Mysql – Select * from statement execute very slowly, innodb io read speed is low

innodbMySQLperformance

I have a very simple query " select * from ap_statistic " running in my servers. the servers have the same hardware and software configuration (CPU 8 core, mem :32G, OS: redhat 5.5, mysql version: 5.1 ) and run the same applications. In server A, the row number of the table ap_statistic is about 22512379, in server B, the row number of the table is 41438751. Of course the query running on server A is faster than server B, but what is strange is the query on server B is extreme slow, it takes more than 3 hours where in server A it just takes 10 minutes.

I use some tool to monitor system status and find that when the query is running in server A, system IO read speed is about 20~30M/s, but in server B it's 2~3M/s. I've tried to clean linux cache and restart mysql server, all is the same result. And I tried to restored DB from server B to server A, so the query in Server A is very very slow and io read speed is very slow. I want to know why this happen?

the ap_statistic table data in server A is generated by normally running and table data in server B is generated by a stored procedure. the table scheme is:

CREATE TABLE `ap_statistic` (
  `ap_statisticId` BIGINT(20) UNSIGNED NOT NULL,
  `deviceId` INT(11) UNSIGNED NOT NULL DEFAULT '0',
  `macaddress` VARCHAR(100) DEFAULT NULL,
  `check_time` TIMESTAMP NOT NULL DEFAULT '0000-00-00 00:00:00',
  `ap_count` INT(10) UNSIGNED NOT NULL DEFAULT '0',
  `wlan` VARCHAR(64) DEFAULT NULL,
  `radio` VARCHAR(50) DEFAULT NULL,
  `bssid` VARCHAR(32) DEFAULT NULL,
  `zd_ap_name` VARCHAR(64) DEFAULT NULL,
  `channel` INT(2) DEFAULT NULL,
  `uplinkRSSI` INT(3) DEFAULT '0',
  `downlinkRSSI` INT(3) DEFAULT '0',
  `txBytes` BIGINT(20) DEFAULT '0',
  `rxBytes` BIGINT(20) DEFAULT '0',
  `txPkts` BIGINT(20) DEFAULT '0',
  `rxPkts` BIGINT(20) DEFAULT '0',
  `hops` INT(1) DEFAULT '0',
  `numDownlink` INT(3) DEFAULT '0',
  `distance` INT(4) DEFAULT '0',
  `phyerr` INT(11) DEFAULT '0',
  `max_num_clients` INT(3) DEFAULT '0',
  `max_mesh_downlinks` INT(1) DEFAULT '0',
  `airtime` INT(3) DEFAULT '0',
  `uptimePercentage` INT(3) DEFAULT '0',
  `total_num_clients` INT(3) DEFAULT '0',
  `tx_actual_throughput` BIGINT(20) DEFAULT '0',
  `rx_actual_throughput` BIGINT(20) DEFAULT '0',
  `tunnelMode` VARCHAR(32) DEFAULT NULL,
  `externalIp` VARCHAR(64) DEFAULT NULL,
  `externalPort` VARCHAR(32) DEFAULT NULL,
  `level` INT(1) DEFAULT '1' 
  `essid` VARCHAR(64) DEFAULT NULL,
  `total_client_join` INT(11) DEFAULT '0',
  PRIMARY KEY (`ap_statisticId`),
  KEY `check_time` (`check_time`),
  KEY `macaddress` (`macaddress`),
  KEY `deviceId` (`deviceId`)
) ENGINE=INNODB DEFAULT CHARSET=utf8

the follows are the table file info and some outputs of the monitor tools

Server B

  -rw-rw---- 1 mysql mysql 18568183808 Oct 11 14:52 ap_statistic.ibd

  [root@localhost itms]# filefrag ./ap_statistic.ibd
  ./ap_statistic.ibd: 164 extents found, perfection would be 159 extents


