I am facing a possible memory leak in Mariadb. I hope reading the warning messages from all the thread could lead me to what is causing it. The problem is warning are not logged anywhere. I can see from the network traffic dump that some threads have a high number of warnings but I can not access them. The application using the database is not logging anything related to database either. How can I read all the threads warnings. I have full access to the server.
I want to have access to these warnings, I don't have any control on the app node to log them
I found the cause of the leak. Whenever there was a jump in memory usage, there was a jump at number of subqueries. By disabling subquery cache problem was solved. Still the root cause is unknown.
Related
We are having a problem where our cloudSQL database crashes periodically.
The error we are seeing in the logs is:
[ERROR] InnoDB: Write to file ./ib_logfile1failed at offset 237496832, 1024 bytes should have been written, only 0 were written. Operating system error number 12. Check that your OS and file system support files of this size. Check also that the disk is not full or a disk quota exceeded.
From what I understand, error number 12 means 'Cannot allocate memory'. Is there a way we can configure cloudsql to leave a larger buffer of free memory? The alternative would be to upgrade to have more memory, but from what I understand cloudSQL automatically uses all the memory available to it... Is this likely to reduce the problem or would it likely continue in the same way?
Are there any other things we can do to reduce this issue?
It is possible your system is running out of disk space rather than memory, especially if you are running in a HA config.
(If disk isn't the issue you should file a GCP support ticket rather than here)
FINAL UPDATE: We fixed this problem by finding a way to accomplish our goals without forking. But forking was the cause of the problem.
---Original Post---
I'm running a ruby on rails stack, our mysql server is separate, but housed at the same site as our app servers. (we've tried swapping it out for a different mysql server with double the specs, but no improvement was seen.
during business hours we get a handful of these from no particular query.
ActiveRecord::StatementInvalid: Mysql2::Error: Lost connection to MySQL server during query
most of the queries that fail are really simple, and there seems to be no pattern between one query and another. This all started when I upgraded from Rails 4.1 to 4.2.
I'm at a loss as to what to try. Our database server is less than 5% CPU throughout the day. I do get bug reports from users who have random interactions fail due to this, so it's not queries that have been running for hours or anything like that, of course when they retry the exact same thing it works.
Our servers are configured by cloud66.
So in short: our mysql server is going away for some reason, but it's not because of lack of resources, it's also a brand new server as we migrated from another server when this problem started.
this also happens to me on localhost while developing features sometimes, so I don't believe it's a load issue.
We're running the following:
ruby 2.2.5
rails 4.2.6
mysql2 0.4.8
UPDATE: per the first answer below I increased our max_connections variable to 500 last night, and confirmed the increase via
show global variables like 'max_connections';
I'm still getting dropped connection, the first one today was dropped only a few minutes ago....
ActiveRecord::StatementInvalid: Mysql2::Error: Lost connection to MySQL server during query
I ran select * from information_schema.processlist; and I got 36 rows back. Does this mean my app servers were running 36 connections at that moment? or can a process be multiple connections?
UPDATE: I just set net_read_timeout = 60 (it was 30 before) I'll see if that helps
UPDATE: It didn't help, I'm still looking for a solution...
Heres my Database.yml with credentials removed.
production:
adapter: mysql2
encoding: utf8
host: localhost
database:
username:
password:
port: 3306
reconnect: true
The connection to MySQL can be disrupted by a number of means, but I would recommend revisiting Mario Carrion's answer since it's a very wise answer.
It seems likely that connection is disrupted because it's being shared with the other processes, causing communication protocol errors...
...this could easily happen if the connection pool is process bound, which I believe it is, in ActiveRecord, meaning that the same connection could be "checked-out" a number of times simultaneously in different processes.
The solution is that database connections must be established only AFTER the fork statement in the application server.
I'm not sure which server you're using, but if you're using a warmup feature - don't.
If you're running any database calls before the first network request - don't.
Either of these actions could potentially initialize the connection pool before forking occurs, causing the MySQL connection pool to be shared between processes while the locking system isn't.
I'm not saying this is the only possible reason for the issue, as stated by #sloth-jr, there are other options... but most of them seem less likely according to your description.
Sidenote:
I ran select * from information_schema.processlist; and I got 36 rows back. Does this mean my app servers were running 36 connections at that moment? or can a process be multiple connections?
