Merge pull request #6705 from ThomasWaldmann/repoindex

borg2: repoindex improvements
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TW 2022-06-14 14:51:18 +02:00 committed by GitHub
commit dc4a1e6d2d
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5 changed files with 269 additions and 62 deletions

View file

@ -77,6 +77,20 @@ assert UINT32_MAX == 2**32-1
assert _MAX_VALUE % 2 == 1
def hashindex_variant(fn):
"""peek into an index file and find out what it is"""
with open(fn, 'rb') as f:
hh = f.read(18) # len(HashHeader)
magic = hh[0:8]
if magic == b'BORG_IDX':
key_size = hh[16]
value_size = hh[17]
return f'k{key_size}_v{value_size}'
if magic == b'12345678': # used by unit tests
return 'k32_v16' # just return the current variant
raise ValueError(f'unknown hashindex format, magic: {magic!r}')
@cython.internal
cdef class IndexBase:
cdef HashIndex *index
@ -196,8 +210,115 @@ cdef class FuseVersionsIndex(IndexBase):
return hashindex_get(self.index, <unsigned char *>key) != NULL
NSIndexEntry = namedtuple('NSIndexEntry', 'segment offset size')
cdef class NSIndex(IndexBase):
value_size = 16
def __getitem__(self, key):
assert len(key) == self.key_size
data = <uint32_t *>hashindex_get(self.index, <unsigned char *>key)
if not data:
raise KeyError(key)
cdef uint32_t segment = _le32toh(data[0])
assert segment <= _MAX_VALUE, "maximum number of segments reached"
return NSIndexEntry(segment, _le32toh(data[1]), _le32toh(data[2]))
def __setitem__(self, key, value):
assert len(key) == self.key_size
cdef uint32_t[4] data
cdef uint32_t segment = value[0]
assert segment <= _MAX_VALUE, "maximum number of segments reached"
data[0] = _htole32(segment)
data[1] = _htole32(value[1])
data[2] = _htole32(value[2])
data[3] = 0 # init flags to all cleared
if not hashindex_set(self.index, <unsigned char *>key, data):
raise Exception('hashindex_set failed')
def __contains__(self, key):
cdef uint32_t segment
assert len(key) == self.key_size
data = <uint32_t *>hashindex_get(self.index, <unsigned char *>key)
if data != NULL:
segment = _le32toh(data[0])
assert segment <= _MAX_VALUE, "maximum number of segments reached"
return data != NULL
def iteritems(self, marker=None, mask=0, value=0):
"""iterate over all items or optionally only over items having specific flag values"""
cdef const unsigned char *key
assert isinstance(mask, int)
assert isinstance(value, int)
iter = NSKeyIterator(self.key_size, mask, value)
iter.idx = self
iter.index = self.index
if marker:
key = hashindex_get(self.index, <unsigned char *>marker)
if marker is None:
raise IndexError
iter.key = key - self.key_size
return iter
def flags(self, key, mask=0xFFFFFFFF, value=None):
"""query and optionally set flags"""
assert len(key) == self.key_size
assert isinstance(mask, int)
data = <uint32_t *>hashindex_get(self.index, <unsigned char *>key)
if not data:
raise KeyError(key)
flags = _le32toh(data[3])
if isinstance(value, int):
new_flags = flags & ~mask # clear masked bits
new_flags |= value & mask # set value bits
data[3] = _htole32(new_flags)
return flags & mask # always return previous flags value
cdef class NSKeyIterator:
cdef NSIndex idx
cdef HashIndex *index
cdef const unsigned char *key
cdef int key_size
cdef int exhausted
cdef int flag_mask
cdef int flag_value
def __cinit__(self, key_size, mask, value):
self.key = NULL
self.key_size = key_size
# note: mask and value both default to 0, so they will match all entries
self.flag_mask = _htole32(mask)
self.flag_value = _htole32(value)
self.exhausted = 0
def __iter__(self):
return self
def __next__(self):
cdef uint32_t *value
if self.exhausted:
raise StopIteration
while True:
self.key = hashindex_next_key(self.index, <unsigned char *>self.key)
if not self.key:
self.exhausted = 1
raise StopIteration
value = <uint32_t *> (self.key + self.key_size)
if value[3] & self.flag_mask == self.flag_value:
# we found a matching entry!
break
cdef uint32_t segment = _le32toh(value[0])
assert segment <= _MAX_VALUE, "maximum number of segments reached"
return ((<char *>self.key)[:self.key_size],
NSIndexEntry(segment, _le32toh(value[1]), _le32toh(value[2])))
cdef class NSIndex1(IndexBase): # legacy borg 1.x
value_size = 8
def __getitem__(self, key):
@ -230,7 +351,7 @@ cdef class NSIndex(IndexBase):
def iteritems(self, marker=None):
cdef const unsigned char *key
iter = NSKeyIterator(self.key_size)
iter = NSKeyIterator1(self.key_size)
iter.idx = self
iter.index = self.index
if marker:
@ -241,8 +362,8 @@ cdef class NSIndex(IndexBase):
return iter
cdef class NSKeyIterator:
cdef NSIndex idx
cdef class NSKeyIterator1: # legacy borg 1.x
cdef NSIndex1 idx
cdef HashIndex *index
cdef const unsigned char *key
cdef int key_size