    TABLE         Non_unique  Key_name    Seq_in_index  Column_name     COLLATION  Cardinality  Sub_part  Packed  NULL    Index_type  COMMENT
    ------------  ----------  ----------  ------------  --------------  ---------  -----------  --------  ------  ------  ----------  -------
    ap_statistic           0  PRIMARY                1  ap_statisticId  A             41438751    (NULL)  (NULL)          BTREE              
    ap_statistic           1  check_time             1  check_time      A                10320    (NULL)  (NULL)          BTREE              
    ap_statistic           1  macaddress             1  macaddress      A                   16    (NULL)  (NULL)  YES     BTREE              
    ap_statistic           1  deviceId               1  deviceId        A                   16    (NULL)  (NULL)          BTREE    


  mysql>show status;

        Variable_name   Value
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        Binlog_cache_disk_use   0
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        Bytes_received  1256
        Bytes_sent  8844
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        Innodb_data_written 1792826880
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        Innodb_dblwr_writes 830
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        Innodb_row_lock_current_waits   0
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        Innodb_rows_deleted 28637
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        Innodb_rows_updated 887251
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        Last_query_cost 9142769.199000
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        Queries 1578897
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        Ssl_callback_cache_hits 0
        Ssl_cipher  
        Ssl_cipher_list 
        Ssl_client_connects 0
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        Table_locks_immediate   1549525
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        Threads_cached  0
        Threads_connected   17
        Threads_created 322
        Threads_running 2
        Uptime  8093
        Uptime_since_flush_status   8093

        mysql>show variables;

        Variable_name   Value
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        binlog_cache_size   32768
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        binlog_format   STATEMENT
        bulk_insert_buffer_size 8388608
        character_set_client    utf8
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        character_set_database  utf8
        character_set_filesystem    binary
        character_set_results   utf8
        character_set_server    utf8
        character_set_system    utf8
        collation_connection    utf8_general_ci
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        completion_type 0
        concurrent_insert   1
        connect_timeout 10
        date_format %Y-%m-%d
        datetime_format %Y-%m-%d %H:%i:%s
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        engine_condition_pushdown   ON
        error_count 0
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        ft_boolean_syntax   + -><()~*:""&|
        ft_max_word_len 84
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        have_community_features YES
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        innodb_locks_unsafe_for_binlog  ON
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        innodb_log_files_in_group   2
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        innodb_use_legacy_cardinality_algorithm ON
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        join_buffer_size    268435456
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        key_buffer_size 268435456
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        key_cache_division_limit    100         
        large_files_support ON
        large_page_size 0
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        last_insert_id  0
        lc_time_names   en_US
        license Commercial
        local_infile    ON
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        sql_slave_skip_counter  
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        ssl_ca  
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        time_format %H:%i:%s
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        version 5.1.53-enterprise-commercial-pro
        version_comment MySQL Enterprise Server - Pro Edition (Commercial)
        version_compile_machine x86_64
        version_compile_os  unknown-linux-gnu
        wait_timeout    28800
        warning_count   0


