#1
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    Contributing User
    Devshed Regular (2000 - 2499 posts)

    Join Date
    Sep 2006
    Posts
    2,013
    Rep Power
    534

    MySQL running very slow


    I have two servers.

    One is a VPS where my provider installed CentOS 6.4. I then installed MySQL 5.1.69 via yum with the CentOS repo. The second is a laptop where I installed CentOS 6.4 basic server and then installed MySQL 5.1.69 via yum with the CentOS repo. CPU info for both is shown below.

    My PHP script has been running very slowly on the laptop, and I believe the cause is MySQL is executing very slowly. The way I tested this is executing a sql file from the command line on both servers, and looking at the time displayed next to each query. The VPS showed typically 0 seconds per query where the laptop showed about 0.05 seconds per query. Not very scientific, but hopefully proved that MySQL is the culprit.

    The laptop used to run fine using CentOS 5.8 and I think MySQL 5.1, so I do not think it is the hardware.

    my.cnf is identical on both machines.
    Code:
    [root@server1 ~]# cat /etc/my.cnf
    [mysqld]
    datadir=/var/lib/mysql
    socket=/var/lib/mysql/mysql.sock
    user=mysql
    # Disabling symbolic-links is recommended to prevent assorted security risks
    symbolic-links=0
    
    [mysqld_safe]
    log-error=/var/log/mysqld.log
    pid-file=/var/run/mysqld/mysqld.pid
    
    innodb_strict_mode=on
    sql_mode=TRADITIONAL
    # sql_mode=STRICT_TRANS_TABLES,NO_ZERO_DATE,NO_ZERO_IN_DATE
    character-set-server=utf8
    collation-server=utf8_general_ci
    log=/var/log/mysqld_all.log
    
    [root@server1 ~]#
    How should I troubleshoot this? I've recently installed sysbench. Is this a good tool for doing so? My first attempt showed an error, but I expect it shouldn't be too difficult to figure out. EDIT. Got sysbench working. See results at end of page.
    Thanks for your help!

    Code:
    [root@server1 ~]# sysbench --test=oltp --oltp-table-size=1000000 --mysql-db=test_database --mysql-user=root --mysql-password=xxx prepare
    sysbench 0.4.12:  multi-threaded system evaluation benchmark
    
    FATAL: no database driver specified
    FATAL: failed to initialize database driver!
    [root@server1 ~]#

    VPS:
    Code:
    [root@vps ~]# cat /proc/cpuinfo
    processor       : 0
    vendor_id       : GenuineIntel
    cpu family      : 6
    model           : 44
    model name      : Intel(R) Xeon(R) CPU           E5620  @ 2.40GHz
    stepping        : 2
    cpu MHz         : 2400.194
    cache size      : 12288 KB
    physical id     : 0
    siblings        : 8
    core id         : 0
    cpu cores       : 4
    apicid          : 0
    fdiv_bug        : no
    hlt_bug         : no
    f00f_bug        : no
    coma_bug        : no
    fpu             : yes
    fpu_exception   : yes
    cpuid level     : 11
    wp              : yes
    flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe nx pdpe1gb rdtscp lm constant_tsc ida nonstop_tsc arat pni monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr sse4_1 sse4_2 popcnt lahf_lm [8]
    bogomips        : 4800.38
    
    processor       : 1
    vendor_id       : GenuineIntel
    cpu family      : 6
    model           : 44
    model name      : Intel(R) Xeon(R) CPU           E5620  @ 2.40GHz
    stepping        : 2
    cpu MHz         : 2400.194
    cache size      : 12288 KB
    physical id     : 0
    siblings        : 8
    core id         : 0
    cpu cores       : 4
    apicid          : 1
    fdiv_bug        : no
    hlt_bug         : no
    f00f_bug        : no
    coma_bug        : no
    fpu             : yes
    fpu_exception   : yes
    cpuid level     : 11
    wp              : yes
    flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe nx pdpe1gb rdtscp lm constant_tsc ida nonstop_tsc arat pni monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr sse4_1 sse4_2 popcnt lahf_lm [8]
    bogomips        : 4800.13
    
    processor       : 2
    vendor_id       : GenuineIntel
    cpu family      : 6
    model           : 44
    model name      : Intel(R) Xeon(R) CPU           E5620  @ 2.40GHz
    stepping        : 2
    cpu MHz         : 2400.194
    cache size      : 12288 KB
    physical id     : 0
    siblings        : 8
    core id         : 1
    cpu cores       : 4
    apicid          : 2
    fdiv_bug        : no
    hlt_bug         : no
    f00f_bug        : no
    coma_bug        : no
    fpu             : yes
    fpu_exception   : yes
    cpuid level     : 11
    wp              : yes
    flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe nx pdpe1gb rdtscp lm constant_tsc ida nonstop_tsc arat pni monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr sse4_1 sse4_2 popcnt lahf_lm [8]
    bogomips        : 4800.15
    