View file

@ -13,7 +13,7 @@ from functools import partial
from itertools import islice
from .constants import * # NOQA
from .hashindex import NSIndex
from .hashindex import NSIndexEntry, NSIndex, NSIndex1, hashindex_variant
from .helpers import Error, ErrorWithTraceback, IntegrityError, format_file_size, parse_file_size
from .helpers import Location
from .helpers import ProgressIndicatorPercent
@ -52,6 +52,18 @@ MAX_TAG_ID = 15
FreeSpace = partial(defaultdict, int)
def header_size(tag):
if tag == TAG_PUT2:
size = LoggedIO.HEADER_ID_SIZE + LoggedIO.ENTRY_HASH_SIZE
elif tag == TAG_PUT or tag == TAG_DELETE:
size = LoggedIO.HEADER_ID_SIZE
elif tag == TAG_COMMIT:
size = LoggedIO.header_fmt.size
else:
raise ValueError(f"unsupported tag: {tag!r}")
return size
class Repository:
"""
Filesystem based transactional key value store
@ -525,10 +537,14 @@ class Repository:
if transaction_id is None:
return NSIndex()
index_path = os.path.join(self.path, 'index.%d' % transaction_id)
variant = hashindex_variant(index_path)
integrity_data = self._read_integrity(transaction_id, 'index')
try:
with IntegrityCheckedFile(index_path, write=False, integrity_data=integrity_data) as fd:
return NSIndex.read(fd)
if variant == 'k32_v16':
return NSIndex.read(fd)
if variant == 'k32_v8': # legacy
return NSIndex1.read(fd)
except (ValueError, OSError, FileIntegrityError) as exc:
logger.warning('Repository index missing or corrupted, trying to recover from: %s', exc)
os.unlink(index_path)
@ -798,14 +814,14 @@ class Repository:
if tag == TAG_COMMIT:
continue
in_index = self.index.get(key)
is_index_object = in_index == (segment, offset)
is_index_object = in_index and (in_index.segment, in_index.offset) == (segment, offset)
if tag in (TAG_PUT2, TAG_PUT) and is_index_object:
try:
new_segment, offset = self.io.write_put(key, data, raise_full=True)
except LoggedIO.SegmentFull:
complete_xfer()
new_segment, offset = self.io.write_put(key, data)
self.index[key] = new_segment, offset
self.index[key] = NSIndexEntry(new_segment, offset, len(data))
segments.setdefault(new_segment, 0)
segments[new_segment] += 1
segments[segment] -= 1
@ -821,10 +837,7 @@ class Repository:
# do not remove entry with empty shadowed_segments list here,
# it is needed for shadowed_put_exists code (see below)!
pass
if tag == TAG_PUT2:
self.storage_quota_use -= len(data) + self.io.HEADER_ID_SIZE + self.io.ENTRY_HASH_SIZE
elif tag == TAG_PUT:
self.storage_quota_use -= len(data) + self.io.HEADER_ID_SIZE
self.storage_quota_use -= header_size(tag) + len(data)
elif tag == TAG_DELETE and not in_index:
# If the shadow index doesn't contain this key, then we can't say if there's a shadowed older tag,
# therefore we do not drop the delete, but write it to a current segment.
@ -919,27 +932,26 @@ class Repository:
if tag in (TAG_PUT2, TAG_PUT):
try:
# If this PUT supersedes an older PUT, mark the old segment for compaction and count the free space
s, _ = self.index[key]
self.compact[s] += size
self.segments[s] -= 1
in_index = self.index[key]
self.compact[in_index.segment] += header_size(tag) + size
self.segments[in_index.segment] -= 1
except KeyError:
pass
self.index[key] = segment, offset
self.index[key] = NSIndexEntry(segment, offset, size)
self.segments[segment] += 1
self.storage_quota_use += size # note: size already includes the put_header_fmt overhead
self.storage_quota_use += header_size(tag) + size
