Mariadb server constanlty crashing [Error 2013] - mysql

I know this problem was asked several times, but no solution worked for me so far. I am struggling with this for over 2 weeks and I am out of options.
System:Ubuntu 18.04 LTS
MySQL version:mysql Ver 15.1 Distrib 10.4.11-MariaDB, for debian-linux-gnu (x86_64) using readline 5.2
I suspect it may be a problem with one large database (over 4GB) I had to recover from frm idb. I know the method of recovery was successful after recovery of single table I checked and the data was there, not sure if with the other tables something is not corrupted BUT:
I tried recovery method described here and problem is even when I do mysqlcheck --all-databases I get error: 2013: Lost connection to MySQL server during query when executing 'CHECK TABLE ... ' so unable to check.
From what I see in syslog server also crashed when I log into mysql and do use epffilm;
Using other advice from SO i created /etc/my.cnf :
[mysql]
connect_timeout = 43200
max_allowed_packet = 2048M
net_buffer_length = 512M
debug-info = TRUE
also content of my /etc/mysql/my.cnf:
client]
port = 3306
socket = /var/run/mysqld/mysqld.sock
#socket = /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
lc_messages_dir = /usr/share/mysql
lc_messages = en_US
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 = 127.0.0.1
#
# * Fine Tuning
#
max_connections = 100
connect_timeout = 1000000
wait_timeout = 600
max_allowed_packet = 1073741824
thread_cache_size = 128
sort_buffer_size = 4M
bulk_insert_buffer_size = 16M
tmp_table_size = 32M
max_heap_table_size = 32M
net_read_timeout = 31536000
net_write_timeout = 31536000
#
# * MyISAM
#
# This replaces the startup script and checks MyISAM tables if needed
# the first time they are touched. On error, make copy and try a repair.
myisam_recover_options = BACKUP
key_buffer_size = 128M
#open-files-limit = 2000
table_open_cache = 400
myisam_sort_buffer_size = 512M
concurrent_insert = 2
read_buffer_size = 2M
read_rnd_buffer_size = 1M
#
# * Query Cache Configuration
#
# Cache only tiny result sets, so we can fit more in the query cache.
query_cache_limit = 128K
query_cache_size = 64M
# for more write intensive setups, set to DEMAND or OFF
#query_cache_type = DEMAND
#
# * 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 due to /etc/mysql/conf.d/mysqld_safe_syslog.cnf.
#
# we do want to know about network errors and such
log_warnings = 2
#
# Enable the slow query log to see queries with especially long duration
#slow_query_log[={0|1}]
slow_query_log_file = /var/log/mysql/mariadb-slow.log
long_query_time = 10
log_slow_rate_limit = 1000
log_slow_verbosity = query_plan
#log-queries-not-using-indexes
#log_slow_admin_statements
#
# The following can be used as easy to replay backup logs or for replication.
# note: if you are setting up a replication slave, see README.Debian about
# other settings you may need to change.
#server-id = 1
#report_host = master1
#auto_increment_increment = 2
#auto_increment_offset = 1
log_bin = /var/log/mysql/mariadb-bin
log_bin_index = /var/log/mysql/mariadb-bin.index
# not fab for performance, but safer
#sync_binlog = 1
expire_logs_days = 7
max_binlog_size = 100M
# If applications support it, this stricter sql_mode prevents some
# mistakes like inserting invalid dates etc.
#sql_mode = NO_ENGINE_SUBSTITUTION,TRADITIONAL
#
# * InnoDB
#
# InnoDB is enabled by default with a 10MB datafile in /var/lib/mysql/.
# Read the manual for more InnoDB related options. There are many!
default_storage_engine = InnoDB
innodb_buffer_pool_size = 6G
innodb_log_buffer_size = 512M
innodb_file_per_table = 1
innodb_open_files = 400
innodb_io_capacity = 400
innodb_flush_method = O_DIRECT
#
#
# Helpful with recovery
#
innodb_force_recovery=3
innodb_purge_threads=0
# * 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
#
# Allow server to accept connections on all interfaces.
#
#bind-address=0.0.0.0
#
# Optional setting
#wsrep_slave_threads=1
#innodb_flush_log_at_trx_commit=0
[mysqldump]
quick
quote-names
max_allowed_packet = 1024M
[mysql]
#no-auto-rehash # faster start of mysql but no tab completion
[isamchk]
key_buffer = 16M
#
# * IMPORTANT: Additional settings that can override those from this file!
# The files must end with '.cnf', otherwise they'll be ignored.
#
!include /etc/mysql/mariadb.cnf
!includedir /etc/mysql/conf.d/
Any insight is appreciated.
Update:
I put a crash log on pastenbin