    processor       : 3
    vendor_id       : GenuineIntel
    cpu family      : 6
    model           : 44
    model name      : Intel(R) Xeon(R) CPU           E5620  @ 2.40GHz
    stepping        : 2
    cpu MHz         : 2400.194
    cache size      : 12288 KB
    physical id     : 0
    siblings        : 8
    core id         : 1
    cpu cores       : 4
    apicid          : 3
    fdiv_bug        : no
    hlt_bug         : no
    f00f_bug        : no
    coma_bug        : no
    fpu             : yes
    fpu_exception   : yes
    cpuid level     : 11
    wp              : yes
    flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe nx pdpe1gb rdtscp lm constant_tsc ida nonstop_tsc arat pni monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr sse4_1 sse4_2 popcnt lahf_lm [8]
    bogomips        : 4800.08
    
    processor       : 4
    vendor_id       : GenuineIntel
    cpu family      : 6
    model           : 44
    model name      : Intel(R) Xeon(R) CPU           E5620  @ 2.40GHz
    stepping        : 2
    cpu MHz         : 2400.194
    cache size      : 12288 KB
    physical id     : 0
    siblings        : 8
    core id         : 9
    cpu cores       : 4
    apicid          : 18
    fdiv_bug        : no
    hlt_bug         : no
    f00f_bug        : no
    coma_bug        : no
    fpu             : yes
    fpu_exception   : yes
    cpuid level     : 11
    wp              : yes
    flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe nx pdpe1gb rdtscp lm constant_tsc ida nonstop_tsc arat pni monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr sse4_1 sse4_2 popcnt lahf_lm [8]
    bogomips        : 4800.13
    
    processor       : 5
    vendor_id       : GenuineIntel
    cpu family      : 6
    model           : 44
    model name      : Intel(R) Xeon(R) CPU           E5620  @ 2.40GHz
    stepping        : 2
    cpu MHz         : 2400.194
    cache size      : 12288 KB
    physical id     : 0
    siblings        : 8
    core id         : 9
    cpu cores       : 4
    apicid          : 19
    fdiv_bug        : no
    hlt_bug         : no
    f00f_bug        : no
    coma_bug        : no
    fpu             : yes
    fpu_exception   : yes
    cpuid level     : 11
    wp              : yes
    flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe nx pdpe1gb rdtscp lm constant_tsc ida nonstop_tsc arat pni monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr sse4_1 sse4_2 popcnt lahf_lm [8]
    bogomips        : 4800.14
    
    processor       : 6
    vendor_id       : GenuineIntel
    cpu family      : 6
    model           : 44
    model name      : Intel(R) Xeon(R) CPU           E5620  @ 2.40GHz
    stepping        : 2
    cpu MHz         : 2400.194
    cache size      : 12288 KB
    physical id     : 0
    siblings        : 8
    core id         : 10
    cpu cores       : 4
    apicid          : 20
    fdiv_bug        : no
    hlt_bug         : no
    f00f_bug        : no
    coma_bug        : no
    fpu             : yes
    fpu_exception   : yes
    cpuid level     : 11
    wp              : yes
    flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe nx pdpe1gb rdtscp lm constant_tsc ida nonstop_tsc arat pni monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr sse4_1 sse4_2 popcnt lahf_lm [8]
    bogomips        : 4800.15
    
    processor       : 7
    vendor_id       : GenuineIntel
    cpu family      : 6
    model           : 44
    model name      : Intel(R) Xeon(R) CPU           E5620  @ 2.40GHz
    stepping        : 2
    cpu MHz         : 2400.194
    cache size      : 12288 KB
    physical id     : 0
    siblings        : 8
    core id         : 10
    cpu cores       : 4
    apicid          : 21
    fdiv_bug        : no
    hlt_bug         : no
    f00f_bug        : no
    coma_bug        : no
    fpu             : yes
    fpu_exception   : yes
    cpuid level     : 11
    wp              : yes
    flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe nx pdpe1gb rdtscp lm constant_tsc ida nonstop_tsc arat pni monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr sse4_1 sse4_2 popcnt lahf_lm [8]
    bogomips        : 4800.14
    