elif tag == TAG_DELETE:
try:
# if the deleted PUT is not in the index, there is nothing to clean up
s, offset = self.index.pop(key)
in_index = self.index.pop(key)
except KeyError:
pass
else:
if self.io.segment_exists(s):
if self.io.segment_exists(in_index.segment):
# the old index is not necessarily valid for this transaction (e.g. compaction); if the segment
# is already gone, then it was already compacted.
self.segments[s] -= 1
size = self.io.read(s, offset, key, read_data=False)
self.compact[s] += size
self.segments[in_index.segment] -= 1
self.compact[in_index.segment] += header_size(tag) + in_index.size
elif tag == TAG_COMMIT:
continue
else:
@ -968,12 +980,13 @@ class Repository:
self.compact[segment] = 0
for tag, key, offset, size in self.io.iter_objects(segment, read_data=False):
if tag in (TAG_PUT2, TAG_PUT):
if self.index.get(key, (-1, -1)) != (segment, offset):
in_index = self.index.get(key)
if not in_index or (in_index.segment, in_index.offset) != (segment, offset):
# This PUT is superseded later
self.compact[segment] += size
self.compact[segment] += header_size(tag) + size
elif tag == TAG_DELETE:
# The outcome of the DELETE has been recorded in the PUT branch already
self.compact[segment] += size
self.compact[segment] += header_size(tag) + size
def check(self, repair=False, save_space=False, max_duration=0):
"""Check repository consistency
@ -1169,7 +1182,7 @@ class Repository:
self.index = self.open_index(transaction_id)
at_start = marker is None
# smallest valid seg is <uint32> 0, smallest valid offs is <uint32> 8
start_segment, start_offset = (0, 0) if at_start else self.index[marker]
start_segment, start_offset, _ = (0, 0, 0) if at_start else self.index[marker]
result = []
for segment, filename in self.io.segment_iterator(start_segment):
obj_iterator = self.io.iter_objects(segment, start_offset, read_data=False, include_data=False)
@ -1186,19 +1199,21 @@ class Repository:
# also, for the next segment, we need to start at offset 0.
start_offset = 0
continue
if tag in (TAG_PUT2, TAG_PUT) and (segment, offset) == self.index.get(id):
# we have found an existing and current object
result.append(id)
if len(result) == limit:
return result
if tag in (TAG_PUT2, TAG_PUT):
in_index = self.index.get(id)
if in_index and (in_index.segment, in_index.offset) == (segment, offset):
# we have found an existing and current object
result.append(id)
if len(result) == limit:
return result
return result
def get(self, id):
if not self.index:
self.index = self.open_index(self.get_transaction_id())
try:
segment, offset = self.index[id]
return self.io.read(segment, offset, id)
in_index = NSIndexEntry(*((self.index[id] + (None, ))[:3])) # legacy: index entriess have no size element
return self.io.read(in_index.segment, in_index.offset, id, expected_size=in_index.size)
except KeyError:
raise self.ObjectNotFound(id, self.path) from None
@ -1215,7 +1230,7 @@ class Repository:
if not self._active_txn:
self.prepare_txn(self.get_transaction_id())
try:
segment, offset = self.index[id]
in_index = self.index[id]
except KeyError:
pass
else:
@ -1223,12 +1238,12 @@ class Repository:
# we do not want to update the shadow_index here, because
# we know already that we will PUT to this id, so it will
# be in the repo index (and we won't need it in the shadow_index).
self._delete(id, segment, offset, update_shadow_index=False)
