
    sys     0m1.804s

    [bitmaps with pack reuse (what you get with this patch)]
    $ time git pack-objects --all --stdout </dev/null >/dev/null
    Reusing existing pack: 3237103, done.
    Total 3237103 (delta 0), reused 0 (delta 0)

    real    0m1.636s
    user    0m1.460s
    sys     0m0.172s

Signed-off-by: Vicent Marti <tanoku@gmail.com>
rev-list: add bitmap mode to speed up object lists

The bitmap reachability index used to speed up the counting objects
phase during `pack-objects` can also be used to optimize a normal
rev-list if the only thing required are the SHA1s of the objects during
the list (i.e., not the path names at which trees and blobs were found).

Calling `git rev-list --objects --use-bitmap-index [committish]` will
perform an object iteration based on a bitmap result instead of actually
walking the object graph.

These are some example timings for `torvalds/linux` (warm cache,
best-of-five):

    $ time git rev-list --objects master > /dev/null

    real    0m34.191s
    user    0m33.904s
    sys     0m0.268s

    $ time git rev-list --objects --use-bitmap-index master > /dev/null

    real    0m1.041s
    user    0m0.976s
    sys     0m0.064s

Likewise, using `git rev-list --count --use-bitmap-index` will speed up
the counting operation by building the resulting bitmap and performing a
fast popcount (number of bits set on the bitmap) on the result.

Here are some sample timings of different ways to count commits in
`torvalds/linux`:

    $ time git rev-list master | wc -l
        399882

        real    0m6.524s
        user    0m6.060s
        sys     0m3.284s

    $ time git rev-list --count master
        399882

        real    0m4.318s
        user    0m4.236s
        sys     0m0.076s

    $ time git rev-list --use-bitmap-index --count master
        399882

        real    0m0.217s
        user    0m0.176s
        sys     0m0.040s

This also respects negative refs, so you can use it to count
a slice of history:

        $ time git rev-list --count v3.0..master
        144843

        real    0m1.971s
        user    0m1.932s
        sys     0m0.036s

        $ time git rev-list --use-bitmap-index --count v3.0..master
        real    0m0.280s
        user    0m0.220s
        sys     0m0.056s

Though note that the closer the endpoints, the less it helps. In the
traversal case, we have fewer commits to cross, so we take less time.
But the bitmap time is dominated by generating the pack revindex, which
is constant with respect to the refs given.

Note that you cannot yet get a fast --left-right count of a symmetric
difference (e.g., "--count --left-right master...topic"). The slow part
of that walk actually happens during the merge-base determination when
we parse "master...topic". Even though a count does not actually need to
know the real merge base (it only needs to take the symmetric difference
of the bitmaps), the revision code would require some refactoring to
handle this case.

Additionally, a `--test-bitmap` flag has been added that will perform
the same rev-list manually (i.e. using a normal revwalk) and using
bitmaps, and verify that the results are the same. This can be used to
exercise the bitmap code, and also to verify that the contents of the
.bitmap file are sane.

Signed-off-by: Vicent Marti <tanoku@gmail.com>
pack-objects: implement bitmap writing

This commit extends more the functionality of `pack-objects` by allowing
it to write out a `.bitmap` index next to any written packs, together
with the `.idx` index that currently gets written.

If bitmap writing is enabled for a given repository (either by calling
`pack-objects` with the `--write-bitmap-index` flag or by having
`pack.writebitmaps` set to `true` in the config) and pack-objects is
writing a packfile that would normally be indexed (i.e. not piping to
stdout), we will attempt to write the corresponding bitmap index for the
packfile.

Bitmap index writing happens after the packfile and its index has been
successfully written to disk (`finish_tmp_packfile`). The process is
performed in several steps:

    1. `bitmap_writer_set_checksum`: this call stores the partial
       checksum for the packfile being written; the checksum will be
       written in the resulting bitmap index to verify its integrity

    2. `bitmap_writer_build_type_index`: this call uses the array of
       `struct object_entry` that has just been sorted when writing out
       the actual packfile index to disk to generate 4 type-index bitmaps
       (one for each object type).

