Fix PackInvalidException when fetch and repack run concurrently
We are running several servers with jGit. We need to run repack from
time to time to keep the repos performant. I.e. after push we test how
many small packs are in the repo and when a threshold is reached we run
the repack.
After upgrading jGit version we've found that if someone does the clone
at the time repack is running the clone sometimes (not always) fails
because the repack removes .pack file used by the clone. Server
exception and client error attached.
I've tracked down the cause and it seems to be introduced between jGit
5.2 (which we upgraded from) and 5.3 and being caused by this commit:
Move throw of PackInvalidException outside the catch -
afef866a44
The problem is that when the throw was inside of the try block the last
catch block catched the exception and called openFailed(false) method.
It is true that it called it with invalidate = false, which is wrong.
The real problem though is that with the throw outside of the try block
the openFail is not called at all and the fields activeWindows and
activeCopyRawData are not set to 0. Which affects the later called tests
like: if (++activeCopyRawData == 1 && activeWindows == 0).
The fix for this is relatively simple keeping the throw outside of the
try block and still having the invalid field set to true. I did
exhaustive testing of the change running concurrent clones and pushes
indefinitely and with the patch applied it never fails while without the
patch it takes relatively short to get the error.
See: https://www.eclipse.org/lists/jgit-dev/msg04014.html
Bug: 569349
Change-Id: I9dbf8801c8d3131955ad7124f42b62095d96da54
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>
Use Instant instead of milliseconds for filesystem timestamp handling
This enables higher file timestamp resolution on filesystems like ext4,
Mac APFS (1ns) or NTFS (100ns) providing high timestamp resolution on
filesystem level.
Note:
- on some OSes Java 8,9 truncate milliseconds, see
https://bugs.openjdk.java.net/browse/JDK-8177809, fixed in Java 10
- UnixFileAttributes truncates timestamp resolution to microseconds when
converting the internal representation to FileTime exposed in the API,
see https://bugs.openjdk.java.net/browse/JDK-8181493
- WindowsFileAttributes also provides only microsecond resolution
Change-Id: I25ffff31a3c6f725fc345d4ddc2f26da3b88f6f2
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>
Extend FileSnapshot for packfiles to also use checksum to detect changes
If the attributes of FileSnapshot don't detect modification of a
packfile read the packfile's checksum and compare it against the
checksum cached in the loaded packfile.
Since reading the checksum needs less IO than reloading the complete
packfile this may help to reduce the overhead to detect modficiation
when a gc completes while ObjectDirectory scans for packfiles in another
thread.
Bug: 546891
Change-Id: I9811b497eb11b8a85ae689081dc5d949ca8c4be5
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>
Keep track of the original cause for a packfile invalidation.
It is needed for the sysadmin to understand if there is a real
underlying filesystem problem and repository corruption or if it is
simply a consequence of a concurrency of Git operations (e.g. repack
or GC).
Change-Id: I06ddda9ec847844ec31616ab6d17f153a5a34e33
Signed-off-by: Luca Milanesio <luca.milanesio@gmail.com>
Signed-off-by: David Pursehouse <david.pursehouse@gmail.com>
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>
When reading from a packfile, make sure that is valid
and has a non-null file-descriptor.
Because of concurrency between a thread invalidating a packfile
and another trying to read it, the read() may result into a NPE
that won't be able to be automatically recovered.
Throwing a PackInvalidException would instead cause the packlist
to be refreshed and the read to eventually succeed.
Bug: 544199
Change-Id: I27788b3db759d93ec3212de35c0094ecaafc2434
Signed-off-by: Luca Milanesio <luca.milanesio@gmail.com>
Move throw of PackInvalidException outside the catch
When a packfile is invalid, throw an exception explicitly
outside any catch scope, so that is not accidentally caught
by the generic catch-all cause, which would set the packfile
as valid again.
Flagging an invalid packfile as valid again would have
dangerous consequences such as the corruption of the in-memory
packlist.
Bug: 544199
Change-Id: If7a3188a68d7985776b509d636d5ddf432bec798
Signed-off-by: Luca Milanesio <luca.milanesio@gmail.com>
Do not redundantly call File.lastModified() for extracting the
timestamp of the PackFile but rather use consistently the FileSnapshot
which reads all file attributes in a single bulk call.
Change-Id: I932675ae4fe56dcd3833dac249816f097303bb09
Signed-off-by: Luca Milanesio <luca.milanesio@gmail.com>
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>
The pack reload mechanism from the filesystem works only by name
and does not check the actual last modified date of the packfile.
This lead to concurrency issues where multiple threads were loading
and removing from each other list of packfiles when one of those
was failing the checksum.