Hello this has already occurred to me ...
In my case my server was low on memory ...
And my database was full of posts.
That is ... he had a lot of information on two types of decodes. (MyISAM & Innodb) in the same bank ...
The solution I found was to export this database ...
This is a backup ...
Create a database from scratch by deciding on single encoding (Innodb) only.
And doing the import little by little checking all the tables and possible errors.
Another option I made was to remove what was old and put it in another database. To be part of another site.
Data integration would be through links between the two sites ...
I hope it helped you!
Strong hug. Good luck!
Send news!

Where did you get these?? (I will comment on it.)
max_allowed_packet = 2048M
net_buffer_length = 512M
They are much too large. These could explain running out of memory and crashing.
Remove those from my.cnf. If some large values are needed for a single load, then set them only within that connection. And shrink innodb_buffer_pool_size by 2.5G to allow room for such a one-time task.
How much RAM do you have?

Related

group_concat_max_length system variable not changed even after changing my.cnf file

I have currently installed MySQL version 5.6 installed on my local system. I want to permanently set the group_concat_max_length system variable to some value.
When I do it using
set global group_concat_max_len = 100000;
command in the mysql terminal, the value is set but the value changes to default on restart.
I have also changed my.cnf file and put it under [mysqld] header.
Can anyone suggest what might be the problem?
Edit:
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
lc-messages-dir = /usr/share/mysql
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 = 127.0.0.1
#max_connections=200 (mysql connections)
#
# * Fine Tuning
#
key_buffer = 16M
max_allowed_packet = 16M
thread_stack = 192K
thread_cache_size = 8
# This replaces the startup script and checks MyISAM tables if needed
# the first time they are touched
myisam-recover = BACKUP
#max_connections = 100
#table_cache = 64
#thread_concurrency = 10
#
# * Query Cache Configuration
#
innodb_buffer_pool_size = 8G
innodb_flush_log_at_trx_commit = 2
query_cache_size=268435456
query_cache_type=1
query_cache_limit=8388608
group_concat_max_len=100000
#query_cache_limit = 1M
#query_cache_size = 16M
#
# * 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 log - should be very few entries.
#
log_error = /var/log/mysql/error.log
#
# 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.
# note: if you are setting up a replication slave, see README.Debian about
# other settings you may need to change.
#server-id = 1
#log_bin = /var/log/mysql/mysql-bin.log
expire_logs_days = 10
max_binlog_size = 100M
#binlog_do_db = include_database_name
#binlog_ignore_db = include_database_name
#
# * InnoDB
#
# InnoDB is enabled by default with a 10MB datafile in /var/lib/mysql/.
# Read the manual for more InnoDB related options. There are many!
#
# * 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
#
# * IMPORTANT: Additional settings that can override those from this file!
# The files must end with '.cnf', otherwise they'll be ignored.
#
!includedir /etc/mysql/conf.d/
mysql file in /etc/init.d/
...
SELF=$(cd $(dirname $0); pwd -P)/$(basename $0)
CONF=/etc/mysql/my.cnf
MYADMIN="/usr/bin/mysqladmin --defaults-file=/etc/mysql/debian.cnf"
# priority can be overriden and "-s" adds output to stderr
ERR_LOGGER="logger -p daemon.err -t /etc/init.d/mysql -i"
...
After mysql restart:
mysql> show variables like '%group_concat_max%';
+----------------------+-------+
| Variable_name | Value |
+----------------------+-------+
| group_concat_max_len | 1024 |
+----------------------+-------+
1 row in set (0.00 sec)
The single line from your configuration file NEEDS to be listed as 6 lines because initialization can only deal with one variable per line, imho.
You will likely find that your query cache size of about 268M and query_cache_limit of about 8M would be more effective at 50M and 1M respectively.
The reason being when one row is changed in a table, every cached query result for the updated table is marked invalid - i.e. cpu cycles are consumed to mark the cache results individually.
After restart, please confirm SHOW GLOBAL VARIABLES LIKE 'group_concat_max_length' has your intended value. It should be visible.

