Is it safe to delete virtuoso.trx? - virtuoso

I just looked into one of our Virtuoso db directories and noticed that virtuoso.db is not the biggest file there -- virtuoso.trx (transaction log) is.
Assuming that I am happy with the data in virtuoso.db and do not anticipate needing to reverse any transactions, is it safe to delete that file and restart (to conserve disk space)?
RELATED: Virtuoso Data Backup & Recovery

virtuoso.db was the active DB immediately following the last CHECKPOINT.
virtuoso.trx is the transaction log, which holds all changes made since the last CHECKPOINT was run.
virtuoso.db plus virtuoso.trx delivers your current active DB.
You should not delete the virtuoso.trx if you want the virtuoso.db to stay as it is. You should start an iSQL or similar session, and run a CHECKPOINT(). The .trx file will be reduced to zero as part of this process.
If you delete this file without running a CHECKPOINT, you will lose all that activity -- whether it was INSERT, UPDATE, DELETE, or otherwise.
Default configuration has CheckpointInterval of 60 minutes -- so a CHECKPOINT(); will run every 60 minutes, and the transaction log will not grow excessively.
See --
6.1.1. Database — Virtuoso Configuration File — [Parameters] — CheckpointInterval=60
9.21. CHECKPOINT, SHUTDOWN Statement
12.5. Database Shutdown
Tips & Tricks — How can I handle checkpoint condition?
Virtuoso Functions Guide & Reference — checkpoint_interval() — Configure database checkpointing

Related

Sqoop from Oracle: "Snapshot too Old"

I am setting up an automated process to sqoop from an oracle table to an hdfs directory with this command:
sqoop-import --connect jdbc:oracle:thin:#redacted.company.com:1234/db --username redacted --password secret123 --num-mappers 1 --table table --target-dir /data/destination/directory/ --as-avrodatafile --compress --compression-codec org.apache.hadoop.io.compress.BZip2Codec
Unfortunately, I'm getting the following error message:
Error:java.io.IOException: SQLException in nextKeyValue
...
Caused by: java.sql.SQLException: ORA-01555: snapshot too old: rollback segment number 336 with name "_SYSSMU336_879580159$" too small
at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:447)
at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:396)
at oracle.jdbc.driver.T4C8Oall.processError(T4C8Oall.java:951)
at oracle.jdbc.driver.T4CTTIfun.receive(T4CTTIfun.java:513)
at oracle.jdbc.driver.T4CTTIfun.doRPC(T4CTTIfun.java:227)
at oracle.jdbc.driver.T4C8Oall.doOALL(T4C8Oall.java:531)
at oracle.jdbc.driver.T4CPreparedStatement.doOall8(T4CPreparedStatement.java:208)
The business requirement I am attempting to fulfill is that the entire table is imported into our hdfs. Since we do not own or administrate this database, I lack control over the UNDO tablespace and related parameters. The job is scheduled to run at 1am which is not a peak time, but since automated processes touch it, I cannot coax people to stop using it during the job.
How should I modify my sqoop-import statement to avoid this error?
It is not a Sqoop issue. You would get the same error executing the same statment directly on Oracle. It is an undo tablespace issue. You have to get your query faster or you have to increase the Oracle undo tablespace size.
List of possible fixes:
Schedule your task when there are less database activity (maybe even
ask people to stop working for a while).
Optimize the query that is failing with this error to read less data
and take less time Increase the size of the UNDO tablespace.
Increase the size of the UNDO_RETENTION parameter.
Set the UNDO tablespace in GUARANTEE mode.
If you are exporting a table, consider exporting with the
CONSISTENT=no parameter.
Do not commit inside a cursor loop
Regards
Giova
Usage of --num-mappers=10 (i.e. increased parallelism) was sufficient enough to overcome the problem in this instance without impacting the source too much.
Additionally, adding the --direct parameter will cause Sqoop to use an Oracle specific connector which will speed things up further, and will be added to my solution as soon as I convince the DBA on that database to open up the necessary privileges. Direct also supports the option -Doraoop.import.consistent.read={true|false} which seems to mirror the Oracle export utility's CONSISTENT parameter in function (note, defaults to false), in the sense that the undo tablespace would not be used to try to preserve consistency, eliminating the need to race to import before the Undo tablespace fills up altogether.