        mysql> show innodb status\G;
        *************************** 1. row ***************************
          Type: InnoDB
          Name:
        Status:
        =====================================
        121011 10:22:13 INNODB MONITOR OUTPUT
        =====================================
        Per second averages calculated from the last 39 seconds
        ----------
        SEMAPHORES
        ----------
        OS WAIT ARRAY INFO: reservation count 3806, signal count 3778
        Mutex spin waits 0, rounds 282892, OS waits 2075
        RW-shared spins 1969, OS waits 864; RW-excl spins 2336, OS waits 749
        ------------
        TRANSACTIONS
        ------------
        Trx id counter 0 5303968
        Purge done for trx's n:o < 0 5303951 undo n:o < 0 0
        History list length 1
        LIST OF TRANSACTIONS FOR EACH SESSION:
        ---TRANSACTION 0 0, not started, process no 30336, OS thread id 1189509440
        MySQL thread id 520, query id 1861594 localhost root
        show innodb status
        ---TRANSACTION 0 5303967, not started, process no 30336, OS thread id 1188710720
        MySQL thread id 526, query id 1861593 127.0.0.1 root
        ---TRANSACTION 0 5303962, not started, process no 30336, OS thread id 1186314560
        MySQL thread id 519, query id 1861555 127.0.0.1 root
        ---TRANSACTION 0 5303952, not started, process no 30336, OS thread id 1188444480
        MySQL thread id 515, query id 1861567 127.0.0.1 root
        ---TRANSACTION 0 5303948, not started, process no 30336, OS thread id 1187912000
        MySQL thread id 516, query id 1861566 127.0.0.1 root
        ---TRANSACTION 0 5303937, not started, process no 30336, OS thread id 1190308160
        MySQL thread id 511, query id 1861568 127.0.0.1 root
        ---TRANSACTION 0 0, not started, process no 30336, OS thread id 1090791744
        MySQL thread id 18, query id 1596073 172.18.112.84 root
        ---TRANSACTION 0 5303959, ACTIVE 63 sec, process no 30336, OS thread id 1090525504 fetching rows, thread declared inside InnoDB 500
        mysql tables in use 1, locked 0
        MySQL thread id 17, query id 1861400 localhost root Sending data
        select * from ap_statistic
        Trx read view will not see trx with id >= 0 5303960, sees < 0 5303960
        --------
        FILE I/O
        --------
        I/O thread 0 state: waiting for i/o request (insert buffer thread)
        I/O thread 1 state: waiting for i/o request (log thread)
        I/O thread 2 state: waiting for i/o request (read thread)
        I/O thread 3 state: waiting for i/o request (write thread)
        Pending normal aio reads: 0, aio writes: 0,
         ibuf aio reads: 0, log i/o's: 0, sync i/o's: 0
        Pending flushes (fsync) log: 0; buffer pool: 0
        63521 OS file reads, 294656 OS file writes, 5641 OS fsyncs
        1 pending preads, 0 pending pwrites
        149.38 reads/s, 16384 avg bytes/read, 0.00 writes/s, 0.00 fsyncs/s
        -------------------------------------
        INSERT BUFFER AND ADAPTIVE HASH INDEX
        -------------------------------------
        Ibuf: size 1, free list len 318, seg size 320,
        63593 inserts, 63593 merged recs, 9674 merges
        Hash table size 22086161, node heap has 607 buffer(s)
        0.08 hash searches/s, 0.26 non-hash searches/s
        ---
        LOG
        ---
        Log sequence number 15 2873617336
        Log flushed up to   15 2873617336
        Last checkpoint at  15 2873617336
        0 pending log writes, 0 pending chkp writes
        269102 log i/o's done, 0.00 log i/o's/second
        ----------------------
        BUFFER POOL AND MEMORY
        ----------------------
        Total memory allocated 12452785320; in additional pool allocated 15261440
        Dictionary memory allocated 789024
        Buffer pool size   681152
        Free buffers       610013
        Database pages     70532
        Modified db pages  0
        Pending reads 1
        Pending writes: LRU 0, flush list 0, single page 0
        Pages read 65043, created 5488, written 45924
        149.38 reads/s, 0.00 creates/s, 0.00 writes/s
        Buffer pool hit rate 888 / 1000
        --------------
        ROW OPERATIONS
        --------------
        1 queries inside InnoDB, 0 queries in queue
        2 read views open inside InnoDB
        Main thread process no. 30336, id 1185782080, state: waiting for server activity
        Number of rows inserted 336555, updated 1112311, deleted 28681, read 29200669
        0.00 inserts/s, 0.00 updates/s, 0.00 deletes/s, 8258.58 reads/s
        ----------------------------
        END OF INNODB MONITOR OUTPUT
        ============================

        1 row in set, 1 warning (0.00 sec)