self._delete(id, in_index.segment, in_index.offset, in_index.size, update_shadow_index=False)
segment, offset = self.io.write_put(id, data)
self.storage_quota_use += len(data) + self.io.HEADER_ID_SIZE + self.io.ENTRY_HASH_SIZE
self.storage_quota_use += header_size(TAG_PUT2) + len(data)
self.segments.setdefault(segment, 0)
self.segments[segment] += 1
self.index[id] = segment, offset
self.index[id] = NSIndexEntry(segment, offset, len(data))
if self.storage_quota and self.storage_quota_use > self.storage_quota:
self.transaction_doomed = self.StorageQuotaExceeded(
format_file_size(self.storage_quota), format_file_size(self.storage_quota_use))
@ -1243,22 +1258,21 @@ class Repository:
if not self._active_txn:
self.prepare_txn(self.get_transaction_id())
try:
segment, offset = self.index.pop(id)
in_index = self.index.pop(id)
except KeyError:
raise self.ObjectNotFound(id, self.path) from None
# if we get here, there is an object with this id in the repo,
# we write a DEL here that shadows the respective PUT.
# after the delete, the object is not in the repo index any more,
# for the compaction code, we need to update the shadow_index in this case.
self._delete(id, segment, offset, update_shadow_index=True)
self._delete(id, in_index.segment, in_index.offset, in_index.size, update_shadow_index=True)
def _delete(self, id, segment, offset, *, update_shadow_index):
def _delete(self, id, segment, offset, size, *, update_shadow_index):
# common code used by put and delete
if update_shadow_index:
self.shadow_index.setdefault(id, []).append(segment)
self.segments[segment] -= 1
size = self.io.read(segment, offset, id, read_data=False)
self.compact[segment] += size
self.compact[segment] += header_size(TAG_PUT2) + size
segment, size = self.io.write_delete(id)
self.compact[segment] += size
self.segments.setdefault(segment, 0)
@ -1448,6 +1462,9 @@ class LoggedIO:
del self.fds[k]
clean_old()
if self._write_fd is not None:
# without this, we have a test failure now
self._write_fd.sync()
try:
ts, fd = self.fds[segment]
except KeyError:
@ -1515,7 +1532,8 @@ class LoggedIO:
if include_data:
yield tag, key, offset, data
else:
yield tag, key, offset, size
yield tag, key, offset, size - header_size(tag) # corresponds to len(data)
assert size >= 0
offset += size
# we must get the fd via get_fd() here again as we yielded to our caller and it might
# have triggered closing of the fd we had before (e.g. by calling io.read() for
@ -1580,7 +1598,7 @@ class LoggedIO:
h.update(d)
return h.digest()
def read(self, segment, offset, id, read_data=True):
def read(self, segment, offset, id, read_data=True, *, expected_size=None):
"""
Read entry from *segment* at *offset* with *id*.
If read_data is False the size of the entry is returned instead.
@ -1596,7 +1614,11 @@ class LoggedIO:
if id != key:
raise IntegrityError('Invalid segment entry header, is not for wanted id [segment {}, offset {}]'.format(
segment, offset))
return data if read_data else size
data_size_from_header = size - header_size(tag)
if expected_size is not None and expected_size != data_size_from_header:
raise IntegrityError(f'size from repository index: {expected_size} != '
f'size from entry header: {data_size_from_header}')
return data if read_data else data_size_from_header
def _read(self, fd, header, segment, offset, acceptable_tags, read_data=True):
"""

