One of my MySQL databases is currently using over 99% CPU when running PHP/Drupal queries.
I am investigating what the root cause is.
Using the following profiling and configuration data, can you suggest a main database setup problems or missing/incorrect configuration?
Output of free in Bash:
total used free shared buffers cached
Mem: 2048 1635 412 0 0 0
-/+ buffers/cache: 1635 412
Swap: 0 0 0
Output of ps auxf:
root 7430 0.0 0.0 9176 1400 ? S May30 0:00
/bin/sh /usr/local/mysql/bin/mysqld_safe --user=mysql --datadir=/usr/local/mysql/data --pid-file=/usr/local/mysql/data/db.pid
mysql 7617 0.6 12.3 486900 258956 ? Sl May30 114:26 \_ /usr/local/mysql/bin/mysqld --basedir=/usr/local/mysql --datadir=/usr/local/mysql/data --plugin-dir=/usr/local/mysql/lib/plugin --user=mysql --log-error=/usr/local/mysql/data/db.err --pid-file=/usr/local/mysql/data/db.pid --socket=/tmp/mysql.sock
Here is the my.cnf file:
[mysqld]
socket=/tmp/mysql.sock
local-infile=0
tmpdir=/dev/shm
max_allowed_packet=100M
Here is the output of sql show status:
SQL result
Host: localhost
Database: db
Generation Time: Jun 11, 2012 at 09:22 AM
Generated by: phpMyAdmin 3.4.7.1 / MySQL 5.5.24
SQL query: SHOW STATUS;
Rows: 310
Variable_name Value
Aborted_clients 242
Aborted_connects 50
Binlog_cache_disk_use 0
Binlog_cache_use 0
Binlog_stmt_cache_disk_use 0
Binlog_stmt_cache_use 0
Bytes_received 221
Bytes_sent 1421
Com_admin_commands 0
Com_assign_to_keycache 0
Com_alter_db 0
Com_alter_db_upgrade 0
Com_alter_event 0
Com_alter_function 0
Com_alter_procedure 0
Com_alter_server 0
Com_alter_table 0
Com_alter_tablespace 0
Com_analyze 0
Com_begin 0
Com_binlog 0
Com_call_procedure 0
Com_change_db 1
Com_change_master 0
Com_check 0
Com_checksum 0
Com_commit 0
Com_create_db 0
Com_create_event 0
Com_create_function 0
Com_create_index 0
Com_create_procedure 0
Com_create_server 0
Com_create_table 0
Com_create_trigger 0
Com_create_udf 0
Com_create_user 0
Com_create_view 0
Com_dealloc_sql 0
Com_delete 0
Com_delete_multi 0
Com_do 0
Com_drop_db 0
Com_drop_event 0
Com_drop_function 0
Com_drop_index 0
Com_drop_procedure 0
Com_drop_server 0
Com_drop_table 0
Com_drop_trigger 0
Com_drop_user 0
Com_drop_view 0
Com_empty_query 0
Com_execute_sql 0
Com_flush 0
Com_grant 0
Com_ha_close 0
Com_ha_open 0
Com_ha_read 0
Com_help 0
Com_insert 0
Com_insert_select 0
Com_install_plugin 0
Com_kill 0
Com_load 0
Com_lock_tables 0
Com_optimize 0
Com_preload_keys 0
Com_prepare_sql 0
Com_purge 0
Com_purge_before_date 0
Com_release_savepoint 0
Com_rename_table 0
Com_rename_user 0
Com_repair 0
Com_replace 0
Com_replace_select 0
Com_reset 0
Com_resignal 0
Com_revoke 0
Com_revoke_all 0
Com_rollback 0
Com_rollback_to_savepoint 0
Com_savepoint 0
Com_select 0
Com_set_option 2
Com_signal 0
Com_show_authors 0
Com_show_binlog_events 0
Com_show_binlogs 0
Com_show_charsets 0
Com_show_collations 0
Com_show_contributors 0
Com_show_create_db 0
Com_show_create_event 0
Com_show_create_func 0
Com_show_create_proc 0
Com_show_create_table 0
Com_show_create_trigger 0
Com_show_databases 0
Variable_name Value
Com_show_engine_logs 0
Com_show_engine_mutex 0
Com_show_engine_status 0
Com_show_events 0
Com_show_errors 0
Com_show_fields 0
Com_show_function_status 0
Com_show_grants 0
Com_show_keys 0
Com_show_master_status 0
Com_show_open_tables 0
Com_show_plugins 1
Com_show_privileges 0
Com_show_procedure_status 0
Com_show_processlist 0
Com_show_profile 0
Com_show_profiles 0
Com_show_relaylog_events 0
Com_show_slave_hosts 0
Com_show_slave_status 0
Com_show_status 1
Com_show_storage_engines 0
Com_show_table_status 0
Com_show_tables 0
Com_show_triggers 0
Com_show_variables 0
Com_show_warnings 0
Com_slave_start 0
Com_slave_stop 0
Com_stmt_close 0
Com_stmt_execute 0
Com_stmt_fetch 0
Com_stmt_prepare 0
Com_stmt_reprepare 0
Com_stmt_reset 0
Com_stmt_send_long_data 0
Com_truncate 0
Com_uninstall_plugin 0
Com_unlock_tables 0
Com_update 0
Com_update_multi 0
Com_xa_commit 0
Com_xa_end 0
Com_xa_prepare 0
Com_xa_recover 0
Com_xa_rollback 0
Com_xa_start 0
Compression OFF
Connections 9376
Created_tmp_disk_tables 1
Created_tmp_files 6
Created_tmp_tables 1
Delayed_errors 0
Delayed_insert_threads 0
Delayed_writes 0
Flush_commands 1
Handler_commit 0