MySQL CPU Maxing

Currently have a MySQL database and experiencing an issue with MySQL running at 600% of the CPU usage.
Specs:
2.3 GHz Intel Xeon® E5-2686 v4 (Broadwell) processors or 2.4 GHz Intel Xeon® E5-2676 v3 (Haswell) processors
8 vCPU's
32GB of RAM
100GB Hard Drive.
Instance is currently hosted with AWS, running Ubuntu 14.04.4 LTS and MySQL version 5.6.33-0ubuntu0.14.04.1-log.
Please see below my.cnf configuration:
# 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
log_error=/var/log/mysql/mysql_error.log
[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
lc-messages-dir = /usr/share/mysql
skip-external-locking
innodb_io_capacity = 2000
innodb_read_io_threads = 64
innodb_thread_concurrency = 0
innodb_write_io_threads = 64
innodb_buffer_pool_size = 2G
innodb_log_file_size = 1G
# Skip reverse DNS lookup of clients
skip-name-resolve
#
# Instead of skip-networking the default is now to listen only on
# localhost which is more compatible and is not less secure.
bind-address = 127.0.0.1
#
# * Fine Tuning
#
key_buffer = 11G
max_allowed_packet = 16M
thread_stack = 192K
thread_cache_size = 8
# This replaces the startup script and checks MyISAM tables if needed
# the first time they are touched
myisam-recover = BACKUP
#max_connections = 100
#table_cache = 64
#thread_concurrency = 10
#
# * Query Cache Configuration
#
query_cache_limit = 1M
query_cache_size = 16M
query_cache_type = 0
#
# * 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 log - should be very few entries.
#
log_error = /var/log/mysql/mysql_error.log
#
# 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.
# note: if you are setting up a replication slave, see README.Debian about
# other settings you may need to change.
#server-id = 1
#log_bin = /var/log/mysql/mysql-bin.log
expire_logs_days = 10
max_binlog_size = 100M
#binlog_do_db = include_database_name
#binlog_ignore_db = include_database_name
#
# * InnoDB
#
# InnoDB is enabled by default with a 10MB datafile in /var/lib/mysql/.
# Read the manual for more InnoDB related options. There are many!
#
# * 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 = 512M
#
# * IMPORTANT: Additional settings that can override those from this file!
# The files must end with '.cnf', otherwise they'll be ignored.
#
!includedir /etc/mysql/conf.d/
First, start by disabling the general_log, no need to have it enabled all the time. The general log is very useful for troubleshooting and/or testing purposes, but it is a performance query killer on production database.
Also, if your are using mixed engines (MyISAM and InnoDB), you can give the innodb_buffer_pool_size more memory. But if you are only using Innodb, you can set this variable to 24G for example, and the key_buffer_size a few hundred of megabytes.
If you are using MyIsam only, please deactivate Innodb engine completely (skip-innodb) and increase Myisam memroy related parameters like key_buffer_size.
Hope it helps.

