def main(fname):
fs = FileStorage(fname, read_only=1)
cn = ZODB.DB(fs).open()
rt = cn.root()
todo = []
add_if_new_persistent(todo, rt, '')
found = 0
while todo:
obj, path = todo.pop(0)
found += 1
if not path:
print "<root>", repr(obj)
else:
print path, repr(obj)
mod = str(obj.__class__.__module__)
if mod.startswith("BTrees"):
if hasattr(obj, "_check"):
try:
obj._check()
except AssertionError, msg:
print "*" * 60
print msg
print "*" * 60
try:
check(obj)
except AssertionError, msg:
print "*" * 60
print msg
print "*" * 60
def testDeletes(self):
# Delete keys in all possible orders, checking each tree along
# the way.
# This is a tough test. Previous failure modes included:
# 1. A variety of assertion failures in _checkRanges.
# 2. Assorted "Invalid firstbucket pointer" failures at
# seemingly random times, coming out of the BTree destructor.
# 3. Under Python 2.3 CVS, some baffling
# RuntimeWarning: tp_compare didn't return -1 or -2 for exception
# warnings, possibly due to memory corruption after a BTree
# goes insane.
# On CPython in PURE_PYTHON mode, this is a *slow* test, taking 15+s
# on a 2015 laptop.
from BTrees.check import check
t, keys = self._build_degenerate_tree()
for oneperm in permutations(keys):
t, keys = self._build_degenerate_tree()
for key in oneperm:
t.remove(key)
keys.remove(key)
t._check()
check(t)
self._checkRanges(t, keys)
# We removed all the keys, so the tree should be empty now.
self.assertEqual(t.__getstate__(), None)
# A damaged tree may trigger an "invalid firstbucket pointer"
# failure at the time its destructor is invoked. Try to force
# that to happen now, so it doesn't look like a baffling failure
# at some unrelated line.
del t # trigger destructor
def testKeysSwapped(self):
# Damage an invariant by swapping two key/value pairs.
s = self.state
# Looks like (state, first_bucket)
# where state looks like (bucket0, 15, bucket1).
(b0, num, b1), firstbucket = s
self.assertEqual(b0[4], 8)
self.assertEqual(b0[5], 10)
b0state = b0.__getstate__()
self.assertEqual(len(b0state), 2)
# b0state looks like
# ((k0, v0, k1, v1, ...), nextbucket)
pairs, nextbucket = b0state
self.assertEqual(pairs[8], 4)
self.assertEqual(pairs[9], 8)
self.assertEqual(pairs[10], 5)
self.assertEqual(pairs[11], 10)
newpairs = pairs[:8] + (5, 10, 4, 8) + pairs[12:]
b0.__setstate__((newpairs, nextbucket))
self.t._check() # not caught
try:
check(self.t)
except AssertionError, detail:
self.failUnless(str(detail).find(
"key 5 at index 4 >= key 4 at index 5") > 0)
def testDeletes(self):
# Delete keys in all possible orders, checking each tree along
# the way.
# This is a tough test. Previous failure modes included:
# 1. A variety of assertion failures in _checkRanges.
# 2. Assorted "Invalid firstbucket pointer" failures at
# seemingly random times, coming out of the BTree destructor.
# 3. Under Python 2.3 CVS, some baffling
# RuntimeWarning: tp_compare didn't return -1 or -2 for exception
# warnings, possibly due to memory corruption after a BTree
# goes insane.
from BTrees.check import check
t, keys = self._build_degenerate_tree()
for oneperm in permutations(keys):
t, keys = self._build_degenerate_tree()
for key in oneperm:
t.remove(key)
keys.remove(key)
t._check()
check(t)
self._checkRanges(t, keys)
# We removed all the keys, so the tree should be empty now.
self.assertEqual(t.__getstate__(), None)
# A damaged tree may trigger an "invalid firstbucket pointer"
# failure at the time its destructor is invoked. Try to force
# that to happen now, so it doesn't look like a baffling failure
# at some unrelated line.
del t # trigger destructor
def testKeysSwapped(self):