Handler_delete 0
Handler_discover 0
Handler_prepare 0
Handler_read_first 0
Handler_read_key 0
Handler_read_last 0
Handler_read_next 0
Handler_read_prev 0
Handler_read_rnd 0
Handler_read_rnd_next 21
Handler_rollback 0
Handler_savepoint 0
Handler_savepoint_rollback 0
Handler_update 0
Handler_write 20
Innodb_buffer_pool_pages_data 8142
Innodb_buffer_pool_pages_dirty 0
Innodb_buffer_pool_pages_flushed 1269726
Innodb_buffer_pool_pages_free 0
Innodb_buffer_pool_pages_misc 49
Innodb_buffer_pool_pages_total 8191
Innodb_buffer_pool_read_ahead_rnd 0
Innodb_buffer_pool_read_ahead 1306
Innodb_buffer_pool_read_ahead_evicted 8907
Innodb_buffer_pool_read_requests 139892912
Innodb_buffer_pool_reads 308579
Innodb_buffer_pool_wait_free 0
Innodb_buffer_pool_write_requests 5066182
Innodb_data_fsyncs 313257
Innodb_data_pending_fsyncs 0
Innodb_data_pending_reads 0
Innodb_data_pending_writes 0
Innodb_data_read 5084336128
Innodb_data_reads 308981
Innodb_data_writes 658963
Innodb_data_written 22884830208
Innodb_dblwr_pages_written 634863
Innodb_dblwr_writes 19355
Innodb_have_atomic_builtins ON
Innodb_log_waits 0
Innodb_log_write_requests 3971026
Innodb_log_writes 266658
Innodb_os_log_fsyncs 273603
Variable_name Value
Innodb_os_log_pending_fsyncs 0
Innodb_os_log_pending_writes 0
Innodb_os_log_written 2077984256
Innodb_page_size 16384
Innodb_pages_created 55793
Innodb_pages_read 310189
Innodb_pages_written 634863
Innodb_row_lock_current_waits 0
Innodb_row_lock_time 185765
Innodb_row_lock_time_avg 476
Innodb_row_lock_time_max 30082
Innodb_row_lock_waits 390
Innodb_rows_deleted 96261
Innodb_rows_inserted 243234
Innodb_rows_read 73669737
Innodb_rows_updated 367966
Innodb_truncated_status_writes 0
Key_blocks_not_flushed 0
Key_blocks_unused 6657
Key_blocks_used 851
Key_read_requests 33873766
Key_reads 3991
Key_write_requests 5515715
Key_writes 11500
Last_query_cost 2.399000
Max_used_connections 22
Not_flushed_delayed_rows 0
Open_files 41
Open_streams 0
Open_table_definitions 400
Open_tables 400
Opened_files 141222
Opened_table_definitions 0
Opened_tables 0
Performance_schema_cond_classes_lost 0
Performance_schema_cond_instances_lost 0
Performance_schema_file_classes_lost 0
Performance_schema_file_handles_lost 0
Performance_schema_file_instances_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_table_handles_lost 0
Performance_schema_table_instances_lost 0
Performance_schema_thread_classes_lost 0
Performance_schema_thread_instances_lost 0
Prepared_stmt_count 0
Qcache_free_blocks 0
Qcache_free_memory 0
Qcache_hits 0
Qcache_inserts 0
Qcache_lowmem_prunes 0
Qcache_not_cached 0
Qcache_queries_in_cache 0
Qcache_total_blocks 0
Queries 4346053
Questions 5
Rpl_status AUTH_MASTER
Select_full_join 0
Select_full_range_join 0
Select_range 0
Select_range_check 0
Select_scan 1
Slave_heartbeat_period 0.000
Slave_open_temp_tables 0
Slave_received_heartbeats 0
Slave_retried_transactions 0
Slave_running OFF
Slow_launch_threads 0
Slow_queries 0
Sort_merge_passes 0
Sort_range 0
Sort_rows 0
Sort_scan 0
Ssl_accept_renegotiates 0
Ssl_accepts 0
Ssl_callback_cache_hits 0
Ssl_cipher
Ssl_cipher_list
Ssl_client_connects 0
Ssl_connect_renegotiates 0
Ssl_ctx_verify_depth 0
Ssl_ctx_verify_mode 0
Ssl_default_timeout 0
Ssl_finished_accepts 0
Ssl_finished_connects 0
Ssl_session_cache_hits 0
Ssl_session_cache_misses 0
Ssl_session_cache_mode NONE
Ssl_session_cache_overflows 0
Ssl_session_cache_size 0
Ssl_session_cache_timeouts 0
Ssl_sessions_reused 0
Ssl_used_session_cache_entries 0
Ssl_verify_depth 0
Ssl_verify_mode 0
Ssl_version
Table_locks_immediate 5113600
Variable_name Value
Table_locks_waited 17
Tc_log_max_pages_used 0
Tc_log_page_size 0
Tc_log_page_waits 0
Threads_cached 0
Threads_connected 1
Threads_created 9375
Threads_running 1
Uptime 1074227
Uptime_since_flush_status 1074227
I’d also examine carefully which queries are performed and on what tables. I don’t know if Drupal has some kind of debugging/profiling mode for queries, but it’s worth a try to investigate this.
From these, also trying to examine them with EXPLAIN (for example, some tables may need indexes).
I understand your site is in Drupal, which should be already optimized at least on its core tables.