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Help requested optimizing MySQL

Discussion in 'Workarounds and Optimization' started by AhmedEgy, Apr 15, 2014.

  1. AhmedEgy

    AhmedEgy Registered

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    Hello

    Mysql cpu load to high 98%, Query very slow , 0% installed RAM, browsing very slow + blank page

    Server

    DualXeonE5-2620 - 24 CPU, 64 GB RAM

    Code:
    [client]                                                                                                                                                      
    port            = 3306                                                                                                                                        
    socket          = /var/lib/mysql/mysql.sock                                                                                                                   
    
    [mysqld]                                                                                                                                       
    wait_timeout=3                                                                                                                                               
    datadir=/var/lib/mysql                                                                                                                                        
    socket=/var/lib/mysql/mysql.sock                                                                                                                              
    user=mysql
    bind-address=127.0.0.1                                                                                                                                  
    symbolic-links=0                                                                                                                                              
    port=3306
    skip-external-locking
    
    #skip-innodb                                                                                                                                                  
    max_connections = 2000
    interactive_timeout=3
    key_buffer = 5G                                                                                                                                               
    myisam_sort_buffer_size = 512M                                                                                                                                
    join_buffer_size = 6M                                                                                                                                         
    read_buffer_size = 8M                                                                                                                                         
    sort_buffer_size = 6M                                                                                                                                         
    table_cache = 1024                                                                                                                                             
    read_rnd_buffer_size=6144K
    thread_cache_size = 300k 
    thread_stack=128K        
    thread_concurrency=12
    wait_timeout = 20                                                                                                                                            
    connect_timeout = 10                                                                                                                                          
    max_allowed_packet = 32M         
    max_connect_errors = 10
    query_cache_limit = 1M
    query_cache_size = 32M
    query_cache_type = 1
    #skip-locking
    #skip-bdb
    max_binlog_size=100M
    default-storage-engine=MyISAM
    tmp_table_size=2500M
    max_heap_table_size=2500M
    table_definition_cache = 500
    #slow_query_log=1
    #slow_query_log_file=mysql-slow.log
    #long_query_time=5
    log-queries-not-using-indexes
    low_priority_updates=1
    concurrent_insert=2
    #skip-federated
    #log-bin=mysql-bin
    server-id = 1
    
    [mysqld_safe]
    #log-error=/var/log/mysqld.log
    pid-file=/var/run/mysqld/mysqld.pid
    open_files_limit = 35000
    socket=/var/run/mysqld/mysqld.sock
    nice=0
    
    [mysqldump]
    #quick
    #max_allowed_packet = 16M
    #quote-names
    
    [myisamchk]
    key_buffer = 512M
    sort_buffer = 512M
    read_buffer = 128M
    write_buffer = 128M
    
    [isamchk]
    key_buffer = 512M
    sort_buffer = 512M
    read_buffer = 128M
    write_buffer = 128M
    
    [mysql.server]
    #basedir=/var/lib/mysql
    
    [mysqlhotcopy]
    interactive-timeout
    safe-show-database
    set-variable=local-infile=0
    

    ./tuning-primer.sh


    Code:
    [root@ne-t194-320cl home]# ./tuning-primer.sh
    
    -- MYSQL PERFORMANCE TUNING PRIMER --
         - By: Matthew Montgomery -
    
    MySQL Version 5.1.73 x86_64
    
    Uptime = 0 days 0 hrs 26 min 4 sec
    Avg. qps = 16
    Total Questions = 25741
    Threads Connected = 258
    
    Warning: Server has not been running for at least 48hrs.
    It may not be safe to use these recommendations
    
    To find out more information on how each of these
    runtime variables effects performance visit:
    [url=http://dev.mysql.com/doc/refman/5.1/en/server-system-variables.html]MySQL :: MySQL 5.1 Reference Manual :: 5.1.4 Server System Variables[/url]
    Visit [url]http://www.mysql.com/products/enterprise/advisors.html[/url]
    for info about MySQL's Enterprise Monitoring and Advisory Service
    