sqlite disk i/o error when performing SELECT statement [duplicate]

We have a new beta version of our software with some changes, but not around our database layer.
We've just started getting Error 3128 reported in our server logs. It seems that once it happens, it happens for as long as the app is open. The part of the code where it is most apparent is where we log data every second via SQLite. We've generated 47k errors on our server this month alone.
3128 Disk I/O error occurred. Indicates that an operation could not be completed because of a disk I/O error. This can happen if the runtime is attempting to delete a temporary file and another program (such as a virus protection application) is holding a lock on the file. This can also happen if the runtime is attempting to write data to a file and the data can't be written.
I don't know what could be causing this error. Maybe an anti-virus program? Maybe our app is getting confused and writing data on top of each other? We're using async connections.
It's causing lots of issues and we're at a loss. It has happened in our older version, but maybe 100 times in a month rather than 47,000 times. Either way I'd like to make it happen "0" times.
Possible solution: Exception Message: Some kind of disk I/O error occurred
Summary: There is probably not a problem with the database but a problem creating (or deleting) the temporary file once the database is opened. AIR may have permissions to the database, but not to create or delete files in the directory.
One answer that has worked for me is to use the PRAGMA statement to set the journal_mode value to something other than DELETE. You do this by issuing a PRAGMA statement in the same way you would issue a query statement.
PRAGMA journal_mode = OFF
Unfortunately, if the application crashes in the middle of a transaction when the OFF journaling mode is set, then the database file will very likely go corrupt.1.
1 http://www.sqlite.org/pragma.html#pragma_journal_mode
The solution was to make sure database delete, update, insert only happened one at at time by wrapping a little wrapper. On top of that, we had to watch for error 3128 and retry. I think this is because we have a trigger running that could lock the database after we inserted data.

Just started getting AIR SQLite Error 3182 Disk I/O error occurred

We have a new beta version of our software with some changes, but not around our database layer.
We've just started getting Error 3128 reported in our server logs. It seems that once it happens, it happens for as long as the app is open. The part of the code where it is most apparent is where we log data every second via SQLite. We've generated 47k errors on our server this month alone.
3128 Disk I/O error occurred. Indicates that an operation could not be completed because of a disk I/O error. This can happen if the runtime is attempting to delete a temporary file and another program (such as a virus protection application) is holding a lock on the file. This can also happen if the runtime is attempting to write data to a file and the data can't be written.
I don't know what could be causing this error. Maybe an anti-virus program? Maybe our app is getting confused and writing data on top of each other? We're using async connections.
It's causing lots of issues and we're at a loss. It has happened in our older version, but maybe 100 times in a month rather than 47,000 times. Either way I'd like to make it happen "0" times.
Possible solution: Exception Message: Some kind of disk I/O error occurred
Summary: There is probably not a problem with the database but a problem creating (or deleting) the temporary file once the database is opened. AIR may have permissions to the database, but not to create or delete files in the directory.
One answer that has worked for me is to use the PRAGMA statement to set the journal_mode value to something other than DELETE. You do this by issuing a PRAGMA statement in the same way you would issue a query statement.
PRAGMA journal_mode = OFF
Unfortunately, if the application crashes in the middle of a transaction when the OFF journaling mode is set, then the database file will very likely go corrupt.1.
1 http://www.sqlite.org/pragma.html#pragma_journal_mode
The solution was to make sure database delete, update, insert only happened one at at time by wrapping a little wrapper. On top of that, we had to watch for error 3128 and retry. I think this is because we have a trigger running that could lock the database after we inserted data.