Parameter database MariaDB my.cnf

I pass an app (hotline for our customers) that runs on Java with a DB2 BDD (on an AS400 race beast) to a MariaDB BDD that runs on a Unix server.
I have a performances problem.
The new Unix server has two processors * 1 core and 5GB of RAM. I could negotiate 2 hearts more but hardly beyond.
The app can be solicited by 100 users / day, and 10-15 active users at the same time.
My main table has 20000 records (number of hotline tickets) but the dependent tables can reach some 150 000 records.
I use the InnoDB engine,because I am obliged to keep the constraints of foreign keys.
I created the most logical indexes.
Each table has an average of 50 fields. (Decimal and varchar 10 or 20)
The problem is that I have queries with 5 views that use 4 tables each (see other views), which is very greedy with several tens of thousands of records per table. I can hardly modify these queries unless I completely rewrite the app. (I remind you that this is just a change of BDD).
Can anyone tell me if my.cnf setting is OK or not. I tuned in looking for info on the web but I'm not an expert.
# MariaDB database server configuration file.
#
# You can copy this file 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
lc_messages_dir = /usr/share/mysql
lc_messages = en_US
skip-external-locking
lower_case_table_names = 1
character-set-server=utf8
collation-server=utf8_general_ci
#
# Instead of skip-networking the default is now to listen only on
# localhost which is more compatible and is not less secure.
bind-address = 10.10.64.51
#
# * Fine Tuning
#
max_connections = 100
connect_timeout = 5
wait_timeout = 600
max_allowed_packet = 16M
thread_cache_size = 128
#sort_buffer_size = 4M
sort_buffer_size = 8M
bulk_insert_buffer_size = 16M
#tmp_table_size = 32M
#max_heap_table_size = 32M
#tmp_table_size = 256M
tmp_table_size = 512M
#max_heap_table_size = 256M
max_heap_table_size = 512M
#
# * MyISAM
#
# This replaces the startup script and checks MyISAM tables if needed
# the first time they are touched. On error, make copy and try a repair.
myisam_recover_options = BACKUP
key_buffer_size = 128M
#open-files-limit = 2000
#table_open_cache = 400
table_open_cache = 600
myisam_sort_buffer_size = 512M
concurrent_insert = 2
read_buffer_size = 2M
#read_rnd_buffer_size = 1M
read_rnd_buffer_size = 2M
#
# * Query Cache Configuration
#
# Cache only tiny result sets, so we can fit more in the query cache.
#query_cache_limit = 128K
query_cache_limit = 512K
#query_cache_size = 256M
query_cache_size = 512M
#query_cache_type = DEMAND
#
# * 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 due to /etc/mysql/conf.d/mysqld_safe_syslog.cnf.
#
# we do want to know about network errors and such
log_warnings = 2
#
# Enable the slow query log to see queries with especially long duration
#slow_query_log[={0|1}]
slow_query_log_file = /var/log/mysql/mariadb-slow.log
long_query_time = 10
#log_slow_rate_limit = 1000
log_slow_verbosity = query_plan
#log-queries-not-using-indexes
#log_slow_admin_statements
#
# The following can be used as easy to replay backup logs or for replication.
# note: if you are setting up a replication slave, see README.Debian about
# other settings you may need to change.
#server-id = 1
#report_host = master1
#auto_increment_increment = 2
#auto_increment_offset = 1
log_bin = /var/log/mysql/mariadb-bin
log_bin_index = /var/log/mysql/mariadb-bin.index
# not fab for performance, but safer
#sync_binlog = 1
expire_logs_days = 10
max_binlog_size = 100M
# slaves
#relay_log = /var/log/mysql/relay-bin
#relay_log_index = /var/log/mysql/relay-bin.index
#relay_log_info_file = /var/log/mysql/relay-bin.info
#log_slave_updates
#read_only
#
# If applications support it, this stricter sql_mode prevents some
# mistakes like inserting invalid dates etc.
#sql_mode = NO_ENGINE_SUBSTITUTION,TRADITIONAL
#
# * InnoDB
#
# InnoDB is enabled by default with a 10MB datafile in /var/lib/mysql/.
# Read the manual for more InnoDB related options. There are many!
default_storage_engine = InnoDB
# you can't just change log file size, requires special procedure
#innodb_log_file_size = 50M
#innodb_buffer_pool_size = 256M
#innodb_buffer_pool_size = 512M
innodb_buffer_pool_size = 1G
innodb_log_buffer_size = 8M
innodb_file_per_table = 1
innodb_open_files = 400
innodb_io_capacity = 400
innodb_flush_method = O_DIRECT
#
# * 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
#
# * Galera-related settings
#
[galera]
# Mandatory settings
#wsrep_on=ON
#wsrep_provider=
#wsrep_cluster_address=
#binlog_format=row
#default_storage_engine=InnoDB
#innodb_autoinc_lock_mode=2
#
# Allow server to accept connections on all interfaces.
#
#bind-address=0.0.0.0
#
# Optional setting
#wsrep_slave_threads=1
#innodb_flush_log_at_trx_commit=0
[mysqldump]
quick
quote-names
max_allowed_packet = 16M
[mysql]
#no-auto-rehash # faster start of mysql but no tab completion
[isamchk]
key_buffer = 16M
#
# * IMPORTANT: Additional settings that can override those from this file!
# The files must end with '.cnf', otherwise they'll be ignored.
#
!includedir /etc/mysql/conf.d/
Best regards
Change these:
tmp_table_size = 50M
max_heap_table_size = 50M
query_cache_size = 50m
# Mickael : yeah I ran several other tests.
# rick : BDD = database, heart is the core of the CPU. Sorry for bad translation from French
# Rick why are you setting these parameters to lower values ??