    SLOW QUERIES
    The slow query log is NOT enabled.
    Current long_query_time = 10.000000 sec.
    You have 514 out of 25762 that take longer than 10.000000 sec. to complete
    Your long_query_time seems to be fine
    
    BINARY UPDATE LOG
    The binary update log is NOT enabled.
    You will not be able to do point in time recovery
    See [url=http://dev.mysql.com/doc/refman/5.1/en/point-in-time-recovery.html]MySQL :: MySQL 5.1 Reference Manual :: 7.5 Point-in-Time (Incremental) Recovery Using the Binary Log[/url]
    
    WORKER THREADS
    Current thread_cache_size = 16384
    Current threads_cached = 255
    Current threads_per_sec = 0
    Historic threads_per_sec = 0
    Your thread_cache_size is fine
    
    MAX CONNECTIONS
    Current max_connections = 2000
    Current threads_connected = 258
    Historic max_used_connections = 513
    The number of used connections is 25% of the configured maximum.
    Your max_connections variable seems to be fine.
    
    INNODB STATUS
    Current InnoDB index space = 0 bytes
    Current InnoDB data space = 0 bytes
    Current InnoDB buffer pool free = 96 %
    Current innodb_buffer_pool_size = 8 M
    Depending on how much space your innodb indexes take up it may be safe
    to increase this value to up to 2 / 3 of total system memory
    
    MEMORY USAGE
    Max Memory Ever Allocated : 18.12 G
    Configured Max Per-thread Buffers : 51.02 G
    Configured Max Global Buffers : 5.04 G
    Configured Max Memory Limit : 56.06 G
    Physical Memory : 62.88 G
    Max memory limit seem to be within acceptable norms
    
    KEY BUFFER
    Current MyISAM index space = 919 M
    Current key_buffer_size = 5.00 G
    Key cache miss rate is 1 : 3613
    Key buffer free ratio = 80 %
    Your key_buffer_size seems to be fine
    
    QUERY CACHE
    Query cache is enabled
    Current query_cache_size = 32 M
    Current query_cache_used = 20 K
    Current query_cache_limit = 1 M
    Current Query cache Memory fill ratio = .06 %
    Current query_cache_min_res_unit = 4 K
    Your query_cache_size seems to be too high.
    Perhaps you can use these resources elsewhere
    MySQL won't cache query results that are larger than query_cache_limit in size
    
    SORT OPERATIONS
    Current sort_buffer_size = 6 M
    Current read_rnd_buffer_size = 6 M
    No sort operations have been performed
    Sort buffer seems to be fine
    
    JOINS
    Current join_buffer_size = 6.00 M
    You have had 0 queries where a join could not use an index properly
    Your joins seem to be using indexes properly
    join_buffer_size >= 4 M
    This is not advised
    
    OPEN FILES LIMIT
    Current open_files_limit = 35000 files
    The open_files_limit should typically be set to at least 2x-3x
    that of table_cache if you have heavy MyISAM usage.
    Your open_files_limit value seems to be fine
    
    TABLE CACHE
    Current table_open_cache = 1024 tables
    Current table_definition_cache = 500 tables
    You have a total of 651 tables
    You have 1024 open tables.
    Current table_cache hit rate is 87%
    , while 100% of your table cache is in use
    You should probably increase your table_cache
    You should probably increase your table_definition_cache value.
    