    [root@vps ~]
    Laptop:
    Code:
    [root@server1 ~]# cat /proc/cpuinfo
    processor       : 0
    vendor_id       : GenuineIntel
    cpu family      : 6
    model           : 15
    model name      : Intel(R) Core(TM)2 Duo CPU     T7100  @ 1.80GHz
    stepping        : 13
    cpu MHz         : 800.000
    cache size      : 2048 KB
    physical id     : 0
    siblings        : 2
    core id         : 0
    cpu cores       : 2
    apicid          : 0
    initial apicid  : 0
    fpu             : yes
    fpu_exception   : yes
    cpuid level     : 10
    wp              : yes
    flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm constant_tsc arch_perfmon pebs bts rep_good aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm lahf_lm ida dts tpr_shadow vnmi flexpriority
    bogomips        : 3591.39
    clflush size    : 64
    cache_alignment : 64
    address sizes   : 36 bits physical, 48 bits virtual
    power management:
    
    processor       : 1
    vendor_id       : GenuineIntel
    cpu family      : 6
    model           : 15
    model name      : Intel(R) Core(TM)2 Duo CPU     T7100  @ 1.80GHz
    stepping        : 13
    cpu MHz         : 800.000
    cache size      : 2048 KB
    physical id     : 0
    siblings        : 2
    core id         : 1
    cpu cores       : 2
    apicid          : 1
    initial apicid  : 1
    fpu             : yes
    fpu_exception   : yes
    cpuid level     : 10
    wp              : yes
    flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm constant_tsc arch_perfmon pebs bts rep_good aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm lahf_lm ida dts tpr_shadow vnmi flexpriority
    bogomips        : 3591.39
    clflush size    : 64
    cache_alignment : 64
    address sizes   : 36 bits physical, 48 bits virtual
    power management:
    
    [root@server1 ~]#
    EDIT

    VPS sysbench:
    Code:
    [root@vps ~]# cat *
    sysbench 0.4.12:  multi-threaded system evaluation benchmark
    
    Running the test with following options:
    Number of threads: 1
    
    Doing CPU performance benchmark
    
    Threads started!
    Done.
    
    Maximum prime number checked in CPU test: 20000
    
    
    Test execution summary:
        total time:                          40.4731s
        total number of events:              10000
        total time taken by event execution: 40.4686
        per-request statistics:
             min:                                  3.09ms
             avg:                                  4.05ms
             max:                                  6.67ms
             approx.  95 percentile:               5.37ms
    
    Threads fairness:
        events (avg/stddev):           10000.0000/0.00
        execution time (avg/stddev):   40.4686/0.00
    
    sysbench 0.4.12:  multi-threaded system evaluation benchmark
    
    Running the test with following options:
    Number of threads: 1
    Initializing random number generator from timer.
    
    
    Extra file open flags: 0
    128 files, 3.125Mb each
    400Mb total file size
    Block size 16Kb
    Number of random requests for random IO: 0
    Read/Write ratio for combined random IO test: 1.50
    Periodic FSYNC enabled, calling fsync() each 100 requests.
    Calling fsync() at the end of test, Enabled.
    Using synchronous I/O mode
    Doing random r/w test
    Threads started!
    Time limit exceeded, exiting...
    Done.
    
    Operations performed:  56640 Read, 37760 Write, 120710 Other = 215110 Total
    Read 885Mb  Written 590Mb  Total transferred 1.4404Gb  (4.9149Mb/sec)
      314.55 Requests/sec executed
    
    Test execution summary:
        total time:                          300.1072s
        total number of events:              94400
        total time taken by event execution: 1.0341
        per-request statistics:
             min:                                  0.00ms
             avg:                                  0.01ms
             max:                                  7.08ms
             approx.  95 percentile:               0.02ms
    
    Threads fairness:
        events (avg/stddev):           94400.0000/0.00
        execution time (avg/stddev):   1.0341/0.00
    
    sysbench 0.4.12:  multi-threaded system evaluation benchmark
    
    Running the test with following options:
    Number of threads: 8
    
    Doing OLTP test.
    Running mixed OLTP test
    Doing read-only test
    Using Special distribution (12 iterations,  1 pct of values are returned in 75 pct cases)
    Using "BEGIN" for starting transactions
    Using auto_inc on the id column
    Threads started!
    Time limit exceeded, exiting...
    (last message repeated 7 times)
    Done.
    
    OLTP test statistics:
        queries performed:
            read:                            1449966
            write:                           0
            other:                           207138
            total:                           1657104
        transactions:                        103569 (1726.01 per sec.)
        deadlocks:                           0      (0.00 per sec.)
        read/write requests:                 1449966 (24164.08 per sec.)
        other operations:                    207138 (3452.01 per sec.)
    
