I have a machine with a large MySQL 5.6 database (multiple tables with 10-100 million rows). It has a considerable amount of load, especially during the evening and is running on a 16 core machine.

No matter what the load is though, we always get these intermittent spikes that can cause problems. Our CPU load looks like this:

(these are very load-light times, especially the time before 6am, should be basically "idle")

The only solution to the problem I have found so far is setting up a new server, mirroring the data and switching to that one. This usually buys me about 2-3 months, then the spikes start appearing again. Just restarting MySQL or rebooting the server does not change anything.

These are also not caused by cronjobs. Even if I disable all of them, this still happens.

Here is a gist of the InnoDB status right now:

https://gist.github.com/fleshgolem/de1d4a661fb545fabfda

And here is a dump of the server variables:

Variable_name   Value
auto_increment_increment    1
auto_increment_offset   1
autocommit  ON
automatic_sp_privileges ON
back_log    200
basedir /usr
big_tables  OFF
bind_address    *
binlog_cache_size   32768
binlog_checksum CRC32
binlog_direct_non_transactional_updates OFF
binlog_format   ROW
binlog_max_flush_queue_time 0
binlog_order_commits    ON
binlog_row_image    FULL
binlog_rows_query_log_events    OFF
binlog_stmt_cache_size  32768
block_encryption_mode   aes-128-ecb
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 NO_CHAIN
concurrent_insert   AUTO
connect_timeout 10
core_file   OFF
datadir /var/lib/mysql/
date_format %Y-%m-%d
datetime_format %Y-%m-%d %H:%i:%s
default_storage_engine  InnoDB
default_tmp_storage_engine  InnoDB
default_week_format 0
delay_key_write ON
delayed_insert_limit    100
delayed_insert_timeout  300
delayed_queue_size  1000
disconnect_on_expired_password  ON
div_precision_increment 4
end_markers_in_json OFF
enforce_gtid_consistency    ON
eq_range_index_dive_limit   10
error_count 0
event_scheduler OFF
expire_logs_days    0
explicit_defaults_for_timestamp OFF
external_user   
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/lib/mysql/xxxx.log
group_concat_max_len    1024
gtid_executed   
gtid_mode   ON
gtid_next   AUTOMATIC
gtid_owned  
gtid_purged 
have_compress   YES
have_crypt  YES
have_dynamic_loading    YES
have_geometry   YES
have_openssl    DISABLED
have_profiling  YES
have_query_cache    YES
have_rtree_keys YES
have_ssl    DISABLED
have_symlink    DISABLED
host_cache_size 640
hostname    xxxx
identity    0
ignore_builtin_innodb   OFF
ignore_db_dirs  
init_connect    
init_file   
init_slave  
innodb_adaptive_flushing    ON
innodb_adaptive_flushing_lwm    10
innodb_adaptive_hash_index  ON
innodb_adaptive_max_sleep_delay 150000
innodb_additional_mem_pool_size 8388608
innodb_api_bk_commit_interval   5
innodb_api_disable_rowlock  OFF
innodb_api_enable_binlog    OFF
innodb_api_enable_mdl   OFF
innodb_api_trx_level    0
innodb_autoextend_increment 64
innodb_autoinc_lock_mode    1
innodb_buffer_pool_dump_at_shutdown OFF
innodb_buffer_pool_dump_now OFF
innodb_buffer_pool_filename ib_buffer_pool
innodb_buffer_pool_instances    8
innodb_buffer_pool_load_abort   OFF
innodb_buffer_pool_load_at_startup  OFF
innodb_buffer_pool_load_now OFF
innodb_buffer_pool_size 42949672960
innodb_change_buffer_max_size   25
innodb_change_buffering all
innodb_checksum_algorithm   innodb
innodb_checksums    ON
innodb_cmp_per_index_enabled    OFF
innodb_commit_concurrency   0
innodb_compression_failure_threshold_pct    5
innodb_compression_level    6
innodb_compression_pad_pct_max  50
innodb_concurrency_tickets  5000
innodb_data_file_path   ibdata1:12M:autoextend
innodb_data_home_dir    
innodb_disable_sort_file_cache  OFF
innodb_doublewrite  OFF
innodb_fast_shutdown    1
innodb_file_format  Antelope
innodb_file_format_check    ON
innodb_file_format_max  Antelope
innodb_file_per_table   ON
innodb_flush_log_at_timeout 1
innodb_flush_log_at_trx_commit  2
innodb_flush_method O_DIRECT
innodb_flush_neighbors  0
innodb_flushing_avg_loops   30
innodb_force_load_corrupted OFF
innodb_force_recovery   0
innodb_ft_aux_table 