# Damage an invariant by swapping two key/value pairs.
s = self.state
# Looks like (state, first_bucket)
# where state looks like (bucket0, 15, bucket1).
(b0, num, b1), firstbucket = s
self.assertEqual(b0[4], 8)
self.assertEqual(b0[5], 10)
b0state = b0.__getstate__()
self.assertEqual(len(b0state), 2)
# b0state looks like
# ((k0, v0, k1, v1, ...), nextbucket)
pairs, nextbucket = b0state
self.assertEqual(pairs[8], 4)
self.assertEqual(pairs[9], 8)
self.assertEqual(pairs[10], 5)
self.assertEqual(pairs[11], 10)
newpairs = pairs[:8] + (5, 10, 4, 8) + pairs[12:]
b0.__setstate__((newpairs, nextbucket))
self.t._check() # not caught
try:
check(self.t)
except AssertionError, detail:
self.failUnless(str(detail).find(
"key 5 at index 4 >= key 4 at index 5") > 0)
def is_ordered(self, item):
if item is None:
return True
try:
check(item)
except AssertionError:
return False
return True
def is_ordered(self, item):
if item is None:
return True
try:
check(item)
except AssertionError:
return False
return True
def testNormal(self):
s = self.state
# Looks like (state, first_bucket)
# where state looks like (bucket0, 15, bucket1).
self.assertEqual(len(s), 2)
self.assertEqual(len(s[0]), 3)
self.assertEqual(s[0][1], 15)
self.t._check() # shouldn't blow up
check(self.t) # shouldn't blow up
def testNormal(self):
s = self.state
# Looks like (state, first_bucket)
# where state looks like (bucket0, 15, bucket1).
self.assertEqual(len(s), 2)
self.assertEqual(len(s[0]), 3)
self.assertEqual(s[0][1], 15)
self.t._check() # shouldn't blow up
check(self.t) # shouldn't blow up
def testKeyTooSmall(self):
# Damage an invariant by bumping the BTree key to 16.
s = self.state
news = (s[0][0], 16, s[0][2]), s[1]
self.t.__setstate__(news)
self.t._check() # not caught
try:
# Expecting "... key %r < lower bound %r at index %d"
check(self.t)
except AssertionError, detail:
self.failUnless(str(detail).find("< lower bound") > 0)
def testKeyTooSmall(self):
# Damage an invariant by bumping the BTree key to 16.
s = self.state
news = (s[0][0], 16, s[0][2]), s[1]
self.t.__setstate__(news)
self.t._check() # not caught
try:
# Expecting "... key %r < lower bound %r at index %d"
check(self.t)
except AssertionError, detail:
self.failUnless(str(detail).find("< lower bound") > 0)
def main(fname=None):
if fname is None:
import sys
try:
fname, = sys.argv[1:]
except:
print(__doc__)
sys.exit(2)
fs = FileStorage(fname, read_only=1)
cn = ZODB.DB(fs).open()
rt = cn.root()
todo = []
add_if_new_persistent(todo, rt, '')
found = 0
while todo:
obj, path = todo.pop(0)
found += 1
if not path:
print("<root>", repr(obj))
else:
print(path, repr(obj))
mod = str(obj.__class__.__module__)
if mod.startswith("BTrees"):
if hasattr(obj, "_check"):
try:
obj._check()
except AssertionError as msg:
print("*" * 60)
print(msg)
print("*" * 60)
try:
check(obj)
except AssertionError as msg:
print("*" * 60)
print(msg)
print("*" * 60)
if found % 100 == 0:
cn.cacheMinimize()
for k, v in get_subobjects(obj):
if k.startswith('['):
# getitem
newpath = "%s%s" % (path, k)
else:
newpath = "%s.%s" % (path, k)
add_if_new_persistent(todo, v, newpath)
print("total", len(fs._index), "found", found)
def _build_degenerate_tree(self):
# Build the buckets and chain them together.
from BTrees.IIBTree import IISet
from BTrees.IIBTree import IITreeSet
from BTrees.check import check
bucket11 = IISet([11])
bucket7 = IISet()
bucket7.__setstate__(((7,), bucket11))
bucket5 = IISet()
bucket5.__setstate__(((5,), bucket7))
bucket3 = IISet()
bucket3.__setstate__(((3,), bucket5))
bucket1 = IISet()
bucket1.__setstate__(((1,), bucket3))
# Build the deepest layers of indirection nodes.
ts = IITreeSet
tree1 = ts()
tree1.__setstate__(((bucket1,), bucket1))
tree3 = ts()
tree3.__setstate__(((bucket3,), bucket3))
tree5lower = ts()
tree5lower.__setstate__(((bucket5,), bucket5))
tree5 = ts()
tree5.__setstate__(((tree5lower,), bucket5))
tree7 = ts()
tree7.__setstate__(((bucket7,), bucket7))
tree11 = ts()
tree11.__setstate__(((bucket11,), bucket11))