    TEMP TABLES
    Current max_heap_table_size = 2.44 G
    Current tmp_table_size = 2.44 G
    Of 519 temp tables, 5% were created on disk
    Created disk tmp tables ratio seems fine
    
    TABLE SCANS
    Current read_buffer_size = 8 M
    Current table scan ratio = 103 : 1
    read_buffer_size seems to be fine
    TABLE LOCKING
    Current Lock Wait ratio = 1 : 0
    You may benefit from selective use of InnoDB.[/QUOTE]
    
    
    [root@ne-t194-320cl home]# netstat -an | grep :80 | wc -l
    36000
    
    mtop
    [QUOTE]load average: 232.58, 224.72, 209.72 mysqld 5.1.73 up 0 day(s),  0:29 hrs
    257 threads: 257 running, 256 cached. Queries/slow: 697/0 Cache Hit: 99.98%
    Opened tables: 0  RRN: 278  TLW: 20.0K  SFJ: 0  SMP: 0  QPS: 0
     
  2. cPanelMichael

    cPanelMichael Forums Analyst
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  3. thinkbot

    thinkbot Well-Known Member

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    run mysqltuner.pl and post results
     
  4. AhmedEgy

    AhmedEgy Registered

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    more information about the database



    Tables 30
    Rows 13,591,548
    Data 1.3 GiB
    Indexes 265.2 MiB
    Total 1.5 GiB
    Overhead 96 B

    - - - Updated - - -

    Code:
    [root@ne-t194-320cl home]# ./tuning-primer.sh
    
    -- MYSQL PERFORMANCE TUNING PRIMER --
         - By: Matthew Montgomery -
    
    MySQL Version 5.1.73 x86_64
    
    Uptime = 0 days 21 hrs 18 min 18 sec
    Avg. qps = 17
    Total Questions = 1343273
    Threads Connected = 253
    
    Warning: Server has not been running for at least 48hrs.
    It may not be safe to use these recommendations
    
    To find out more information on how each of these
    runtime variables effects performance visit:
    http://dev.mysql.com/doc/refman/5.1/en/server-system-variables.html
    Visit http://www.mysql.com/products/enterprise/advisors.html
    for info about MySQL's Enterprise Monitoring and Advisory Service
    
    SLOW QUERIES
    The slow query log is NOT enabled.
    Current long_query_time = 10.000000 sec.
    You have 28844 out of 1343294 that take longer than 10.000000 sec. to complete
    Your long_query_time seems to be fine
    
    BINARY UPDATE LOG
    The binary update log is NOT enabled.
    You will not be able to do point in time recovery
    See http://dev.mysql.com/doc/refman/5.1/en/point-in-time-recovery.html
    
    WORKER THREADS
    Current thread_cache_size = 16384
    Current threads_cached = 5
    Current threads_per_sec = 0
    Historic threads_per_sec = 0
    Your thread_cache_size is fine
    
    MAX CONNECTIONS
    Current max_connections = 2000
    Current threads_connected = 253
    Historic max_used_connections = 258
    The number of used connections is 12% of the configured maximum.
    Your max_connections variable seems to be fine.
    
    INNODB STATUS
    Current InnoDB index space = 0 bytes
    Current InnoDB data space = 0 bytes
    Current InnoDB buffer pool free = 96 %
    Current innodb_buffer_pool_size = 8 M
    Depending on how much space your innodb indexes take up it may be safe
    to increase this value to up to 2 / 3 of total system memory
    
    MEMORY USAGE
    Max Memory Ever Allocated : 11.62 G
    Configured Max Per-thread Buffers : 51.02 G
    Configured Max Global Buffers : 5.04 G
    Configured Max Memory Limit : 56.06 G
    Physical Memory : 62.88 G
    Max memory limit seem to be within acceptable norms
    
    KEY BUFFER
    Current MyISAM index space = 919 M
    Current key_buffer_size = 5.00 G
    Key cache miss rate is 1 : 172564
    Key buffer free ratio = 80 %
    Your key_buffer_size seems to be too high.
    Perhaps you can use these resources elsewhere
    