Each process could hold a number of connections. In your case, you might have up to 500X36 connections. (see edit)
In general, the number of connections in the pool can often be the same as the number of threads in each process (it shouldn't be less than the number of thread, or contention will slow you down). Sometimes it's good to add a few more depending on your application.
EDIT:
I apologize for ignoring the fact that the process count was referencing the MySQL data and not the application data.
The process count you showed is the MySQL server data, which seems to use a thread per connection IO scheme. The "Process" data actually counts active connections and not actual processes or threads (although it should translate to the number of threads as well).
This means that out of possible 500 connections per application processes (i.e., if you're using 8 processes for your application, that would be 8X500=4,000 allowed connections) your application only opened 36 connections so far.
This indicates a timeout error. It's usually a general resource or connection error.
I would check your MySQL config for max connections on MySQL console:
show global variables like 'max_connections';
And ensure the number of pooled connections used by Rails database.yml is less than that:
pool: 10
Note that database.yml reflects number of connections that will be pooled by a single Rails process. If you have multiple processes or other servers like Sidekiq, you'll need to add them together.
Increase max_connections if necessary in your MySQL server config (my.cnf), assuming your kit can handle it.
[mysqld]
max_connections = 100
Note other things might be blocking too, e.g. open files, but looking at connections is a good starting point.
You can also monitor active queries:
select * from information_schema.processlist;
as well as monitoring the MySQL slow log.
One issue may be a long-running update command. If you have a slow-running command that affects a lot of records (e.g. a whole table), it might be blocking even the simplest queries. This means you could see random queries timeout, but if you check MySQL status, the real cause is another long-running query.
Things you did not mention but you should take a look:
Are you using unicorn? If so, are your reconnecting and disconnecting in your after_fork and before_fork?
Is reconnect: true set in your database.yml configuration?
Well,at first glance this sounds like your webserver is keeping the mysql sessions open and sometimes a user runs into a timeout. Try disabling the keep mysql sessions alive.
It will be a hog but you only use 5% ...
other tipps:
Enable the mysql "Slow Query Log" and take a look.
write a short script which pulls and logs the mysql processlist every minute and cross check the log with timeouts
look at the pool size in your db connection or set one!
http://guides.rubyonrails.org/configuring.html#database-pooling
should be equal to the max-connections mysql likes to have!
Good luck!
Find out if your database is limited in terms of multiple connections. Because normally a SQL database is supposed to have more than one active connection.
(Contact your network provider)
Would you mind posting some of your queries? The MySQL documentation has this to say about it:
https://dev.mysql.com/doc/refman/5.7/en/error-lost-connection.html
TL;DR:
Network problems; are any of your boxes renewing leases
periodically, or experiencing other network connection errors
(netstat / ss), firewall timeouts, etc. Not sure how managed your
hosts are by cloud66....
Query timed out. This can happen if you've got commands backed up
behind blocking statements (eg, alters/locking backups on MyISAM
tables). How simple are your queries? No cartesian products in-play?
EXPLAIN query could help.
Exceeding MAX_PACKET_SIZE. Are you storing pictures, video content, etc.?
There are lots of possibilities here, and without more information, will be difficult to pinpoint this.
Would look first at mysql_error.log, then work your way from the DB server back to your application.
UPDATE: this didn't work.
Heres the solution, special thanks to #Myst for pointing out that forking can cause issues, I had no idea to look at this particular code. As the errors seemed random because we forked in this fashion in several places.
It turns out that when I was forking processes, rails was using the same database connection for all forked processes, This created a situation where when one of the processes (the parent process?) terminated the database connection, the remaining process would have its connection interrupted.
The solution was to change this code:
def recalculate_completion
Process.fork do
if self.course
self.course.user_groups.includes(user:[:events]).each do |ug|
ug.recalculate_completion
end
end
end
end
into this code:
def recalculate_completion
ActiveRecord::Base.remove_connection
Process.fork do
ActiveRecord::Base.establish_connection
if self.course
self.course.user_groups.includes(user:[:events]).each do |ug|
ug.recalculate_completion
end
end
ActiveRecord::Base.remove_connection
end
ActiveRecord::Base.establish_connection
end
Making this change stopped the errors from our servers and everything appears to be working well now. If anyone has any more info as to why this worked I would be happy to hear it, as I would like to have a deeper understanding of this.