How to lock node for deletion process

Within alfresco, I want to delete a node but I don't want to be used by any other users in a cluster environment.
I know that I will use LockService for lock a node (in a cluster environment) as in the folloing lines:
lockService.lock(deleteNode);
nodeService.deleteNode(deleteNode);
lockService.unlock(deleteNode);
the last line may cause an exception because the node has already been deleted, and indeed it causes the exception is
A system error happened during the operation: Node does not exist: workspace://SpacesStore/cb6473ed-1f0c-4fa3-bfdf-8f0bc86f3a12
So how to ensure concurrency in a cluster environment when delete a node to prevent two users to access the same node at the same time one of them want to update it and the second once want o delete it?
Depending on your cluster environment (e.g. same DB server used by all Alfresco instances), transactions might most likely just be enough to ensure no stale content is used:
serverA(readNode)
serverB(deleteNode)
serverA(updateNode) <--- transaction failure
The JobLockService allows more control in case of more complex operations, which might involve multiple, dynamic nodes (or no nodes at all, e.g. sending emails or similar):
serverA(acquireLock)
serverB(acquireLock) <--- wait for the lock to be released
serverA(readNode1)
serverA(if something then updateNode2)
serverA(updateNode1)
serverA(releaseLock)
serverB(readNode2)
serverB(releaseLock)

How do I unlock a SQLite database?

