Subject: [PATCH 11/23] midx: sort and deduplicate objects from packfiles

From: Derrick Stolee <[email-masked]>
Date: Thu, 7 Jun 2018 10:03:26 -0400

Before writing a list of objects and their offsets to a multi-pack-index
(MIDX), we need to collect the list of objects contained in the
packfiles. There may be multiple copies of some objects, so this list
must be deduplicated.

It is possible to artificially get into a state where there are many
duplicate copies of objects. That can create high memory pressure if we
are to create a list of all objects before de-duplication. To reduce
this memory pressure without a significant performance drop,
automatically group objects by the first byte of their object id. Use
the IDX fanout tables to group the data, copy to a local array, then
sort.

Copy only the de-duplicated entries. Select the duplicate based on the
most-recent modified time of a packfile containing the object.

Signed-off-by: Derrick Stolee <[email-masked]>
---
 midx.c | 138 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 138 insertions(+)

diff --git a/midx.c b/midx.c
index 923acda72e..b20d52713c 100644
--- a/midx.c
+++ b/midx.c
@@ -4,6 +4,7 @@
 #include "csum-file.h"
 #include "lockfile.h"
 #include "object-store.h"
+#include "packfile.h"
 #include "midx.h"
 
 #define MIDX_SIGNATURE 0x4d494458 /* "MIDX" */
@@ -190,6 +191,140 @@ static void sort_packs_by_name(char **pack_names, uint32_t nr_packs, uint32_t *p
 	}
 }
 