    Test execution summary:
        total time:                          60.0050s
        total number of events:              103569
        total time taken by event execution: 479.1544
        per-request statistics:
             min:                                  1.98ms
             avg:                                  4.63ms
             max:                                330.73ms
             approx.  95 percentile:               8.26ms
    
    Threads fairness:
        events (avg/stddev):           12946.1250/381.09
        execution time (avg/stddev):   59.8943/0.00
    
    [root@vps ~]#
    Laptop sysbench:
    Code:
    [root@server1 ~]# cat *.txt
    sysbench 0.4.12:  multi-threaded system evaluation benchmark
    
    Running the test with following options:
    Number of threads: 1
    
    Doing CPU performance benchmark
    
    Threads started!
    Done.
    
    Maximum prime number checked in CPU test: 20000
    
    
    Test execution summary:
        total time:                          59.5999s
        total number of events:              10000
        total time taken by event execution: 59.5873
        per-request statistics:
             min:                                  5.94ms
             avg:                                  5.96ms
             max:                                 14.62ms
             approx.  95 percentile:               5.98ms
    
    Threads fairness:
        events (avg/stddev):           10000.0000/0.00
        execution time (avg/stddev):   59.5873/0.00
    
    sysbench 0.4.12:  multi-threaded system evaluation benchmark
    
    Running the test with following options:
    Number of threads: 1
    Initializing random number generator from timer.
    
    
    Extra file open flags: 0
    128 files, 3.125Mb each
    400Mb total file size
    Block size 16Kb
    Number of random requests for random IO: 0
    Read/Write ratio for combined random IO test: 1.50
    Periodic FSYNC enabled, calling fsync() each 100 requests.
    Calling fsync() at the end of test, Enabled.
    Using synchronous I/O mode
    Doing random r/w test
    Threads started!
    Time limit exceeded, exiting...
    Done.
    
    Operations performed:  46380 Read, 30920 Write, 98885 Other = 176185 Total
    Read 724.69Mb  Written 483.12Mb  Total transferred 1.1795Gb  (4.026Mb/sec)
      257.67 Requests/sec executed
    
    Test execution summary:
        total time:                          300.0006s
        total number of events:              77300
        total time taken by event execution: 2.0379
        per-request statistics:
             min:                                  0.01ms
             avg:                                  0.03ms
             max:                                  0.24ms
             approx.  95 percentile:               0.04ms
    
    Threads fairness:
        events (avg/stddev):           77300.0000/0.00
        execution time (avg/stddev):   2.0379/0.00
    
    sysbench 0.4.12:  multi-threaded system evaluation benchmark
    
    Running the test with following options:
    Number of threads: 8
    
    Doing OLTP test.
    Running mixed OLTP test
    Doing read-only test
    Using Special distribution (12 iterations,  1 pct of values are returned in 75 pct cases)
    Using "BEGIN" for starting transactions
    Using auto_inc on the id column
    Threads started!
    Time limit exceeded, exiting...
    (last message repeated 7 times)
    Done.
    
    OLTP test statistics:
        queries performed:
            read:                            634718
            write:                           0
            other:                           90674
            total:                           725392
        transactions:                        45337  (755.56 per sec.)
        deadlocks:                           0      (0.00 per sec.)
        read/write requests:                 634718 (10577.78 per sec.)
        other operations:                    90674  (1511.11 per sec.)
    
    Test execution summary:
        total time:                          60.0048s
        total number of events:              45337
        total time taken by event execution: 479.4912
        per-request statistics:
             min:                                  2.04ms
             avg:                                 10.58ms
             max:                                 85.56ms
             approx.  95 percentile:              19.70ms
    
    Threads fairness:
        events (avg/stddev):           5667.1250/42.18
        execution time (avg/stddev):   59.9364/0.00
    
    [root@server1 ~]#
    Last edited by NotionCommotion; June 25th, 2013 at 04:39 PM.
  2. #2
  3. No Profile Picture
    Contributing User
    Devshed Regular (2000 - 2499 posts)

    Join Date
    Sep 2006
    Posts
    2,013
    Rep Power
    534
    Anything look out of whack from SHOW VARIABLES?

