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

[jc: stripped debug-only code per Peff's $gmane/239768]

Signed-off-by: Vicent Marti <[email protected]>
Signed-off-by: Jeff King <[email protected]>
Helped-by: Ramsay Jones <[email protected]>
Signed-off-by: Junio C Hamano <[email protected]>

Makefile

@@ -667,6 +667,8 @@ LIB_H += diff.h
 LIB_H += diffcore.h
 LIB_H += dir.h
 LIB_H += exec_cmd.h
+LIB_H += ewah/ewok.h
+LIB_H += ewah/ewok_rlw.h
 LIB_H += fetch-pack.h
 LIB_H += fmt-merge-msg.h
 LIB_H += fsck.h
@@ -800,6 +802,10 @@ LIB_OBJS += dir.o
 LIB_OBJS += editor.o
 LIB_OBJS += entry.o
 LIB_OBJS += environment.o
+LIB_OBJS += ewah/bitmap.o
+LIB_OBJS += ewah/ewah_bitmap.o
+LIB_OBJS += ewah/ewah_io.o
+LIB_OBJS += ewah/ewah_rlw.o
 LIB_OBJS += exec_cmd.o
 LIB_OBJS += fetch-pack.o
 LIB_OBJS += fsck.o
@@ -2474,8 +2480,9 @@ profile-clean:
 	$(RM) $(addsuffix *.gcno,$(addprefix $(PROFILE_DIR)/, $(object_dirs)))
 
 clean: profile-clean coverage-clean
-	$(RM) *.o *.res block-sha1/*.o ppc/*.o compat/*.o compat/*/*.o xdiff/*.o vcs-svn/*.o \
-		builtin/*.o $(LIB_FILE) $(XDIFF_LIB) $(VCSSVN_LIB)
+	$(RM) *.o *.res block-sha1/*.o ppc/*.o compat/*.o compat/*/*.o
+	$(RM) xdiff/*.o vcs-svn/*.o ewah/*.o builtin/*.o
+	$(RM) $(LIB_FILE) $(XDIFF_LIB) $(VCSSVN_LIB)
 	$(RM) $(ALL_PROGRAMS) $(SCRIPT_LIB) $(BUILT_INS) git$X
 	$(RM) $(TEST_PROGRAMS) $(NO_INSTALL)
 	$(RM) -r bin-wrappers $(dep_dirs)