Rely on FileSnapshot rather than directly checking lastModified
timestamp so that more checks can be performed.
Bug: 544199
Change-Id: I173328f29d9914007fd5eae3b4c07296ab292390
Signed-off-by: Luca Milanesio <luca.milanesio@gmail.com>
In case of concurrent pack file access, threads may wait on the idx()
function even for already open files. This happens especially with a
slow file system.
Performance numbers are listed in the bug report.
Bug: 543739
Change-Id: Iff328d347fa65ae07ecce3267d44184161248978
Signed-off-by: Juergen Denner <j.denner@sap.com>
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>
PackFile: report correct message for checksum mismatch
When the packfile checksum does not match the expected one
report the correct checksum error instead of reporting that
the number of objects is incorrect.
Change-Id: I040f36dacc4152ae05453e7acbf8dfccceb46e0d
Signed-off-by: Luca Milanesio <luca.milanesio@gmail.com>
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>
(cherry picked from commit 436c99ce59)
PackFile: report correct message for checksum mismatch
When the packfile checksum does not match the expected one
report the correct checksum error instead of reporting that
the number of objects is incorrect.
Change-Id: I040f36dacc4152ae05453e7acbf8dfccceb46e0d
Signed-off-by: Luca Milanesio <luca.milanesio@gmail.com>
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>
Remove it from
* package private functions.
* try blocks
* for loops
this was done with the following python script:
$ cat f.py
import sys
import re
import os
def replaceFinal(m):
return m.group(1) + "(" + m.group(2).replace('final ', '') + ")"
methodDecl = re.compile(r"^([\t ]*[a-zA-Z_ ]+)\(([^)]*)\)")
def subst(fn):
input = open(fn)
os.rename(fn, fn + "~")
dest = open(fn, 'w')
for l in input:
l = methodDecl.sub(replaceFinal, l)
dest.write(l)
dest.close()
for root, dirs, files in os.walk(".", topdown=False):
for f in files:
if not f.endswith('.java'):
continue
full = os.path.join(root, f)
print full
subst(full)
Change-Id: If533a75a417594fc893e7c669d2c1f0f6caeb7ca
Signed-off-by: Han-Wen Nienhuys <hanwen@google.com>
CorruptObjectException has a constructor that takes Throwable and
calls initCause with it. Use that instead of instantiating the
exception and explicitly calling initCause.
Change-Id: I1f2747d6c4cc5249e93401b9787eb4ceb50cb995
Signed-off-by: David Pursehouse <david.pursehouse@gmail.com>
Use new StoredObjectRepresentationNotAvailableException constructor
In 5e7eed4 a new StoredObjectRepresentationNotAvailableException
constructor was added, that takes a Throwable to initialize the
exception cause.
Update more call sites to use this constructor instead of first
instantiating it and explicitly calling initCause().
All callers now use the new constructor, so annotate the other one as
deprecated.
Change-Id: I6d2a7e289a95f0360ddebf904cfd8b6c18fef10c
Signed-off-by: David Pursehouse <david.pursehouse@gmail.com>
Fix exception handling for opening bitmap index files
When creating a new PackFile instance it is specified whether this pack
has an associated bitmap index file or not. This information is cached
and the public method getBitmapIndex() will always assume a bitmap index
file must exist if the cached data tells so. But it may happen that the
packfiles are repacked during a gc in a different process causing the
packfile, bitmap-index and index file to be deleted. Since JGit still
has an open FileHandle on the packfile this file is not really deleted
and can still be accessed. But index and bitmap index file are deleted.
Fix getBitmapIndex() to invalidate the cached packfile instance if such
a situation occurs.
This problem showed up when a gerrit server was serving repositories
which where garbage collected with native git regularly. Fetch and
clone commands for certain repositories failed permanently after a
native git gc had deleted old bitmap index files.
Change-Id: I8e620bec74dd3f310ba42024f9a657062f868f0e
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>
Only mark packfile invalid if exception signals permanent problem
Add NoPackSignatureException and UnsupportedPackVersionException to
explicitly mark permanent unrecoverable problems with a pack
Assume problem with a pack is permanent only if we are sure the
exception signals a non-transient problem we can't recover from:
- AccessDeniedException: we lack permissions
- CorruptObjectException: we detected corruption
- EOFException: file ended unexpectedly
- NoPackSignatureException: pack has no pack signature
- NoSuchFileException: file has gone missing
- PackMismatchException: pack no longer matches its index
- UnpackException: unpacking failed
- UnsupportedPackIndexVersionException: unsupported pack index version
- UnsupportedPackVersionException: unsupported pack version
Do not attempt to handle Errors since they are thrown for serious
problems applications should not try to recover from.