    QUERY CACHE
    Query cache is enabled
    Current query_cache_size = 32 M
    Current query_cache_used = 61 K
    Current query_cache_limit = 1 M
    Current Query cache Memory fill ratio = .18 %
    Current query_cache_min_res_unit = 4 K
    Your query_cache_size seems to be too high.
    Perhaps you can use these resources elsewhere
    MySQL won't cache query results that are larger than query_cache_limit in size
    
    SORT OPERATIONS
    Current sort_buffer_size = 6 M
    Current read_rnd_buffer_size = 6 M
    No sort operations have been performed
    Sort buffer seems to be fine
    
    JOINS
    Current join_buffer_size = 6.00 M
    You have had 0 queries where a join could not use an index properly
    Your joins seem to be using indexes properly
    join_buffer_size >= 4 M
    This is not advised
    
    
    OPEN FILES LIMIT
    Current open_files_limit = 35000 files
    The open_files_limit should typically be set to at least 2x-3x
    that of table_cache if you have heavy MyISAM usage.
    Your open_files_limit value seems to be fine
    
    TABLE CACHE
    Current table_open_cache = 1024 tables
    Current table_definition_cache = 500 tables
    You have a total of 651 tables
    You have 907 open tables.
    The table_cache value seems to be fine
    You should probably increase your table_definition_cache value.
    
    TEMP TABLES
    Current max_heap_table_size = 2.44 G
    Current tmp_table_size = 2.44 G
    Of 1941 temp tables, 6% were created on disk
    Created disk tmp tables ratio seems fine
    
    TABLE SCANS
    Current read_buffer_size = 8 M
    Current table scan ratio = 514 : 1
    read_buffer_size seems to be fine
    
    TABLE LOCKING
    Current Lock Wait ratio = 1 : 0
    You may benefit from selective use of InnoDB.
    
    Code:
    [root@ne-t194-320cl home]# netstat -an | grep :80 | wc -l
    16054
     
  5. thinkbot

    thinkbot Well-Known Member

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    mysqltuner.pl not tuning-primer

    anyway adjust:
    thread_cache_size = 200
    max_connections = 500
    sort_buffer_size = 256K
    read_rnd_buffer_size = 256K
    read_buffer_size=128K
    join_buffer_size=2M
    table_definition_cache = 1000

    max_heap_table_size = 200M
    tmp_table_size = 200M


    remove those:
    thread_cache_size = 300k
    thread_stack=128K
    thread_concurrency=12
    max_connect_errors = 10
    low_priority_updates=1


    "Mysql cpu load to high 98%,"
    to make it simple, if you got 24 cores, you can have 24x100% = 2400%

    you should also review your slow queries, and optimize them, add some indexes if necessary etc.
     
  6. AhmedEgy

    AhmedEgy Registered

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    Code:
    $sql3 =  mysql_query("SELECT * FROM config LIMIT 1");
    $row3 = mysql_fetch_assoc($sql3);
    $log=$row3['con_log'];
    $sql2 = mysql_query("SELECT sl_start,sl_id FROM ss_list2 WHERE sl_ss='0' ORDER BY sl_id LIMIT 40");
    while($row2 = mysql_fetch_assoc($sql2)){
    echo "crk|".$row2['sl_start']."|".$log."-";
    $sl_id = $row2['sl_id'];
    mysql_query("UPDATE scan_list2 SET sl_ss='1' WHERE sl_id='$sl_id'");
    Is there any better solution for this problem to make the query faster, that one take more than 5 mint.
     
  7. thinkbot

    thinkbot Well-Known Member

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    it would be better to copy more content here

    Make sure there are idexes on sl_id in scan_list2 table
    and 1 index containing 2 columns (sl_ss, sl_id)

    you can show us the result of those queries (you can run them from phpmyadmin):
    explain extended SELECT sl_start,sl_id FROM ss_list2 WHERE sl_ss='0' ORDER BY sl_id LIMIT 40
    explain extended SELECT sl_ss FROM scan_list2 WHERE sl_id='1'

    to check if there are indexes on it used well
     
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