        ERROR:
        No query specified



        iostat -dx 2

        Device:    rrqm/s wrqm/s   r/s   w/s  rsec/s  wsec/s    rkB/s    wkB/s avgrq-sz avgqu-sz   await  svctm  %util
        sda          0.00   2.50 141.50 11.50 4516.00  112.00  2258.00    56.00    30.25     0.95    6.23   5.70  87.25
        sda1         0.00   0.00  0.00  0.00    0.00    0.00     0.00     0.00     0.00     0.00    0.00   0.00   0.00
        sda2         0.00   2.50 141.50 11.50 4516.00  112.00  2258.00    56.00    30.25     0.95    6.23   5.70  87.25
        dm-0         0.00   0.00 141.50 14.00 4516.00  112.00  2258.00    56.00    29.76     0.97    6.24   5.62  87.35
        dm-1         0.00   0.00  0.00  0.00    0.00    0.00     0.00     0.00     0.00     0.00    0.00   0.00   0.00

        Device:    rrqm/s wrqm/s   r/s   w/s  rsec/s  wsec/s    rkB/s    wkB/s avgrq-sz avgqu-sz   await  svctm  %util
        sda          3.00   0.00 154.50  0.00 4932.00    0.00  2466.00     0.00    31.92     0.93    6.04   6.04  93.25
        sda1         0.00   0.00  0.00  0.00    0.00    0.00     0.00     0.00     0.00     0.00    0.00   0.00   0.00
        sda2         3.00   0.00 154.50  0.00 4932.00    0.00  2466.00     0.00    31.92     0.93    6.04   6.04  93.25
        dm-0         0.00   0.00 157.50  0.00 4932.00    0.00  2466.00     0.00    31.31     0.95    6.04   5.93  93.40
        dm-1         0.00   0.00  0.00  0.00    0.00    0.00     0.00     0.00     0.00     0.00    0.00   0.00   0.00

        Device:    rrqm/s wrqm/s   r/s   w/s  rsec/s  wsec/s    rkB/s    wkB/s avgrq-sz avgqu-sz   await  svctm  %util
        sda          3.00   1.50 150.50  1.50 4804.00   24.00  2402.00    12.00    31.76     0.94    6.15   6.14  93.40
        sda1         0.00   0.00  0.00  0.00    0.00    0.00     0.00     0.00     0.00     0.00    0.00   0.00   0.00
        sda2         3.00   1.50 150.50  1.50 4804.00   24.00  2402.00    12.00    31.76     0.94    6.15   6.14  93.40
        dm-0         0.00   0.00 153.50  3.00 4804.00   24.00  2402.00    12.00    30.85     0.95    6.08   5.97  93.50
        dm-1         0.00   0.00  0.00  0.00    0.00    0.00     0.00     0.00     0.00     0.00    0.00   0.00   0.00


        vmstat 2

        procs -----------memory---------- ---swap-- -----io---- --system-- -----cpu------
         r  b   swpd   free   buff  cache   si   so    bi    bo   in   cs us sy id wa st
         1  1     16 27358488  18152 115500    0    0  2558     0 1193 8634 14  1 73 12  0
         1  1     16 27346840  18168 115500    0    0  2356    12 1174 9129 14  2 73 12  0
         2  1     16 27334320  18172 115504    0    0  2522     0 1184 8918 14  1 73 12  0
         1  1     16 27321812  18180 115496    0    0  2456    12 1183 7357 13  1 74 12  0
         1  1     16 27310132  18180 115504    0    0  2344    12 1174 6990 12  2 74 12  0
         1  1     16 27297608  18184 115508    0    0  2506     0 1182 6203 12  2 74 11  0
         1  1     16 27285444  18200 115504    0    0  2420    90 1187 9667 13  2 73 12  0
         1  1     16 27277640  18200 115508    0    0  2248     0 1165 8103 19  2 69 11  0
         2  1     16 27265380  18204 115504    0    0  2498     0 1179 5690 13  1 74 12  0
         4  1     16 27252972  18216 115508    0    0  2434    12 1178 6096 14  1 74 12  0
         1  1     16 27241032  18232 115496    0    0  2520     0 1181 9252 12  1 75 11  0
         2  1     16 27229136  18240 115508    0    0  2468    10 1178 7116 13  1 74 12  0
         1  0     16 27630612  18248 115508    0    0  1536    20 1121 4082 13  1 79  7  0