Change-Id: I2c416ce2b0e23255c4fb03a3f9a0ee237f7a484a
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>
Don't flag a packfile invalid if opening existing file failed
A packfile random file open operation may fail with a
FileNotFoundException even if the file exists, possibly
for the temporary lack of resources.
Instead of managing the FileNotFoundException as any generic
IOException it is best to rethrow the exception but prevent
the packfile for being flagged as invalid until it is actually
opened and read successfully or unsuccessfully.
Bug: 514170
Change-Id: Ie37edba2df77052bceafc0b314fd1d487544bf35
Signed-off-by: Luca Milanesio <luca.milanesio@gmail.com>
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>
Don't remove pack when FileNotFoundException is transient
The FileNotFoundException is typically raised in three conditions:
1. file doesn't exist
2. incompatible read vs. read/write open modes
3. filesystem locking
4. temporary lack of resources (e.g. too many open files)
1. is already managed, 2. would never happen as packs are not
overwritten while with 3. and 4. it is worth logging the exception and
retrying to read the pack again.
Log transient errors using an exponential backoff strategy to avoid
flooding the logs with the same error if consecutive retries to access
the pack fail repeatedly.
Bug: 513435
Change-Id: I03c6f6891de3c343d3d517092eaa75dba282c0cd
Signed-off-by: Luca Milanesio <luca.milanesio@gmail.com>
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>
Enable and fix 'Should be tagged with @Override' warning
Set missingOverrideAnnotation=warning in Eclipse compiler preferences
which enables the warning:
The method <method> of type <type> should be tagged with @Override
since it actually overrides a superclass method
Justification for this warning is described in:
http://stackoverflow.com/a/94411/381622
Enabling this causes in excess of 1000 warnings across the entire
code-base. They are very easy to fix automatically with Eclipse's
"Quick Fix" tool.
Fix all of them except 2 which cause compilation failure when the
project is built with mvn; add TODO comments on those for further
investigation.
Change-Id: I5772061041fd361fe93137fd8b0ad356e748a29c
Signed-off-by: David Pursehouse <david.pursehouse@gmail.com>
Previously it was looking for a keep file with the name of a pack file
(extenstion included) appended with a '.keep'. However, the keep file
name should be the pack file name with a '.keep' extension
Change-Id: I9dc4c7c393ae20aefa0b9507df8df83610ce4d42
Signed-off-by: James Melvin <jmelvin@codeaurora.org>
[performance] Remove synthetic access$ methods in pack and file packages
Java compiler must generate synthetic access methods for private methods
and fields of the enclosing class if they are accessed from inner
classes and vice versa.
While invisible in the code, those synthetic access methods exist in the
bytecode and seem to produce some extra execution overhead at runtime
(compared with the direct access to this fields or methods), see
https://git.eclipse.org/r/58948/.
By removing the "private" access modifier from affected methods and
fields we help compiler to avoid generation of synthetic access methods
and hope to improve execution performance.
To validate changes, one can either use javap or use Bytecode Outline
plugin in Eclipse. In both cases one should look for "synthetic
access$<number>" methods at the end of the class and inner class files
in question - there should be none.
NB: don't mix this "synthetic access$" methods up with "public synthetic
bridge" methods generated to allow generic method override return types.
Change-Id: If53ec94145bae47b74e2561305afe6098012715c
Signed-off-by: Andrey Loskutov <loskutov@gmx.de>
Set "potentialNullReference" to "error" level and fixed all issues
There should be no functional change, the logic updated only to make
code simple so that compiler can understand what is going for. Removed
all @SuppressWarnings("null") annotations since they cannot be used if
"org.eclipse.jdt.core.compiler.problem.potentialNullReference" option is
set to the "error" level.
Bug: 470647
Change-Id: Ie93c249fa46e792198d362e531d5cbabaf41fdc4
Signed-off-by: Andrey Loskutov <loskutov@gmx.de>
Don't invalidate pack file on InterruptedIOException
If the thread reading a pack file is interrupted don't invalidate that
pack file.
This could happen when Gerrit invoked JGit for computing a diff in one
thread and waited for the call to finish from another thread, with a
timeout. When the timeout was reached the "diff" thread was interrupted.
If it happened to be in an IO operation, reading a pack file, an
InterruptedIOException was thrown and the pack file was marked as
invalid and removed from the pack list.
Invalidating the pack in that case could cause the project disappearing in
Gerrit as discussed in [1] and [2].