    Code:
    auto_increment_increment    1
    auto_increment_offset   1
    autocommit  ON
    automatic_sp_privileges ON
    back_log    50
    basedir /usr/
    big_tables  OFF
    binlog_cache_size   32768
    binlog_direct_non_transactional_updates OFF
    binlog_format   STATEMENT
    bulk_insert_buffer_size 8388608
    character_set_client    utf8
    character_set_connection    utf8
    character_set_database  latin1
    character_set_filesystem    binary
    character_set_results   utf8
    character_set_server    latin1
    character_set_system    utf8
    character_sets_dir  /usr/share/mysql/charsets/
    collation_connection    utf8_general_ci
    collation_database  latin1_swedish_ci
    collation_server    latin1_swedish_ci
    completion_type 0
    concurrent_insert   1
    connect_timeout 10
    datadir /var/lib/mysql/
    date_format %Y-%m-%d
    datetime_format %Y-%m-%d %H:%i:%s
    default_week_format 0
    delay_key_write ON
    delayed_insert_limit    100
    delayed_insert_timeout  300
    delayed_queue_size  1000
    div_precision_increment 4
    engine_condition_pushdown   ON
    error_count 0
    event_scheduler OFF
    expire_logs_days    0
    flush   OFF
    flush_time  0
    foreign_key_checks  ON
    ft_boolean_syntax   + -><()~*:""&|
    ft_max_word_len 84
    ft_min_word_len 4
    ft_query_expansion_limit    20
    ft_stopword_file    (built-in)
    general_log OFF
    general_log_file    /var/run/mysqld/mysqld.log
    group_concat_max_len    1024
    have_community_features YES
    have_compress   YES
    have_crypt  YES
    have_csv    YES
    have_dynamic_loading    YES
    have_geometry   YES
    have_innodb YES
    have_ndbcluster NO
    have_openssl    DISABLED
    have_partitioning   YES
    have_query_cache    YES
    have_rtree_keys YES
    have_ssl    DISABLED
    have_symlink    DISABLED
    hostname    server1.site2.com
    identity    0
    ignore_builtin_innodb   OFF
    init_connect    
    init_file   
    init_slave  
    innodb_adaptive_hash_index  ON
    innodb_additional_mem_pool_size 1048576
    innodb_autoextend_increment 8
    innodb_autoinc_lock_mode    1
    innodb_buffer_pool_size 8388608
    innodb_checksums    ON
    innodb_commit_concurrency   0
    innodb_concurrency_tickets  500
    innodb_data_file_path   ibdata1:10M:autoextend
    innodb_data_home_dir    
    innodb_doublewrite  ON
    innodb_fast_shutdown    1
    innodb_file_io_threads  4
    innodb_file_per_table   OFF
    innodb_flush_log_at_trx_commit  1
    innodb_flush_method 
    innodb_force_recovery   0
    innodb_lock_wait_timeout    50
    innodb_locks_unsafe_for_binlog  OFF
    innodb_log_buffer_size  1048576
    innodb_log_file_size    5242880
    innodb_log_files_in_group   2
    innodb_log_group_home_dir   ./
    innodb_max_dirty_pages_pct  90
    innodb_max_purge_lag    0
    innodb_mirrored_log_groups  1
    innodb_open_files   300
    innodb_rollback_on_timeout  OFF
    innodb_stats_method nulls_equal
    innodb_stats_on_metadata    ON
    innodb_support_xa   ON
    innodb_sync_spin_loops  20
    innodb_table_locks  ON
    innodb_thread_concurrency   8
    innodb_thread_sleep_delay   10000
    innodb_use_legacy_cardinality_algorithm ON
    insert_id   0
    interactive_timeout 28800
    join_buffer_size    131072
    keep_files_on_create    OFF
    key_buffer_size 8384512
    key_cache_age_threshold 300
    key_cache_block_size    1024
    key_cache_division_limit    100
    language    /usr/share/mysql/english/
    large_files_support ON
    large_page_size 0
    large_pages OFF
    last_insert_id  0
    lc_time_names   en_US
    license GPL
    local_infile    ON
    locked_in_memory    OFF
    log OFF
    log_bin OFF
    log_bin_trust_function_creators OFF
    log_bin_trust_routine_creators  OFF
    log_error   /var/log/mysqld.log
    log_output  FILE
    log_queries_not_using_indexes   OFF
    log_slave_updates   OFF
    log_slow_queries    OFF
    log_warnings    1
    long_query_time 10.000000
    low_priority_updates    OFF
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  4. #3
  5. No Profile Picture
    Contributing User
    Devshed Regular (2000 - 2499 posts)

    Join Date
    Sep 2006
    Posts
    2,013
    Rep Power
    534
    Hi again,

    Any suggestions? Makes no sense that it used to run great, then I upgrade CentOS and it runs 50x slower. I've been spending days on this, and would really appreciate advice from someone smarter than me.

    I know I probably should just get a new computer. Problem is I have a RS-232 serial fax modem, and trying to find something which will work with it has been challenging.

    Thanks

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