-1

I am hoping for a bit of help or direction on how best to troubleshoot this issue. We have recently increased our application load (more processes interacting with the DB) and the DB CPU is constantly between 30-90% sometimes going to 100%. This even happens during non busy times.

Here is some data taken from right now during a low traffic time where the CPU is sitting around 30% which seems high.

Any help would be much appreciated!

This is on an Amazon RDS db.t2.medium which has 4GB ram.

CPU 5 mins: CPU 5 minutes

Performance Insights: enter image description here

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SHOW VARIABLES:

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Key_writes  119
Last_query_cost 0.000000
Last_query_partial_plans    0
Max_used_connections    47
Not_flushed_delayed_rows    0
Open_files  152
Open_streams    0
Open_table_definitions  263
Open_tables 1793
Opened_files    1362637
Opened_table_definitions    2584
Opened_tables   7341
Performance_schema_accounts_lost    0
Performance_schema_cond_classes_lost    0
Performance_schema_cond_instances_lost  0
Performance_schema_digest_lost  0
Performance_schema_file_classes_lost    0
Performance_schema_file_handles_lost    0
Performance_schema_file_instances_lost  0
Performance_schema_hosts_lost   0
Performance_schema_locker_lost  0
Performance_schema_mutex_classes_lost   0
Performance_schema_mutex_instances_lost 0
Performance_schema_rwlock_classes_lost  0
Performance_schema_rwlock_instances_lost    0
Performance_schema_session_connect_attrs_lost   0
Performance_schema_socket_classes_lost  0
Performance_schema_socket_instances_lost    0
Performance_schema_stage_classes_lost   0
Performance_schema_statement_classes_lost   0
Performance_schema_table_handles_lost   0
Performance_schema_table_instances_lost 0
Performance_schema_thread_classes_lost  0
Performance_schema_thread_instances_lost    0
Performance_schema_users_lost   0
Prepared_stmt_count 5
Qcache_free_blocks  1
Qcache_free_memory  1031360
Qcache_hits 0
Qcache_inserts  0
Qcache_lowmem_prunes    0
Qcache_not_cached   499229802
Qcache_queries_in_cache 0
Qcache_total_blocks 1
Queries 1690793956
Questions   594029638
Rsa_public_key  
Select_full_join    4242
Select_full_range_join  44
Select_range    3438367
Select_range_check  0
Select_scan 16832756
Slave_heartbeat_period  0.000
Slave_last_heartbeat    
Slave_open_temp_tables  0
Slave_received_heartbeats   0
Slave_retried_transactions  0
Slave_running   OFF
Slow_launch_threads 0
Slow_queries    837
Sort_merge_passes   2098
Sort_range  250992
Sort_rows   28892235
Sort_scan   2179832
Ssl_accept_renegotiates 0
Ssl_accepts 723
Ssl_callback_cache_hits 0
Ssl_cipher  
Ssl_cipher_list 
Ssl_client_connects 0
Ssl_connect_renegotiates    0
Ssl_ctx_verify_depth    18446744073709551615
Ssl_ctx_verify_mode 5
Ssl_default_timeout 0
Ssl_finished_accepts    717
Ssl_finished_connects   0
Ssl_server_not_after    
Ssl_server_not_before   
Ssl_session_cache_hits  5
Ssl_session_cache_misses    655
Ssl_session_cache_mode  SERVER
Ssl_session_cache_overflows 410
Ssl_session_cache_size  128
Ssl_session_cache_timeouts  4
Ssl_sessions_reused 0
Ssl_used_session_cache_entries  128
Ssl_verify_depth    0
Ssl_verify_mode 0
Ssl_version 
Table_locks_immediate   2216706048
Table_locks_waited  25050917
Table_open_cache_hits   2783618885
Table_open_cache_misses 7341
Table_open_cache_overflows  615
Tc_log_max_pages_used   0
Tc_log_page_size    0
Tc_log_page_waits   0
Threads_cached  9
Threads_connected   20
Threads_created 402
Threads_running 3
Uptime  8001175
Uptime_since_flush_status   8001175
3
  • 1
    Looks like a big backup or large batch job. Check your slow query log, it looks like some some where registered about the same time.
    – danblack
    Oct 11 at 10:31
  • And, how much RAM do you have? If you have at least 6GB, then OK; if you have 3GB or less, then the buffer_pool is too big.
    – Rick James
    Oct 11 at 17:54
  • This is on an Amazon RDS db.t2.medium which has 4GB ram.
    – ronnz
    Oct 11 at 23:12
0

