MySQL 5.1.49 freezing every two days

Posted by maximus on Server Fault See other posts from Server Fault or by maximus
Published on 2010-09-14T14:52:36Z Indexed on 2011/01/05 23:55 UTC
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Hi all,

our mysql system is "freezing" every two days.

By "freezing" i mean the following:

  • it doesn't respond to ping
  • we can't login with SSH
  • we don't get any answer from MySQL
  • there is no entry in the error logs! neither from linux neither from MySQL.
  • we have already changed to a completely new hardware, we have the same problem, so it's definitely not a hardware problem.
  • we do not have any other software installed except a firewall (iptables rule)
  • we can restart the server from another server using rsyslog (www.rsyslog.com)(software reset)

Could someone help me, by giving me some pointers what could i do to figure out the problem? I have included every detail about our settings.

Thank you in advance for your help. Max.

Our system parameters and settings:

  • System-Memory: 12GB
  • Processor: Intel 7-920 Quadcore
  • Operating system: Debian 5 (lenny) 64bit
  • MySQL 5.1.49
  • Databases: (a) a small phpbb forum (b) a 6GB database 3 tables with about 15 million rows

my.cnf

#
# The MySQL database server configuration file.
#
# You can copy this to one of:
# - "/etc/mysql/my.cnf" to set global options,
# - "~/.my.cnf" to set user-specific options.
# 
# One can use all long options that the program supports.
# Run program with --help to get a list of available options and with
# --print-defaults to see which it would actually understand and use.
#
# For explanations see
# http://dev.mysql.com/doc/mysql/en/server-system-variables.html

# This will be passed to all mysql clients
# It has been reported that passwords should be enclosed with ticks/quotes
# escpecially if they contain "#" chars...
# Remember to edit /etc/mysql/debian.cnf when changing the socket location.
[client]
port        = 3306
socket      = /var/run/mysqld/mysqld.sock

# Here is entries for some specific programs
# The following values assume you have at least 32M ram

# This was formally known as [safe_mysqld]. Both versions are currently parsed.
[mysqld_safe]
socket      = /var/run/mysqld/mysqld.sock
nice        = 0

[mysqld]
#
# * Basic Settings
#
user        = mysql
pid-file    = /var/run/mysqld/mysqld.pid
socket      = /var/run/mysqld/mysqld.sock
port        = 3306
basedir     = /usr
datadir     = /var/lib/mysql
tmpdir      = /tmp
language    = /usr/share/mysql/english
skip-external-locking
#
# Instead of skip-networking the default is now to listen only on
# localhost which is more compatible and is not less secure.
bind-address        = our-ip-address

#
# * Fine Tuning
#
key_buffer      = 16M
max_allowed_packet  = 16M
thread_stack        = 256K
thread_cache_size   = 32 
max_connections         = 300
table_cache             = 2048
#thread_concurrency     = 4

# Used for InnoDB tables recommended to 50%-80% available memory
innodb_buffer_pool_size            = 6G

# 20MB sometimes larger
innodb_additional_mem_pool_size    = 20M

# 8M-16M is good for most situations
innodb_log_buffer_size             = 8M

# Disable XA support because we do not use it
innodb-support-xa          = 0

# 1 is default wich is 100% secure but 2 offers better performance
innodb_flush_log_at_trx_commit     = 1

innodb_flush_method        = O_DIRECT
#innodb_thread_concurency      = 8


# Recommended 64M - 512M depending on server size
innodb_log_file_size           = 512M

# One file per table
innodb_file_per_table


#
# * Query Cache Configuration
#
query_cache_limit       = 1M
query_cache_size        = 16M
#query_cache_type   = 1
#query_cache_min_res_unit= 2K
#join_buffer_size   = 1M

#
# * Logging and Replication
#
# Both location gets rotated by the cronjob.
# Be aware that this log type is a performance killer.
# As of 5.1 you can enable the log at runtime!
#general_log_file        = /var/log/mysql/mysql.log
#general_log             = 1
#
# Error logging goes to syslog. This is a Debian improvement :)
#
# Here you can see queries with especially long duration
log_slow_queries    = /var/log/mysql/mysql-slow.log
long_query_time = 2
log-queries-not-using-indexes

#
# The following can be used as easy to replay backup logs or for replication.
#server-id      = 1
log_bin         = /var/log/mysql/mysql-bin.log
# WARNING: Using expire_logs_days without bin_log crashes the server! See README.Debian!
expire_logs_days    = 10
max_binlog_size         = 100M
#binlog_do_db       = include_database_name
#binlog_ignore_db   = include_database_name
#
# InnoDB is enabled by default with a 10MB datafile in /var/lib/mysql/.
# Read the manual for more InnoDB related options. There are many!
# * InnoDB plugin
# As of MySQL 5.1.38, the InnoDB plugin from Oracle is included in the MySQL source code.
# It has many improvements and better performances than the built-in InnoDB storage engine.
# Please read http://www.innodb.com/products/innodb_plugin/ for more information.
# Uncommenting the two following lines to use the InnoDB plugin.
ignore_builtin_innodb
plugin-load=innodb=ha_innodb_plugin.so

#
# * Security Features
#
# Read the manual, too, if you want chroot!
# chroot = /var/lib/mysql/
#
# For generating SSL certificates I recommend the OpenSSL GUI "tinyca".
#
# ssl-ca=/etc/mysql/cacert.pem
# ssl-cert=/etc/mysql/server-cert.pem
# ssl-key=/etc/mysql/server-key.pem



[mysqldump]
quick
quote-names
max_allowed_packet  = 16M

[mysql]
#no-auto-rehash # faster start of mysql but no tab completition

[isamchk]
key_buffer      = 16M

#
# * NDB Cluster
#
# See /usr/share/doc/mysql-server-*/README.Debian for more information.
#
# The following configuration is read by the NDB Data Nodes (ndbd processes)
# not from the NDB Management Nodes (ndb_mgmd processes).
#
# [MYSQL_CLUSTER]
# ndb-connectstring=127.0.0.1


#
# * IMPORTANT: Additional settings that can override those from this file!
#
!includedir /etc/mysql/conf.d/

UPDATE After installing sysstat and configuring it to collect data after every minute i have the following datas. I used sar to generate the following output:

The log-file is too big so coudn't enter it here but uploaded to box.net. The link is http://www.box.net/shared/xc6rh7qqob

SECOND UPDATE We started a ping command in the background, and that solved the problem. Now the server does work since more then a week. We still don't know what's the problem.

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