# Paste together the middle layers.
tree13 = ts()
tree13.__setstate__(((tree1, 2, tree3), bucket1))
tree5711lower = ts()
tree5711lower.__setstate__(((tree5, 6, tree7, 10, tree11), bucket5))
tree5711 = ts()
tree5711.__setstate__(((tree5711lower,), bucket5))
# One more.
t = ts()
t.__setstate__(((tree13, 4, tree5711), bucket1))
t._check()
check(t)
return t, [1, 3, 5, 7, 11]
def _build_degenerate_tree(self):
# Build the buckets and chain them together.
from BTrees.IIBTree import IISet
from BTrees.IIBTree import IITreeSet
from BTrees.check import check
bucket11 = IISet([11])
bucket7 = IISet()
bucket7.__setstate__(((7,), bucket11))
bucket5 = IISet()
bucket5.__setstate__(((5,), bucket7))
bucket3 = IISet()
bucket3.__setstate__(((3,), bucket5))
bucket1 = IISet()
bucket1.__setstate__(((1,), bucket3))
# Build the deepest layers of indirection nodes.
ts = IITreeSet
tree1 = ts()
tree1.__setstate__(((bucket1,), bucket1))
tree3 = ts()
tree3.__setstate__(((bucket3,), bucket3))
tree5lower = ts()
tree5lower.__setstate__(((bucket5,), bucket5))
tree5 = ts()
tree5.__setstate__(((tree5lower,), bucket5))
tree7 = ts()
tree7.__setstate__(((bucket7,), bucket7))
tree11 = ts()
tree11.__setstate__(((bucket11,), bucket11))
# Paste together the middle layers.
tree13 = ts()
tree13.__setstate__(((tree1, 2, tree3), bucket1))
tree5711lower = ts()
tree5711lower.__setstate__(((tree5, 6, tree7, 10, tree11), bucket5))
tree5711 = ts()
tree5711.__setstate__(((tree5711lower,), bucket5))
# One more.
t = ts()
t.__setstate__(((tree13, 4, tree5711), bucket1))
t._check()
check(t)
return t, [1, 3, 5, 7, 11]
def main(fname=None):
if fname is None:
import sys
try:
fname, = sys.argv[1:]
except:
print(__doc__)
sys.exit(2)
fs = FileStorage(fname, read_only=1)
cn = ZODB.DB(fs).open()
rt = cn.root()
todo = []
add_if_new_persistent(todo, rt, '')
found = 0
while todo:
obj, path = todo.pop(0)
found += 1
if not path:
print("<root>", repr(obj))
else:
print(path, repr(obj))
mod = str(obj.__class__.__module__)
if mod.startswith("BTrees"):
if hasattr(obj, "_check"):
try:
obj._check()
except AssertionError as msg:
print("*" * 60)
print(msg)
print("*" * 60)
try:
check(obj)
except AssertionError as msg:
print("*" * 60)
print(msg)
print("*" * 60)
if found % 100 == 0:
cn.cacheMinimize()
for k, v in get_subobjects(obj):
if k.startswith('['):
# getitem
newpath = "%s%s" % (path, k)
else:
newpath = "%s.%s" % (path, k)
add_if_new_persistent(todo, v, newpath)
print("total", len(fs._index), "found", found)
def hCheck(htree):
"""
Recursively check the btree
"""
check(htree)
for key in htree.keys():
if not htree.has_key(key):
raise AssertionError("Missing value for key: %s" % repr(key))
else:
ob = htree[key]
if isinstance(ob, OOBTree):
hCheck(ob)
return 1
def hCheck(htree):
"""
Recursively check the btree
"""
check(htree)
for key in htree.keys():
if not htree.has_key(key):
raise AssertionError(
"Missing value for key: %s" % repr(key))
else:
ob = htree[key]
if isinstance(ob, OOBTree):
hCheck(ob)
return 1
def _check_tree(self, cn, tree):
# Make sure the BTree is sane at the C level.
retries = 3
while retries:
retries -= 1
try:
check(tree)
tree._check()
except ReadConflictError:
if retries:
transaction.abort()
else:
raise
except:
display(tree)
raise
def _check_tree(self, cn, tree):
# Make sure the BTree is sane at the C level.
retries = 3
while retries:
retries -= 1
try:
check(tree)
tree._check()
except ReadConflictError:
if retries:
transaction.abort()
else:
raise
except:
display(tree)
raise
def __init__(self, tree, base_id=_marker):
self._tree = tree
if base_id is _marker:
tree_id_list = tree.getTreeIdList()
self._count = tree._count
else:
tree_id_list = base_id,
check = tree._checkObjectId
self._keys = lambda: (x for base_id in tree_id_list for x in (
tree._htree if base_id is None else tree._getTree(base_id)).keys()
if check((base_id, x)))
def cleanup_to_mapping(self, iface_name, mapping_key):