ewah/bitmap.c

@@ -0,0 +1,221 @@
+/**
+ * Copyright 2013, GitHub, Inc
+ * Copyright 2009-2013, Daniel Lemire, Cliff Moon,
+ *	David McIntosh, Robert Becho, Google Inc. and Veronika Zenz
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+ */
+#include "git-compat-util.h"
+#include "ewok.h"
+
+#define MASK(x) ((eword_t)1 << (x % BITS_IN_WORD))
+#define BLOCK(x) (x / BITS_IN_WORD)
+
+struct bitmap *bitmap_new(void)
+{
+	struct bitmap *bitmap = ewah_malloc(sizeof(struct bitmap));
+	bitmap->words = ewah_calloc(32, sizeof(eword_t));
+	bitmap->word_alloc = 32;
+	return bitmap;
+}
+
+void bitmap_set(struct bitmap *self, size_t pos)
+{
+	size_t block = BLOCK(pos);
+
+	if (block >= self->word_alloc) {
+		size_t old_size = self->word_alloc;
+		self->word_alloc = block * 2;
+		self->words = ewah_realloc(self->words,
+			self->word_alloc * sizeof(eword_t));
+
+		memset(self->words + old_size, 0x0,
+			(self->word_alloc - old_size) * sizeof(eword_t));
+	}
+
+	self->words[block] |= MASK(pos);
+}
+
+void bitmap_clear(struct bitmap *self, size_t pos)
+{
+	size_t block = BLOCK(pos);
+
+	if (block < self->word_alloc)
+		self->words[block] &= ~MASK(pos);
+}
+
+int bitmap_get(struct bitmap *self, size_t pos)
+{
+	size_t block = BLOCK(pos);
+	return block < self->word_alloc &&
+		(self->words[block] & MASK(pos)) != 0;
+}
+
+struct ewah_bitmap *bitmap_to_ewah(struct bitmap *bitmap)
+{
+	struct ewah_bitmap *ewah = ewah_new();
+	size_t i, running_empty_words = 0;
+	eword_t last_word = 0;
+
+	for (i = 0; i < bitmap->word_alloc; ++i) {
+		if (bitmap->words[i] == 0) {
+			running_empty_words++;
+			continue;
+		}
+
+		if (last_word != 0)
+			ewah_add(ewah, last_word);
+
+		if (running_empty_words > 0) {
+			ewah_add_empty_words(ewah, 0, running_empty_words);
+			running_empty_words = 0;
+		}
+
+		last_word = bitmap->words[i];
+	}
+
+	ewah_add(ewah, last_word);
+	return ewah;
+}
+
+struct bitmap *ewah_to_bitmap(struct ewah_bitmap *ewah)
+{
+	struct bitmap *bitmap = bitmap_new();
+	struct ewah_iterator it;
+	eword_t blowup;
+	size_t i = 0;
+
+	ewah_iterator_init(&it, ewah);
+
+	while (ewah_iterator_next(&blowup, &it)) {
+		if (i >= bitmap->word_alloc) {
+			bitmap->word_alloc *= 1.5;
+			bitmap->words = ewah_realloc(
+				bitmap->words, bitmap->word_alloc * sizeof(eword_t));
+		}
+
+		bitmap->words[i++] = blowup;
+	}
+
+	bitmap->word_alloc = i;
+	return bitmap;
+}
+
+void bitmap_and_not(struct bitmap *self, struct bitmap *other)
+{
+	const size_t count = (self->word_alloc < other->word_alloc) ?
+		self->word_alloc : other->word_alloc;
+
+	size_t i;
+
+	for (i = 0; i < count; ++i)
+		self->words[i] &= ~other->words[i];
+}
+
+void bitmap_or_ewah(struct bitmap *self, struct ewah_bitmap *other)
+{
+	size_t original_size = self->word_alloc;
+	size_t other_final = (other->bit_size / BITS_IN_WORD) + 1;
+	size_t i = 0;
+	struct ewah_iterator it;
+	eword_t word;
+
+	if (self->word_alloc < other_final) {
+		self->word_alloc = other_final;
+		self->words = ewah_realloc(self->words,
+			self->word_alloc * sizeof(eword_t));
+		memset(self->words + original_size, 0x0,
+			(self->word_alloc - original_size) * sizeof(eword_t));
+	}
+
+	ewah_iterator_init(&it, other);
+
+	while (ewah_iterator_next(&word, &it))
+		self->words[i++] |= word;
+}
+
+void bitmap_each_bit(struct bitmap *self, ewah_callback callback, void *data)
+{
+	size_t pos = 0, i;
+
+	for (i = 0; i < self->word_alloc; ++i) {
+		eword_t word = self->words[i];
+		uint32_t offset;
+
+		if (word == (eword_t)~0) {
+			for (offset = 0; offset < BITS_IN_WORD; ++offset)
+				callback(pos++, data);
+		} else {
+			for (offset = 0; offset < BITS_IN_WORD; ++offset) {
+				if ((word >> offset) == 0)
+					break;
+
+				offset += ewah_bit_ctz64(word >> offset);
+				callback(pos + offset, data);
+			}
+			pos += BITS_IN_WORD;
+		}
+	}
+}
+
+size_t bitmap_popcount(struct bitmap *self)
+{
+	size_t i, count = 0;
+
+	for (i = 0; i < self->word_alloc; ++i)
+		count += ewah_bit_popcount64(self->words[i]);
+
+	return count;
+}
+
+int bitmap_equals(struct bitmap *self, struct bitmap *other)
+{
+	struct bitmap *big, *small;
+	size_t i;
+
+	if (self->word_alloc < other->word_alloc) {
+		small = self;
+		big = other;
+	} else {
+		small = other;
+		big = self;
+	}
+
+	for (i = 0; i < small->word_alloc; ++i) {
+		if (small->words[i] != big->words[i])
+			return 0;
+	}
+
+	for (; i < big->word_alloc; ++i) {
+		if (big->words[i] != 0)
+			return 0;
+	}
+
+	return 1;
+}
+
+void bitmap_reset(struct bitmap *bitmap)
+{
+	memset(bitmap->words, 0x0, bitmap->word_alloc * sizeof(eword_t));
+}
+
+void bitmap_free(struct bitmap *bitmap)
+{
+	if (bitmap == NULL)
+		return;
+
+	free(bitmap->words);
+	free(bitmap);
+}