When I enter this query:
sqlite> DELETE FROM mails WHERE (id = 71);
SQLite returns this error:
SQL error: database is locked
How do I unlock the database so this query will work?
In windows you can try this program http://www.nirsoft.net/utils/opened_files_view.html to find out the process is handling db file. Try closed that program for unlock database
In Linux and macOS you can do something similar, for example, if your locked file is development.db:
$ fuser development.db
This command will show what process is locking the file:
> development.db: 5430
Just kill the process...
kill -9 5430
...And your database will be unlocked.
I caused my sqlite db to become locked by crashing an app during a write. Here is how i fixed it:
echo ".dump" | sqlite old.db | sqlite new.db
Taken from: http://random.kakaopor.hu/how-to-repair-an-sqlite-database
The SQLite wiki DatabaseIsLocked page offers an explanation of this error message. It states, in part, that the source of contention is internal (to the process emitting the error). What this page doesn't explain is how SQLite decides that something in your process holds a lock and what conditions could lead to a false positive.
This error code occurs when you try to do two incompatible things with a database at the same time from the same database connection.
Changes related to file locking introduced in v3 and may be useful for future readers and can be found here: File Locking And Concurrency In SQLite Version 3
If you want to remove a "database is locked" error then follow these steps:
Copy your database file to some other location.
Replace the database with the copied database. This will dereference all processes which were accessing your database file.
Deleting the -journal file sounds like a terrible idea. It's there to allow sqlite to roll back the database to a consistent state after a crash. If you delete it while the database is in an inconsistent state, then you're left with a corrupted database. Citing a page from the sqlite site:
If a crash or power loss does occur and a hot journal is left on the disk, it is essential that the original database file and the hot journal remain on disk with their original names until the database file is opened by another SQLite process and rolled back. [...]
We suspect that a common failure mode for SQLite recovery happens like this: A power failure occurs. After power is restored, a well-meaning user or system administrator begins looking around on the disk for damage. They see their database file named "important.data". This file is perhaps familiar to them. But after the crash, there is also a hot journal named "important.data-journal". The user then deletes the hot journal, thinking that they are helping to cleanup the system. We know of no way to prevent this other than user education.
The rollback is supposed to happen automatically the next time the database is opened, but it will fail if the process can't lock the database. As others have said, one possible reason for this is that another process currently has it open. Another possibility is a stale NFS lock, if the database is on an NFS volume. In that case, a workaround is to replace the database file with a fresh copy that isn't locked on the NFS server (mv database.db original.db; cp original.db database.db). Note that the sqlite FAQ recommends caution regarding concurrent access to databases on NFS volumes, because of buggy implementations of NFS file locking.
I can't explain why deleting a -journal file would let you lock a database that you couldn't before. Is that reproducible?
By the way, the presence of a -journal file doesn't necessarily mean that there was a crash or that there are changes to be rolled back. Sqlite has a few different journal modes, and in PERSIST or TRUNCATE modes it leaves the -journal file in place always, and changes the contents to indicate whether or not there are partial transactions to roll back.
the SQLite db files are just files, so the first step would be to make sure it isn't read-only. The other thing to do is to make sure that you don't have some sort of GUI SQLite DB viewer with the DB open. You could have the DB open in another shell, or your code may have the DB open. Typically you would see this if a different thread, or application such as SQLite Database Browser has the DB open for writing.
My lock was caused by the system crashing and not by a hanging process. To resolve this, I simply renamed the file then copied it back to its original name and location.
Using a Linux shell that would be:
mv mydata.db temp.db
cp temp.db mydata.db
If a process has a lock on an SQLite DB and crashes, the DB stays locked permanently. That's the problem. It's not that some other process has a lock.
I had this problem just now, using an SQLite database on a remote server, stored on an NFS mount. SQLite was unable to obtain a lock after the remote shell session I used had crashed while the database was open.
The recipes for recovery suggested above did not work for me (including the idea to first move and then copy the database back). But after copying it to a non-NFS system, the database became usable and not data appears to have been lost.
Some functions, like INDEX'ing, can take a very long time - and it locks the whole database while it runs. In instances like that, it might not even use the journal file!
So the best/only way to check if your database is locked because a process is ACTIVELY writing to it (and thus you should leave it the hell alone until its completed its operation) is to md5 (or md5sum on some systems) the file twice.