[1] https://groups.google.com/forum/#!topic/repo-discuss/CYYoHfDxCfA
[2] https://groups.google.com/forum/#!topic/repo-discuss/ZeGWPyyJlrM
Change-Id: I2eb1f98370936b5be541d96d70c3973cbfc39238
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>
Signed-off-by: Sasa Zivkov <sasa.zivkov@sap.com>
Cached packs are only used when writing over the network or to
a bundle file and reuse validation is always disabled in these
two contexts. The client/consumer of the stream will be SHA-1
checksumming every object.
Reuse validation is most critical during local GC to avoid silently
ignoring corruption by stopping as soon as a problem is found and
leaving everything alone for the end-user to debug and salvage.
Cached packs are not supported during local GC as the bitmap rebuild
logic does not support including a cached pack in the result.
Strip out the validation and force PackWriter to always disable the
cached pack feature if reuseValidation is enabled.
Change-Id: If0d7baf2ae1bf1f7e71bf773151302c9f7887039
Remove AutoCloseable from internal PackFile and friends
PackFile is held by the block cache and cannot be auto closed in a
try-with-resources statement. Remove the interface as JGit does
explicit management of the instances.
ObjectDatabase and RefDatabase are internal details of Repository
and are managed with the Repository. Marking them AutoCloseable
provides no value to the library or an application using the API.
Change-Id: Ibee19eadd66233e6666b601583daa1834a7778f1
Provide more details in exceptions thrown when packfile is invalid
Mention packfile path in exceptions thrown when we detect that a
packfile is invalid and make excplicit that corrupt packs are removed
from the pack list.
Change-Id: I454ada5f8e69307d3f34d1c1b8f3cb87607ddf35
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>
Cleanup use of java.util.Inflater, fixing rare infinite loops
The native implementation of inflate() can set finished to return
true at the same time as it copies the last bytes into the buffer.
Check for finished on each iteration, terminating as soon as libz
knows the stream was completely inflated.
If not finished, it is likely input is required before the next
native call could do any useful work. Most invocations are passing
in a buffer large enough to store the entire result. A partial return
from inflate() will need more input before it can continue. Checking
right away that needsInput() is true saves a native call to determine
no bytes can be inflated without more input.
This should fix a rare infinite loop condition inside of inflation
when an object ends exactly at the end of a block boundary, and
the next block contains only the 20 byte trailing SHA-1.
When the stream is finished each new attempt to inflate() returns
n == 0, as no additional bytes were output. The needsInput() test
tries to add the length of the footer block to itself, but then loops
back around an reloads the same block as the block is smaller than
a full block size. A zero length input is set to the inflater,
which triggers needsInput() condition again.
Change-Id: I95d02bfeab4bf995a254d49166b4ae62d1f21346
Streaming packed deltas is so slow that it never feasibly completes
(it will take hours for it to stream a few hundred megabytes on
relatively fast systems with a large amount of storage). This
was indicated as a "failed experiment" by Shawn in the following
mailing list post:
http://dev.eclipse.org/mhonarc/lists/jgit-dev/msg01674.html
Change-Id: Idc12f59e37b122f13856d7b533a5af9d8867a8a5
Signed-off-by: Doug Kelly <dougk.ff7@gmail.com>
Ignore bitmap indexes that do not match the pack checksum
If `git gc` creates a new pack with the same file name, the
pack checksum may not match that in the .bitmap. Fix the PackFile
implementaion to silently ignore invalid bitmap indexes.
Fixes Issue https://code.google.com/p/gerrit/issues/detail?id=2131
Change-Id: I378673c00de32385ba90f4b639cb812f9574a216
JGit 3.0: move internal classes into an internal subpackage
This breaks all existing callers once. Applications are not supposed
to build against the internal storage API unless they can accept API
churn and make necessary updates as versions change.
Change-Id: I2ab1327c202ef2003565e1b0770a583970e432e9
If a pack file has been marked invalid due to a prior IOException
accessing its contents, do not offer its bitmap index to callers.
The pack cannot be used so its bitmap should be off limits from
any reader trying to work from a bitmap.
Change-Id: Ia44e46558abdddee560bb184158b1e0af9437eee
A pack bitmap index is an additional index of compressed
bitmaps of the object graph. Furthermore, a logical API of the index
functionality is included, as it is expected to be used by the
PackWriter.
Compressed bitmaps are created using the javaewah library, which is a
word-aligned compressed variant of the Java bitset class based on
run-length encoding. The library only works with positive integer
values. Thus, the maximum number of ObjectIds in a pack file that
this index can currently support is limited to Integer.MAX_VALUE.