This plugin helps with CPU and, in some systems, I/O: wordpress.org/plugins/index-wp-mysql-for-speed

Analysis of GLOBAL STATUS and VARIABLES:

Observations:

  • Version: 5.6.51-log
  • 4 GB of RAM??
  • Uptime = 92d 14:32:55
  • 211 Queries/sec : 74.2 Questions/sec

The More Important Issues:

Suggested changes:

general_log = OFF   -- to avoid rapidly filling up disk
max_connections = 60

To advise on innodb_buffer_pool_size (now 2G), I need to know the RAM size (I assumed 4G for this analysis)

I see a lot of prepare+execute (69/sec) but not many proc calls. -- What API are you using to connect to mysqld?

I see an unusually high number of these; what is going on? ALTER DATABASE, DROP/CREATE TRIGGER, FLUSH, PURGE, RENAME TABLE

Compression = ON -- How is that going for you?

Details and other observations:

( general_log ) = general_log = ON -- Log (FILE or TABLE) of all queries run. -- Turn off the general_log (now ON) when not in use. That log can fill up disk very rapidly.

( innodb_buffer_pool_size ) = 2,048 / 4096M = 50.0% -- % of RAM used for InnoDB buffer_pool -- Set to about 70% of available RAM. (To low is less efficient; too high risks swapping.)

( innodb_lru_scan_depth ) = 1,024 -- "InnoDB: page_cleaner: 1000ms intended loop took ..." may be fixed by lowering lru_scan_depth

( innodb_io_capacity ) = 200 -- When flushing, use this many IOPs. -- Reads could be slugghish or spiky.

( innodb_io_capacity_max / innodb_io_capacity ) = 2,000 / 200 = 10 -- Capacity: max/plain -- Recommend 2. Max should be about equal to the IOPs your I/O subsystem can handle. (If the drive type is unknown 2000/200 may be a reasonable pair.)

( Innodb_pages_written / Innodb_buffer_pool_write_requests ) = 74,268,160 / 471798585 = 15.7% -- Write requests that had to hit disk -- Check innodb_buffer_pool_size (now 2147483648)

( Innodb_os_log_written / (Uptime / 3600) / innodb_log_files_in_group / innodb_log_file_size ) = 56,568,371,200 / (8001175 / 3600) / 2 / 128M = 0.0948 -- Ratio -- (see minutes)

( Uptime / 60 * innodb_log_file_size / Innodb_os_log_written ) = 8,001,175 / 60 * 128M / 56568371200 = 316 -- Minutes between InnoDB log rotations Beginning with 5.6.8, this can be changed dynamically; be sure to also change my.cnf. -- (The recommendation of 60 minutes between rotations is somewhat arbitrary.) Adjust innodb_log_file_size (now 134217728). (Cannot change in AWS.)

( innodb_flush_neighbors ) = 1 -- A minor optimization when writing blocks to disk. -- Use 0 for SSD drives; 1 for HDD.

( innodb_io_capacity ) = 200 -- I/O ops per second capable on disk . 100 for slow drives; 200 for spinning drives; 1000-2000 for SSDs; multiply by RAID factor.

( innodb_strict_mode ) = innodb_strict_mode = OFF -- Catches some subtle errors earlier. -- OFF leaves some warnings as warnings; ON makes them errors.