If you get a different checksum, the database is being written, and you really really REALLY don't want to kill -9 that process because you can easily end up with a corrupt table/database if you do.
I'll reiterate, because it's important - the solution is NOT to find the locking program and kill it - it's to find if the database has a write lock for a good reason, and go from there. Sometimes the correct solution is just a coffee break.
The only way to create this locked-but-not-being-written-to situation is if your program runs BEGIN EXCLUSIVE, because it wanted to do some table alterations or something, then for whatever reason never sends an END afterwards, and the process never terminates. All three conditions being met is highly unlikely in any properly-written code, and as such 99 times out of 100 when someone wants to kill -9 their locking process, the locking process is actually locking your database for a good reason. Programmers don't typically add the BEGIN EXCLUSIVE condition unless they really need to, because it prevents concurrency and increases user complaints. SQLite itself only adds it when it really needs to (like when indexing).
Finally, the 'locked' status does not exist INSIDE the file as several answers have stated - it resides in the Operating System's kernel. The process which ran BEGIN EXCLUSIVE has requested from the OS a lock be placed on the file. Even if your exclusive process has crashed, your OS will be able to figure out if it should maintain the file lock or not!! It is not possible to end up with a database which is locked but no process is actively locking it!!
When it comes to seeing which process is locking the file, it's typically better to use lsof rather than fuser (this is a good demonstration of why: https://unix.stackexchange.com/questions/94316/fuser-vs-lsof-to-check-files-in-use). Alternatively if you have DTrace (OSX) you can use iosnoop on the file.
I added "Pooling=true" to connection string and it worked.
This error can be thrown if the file is in a remote folder, like a shared folder. I changed the database to a local directory and it worked perfectly.
I found the documentation of the various states of locking in SQLite to be very helpful. Michael, if you can perform reads but can't perform writes to the database, that means that a process has gotten a RESERVED lock on your database but hasn't executed the write yet. If you're using SQLite3, there's a new lock called PENDING where no more processes are allowed to connect but existing connections can sill perform reads, so if this is the issue you should look at that instead.
I have such problem within the app, which access to SQLite from 2 connections - one was read-only and second for writing and reading. It looks like that read-only connection blocked writing from second connection. Finally, it is turns out that it is required to finalize or, at least, reset prepared statements IMMEDIATELY after use. Until prepared statement is opened, it caused to database was blocked for writing.
DON'T FORGET CALL:
sqlite_reset(xxx);
or
sqlite_finalize(xxx);
I just had something similar happen to me - my web application was able to read from the database, but could not perform any inserts or updates. A reboot of Apache solved the issue at least temporarily.
It'd be nice, however, to be able to track down the root cause.
lsof command on my Linux environment helped me to figure it out that a process was hanging keeping the file open.
Killed the process and problem was solved.
This link solve the problem. : When Sqlite gives : Database locked error
It solved my problem may be useful to you.
And you can use begin transaction and end transaction to not make database locked in future.
Should be a database's internal problem...
For me it has been manifested after trying to browse database with "SQLite manager"...
So, if you can't find another process connect to database and you just can't fix it,
just try this radical solution:
Provide to export your tables (You can use "SQLite manager" on Firefox)
If the migration alter your database scheme delete the last failed migration
Rename your "database.sqlite" file
Execute "rake db:migrate" to make a new working database
Provide to give the right permissions to database for table's importing
Import your backed up tables
Write the new migration
Execute it with "rake db:migrate"
In my experience, this error is caused by: You opened multiple connections.
e.g.:
1 or more sqlitebrowser (GUI)
1 or more electron thread
rails thread
I am nore sure about the details of SQLITE3 how to handle the multiple thread/request, but when I close the sqlitebrowser and electron thread, then rails is running well and won't block any more.
I ran into this same problem on Mac OS X 10.5.7 running Python scripts from a terminal session. Even though I had stopped the scripts and the terminal window was sitting at the command prompt, it would give this error the next time it ran. The solution was to close the terminal window and then open it up again. Doesn't make sense to me, but it worked.
I just had the same error.
After 5 minets google-ing I found that I didun't closed one shell witch were using the db.
Just close it and try again ;)
I had the same problem. Apparently the rollback function seems to overwrite the db file with the journal which is the same as the db file but without the most recent change. I've implemented this in my code below and it's been working fine since then, whereas before my code would just get stuck in the loop as the database stayed locked.
Hope this helps
my python code
##############
#### Defs ####
##############
def conn_exec( connection , cursor , cmd_str ):
done = False
try_count = 0.0