Every ObjectId is given an integer mapping. The integer is the
position of the ObjectId in the complete ObjectId list, sorted
by offset, for the pack file. That integer is what the bitmaps
use to reference the ObjectId. Currently, the new index format can
only be used with pack files that contain a complete closure of the
object graph e.g. the result of a garbage collection.
The index file includes four bitmaps for the Git object types i.e.
commits, trees, blobs, and tags. In addition, a collection of
bitmaps keyed by an ObjectId is also included. The bitmap for each entry
in the collection represents the full closure of ObjectIds reachable
from the keyed ObjectId (including the keyed ObjectId itself). The
bitmaps are further compressed by XORing the current bitmaps against
prior bitmaps in the index, and selecting the smallest representation.
The XOR'd bitmap and offset from the current entry to the position
of the bitmap to XOR against is the actual representation of the entry
in the index file. Each entry contains one byte, which is currently
used to note whether the bitmap should be blindly reused.
Change-Id: Id328724bf6b4c8366a088233098c18643edcf40f
Include supported extensions in PackFile constructor.
Previously a PackFile class was assumed to only support a .pack and .idx
file. Update the constructor to enumerate the supported extensions for
the pack file. This will allow the bitmap code to only be executed if
the bitmap extension file is known to exist.
Change-Id: Ie59041dffec5f60d7ea2771026ffd945106bd4bf
Rename PackConstants to PackExt, a typed pack file extension.
PackConstants previously contained string values for the pack and pack
index extension. Change PackConstant to be PackExt, a typed wrapper
around the string pack file extension.
Change-Id: I86ac4db6da8f33aa42d6f37cfcc119e819444318
Remove packIndex field from FileObjDatabase openPack method.
Previously, the FileObjDatabase required both the pack file path and
index file path to be passed to openPack(). A future change to add
a bitmap index will add a .bitmap file parallel to the pack file
(similar to the .idx file). Update the PackFile to support
automatically loading pack index extensions based on the pack file
path.
Change-Id: Ifc8fc3e57f4afa177ba5a88df87334dbfa799f01
A few classes such as Constanrs are marked with @SuppressWarnings, as are
toString() methods with many liternal, but otherwise $NLS-n$ is used for
string containing text that should not be translated. A few literals may
fall into the gray zone, but mostly I've tried to only tag the obvious
ones.
Change-Id: I22e50a77e2bf9e0b842a66bdf674e8fa1692f590
Implements a garbage collector for FileRepositories. Main ideas are
copied from the garbage collector for DFS based repos
(DfsGarbageCollector). Added functionalities are
- pruning loose objects
- handling of the index
- packing refs
- handling of reflogs (objects referenced from reflog will not be
pruned/)
These are features of a GC which are not handled in this change and
which should come with subsequent changes:
- unpacking packed objects into loose objects (to support that pruning
packed objects doesn't delete them until they are older than two weeks)
- expiration of reflogs
- support for configuration parameters (e.g. gc.pruneExpire)
Change-Id: I14ea5cb7e0fd1b5c50b994fd77f4e05bfbb9d911
Signed-off-by: Christian Halstrick <christian.halstrick@sap.com>
Use Integer, Character, and Long valueOf methods when
passing parameters to MessageFormat and other places
that expect objects instead of primitives
Change-Id: I5942fbdbca6a378136c00d951ce61167f2366ca4
Parsing the size from a packed object header was incorrectly computing
the total inflated length when the length exceeded the range of a Java
int. The next 7 bits of size information was shifted left as an int
using a shift of 25 bits, placing the higher bits of the size into the
sign position. When this size was extended to a long to be added to
the current size accumulator the size went negative, resulting in
NegativeArraySizeException being thrown.
Fix all places where this particular pattern of code is used to read a
pack size field, or a binary delta header, as they both use the same
variable length encoding scheme.
Change-Id: I04008728ed828f18202652c3d5401cf95a441d0a
The 'Counting objects' phase of PackWriter requires good hit rates
from the DeltaBaseCache while walking trees, the deltas need to find
their bases in the cache in order to inflate in a reasonable time.
If JGit is running in a multi-threaded server, such as Gerrit Code
Review, each thread needs its own DeltaBaseCache to prevent one thread
from evicting the other thread's relevant bases. Move the cache to be
per-ObjectReader, lazily allocated when required by a PackFile.
Change-Id: If9d5ed06728e813632ae96dcfb811f4860b276e8
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>
Petr Hrebejk
Matthias Sohn
Luca Milanesio
Juergen Denner
Han-Wen Nienhuys
David Pursehouse
Christian Halstrick
James Melvin
Andrey Loskutov
Saša Živkov
Shawn Pearce
Doug Kelly
Colby Ranger
Robin Rosenberg
Kevin Sawicki