AWS 2x.large server Apache and Mysql config not utilizing cpu and memory well

I have been trying to optimize my AWS server for apache and mysql to use the whole lot of resources allocated to it i.e: CPU: 8 core, RAM: 30GiB
Top command screenshot
whatevere I do, I am not able to get the config work optimistically.
Here is the my.cnf file content
#
# 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
lc-messages-dir = /usr/share/mysql
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 = 127.0.0.1
#skip-networking
#
# * Fine Tuning
#
key_buffer = 512M
max_allowed_packet = 16M
thread_stack = 192K
thread_cache_size = 8
# This replaces the startup script and checks MyISAM tables if needed
# the first time they are touched
myisam-recover = BACKUP
max_connections = 505
max_user_connections = 500
table_cache = 8192
#thread_concurrency = 10
#
# * Query Cache Configuration
#
query_cache_limit = 64M
query_cache_size = 64M
#
# * 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 log - should be very few entries.
#
log_error = /var/log/mysql/error.log
#
# 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.
# note: if you are setting up a replication slave, see README.Debian about
# other settings you may need to change.
#server-id = 1
#log_bin = /var/log/mysql/mysql-bin.log
expire_logs_days = 10
max_binlog_size = 100M
#binlog_do_db = include_database_name
#binlog_ignore_db = include_database_name
#
# * InnoDB
#
# InnoDB is enabled by default with a 10MB datafile in /var/lib/mysql/.
# Read the manual for more InnoDB related options. There are many!
#
# * 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
tmp_table_size = 1G
max_heap_table_size = 1G
innodb_buffer_pool_size = 4G
[mysqldump]
quick
quote-names
max_allowed_packet = 16M
[mysql]
#no-auto-rehash # faster start of mysql but no tab completition
[isamchk]
key_buffer = 256M
#
# * IMPORTANT: Additional settings that can override those from this file!
# The files must end with '.cnf', otherwise they'll be ignored.
#
!includedir /etc/mysql/conf.d/
I would really appriciate if I had any idea what else can be done so that both Mysql and Apache uses the allocated resources
Which engine, MyISAM or InnoDB? If InnoDB, decrease key_buffer_size to 40M. If MyISAM, convert.
Decrease MaxClients in Apache to 20.
The "top" shows a calm system. I interpret it to mean that there is not much to do, not that it is poorly utilizing resources.
If you have particular MySQL queries that are slow; let's see them. Often there are simple fixes.
Some Apache threads are moderately high on CPU -- look at the algorithms involved in the PHP (or whatever) code you have.

Lots of mysql Sleep processes

I am still having trouble with my mysql server. It seems that since i optimize it, the tables were growing and now sometimes is very slow again. I have no idea of how to optimize more.
mySQL server has 48GB of RAM and mysqld is using about 8, most of the tables are innoDB.
Site has about 2000 users online. I also run explain on every query and every one of them is indexed.
mySQL processes:
http://www.pik.ba/mysqlStanje.php
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 = 10.100.27.30
#
# * Fine Tuning
#
key_buffer = 64M
key_buffer_size = 512M
max_allowed_packet = 16M
thread_stack = 128K
thread_cache_size = 8
# This replaces the startup script and checks MyISAM tables if needed
# the first time they are touched
myisam-recover = BACKUP
max_connections = 1000
table_cache = 1000
join_buffer_size = 2M
tmp_table_size = 2G
max_heap_table_size = 2G
innodb_buffer_pool_size = 3G
innodb_additional_mem_pool_size = 128M
innodb_log_file_size = 100M
log-slow-queries = /var/log/mysql/slow.log
sort_buffer_size = 5M
net_buffer_length = 5M
read_buffer_size = 2M
read_rnd_buffer_size = 12M
thread_concurrency = 10
ft_min_word_len = 3
#thread_concurrency = 10
#
# * Query Cache Configuration
#
query_cache_limit = 1M
query_cache_size = 512M
#
# * Logging and Replication
#
# Both location gets rotated by the cronjob.
# Be aware that this log type is a performance killer.
#log = /var/log/mysql/mysql.log
#
# 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.
# note: if you are setting up a replication slave, see README.Debian about
# other settings you may need to change.
#server-id = 1
#log_bin = /var/log/mysql/mysql-bin.log
expire_logs_days = 10
max_binlog_size = 100M
#binlog_do_db = include_database_name
#binlog_ignore_db = include_database_name
#
# * BerkeleyDB
#
# Using BerkeleyDB is now discouraged as its support will cease in 5.1.12.
skip-bdb
#
# * InnoDB
#
# InnoDB is enabled by default with a 10MB datafile in /var/lib/mysql/.
# Read the manual for more InnoDB related options. There are many!
# You might want to disable InnoDB to shrink the mysqld process by circa 100MB.
#skip-innodb
#
# * 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!
# The files must end with '.cnf', otherwise they'll be ignored.
#
!includedir /etc/mysql/conf.d/
I refreshed on your process list page a couple times and quite often the queries I saw included "SELECT tablename.*"
Do you need every column from that table? If not that could help.
Unless your server is strapped for resources I wouldn't worry a whole lot about sleeping processes. They typically don't consume a lot of resources. However if you really do wish to manually set the amount of time before they are killed you can do the following in your config file:
[mysqld]
wait_timeout=20