View file

@ -33,7 +33,7 @@ SELFTEST_CASES = [
ChunkerTestCase,
]
SELFTEST_COUNT = 36
SELFTEST_COUNT = 37
class SelfTestResult(TestResult):

View file

@ -87,8 +87,8 @@ class HashIndexTestCase(BaseTestCase):
del idx
def test_nsindex(self):
self._generic_test(NSIndex, lambda x: (x, x),
'85f72b036c692c8266e4f51ccf0cff2147204282b5e316ae508d30a448d88fef')
self._generic_test(NSIndex, lambda x: (x, x, x),
'7d70671d0b7e9d2f51b2691ecf35184b9f8ecc1202cceb2748c905c8fc04c256')
def test_chunkindex(self):
self._generic_test(ChunkIndex, lambda x: (x, x),
@ -102,7 +102,7 @@ class HashIndexTestCase(BaseTestCase):
initial_size = os.path.getsize(filepath)
self.assert_equal(len(idx), 0)
for x in range(n):
idx[H(x)] = x, x
idx[H(x)] = x, x, x, x
idx.write(filepath)
assert initial_size < os.path.getsize(filepath)
for x in range(n):
@ -114,7 +114,7 @@ class HashIndexTestCase(BaseTestCase):
def test_iteritems(self):
idx = NSIndex()
for x in range(100):
idx[H(x)] = x, x
idx[H(x)] = x, x, x, x
iterator = idx.iteritems()
all = list(iterator)
self.assert_equal(len(all), 100)
@ -153,6 +153,70 @@ class HashIndexTestCase(BaseTestCase):
assert chunks == 1 + 2 + 3
assert unique_chunks == 3
def test_flags(self):
idx = NSIndex()
key = H(0)
self.assert_raises(KeyError, idx.flags, key, 0)
idx[key] = 0, 0, 0 # create entry
# check bit 0 and 1, should be both 0 after entry creation
self.assert_equal(idx.flags(key, mask=3), 0)
# set bit 0
idx.flags(key, mask=1, value=1)
self.assert_equal(idx.flags(key, mask=1), 1)
# set bit 1
idx.flags(key, mask=2, value=2)
self.assert_equal(idx.flags(key, mask=2), 2)
# check both bit 0 and 1, both should be set
self.assert_equal(idx.flags(key, mask=3), 3)
# clear bit 1
idx.flags(key, mask=2, value=0)
self.assert_equal(idx.flags(key, mask=2), 0)
# clear bit 0
idx.flags(key, mask=1, value=0)
self.assert_equal(idx.flags(key, mask=1), 0)
# check both bit 0 and 1, both should be cleared
self.assert_equal(idx.flags(key, mask=3), 0)
def test_flags_iteritems(self):
idx = NSIndex()
keys_flagged0 = {H(i) for i in (1, 2, 3, 42)}
keys_flagged1 = {H(i) for i in (11, 12, 13, 142)}
keys_flagged2 = {H(i) for i in (21, 22, 23, 242)}
keys_flagged3 = {H(i) for i in (31, 32, 33, 342)}
for key in keys_flagged0:
idx[key] = 0, 0, 0 # create entry
idx.flags(key, mask=3, value=0) # not really necessary, unflagged is default
for key in keys_flagged1:
idx[key] = 0, 0, 0 # create entry
idx.flags(key, mask=3, value=1)
for key in keys_flagged2:
idx[key] = 0, 0, 0 # create entry
idx.flags(key, mask=3, value=2)
for key in keys_flagged3:
idx[key] = 0, 0, 0 # create entry
idx.flags(key, mask=3, value=3)
# check if we can iterate over all items
k_all = {k for k, v in idx.iteritems()}
self.assert_equal(k_all, keys_flagged0 | keys_flagged1 | keys_flagged2 | keys_flagged3)
# check if we can iterate over the flagged0 items
k0 = {k for k, v in idx.iteritems(mask=3, value=0)}
self.assert_equal(k0, keys_flagged0)
# check if we can iterate over the flagged1 items
k1 = {k for k, v in idx.iteritems(mask=3, value=1)}
self.assert_equal(k1, keys_flagged1)
# check if we can iterate over the flagged2 items
k1 = {k for k, v in idx.iteritems(mask=3, value=2)}
self.assert_equal(k1, keys_flagged2)
# check if we can iterate over the flagged3 items
k1 = {k for k, v in idx.iteritems(mask=3, value=3)}