       These bitmaps have their nth bit set if the given object is of
       the bitmap's type. E.g. the nth bit of the Commits bitmap will be
       1 if the nth object in the packfile index is a commit.

       This is a very cheap operation because the bitmap writing code has
       access to the metadata stored in the `struct object_entry` array,
       and hence the real type for each object in the packfile.

    3. `bitmap_writer_reuse_bitmaps`: if there exists an existing bitmap
       index for one of the packfiles we're trying to repack, this call
       will efficiently rebuild the existing bitmaps so they can be
       reused on the new index. All the existing bitmaps will be stored
       in a `reuse` hash table, and the commit selection phase will
       prioritize these when selecting, as they can be written directly
       to the new index without having to perform a revision walk to
       fill the bitmap. This can greatly speed up the repack of a
       repository that already has bitmaps.

    4. `bitmap_writer_select_commits`: if bitmap writing is enabled for
       a given `pack-objects` run, the sequence of commits generated
       during the Counting Objects phase will be stored in an array.

       We then use that array to build up the list of selected commits.
       Writing a bitmap in the index for each object in the repository
       would be cost-prohibitive, so we use a simple heuristic to pick
       the commits that will be indexed with bitmaps.

       The current heuristics are a simplified version of JGit's
       original implementation. We select a higher density of commits
       depending on their age: the 100 most recent commits are always
       selected, after that we pick 1 commit of each 100, and the gap
       increases as the commits grow older. On top of that, we make sure
       that every single branch that has not been merged (all the tips
       that would be required from a clone) gets their own bitmap, and
       when selecting commits between a gap, we tend to prioritize the
       commit with the most parents.

       Do note that there is no right/wrong way to perform commit
       selection; different selection algorithms will result in
       different commits being selected, but there's no such thing as
       "missing a commit". The bitmap walker algorithm implemented in
       `prepare_bitmap_walk` is able to adapt to missing bitmaps by
       performing manual walks that complete the bitmap: the ideal
       selection algorithm, however, would select the commits that are
       more likely to be used as roots for a walk in the future (e.g.
       the tips of each branch, and so on) to ensure a bitmap for them
       is always available.

    5. `bitmap_writer_build`: this is the computationally expensive part
       of bitmap generation. Based on the list of commits that were
       selected in the previous step, we perform several incremental
       walks to generate the bitmap for each commit.

       The walks begin from the oldest commit, and are built up
       incrementally for each branch. E.g. consider this dag where A, B,
       C, D, E, F are the selected commits, and a, b, c, e are a chunk
       of simplified history that will not receive bitmaps.

            A---a---B--b--C--c--D
                     \
                      E--e--F

       We start by building the bitmap for A, using A as the root for a
       revision walk and marking all the objects that are reachable
       until the walk is over. Once this bitmap is stored, we reuse the
       bitmap walker to perform the walk for B, assuming that once we
       reach A again, the walk will be terminated because A has already
       been SEEN on the previous walk.

       This process is repeated for C, and D, but when we try to
       generate the bitmaps for E, we can reuse neither the current walk
       nor the bitmap we have generated so far.

       What we do now is resetting both the walk and clearing the
       bitmap, and performing the walk from scratch using E as the
       origin. This new walk, however, does not need to be completed.
       Once we hit B, we can lookup the bitmap we have already stored
       for that commit and OR it with the existing bitmap we've composed
       so far, allowing us to limit the walk early.

       After all the bitmaps have been generated, another iteration
       through the list of commits is performed to find the best XOR
       offsets for compression before writing them to disk. Because of
       the incremental nature of these bitmaps, XORing one of them with
       its predecesor results in a minimal "bitmap delta" most of the
       time. We can write this delta to the on-disk bitmap index, and
       then re-compose the original bitmaps by XORing them again when
       loaded.

       This is a phase very similar to pack-object's `find_delta` (using
       bitmaps instead of objects, of course), except the heuristics
       have been greatly simplified: we only check the 10 bitmaps before
       any given one to find best compressing one. This gives good
       results in practice, because there is locality in the ordering of
       the objects (and therefore bitmaps) in the packfile.