        mpstat -P ALL 2


        02:48:57 PM  CPU   %user   %nice %system %iowait    %irq   %soft   %idle    intr/s
        02:48:59 PM  all   13.69    0.00    1.31   11.56    0.00    0.62   72.81   1190.95
        02:48:59 PM    0   33.67    0.00    0.50    0.00    0.00    0.00   65.83   1006.03
        02:48:59 PM    1    6.53    0.00    0.50   92.96    0.50    0.50    0.00    160.80
        02:48:59 PM    2    1.01    0.00    0.50    0.00    0.00    0.00   98.49      0.00
        02:48:59 PM    3    0.00    0.00    0.00    0.00    0.00    0.00  100.50      3.52
        02:48:59 PM    4   35.68    0.00    1.01    0.00    0.00    1.01   62.81     13.57
        02:48:59 PM    5    4.52    0.00    0.00    0.00    0.00    0.00   96.48      0.50
        02:48:59 PM    6    3.52    0.00    0.00    0.00    0.00    0.00   96.98      0.50
        02:48:59 PM    7   25.13    0.00    7.54    0.00    0.00    4.02   63.82      6.03

        02:48:59 PM  CPU   %user   %nice %system %iowait    %irq   %soft   %idle    intr/s
        02:49:01 PM  all   12.50    0.00    1.19   11.69    0.00    0.56   74.06   1177.11
        02:49:01 PM    0   22.89    0.00    1.49    0.00    0.00    1.49   74.13    995.52
        02:49:01 PM    1    5.97    0.00    0.50   92.54    0.00    0.50    0.00    159.70
        02:49:01 PM    2    0.50    0.00    0.50    0.50    0.00    0.00   98.01      1.99
        02:49:01 PM    3    0.00    0.00    0.00    0.00    0.00    0.00   99.50      2.49
        02:49:01 PM    4   45.77    0.00    1.49    0.00    0.00    0.50   51.24     11.94
        02:49:01 PM    5    0.00    0.00    0.00    0.00    0.00    0.00   99.50      0.50
        02:49:01 PM    6    0.50    0.00    0.00    0.00    0.00    0.00   99.00      0.50
        02:49:01 PM    7   23.38    0.00    5.47    0.00    0.00    1.99   68.16      4.48

        02:49:01 PM  CPU   %user   %nice %system %iowait    %irq   %soft   %idle    intr/s
        02:49:03 PM  all   13.05    0.00    1.12   11.62    0.00    0.50   73.70   1179.00
        02:49:03 PM    0   43.50    0.00    0.50    0.00    0.00    0.00   56.00   1000.50
        02:49:03 PM    1    6.50    0.00    1.00   93.00    0.00    0.50    0.00    157.00
        02:49:03 PM    2    1.50    0.00    0.50    0.00    0.00    0.00   98.50      0.00
        02:49:03 PM    3    0.00    0.00    0.00    0.00    0.00    0.00  100.00      2.50
        02:49:03 PM    4   32.50    0.00    1.50    0.00    0.00    1.00   65.50     13.00
        02:49:03 PM    5   11.00    0.00    4.00    0.00    0.00    1.50   83.50      0.50
        02:49:03 PM    6    0.00    0.00    0.00    0.00    0.00    0.00  100.00      0.00
        02:49:03 PM    7   10.50    0.00    2.00    0.00    0.00    1.00   87.00      5.50

Best Answer

Run OPTIMIZE TABLE on your tables to get them into a fresh state.

If your table is fragmented the system IO read speed gets really slow.