self.assert_equal(k1, keys_flagged3)
# check if we can iterate over the flagged1 + flagged3 items
k1 = {k for k, v in idx.iteritems(mask=1, value=1)}
self.assert_equal(k1, keys_flagged1 | keys_flagged3)
# check if we can iterate over the flagged0 + flagged2 items
k1 = {k for k, v in idx.iteritems(mask=1, value=0)}
self.assert_equal(k1, keys_flagged0 | keys_flagged2)
class HashIndexExtraTestCase(BaseTestCase):
"""These tests are separate because they should not become part of the selftest.
@ -514,9 +578,9 @@ class NSIndexTestCase(BaseTestCase):
def test_nsindex_segment_limit(self):
idx = NSIndex()
with self.assert_raises(AssertionError):
idx[H(1)] = NSIndex.MAX_VALUE + 1, 0
idx[H(1)] = NSIndex.MAX_VALUE + 1, 0, 0, 0
assert H(1) not in idx
idx[H(2)] = NSIndex.MAX_VALUE, 0
idx[H(2)] = NSIndex.MAX_VALUE, 0, 0, 0
assert H(2) in idx
@ -531,38 +595,38 @@ class IndexCorruptionTestCase(BaseTestCase):
from struct import pack
def HH(x, y):
# make some 32byte long thing that depends on x and y.
def HH(x, y, z):
# make some 32byte long thing that depends on x, y, z.
# same x will mean a collision in the hashtable as bucket index is computed from
# first 4 bytes. giving a specific x targets bucket index x.
# y is to create different keys and does not go into the bucket index calculation.
# so, same x + different y --> collision
return pack('<IIQQQ', x, y, 0, 0, 0) # 2 * 4 + 3 * 8 == 32
return pack('<IIIIIIII', x, y, z, 0, 0, 0, 0, 0) # 8 * 4 == 32
idx = NSIndex()
# create lots of colliding entries
for y in range(700): # stay below max load to not trigger resize
idx[HH(0, y)] = (0, y)
idx[HH(0, y, 0)] = (0, y, 0)
assert idx.size() == 1031 * 40 + 18 # 1031 buckets + header
assert idx.size() == 1031 * 48 + 18 # 1031 buckets + header
# delete lots of the collisions, creating lots of tombstones
for y in range(400): # stay above min load to not trigger resize
del idx[HH(0, y)]
del idx[HH(0, y, 0)]
# create lots of colliding entries, within the not yet used part of the hashtable
for y in range(330): # stay below max load to not trigger resize
# at y == 259 a resize will happen due to going beyond max EFFECTIVE load
# if the bug is present, that element will be inserted at the wrong place.
# and because it will be at the wrong place, it can not be found again.
idx[HH(600, y)] = 600, y
idx[HH(600, y, 0)] = 600, y, 0
# now check if hashtable contents is as expected:
assert [idx.get(HH(0, y)) for y in range(400, 700)] == [(0, y) for y in range(400, 700)]
assert [idx.get(HH(0, y, 0)) for y in range(400, 700)] == [(0, y, 0) for y in range(400, 700)]
assert [HH(0, y) in idx for y in range(400)] == [False for y in range(400)] # deleted entries
assert [HH(0, y, 0) in idx for y in range(400)] == [False for y in range(400)] # deleted entries
# this will fail at HH(600, 259) if the bug is present.
assert [idx.get(HH(600, y)) for y in range(330)] == [(600, y) for y in range(330)]
assert [idx.get(HH(600, y, 0)) for y in range(330)] == [(600, y, 0) for y in range(330)]

View file

@ -714,7 +714,7 @@ class RepositoryCheckTestCase(RepositoryTestCaseBase):
def corrupt_object(self, id_):
idx = self.open_index()
segment, offset = idx[H(id_)]
segment, offset, _ = idx[H(id_)]
with open(os.path.join(self.tmppath, 'repository', 'data', '0', str(segment)), 'r+b') as fd:
fd.seek(offset)
fd.write(b'BOOM')