Edit: it turns out this didn't work either.... we still got dropped connections but not as often.
If you have query cache enabled, please reset it and it should work.
RESET QUERY CACHE;
I have a problem with my unix server. This started a week ago. One day after a backup (I used to keep 3 backup files) I visited a website on the server but it wouldn't work. I restarted the server and it seemed to be working fine except the mysql service. My attempts to restart it failed. Then I figured that was because the server was full, so I deleted one of the backups, cleaned up some space and the mysql service restarted successfully. Than I figured tables in one of the databases (MYIsam tables) were corrupt. So I repaired them through myisamchk command via ssh and all worked fine. However, the very next day I woke up they were corrupt again (despite mysql was working fine), and this time there was no disk space problem on the server. I repaired them again. The next day the same thing happenned; and this time innodb tables that were part of another database were corrupt as well. I've fixed them too, so now all is working well but I guess the same thing will happen after tonight's backup.
I can't identify the problem and I don't know what logs to look into to understand the problem. Can anyone please help me out? Thanks very much in advance.
No easy answer here. My immediate thought is that the dbase is still busy when the backups commence, possibly corrupting indexes, interferring with caches, etc. Turn on full logging and check for problems when the backup starts happens. Maybe you will find something.
Look for the my.cnf file. On my CentOs it is located in /etc/my.cnf. It will have a config setting for the location of the error log.
My strongest suspect is OOM kill by the kernel or some other issue that results from running the system out of memory. Try this:
Start top on the server and press M to sort by memory so the biggest memory user is at the top.
note the pid of mysqld
manually perform the backup as you observe the value of the RES column in the top output (resident memory size)
once the backup is over see if the pid of mysqld has changed
If the pid has changed (meaning restart took place), and you saw the memory footprint of mysqld take up something comparable to the total amount of system memory, then my suspicion is correct, and we need to lower some settings in my.cnf to make it use less memory, e.g key_buffer_size and innodb_buffer_pool_size.
EDIT - From the log you posted, there are additional issues although it is not clear how they could be contributing to the table corruption. Your server appears to be running with --skip-innodb and your backup script is not able to deal with the absence of InnoDB storage engine printing exception error messages, but nevertheless continuing. It is also attempting to do a repair, which is failing due to the lack of system privileges (error 1 is Operation not permitted). It is possible that encountering those errors triggers some faulty logic in your backup script that leaves the tables corrupted.
At this point I would recommend disabling MySQL backup using the cPanel tool, and using mysqldump or some other solution (e.g. Xtrabackup (https://www.percona.com/doc/percona-xtrabackup/2.3/index.html)) from a cron job instead.
EDIT2 - from the test results. The manual backup does not run the system out of memory and does not crash the server. The jury is still out on the automatic one.
Don't kill mysqld; shut it down gracefully.
Switch from MyISAM to InnoDB; the latter does not suffer from that 'error'.
I have an Ubuntu LAMJ server running Tomcat6.
One of my JSP applications freezes every couple of days and I am having trouble figuring out why. I have to reboot tomcat to get that one app going again, as it won't cone back on its own. I am getting nothing in my own log4j logs for that app, and can't see anything in Catalina.out either.
This applications shares a javax.sql.DataSource resource with another, via a context element in the server.xml file. I don't think this is the cause of the problem, but I may as well mention it.
Could anyone point me in the right direction to find the cause of this intermittent issue?
thanks in advance,
Christy
Get a Thread dump of the running server
There are two options
Use VisualVM
in your %java_home%/bin folder there will be a file called jvisualvm. Run this and connect to your tomcat server. Click the Threads tab and then "Thread Dump"
Manually from the Command Line
open up a command line and find the process id for your tomcat
ps -ef | grep java
Once you identify the process ID for the running tomcat instance,
kill -3 <pid>
replace the process Id here. This will send your thread dump to the stdout for your tomcat. Most likely catalina.out file.
edit - As per Mark's comments below:
It is normal to take 3 thread dumps ~10s apart and compare them. It
makes it much easier to see which threads are 'stuck' and which ones
are moving
Once you have the thread dump you can analyse it for stuck threads. It may not be stuck threads as the problem, but at least you can see what is going on inside the server to analyze the problem further.