while not done:
try:
cursor.execute( cmd_str )
done = True
except sqlite.IntegrityError:
# Ignore this error because it means the item already exists in the database
done = True
except Exception, error:
if try_count%60.0 == 0.0: # print error every minute
print "\t" , "Error executing command" , cmd_str
print "Message:" , error
if try_count%120.0 == 0.0: # if waited for 2 miutes, roll back
print "Forcing Unlock"
connection.rollback()
time.sleep(0.05)
try_count += 0.05
def conn_comit( connection ):
done = False
try_count = 0.0
while not done:
try:
connection.commit()
done = True
except sqlite.IntegrityError:
# Ignore this error because it means the item already exists in the database
done = True
except Exception, error:
if try_count%60.0 == 0.0: # print error every minute
print "\t" , "Error executing command" , cmd_str
print "Message:" , error
if try_count%120.0 == 0.0: # if waited for 2 miutes, roll back
print "Forcing Unlock"
connection.rollback()
time.sleep(0.05)
try_count += 0.05
##################
#### Run Code ####
##################
connection = sqlite.connect( db_path )
cursor = connection.cursor()
# Create tables if database does not exist
conn_exec( connection , cursor , '''CREATE TABLE IF NOT EXISTS fix (path TEXT PRIMARY KEY);''')
conn_exec( connection , cursor , '''CREATE TABLE IF NOT EXISTS tx (path TEXT PRIMARY KEY);''')
conn_exec( connection , cursor , '''CREATE TABLE IF NOT EXISTS completed (fix DATE, tx DATE);''')
conn_comit( connection )
One common reason for getting this exception is when you are trying to do a write operation while still holding resources for a read operation. For example, if you SELECT from a table, and then try to UPDATE something you've selected without closing your ResultSet first.
I was having "database is locked" errors in a multi-threaded application as well, which appears to be the SQLITE_BUSY result code, and I solved it with setting sqlite3_busy_timeout to something suitably long like 30000.
(On a side-note, how odd that on a 7 year old question nobody found this out already! SQLite really is a peculiar and amazing project...)
Before going down the reboot option, it is worthwhile to see if you can find the user of the sqlite database.
On Linux, one can employ fuser to this end:
$ fuser database.db
$ fuser database.db-journal
In my case I got the following response:
philip 3556 4700 0 10:24 pts/3 00:00:01 /usr/bin/python manage.py shell
Which showed that I had another Python program with pid 3556 (manage.py) using the database.
An old question, with a lot of answers, here's the steps I've recently followed reading the answers above, but in my case the problem was due to cifs resource sharing. This case is not reported previously, so hope it helps someone.
Check no connections are left open in your java code.
Check no other processes are using your SQLite db file with lsof.
Check the user owner of your running jvm process has r/w permissions over the file.
Try to force the lock mode on the connection opening with
final SQLiteConfig config = new SQLiteConfig();
config.setReadOnly(false);
config.setLockingMode(LockingMode.NORMAL);
connection = DriverManager.getConnection(url, config.toProperties());
If your using your SQLite db file over a NFS shared folder, check this point of the SQLite faq, and review your mounting configuration options to make sure your avoiding locks, as described here:
//myserver /mymount cifs username=*****,password=*****,iocharset=utf8,sec=ntlm,file,nolock,file_mode=0700,dir_mode=0700,uid=0500,gid=0500 0 0
I got this error in a scenario a little different from the ones describe here.
The SQLite database rested on a NFS filesystem shared by 3 servers. On 2 of the servers I was able do run queries on the database successfully, on the third one thought I was getting the "database is locked" message.
The thing with this 3rd machine was that it had no space left on /var. Everytime I tried to run a query in ANY SQLite database located in this filesystem I got the "database is locked" message and also this error over the logs:
Aug 8 10:33:38 server01 kernel: lockd: cannot monitor 172.22.84.87
And this one also:
Aug 8 10:33:38 server01 rpc.statd[7430]: Failed to insert: writing /var/lib/nfs/statd/sm/other.server.name.com: No space left on device
Aug 8 10:33:38 server01 rpc.statd[7430]: STAT_FAIL to server01 for SM_MON of 172.22.84.87
After the space situation was handled everything got back to normal.
If you're trying to unlock the Chrome database to view it with SQLite, then just shut down Chrome.
Windows
%userprofile%\Local Settings\Application Data\Google\Chrome\User Data\Default\Web Data
or
%userprofile%\Local Settings\Application Data\Google\Chrome\User Data\Default\Chrome Web Data
Mac
~/Library/Application Support/Google/Chrome/Default/Web Data
From your previous comments you said a -journal file was present.
This could mean that you have opened and (EXCLUSIVE?) transaction and have not yet committed the data. Did your program or some other process leave the -journal behind??
Restarting the sqlite process will look at the journal file and clean up any uncommitted actions and remove the -journal file.
As Seun Osewa has said, sometimes a zombie process will sit in the terminal with a lock aquired, even if you don't think it possible. Your script runs, crashes, and you go back to the prompt, but there's a zombie process spawned somewhere by a library call, and that process has the lock.
Closing the terminal you were in (on OSX) might work. Rebooting will work. You could look for "python" processes (for example) that are not doing anything, and kill them.

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