+static uint32_t get_pack_fanout(struct packed_git *p, uint32_t value)
+{
+	const uint32_t *level1_ofs = p->index_data;
+
+	if (!level1_ofs) {
+		if (open_pack_index(p))
+			return 0;
+		level1_ofs = p->index_data;
+	}
+
+	if (p->index_version > 1) {
+		level1_ofs += 2;
+	}
+
+	return ntohl(level1_ofs[value]);
+}
+
+struct pack_midx_entry {
+	struct object_id oid;
+	uint32_t pack_int_id;
+	time_t pack_mtime;
+	uint64_t offset;
+};
+
+static int midx_oid_compare(const void *_a, const void *_b)
+{
+	struct pack_midx_entry *a = (struct pack_midx_entry *)_a;
+	struct pack_midx_entry *b = (struct pack_midx_entry *)_b;
+	int cmp = oidcmp(&a->oid, &b->oid);
+
+	if (cmp)
+		return cmp;
+
+	if (a->pack_mtime > b->pack_mtime)
+		return -1;
+	else if (a->pack_mtime < b->pack_mtime)
+		return 1;
+
+	return a->pack_int_id - b->pack_int_id;
+}
+
+static void fill_pack_entry(uint32_t pack_int_id,
+			    struct packed_git *p,
+			    uint32_t cur_object,
+			    struct pack_midx_entry *entry)
+{
+	if (!nth_packed_object_oid(&entry->oid, p, cur_object))
+		die("failed to located object %d in packfile", cur_object);
+
+	entry->pack_int_id = pack_int_id;
+	entry->pack_mtime = p->mtime;
+
+	entry->offset = nth_packed_object_offset(p, cur_object);
+}
+
+/*
+ * It is possible to artificially get into a state where there are many
+ * duplicate copies of objects. That can create high memory pressure if
+ * we are to create a list of all objects before de-duplication. To reduce
+ * this memory pressure without a significant performance drop, automatically
+ * group objects by the first byte of their object id. Use the IDX fanout
+ * tables to group the data, copy to a local array, then sort.
+ *
+ * Copy only the de-duplicated entries (selected by most-recent modified time
+ * of a packfile containing the object).
+ */
+static struct pack_midx_entry *get_sorted_entries(struct packed_git **p,
+						  uint32_t *perm,
+						  uint32_t nr_packs,
+						  uint32_t *nr_objects)
+{
+	uint32_t cur_fanout, cur_pack, cur_object;
+	uint32_t nr_fanout, alloc_fanout, alloc_objects, total_objects = 0;
+	struct pack_midx_entry *entries_by_fanout = NULL;
+	struct pack_midx_entry *deduplicated_entries = NULL;
+
+	for (cur_pack = 0; cur_pack < nr_packs; cur_pack++) {
+		if (open_pack_index(p[cur_pack]))
+			continue;
+
+		total_objects += p[cur_pack]->num_objects;
+	}
+
+	/*
+	 * As we de-duplicate by fanout value, we expect the fanout
+	 * slices to be evenly distributed, with some noise. Hence,
+	 * allocate slightly more than one 256th.
+	 */
+	alloc_objects = alloc_fanout = total_objects > 3200 ? total_objects / 200 : 16;
+
+	ALLOC_ARRAY(entries_by_fanout, alloc_fanout);
+	ALLOC_ARRAY(deduplicated_entries, alloc_objects);
+	*nr_objects = 0;
+
+	for (cur_fanout = 0; cur_fanout < 256; cur_fanout++) {
+		nr_fanout = 0;
+
+		for (cur_pack = 0; cur_pack < nr_packs; cur_pack++) {
+			uint32_t start = 0, end;
+
+			if (cur_fanout)
+				start = get_pack_fanout(p[cur_pack], cur_fanout - 1);
+			end = get_pack_fanout(p[cur_pack], cur_fanout);
+
+			for (cur_object = start; cur_object < end; cur_object++) {
+				ALLOC_GROW(entries_by_fanout, nr_fanout + 1, alloc_fanout);
+				fill_pack_entry(perm[cur_pack], p[cur_pack], cur_object, &entries_by_fanout[nr_fanout]);
+				nr_fanout++;
+			}
+		}
+
+		QSORT(entries_by_fanout, nr_fanout, midx_oid_compare);
+
+		/*
+		 * The batch is now sorted by OID and then mtime (descending).
+		 * Take only the first duplicate.
+		 */
+		for (cur_object = 0; cur_object < nr_fanout; cur_object++) {
+			if (cur_object && !oidcmp(&entries_by_fanout[cur_object - 1].oid,
+						  &entries_by_fanout[cur_object].oid))
+				continue;
+
+			ALLOC_GROW(deduplicated_entries, *nr_objects + 1, alloc_objects);
+			memcpy(&deduplicated_entries[*nr_objects],
+			       &entries_by_fanout[cur_object],
+			       sizeof(struct pack_midx_entry));
+			(*nr_objects)++;
+		}
+	}
+
+	FREE_AND_NULL(entries_by_fanout);
+	return deduplicated_entries;
+}
+
 static size_t write_midx_pack_lookup(struct hashfile *f,
 				     char **pack_names,
 				     uint32_t nr_packs)
@@ -254,6 +389,7 @@ int write_midx_file(const char *object_dir)
 	uint64_t written = 0;
 	uint32_t chunk_ids[MIDX_MAX_CHUNKS + 1];
 	uint64_t chunk_offsets[MIDX_MAX_CHUNKS + 1];
+	uint32_t nr_entries;
 
 	midx_name = get_midx_filename(object_dir);
 	if (safe_create_leading_directories(midx_name)) {
@@ -312,6 +448,8 @@ int write_midx_file(const char *object_dir)
 	ALLOC_ARRAY(pack_perm, nr_packs);
 	sort_packs_by_name(pack_names, nr_packs, pack_perm);
 
+	get_sorted_entries(packs, pack_perm, nr_packs, &nr_entries);
+
 	hold_lock_file_for_update(&lk, midx_name, LOCK_DIE_ON_ERROR);
 	f = hashfd(lk.tempfile->fd, lk.tempfile->filename.buf);
 	FREE_AND_NULL(midx_name);
-- 
2.18.0.rc1