I'm seeing a few of these errors during high load times:
mysql_connect() [<a
href='function.mysql-connect'>function.mysql-connect</a>]: [2002] Resource
temporarily unavailable (trying to connect via
unix:///var/lib/mysql/mysql.sock)
From what I can tell the mysql server isn't hitting its max connections limit, but there's something else stopping it from serving the query. What other limits would MySQL be hitting?
I'm running RHEL 6.2 64bit with MySQL 5.5.21
Let's assume your system is currently Unix-based (as given in your problem statement). If this is correct, here's the set of issues you may be running into:
You've run out of memory available to MySQL.
This is the most likely problem you're facing. Each connection in MySQL's connection pool requires memory to function, and if this resource is exhausted, no further connections can be made. Of course, the memory footprints and maximum packet sizes of various operations can be tuned in your equivalent to my.cnf if you discover this to be an issue.
Here's an additional thread that can help there, but you may also consider using simpler profiling tools like top to get a good ballpark estimate of what's going on.
You've run out of file descriptors available to your MySQL user account.
Another common issue: if you're trying to service requests that require file IO above the 1,024 boundary (by default), you will run into cases where the operation simply fails. This is because most systems specify a soft and hard limit on the number of open file descriptors each user can have available at one time, and walking over this threshold can cause problems.
This will usually have a series of glaringly obvious signs expressed in your log files. Check /var/log/messages and your comparable directories (for example, /var/log/mysql to see if you can find anything interesting.
You've run into a livelock or deadlock scenario where your thread is unsatisfiable.
Corollary to memory and file descriptor exhaustion, threads can time out if you've overstepped the computational load your system is capable of handling. It won't throw this error message, but this is something to watch out for in the future.
Your system is running out of PIDs available to fork.
Another common scenario: fork only has so many PIDs available for its use at any given time. If your system is simply overforked, it will cease to be able to service requests.
The easiest check for this is to see if any other services can connect through to the machine. For example, trying to SSH into the box and discovering that you cannot is a big clue.
An upstream proxy or connection manager has run out of resources and ceased servicing requests.
If you have any service layer between your client and MySQL, it bears inspecting to see if it has crashed, hung, or otherwise become unstable. The advice above applies.
Your port mapper has exhausted itself after 65,536 connections.
Unlikely, but again, a possible exhaustion case. Checking the trivial service connection as above is, ehm, also the best port of call here.
In short: this is a resource exhaustion scenario, inclusive of the server simply being "down". You're going to have to profile your system further to see what you're blocking on. All the error message gives us in this case is the fact the resource is unavailable to the client -- we'd need to see more information about the server to determine a more adequate remedy.
I still haven't found which limits it was hitting, but I did manage to work around the problem. There was a problem with our session table (in vbulletin) which uses the MEMORY engine. The indexes for this table were HASH and thus when vbulletin purged this table once an hour it would lock the table just long enough to hold up other queries and push mysql to the limit of its resources.
By changing the indexes to BTREE this allowed MySQL to delete the rows from the session table a lot quicker and avoid any limits there were reached previously. The errors only started when we upgraded our master db server to MySQL 5.5, so I'm guessing MEMORY tables are handled differently in the latest release.
See http://www.mysqlperformanceblog.com/2008/02/01/performance-gotcha-of-mysql-memory-tables/ for information on speed increases from using BTREE indexes over HASH For MEMORY.
Geez, this could be so many things. It could be that the socket buffer space is exhausted. It could be that mysql is not accepting connections as fast as they are coming in and the backlog limit is reached (though I'd expect that to give you a "Connection Refused" error, I don't know for sure that's what you'll get for a Unix domain socket). It could be any of the things #MrGomez pointed out.
Since you are running Apache and MySQL on the same server and this is a problem under high load, it could well be that Apache is starving the system of some resource and you're just not seeing (noticing?) the dropped/failed incoming connections/requests in your logs.
Are you using connection pooling? If not, I'd start there.
I'd also look for errors in the Apache logs and syslog around the same time as the mysql_connect error and see what else turns up. I'd especially recommend getting MySQL moved over to its own separate dedicated server.
In my case, I was working with JSON data types with PDO (PHP Driver).
I was using fetch to retrieve one item but forgot to add LIMIT 1 to the query. Adding it solved the problem.