# Check the BTree consistency, to avoid key errors when deleting
# entries in the BTree.
# If the check method detects an inconsistency, we fix the Btree by
# creating a copy of it.
#
# See http://do3.cc/blog/2012/09/264/debugging-zcrelations---broken-btrees/
# for more information.
try:
check(self.catalog._name_TO_mapping[mapping_key])
except AssertionError:
btree = self.catalog._name_TO_mapping[mapping_key]
self.catalog._name_TO_mapping[mapping_key] = btree.__class__(btree)
logger.warning(
'Inconsistent BTree detected and fixed by recreating it.')
for iface in self.catalog._name_TO_mapping[mapping_key].keys():
if '{}.{}'.format(iface.__module__, iface.__name__) == iface_name:
del self.catalog._name_TO_mapping[mapping_key][iface]
break
def cleanup_to_mapping(self, iface_name, mapping_key):
# Check the BTree consistency, to avoid key errors when deleting
# entries in the BTree.
# If the check method detects an inconsistency, we fix the Btree by
# creating a copy of it.
#
# See http://do3.cc/blog/2012/09/264/debugging-zcrelations---broken-btrees/
# for more information.
try:
check(self.catalog._name_TO_mapping[mapping_key])
except AssertionError:
btree = self.catalog._name_TO_mapping[mapping_key]
self.catalog._name_TO_mapping[mapping_key] = btree.__class__(btree)
logger.warning(
'Inconsistent BTree detected and fixed by recreating it.')
for iface in self.catalog._name_TO_mapping[mapping_key].keys():
if '{}.{}'.format(iface.__module__, iface.__name__) == iface_name:
del self.catalog._name_TO_mapping[mapping_key][iface]
break
def __init__(self, tree, base_id=_marker):
self._tree = tree
if base_id is _marker:
tree_id_list = tree.getTreeIdList()
self._count = tree._count
else:
tree_id_list = base_id,
check = tree._checkObjectId
self._keys = lambda: (x for base_id in tree_id_list
for x in (tree._htree if base_id is None else
tree._getTree(base_id)).keys()
if check((base_id, x)))
def main(fname=None):
if fname is None:
import sys
try:
fname, = sys.argv[1:]
except:
print __doc__
sys.exit(2)
fs = FileStorage(fname, read_only=1)
cn = ZODB.DB(fs).open()
rt = cn.root()
todo = []
add_if_new_persistent(todo, rt, '')
found = 0
while todo:
obj, path = todo.pop(0)
found += 1
if not path:
print "<root>", repr(obj)
else:
print path, repr(obj)
mod = str(obj.__class__.__module__)
if mod.startswith("BTrees"):
if hasattr(obj, "_check"):
try:
obj._check()
except AssertionError, msg:
print "*" * 60
print msg
print "*" * 60
try:
check(obj)
except AssertionError, msg:
print "*" * 60
print msg
print "*" * 60
def _cleanup(self):
"""Cleans up errors in the BTrees.
Certain ZODB bugs have caused BTrees to become slightly insane.
Fortunately, there is a way to clean up damaged BTrees that
always seems to work: make a new BTree containing the items()
of the old one.
Returns 1 if no damage was detected, or 0 if damage was
detected and fixed.
"""
from BTrees.check import check
path = '/'.join(self.getPhysicalPath())
try:
check(self._tree)
for key in self._tree.keys():
if key not in self._tree:
raise AssertionError(
"Missing value for key: %s" % repr(key))
check(self._mt_index)
keys = set(self._tree.keys())
for key, value in self._mt_index.items():
if (key not in self._mt_index
or self._mt_index[key] is not value):
raise AssertionError(
"Missing or incorrect meta_type index: %s"
% repr(key))
check(value)
for k in value.keys():
if k not in value or k not in keys:
raise AssertionError(
"Missing values for meta_type index: %s"
% repr(key))
return 1
except AssertionError:
LOG.warn('Detected damage to %s. Fixing now.' % path,
exc_info=sys.exc_info())
try:
self._tree = OOBTree(self._tree)
keys = set(self._tree.keys())
mt_index = OOBTree()
for key, value in self._mt_index.items():
for name in tuple(value.keys()):
if name not in keys:
del value[name]
mt_index[key] = OIBTree(value)
self._mt_index = mt_index
new = len(keys)
if self._count() != new:
self._count.set(new)
except:
LOG.error('Failed to fix %s.' % path,
exc_info=sys.exc_info())
raise
else:
LOG.info('Fixed %s.' % path)
return 0
def _cleanup(self):
"""Cleans up errors in the BTrees.