     6. `bitmap_writer_finish`: the last step in the process is
	serializing to disk all the bitmap data that has been generated
	in the two previous steps.

	The bitmap is written to a tmp file and then moved atomically to
	its final destination, using the same process as
	`pack-write.c:write_idx_file`.

Signed-off-by: Vicent Marti <tanoku@gmail.com>
repack: stop using magic number for ARRAY_SIZE(exts)

We have a static array of extensions, but hardcode the size
of the array in our loops. Let's pull out this magic number,
which will make it easier to change.
repack: turn exts array into array-of-struct

This is slightly more verbose, but will let us annotate the
extensions with further options in future commits.
repack: handle optional files created by pack-objects

We ask pack-objects to pack to a set of temporary files, and
then rename them into place. Some files that pack-objects
creates may be optional (like a .bitmap file), in which case
we would not want to call rename(). We already call stat()
and make the chmod optional if the file cannot be accessed.
We could simply skip the rename step in this case, but that
would be a minor regression in noticing problems with
non-optional files (like the .pack and .idx files).

Instead, we can now annotate extensions as optional, and
skip them if they don't exist (and otherwise rely on
rename() to barf).
repack: consider bitmaps when performing repacks

Since `pack-objects` will write a `.bitmap` file next to the `.pack` and
`.idx` files, this commit teaches `git-repack` to consider the new
bitmap indexes (if they exist) when performing repack operations.

This implies moving old bitmap indexes out of the way if we are
repacking a repository that already has them, and moving the newly
generated bitmap indexes into the `objects/pack` directory, next to
their corresponding packfiles.

Since `git repack` is now capable of handling these `.bitmap` files,
a normal `git gc` run on a repository that has `pack.writebitmaps` set
to true in its config file will generate bitmap indexes as part of the
garbage collection process.

Alternatively, `git repack` can be called with the `-b` switch to
explicitly generate bitmap indexes if you are experimenting
and don't want them on all the time.

Signed-off-by: Vicent Marti <tanoku@gmail.com>
count-objects: recognize .bitmap in garbage-checking

Count-objects will report any "garbage" files in the packs
directory, including files whose extensions it does not
know (case 1), and files whose matching ".pack" file is
missing (case 2).  Without having learned about ".bitmap"
files, the current code reports all such files as garbage
(case 1), even if their pack exists. Instead, they should be
treated as case 2.

Signed-off-by: Nguyễn Thái Ngọc Duy <pclouds@gmail.com>
t: add basic bitmap functionality tests

Now that we can read and write bitmaps, we can exercise them
with some basic functionality tests. These tests aren't
particularly useful for seeing the benefit, as the test
repo is too small for it to make a difference. However, we
can at least check that using bitmaps does not break anything.
t/perf: add tests for pack bitmaps

This adds a few basic perf tests for the pack bitmap code to
show off its improvements. The tests are:

  1. How long does it take to do a repack (it gets slower
     with bitmaps, since we have to do extra work)?

  2. How long does it take to do a clone (it gets faster
     with bitmaps)?

  3. How does a small fetch perform when we've just
     repacked?

  4. How does a clone perform when we haven't repacked since
     a week of pushes?

Here are results against linux.git:

Test                      origin/master       this tree
-----------------------------------------------------------------------
5310.2: repack to disk    33.64(32.64+2.04)   67.67(66.75+1.84) +101.2%
5310.3: simulated clone   30.49(29.47+2.05)   1.20(1.10+0.10) -96.1%
5310.4: simulated fetch   3.49(6.79+0.06)     5.57(22.35+0.07) +59.6%
5310.6: partial bitmap    36.70(43.87+1.81)   8.18(21.92+0.73) -77.7%

You can see that we do take longer to repack, but we do way
better for further clones. A small fetch performs a bit
worse, as we spend way more time on delta compression (note
the heavy user CPU time, as we have 8 threads) due to the
lack of name hashes for the bitmapped objects.

The final test shows how the bitmaps degrade over time
between packs. There's still a significant speedup over the
non-bitmap case, but we don't do quite as well (we have to
spend time accessing the "new" objects the old fashioned
way, including delta compression).