( innodb_adaptive_hash_index ) = innodb_adaptive_hash_index = ON -- Usually should be ON. -- There are cases where OFF is better. See also innodb_adaptive_hash_index_parts (after 5.7.9) and innodb_adaptive_hash_index_partitions (MariaDB and Percona). ON has been implicated in rare crashes (bug 73890). 10.5.0 decided to default OFF.

( innodb_print_all_deadlocks ) = innodb_print_all_deadlocks = OFF -- Whether to log all Deadlocks. -- If you are plagued with Deadlocks, turn this on. Caution: If you have lots of deadlocks, this may write a lot to disk.

( character_set_server ) = character_set_server = latin1 -- Charset problems may be helped by setting character_set_server (now latin1) to utf8mb4. That is the future default.

( local_infile ) = local_infile = ON -- local_infile (now ON) = ON is a potential security issue

( Com__biggest ) = Com__biggest = Com_stmt_execute -- Which of the "Com_" metrics is biggest. -- Normally it is Com_select (now 499230264). If something else, then it may be a sloppy platform, or may be something else.

( binlog_error_action ) = binlog_error_action = IGNORE_ERROR -- What to do if the binlog cannot be written. -- IGNORE_ERROR is the default for backwards compatibility, but ABORT_SERVER is recommended.

( binlog_format ) = binlog_format = MIXED -- STATEMENT/ROW/MIXED. -- ROW is preferred by 5.7 (10.3)

( simplified_binlog_gtid_recovery ) = 0 -- Percona: Perform a faster crash recovery. -- Set to 1 to speed up binlog recovery with/without GTIDs after a crash.

( long_query_time ) = 10 -- Cutoff (Seconds) for defining a "slow" query. -- Suggest 2

( log_slow_slave_statements ) = log_slow_slave_statements = OFF -- (5.6.11, 5.7.1) By default, replicated statements won't show up in the slowlog; this causes them to show. -- It can be helpful in the slowlog to see writes that could be interfering with Replica reads.

( Max_used_connections / max_connections ) = 47 / 312 = 15.1% -- Peak % of connections -- Since several memory factors can expand based on max_connections (now 312), it is good not to have that setting too high.

You have the Query Cache half-off. You should set both query_cache_type = OFF and query_cache_size = 0 . There is (according to a rumor) a 'bug' in the QC code that leaves some code on unless you turn off both of those settings.

Abnormally small:

Innodb_buffer_pool_bytes_data = 236 /sec

Abnormally large:

Com_alter_db = 0.00045 /HR
Com_create_trigger = 0.0013 /HR
Com_drop_trigger = 0.0013 /HR
Com_flush = 13 /HR
Com_purge_before_date = 12 /HR
Com_rename_table = 0.049 /HR
Com_show_privileges = 0.0022 /HR
Com_stmt_close = 69 /sec
Com_stmt_execute = 69 /sec
Com_stmt_prepare = 69 /sec
Innodb_buffer_pool_reads * innodb_page_size / innodb_buffer_pool_size = 30712.3%
Prepared_stmt_count = 5

Abnormal strings:

Compression = ON
innodb_data_home_dir = /rdsdbdata/db/innodb
innodb_fast_shutdown = 1
log_output = TABLE
optimizer_trace = enabled=off,one_line=off
optimizer_trace_features = greedy_search=on, range_optimizer=on, dynamic_range=on, repeated_subselect=on
relay_log_recovery = ON
slave_rows_search_algorithms = TABLE_SCAN,INDEX_SCAN
time_zone = UTC
2
  • Where could you see these? "I see an unusually high number of these; what is going on? ALTER DATABASE, DROP/CREATE TRIGGER, FLUSH, PURGE, RENAME TABLE"
    – ronnz
    Oct 11 at 23:18
  • @ronnz - SHOW GLOBAL STATUS LIKE 'Com_%' -- shows counters (since restart) for lots of commands and variants of commands (eg, the various PURGEs). I divided by Uptime to get the metrics. But... Note: mysqld has been running for 92 days. Possibly some of that was long ago.
    – Rick James
    Oct 11 at 23:49

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