Certain ZODB bugs have caused BTrees to become slightly insane.
Fortunately, there is a way to clean up damaged BTrees that
always seems to work: make a new BTree containing the items()
of the old one.
Returns 1 if no damage was detected, or 0 if damage was
detected and fixed.
"""
from BTrees.check import check
path = '/'.join(self.getPhysicalPath())
try:
check(self._tree)
for key in self._tree.keys():
if key not in self._tree:
raise AssertionError(
"Missing value for key: %s" % repr(key))
check(self._mt_index)
keys = set(self._tree.keys())
for key, value in self._mt_index.items():
if (key not in self._mt_index
or self._mt_index[key] is not value):
raise AssertionError(
"Missing or incorrect meta_type index: %s"
% repr(key))
check(value)
for k in value.keys():
if k not in value or k not in keys:
raise AssertionError(
"Missing values for meta_type index: %s"
% repr(key))
return 1
except AssertionError:
LOG.warning('Detected damage to %s. Fixing now.' % path,
exc_info=sys.exc_info())
try:
self._tree = OOBTree(self._tree)
keys = set(self._tree.keys())
mt_index = OOBTree()
for key, value in self._mt_index.items():
for name in tuple(value.keys()):
if name not in keys:
del value[name]
mt_index[key] = OIBTree(value)
self._mt_index = mt_index
new = len(keys)
if self._count() != new:
self._count.set(new)
except Exception:
LOG.error('Failed to fix %s.' % path,
exc_info=sys.exc_info())
raise
else:
LOG.info('Fixed %s.' % path)
return 0
def _cleanup(self):
"""Cleans up errors in the BTrees.
Certain ZODB bugs have caused BTrees to become slightly insane.
Fortunately, there is a way to clean up damaged BTrees that
always seems to work: make a new BTree containing the items()
of the old one.
Returns 1 if no damage was detected, or 0 if damage was
detected and fixed.
"""
from BTrees.check import check
path = '/'.join(self.getPhysicalPath())
try:
check(self._tree)
for key in self._tree.keys():
if not self._tree.has_key(key):
raise AssertionError(
"Missing value for key: %s" % repr(key))
check(self._mt_index)
for key, value in self._mt_index.items():
if (not self._mt_index.has_key(key)
or self._mt_index[key] is not value):
raise AssertionError(
"Missing or incorrect meta_type index: %s"
% repr(key))
check(value)
for k in value.keys():
if not value.has_key(k):
raise AssertionError(
"Missing values for meta_type index: %s"
% repr(key))
return 1
except AssertionError:
LOG('BTreeFolder2', WARNING,
'Detected damage to %s. Fixing now.' % path,
error=sys.exc_info())
try:
self._tree = OOBTree(self._tree)
mt_index = OOBTree()
for key, value in self._mt_index.items():
mt_index[key] = OIBTree(value)
self._mt_index = mt_index
except:
LOG('BTreeFolder2', ERROR, 'Failed to fix %s.' % path,
error=sys.exc_info())
raise
else:
LOG('BTreeFolder2', INFO, 'Fixed %s.' % path)
return 0
def _callFUT(self, tree):
from BTrees.check import check
return check(tree)
args = parser.parse_args()
logging.basicConfig(filename='/projects/dami9546/HPSC/final/hostgraph_test2120.out', \
format='%(asctime)s %(message)s',level=logging.DEBUG)
logging.info('Starting graph script')
D = DAG(args.in_file, args.host_mapping)
Grf, H = D.slog2Dict()
I = D.connectGraph(Grf,H)
for i in H.keys():
logging.info("type of rank_dict[i]['MPI_Send']: %s" % (type(H[i]['MPI_Send'])))
logging.info("type of rank_dict[i]['MPI_Wait']: %s" % (type(H[i]['MPI_Wait'])))
logging.info("type of rank_dict[i]: %s" % (type(H[i])))
try:
check(H[i]['MPI_Send'])
check(H[i]['MPI_Wait'])
logging.info('my type: %s' % type(i))
logging.info('%d is clean' % i)
except:
logging.info('my type: %s' % type(i))
logging.error('%d is corrupt' % i)
logging.info("DAG size: %d" % (I.size()))
logging.info("DAG numnodes %d" % (len(I)))
logging.info("number of self-loops: %d" % (I.number_of_selfloops()))
crit_path = D.find_critical(I)
with open(args.crit_file, 'wb') as c:
crit_path = map(lambda x:x+'\n', crit_path)
c.writelines(crit_path)