innodb_ft_cache_size    8000000
innodb_ft_enable_diag_print OFF
innodb_ft_enable_stopword   ON
innodb_ft_max_token_size    84
innodb_ft_min_token_size    3
innodb_ft_num_word_optimize 2000
innodb_ft_result_cache_limit    2000000000
innodb_ft_server_stopword_table 
innodb_ft_sort_pll_degree   2
innodb_ft_total_cache_size  640000000
innodb_ft_user_stopword_table   
innodb_io_capacity  200
innodb_io_capacity_max  2000
innodb_large_prefix OFF
innodb_lock_wait_timeout    50
innodb_locks_unsafe_for_binlog  OFF
innodb_log_buffer_size  8388608
innodb_log_compressed_pages ON
innodb_log_file_size    104857600
innodb_log_files_in_group   2
innodb_log_group_home_dir   ./
innodb_lru_scan_depth   1024
innodb_max_dirty_pages_pct  75
innodb_max_dirty_pages_pct_lwm  0
innodb_max_purge_lag    0
innodb_max_purge_lag_delay  0
innodb_mirrored_log_groups  1
innodb_monitor_disable  
innodb_monitor_enable   
innodb_monitor_reset    
innodb_monitor_reset_all    
innodb_old_blocks_pct   37
innodb_old_blocks_time  1000
innodb_online_alter_log_max_size    134217728
innodb_open_files   2000
innodb_optimize_fulltext_only   OFF
innodb_page_size    16384
innodb_print_all_deadlocks  OFF
innodb_purge_batch_size 300
innodb_purge_threads    1
innodb_random_read_ahead    OFF
innodb_read_ahead_threshold 56
innodb_read_io_threads  16
innodb_read_only    OFF
innodb_replication_delay    0
innodb_rollback_on_timeout  OFF
innodb_rollback_segments    128
innodb_sort_buffer_size 1048576
innodb_spin_wait_delay  6
innodb_stats_auto_recalc    ON
innodb_stats_method nulls_equal
innodb_stats_on_metadata    OFF
innodb_stats_persistent ON
innodb_stats_persistent_sample_pages    20
innodb_stats_sample_pages   8
innodb_stats_transient_sample_pages 8
innodb_status_output    OFF
innodb_status_output_locks  OFF
innodb_strict_mode  OFF
innodb_support_xa   ON
innodb_sync_array_size  1
innodb_sync_spin_loops  30
innodb_table_locks  ON
innodb_thread_concurrency   0
innodb_thread_sleep_delay   10000
innodb_undo_directory   .
innodb_undo_logs    128
innodb_undo_tablespaces 0
innodb_use_native_aio   ON
innodb_use_sys_malloc   ON
innodb_version  5.6.19
innodb_write_io_threads 16
insert_id   0
interactive_timeout 28800
join_buffer_size    262144
keep_files_on_create    OFF
key_buffer_size 8388608
key_cache_age_threshold 300
key_cache_block_size    1024
key_cache_division_limit    100
large_files_support ON
large_page_size 0
large_pages OFF
last_insert_id  0
lc_messages en_US
lc_messages_dir /usr/share/mysql/
lc_time_names   en_US
license GPL
local_infile    ON
lock_wait_timeout   31536000
locked_in_memory    OFF
log_bin ON
log_bin_basename    /var/lib/mysql/xxxx-db1-bin
log_bin_index   /var/lib/mysql/xxxx-db1-bin.index
log_bin_trust_function_creators OFF
log_bin_use_v1_row_events   OFF
log_error   /var/log/mysqld.log
log_output  FILE
log_queries_not_using_indexes   OFF
log_slave_updates   ON
log_slow_admin_statements   OFF
log_slow_slave_statements   OFF
log_throttle_queries_not_using_indexes  0
log_warnings    1
long_query_time 10.000000
low_priority_updates    OFF
lower_case_file_system  OFF
lower_case_table_names  0
master_info_repository  TABLE
master_verify_checksum  OFF
max_allowed_packet  4194304
max_binlog_cache_size   18446744073709547520
max_binlog_size 1073741824
max_binlog_stmt_cache_size  18446744073709547520
max_connect_errors  100
max_connections 750
max_delayed_threads 20
max_error_count 64
max_heap_table_size 16777216
max_insert_delayed_threads  20
max_join_size   18446744073709551615
max_length_for_sort_data    1024
max_prepared_stmt_count 16382
max_relay_log_size  0
max_seeks_for_key   18446744073709551615
max_sort_length 1024a
max_sp_recursion_depth  0
max_tmp_tables  32
max_user_connections    0
max_write_lock_count    18446744073709551615
metadata_locks_cache_size   1024
metadata_locks_hash_instances   8
min_examined_row_limit  0
multi_range_count   256
myisam_data_pointer_size    6
myisam_max_sort_file_size   9223372036853727232
myisam_mmap_size    18446744073709551615
myisam_recover_options  OFF
myisam_repair_threads   1
myisam_sort_buffer_size 8388608
myisam_stats_method nulls_unequal
myisam_use_mmap OFF
net_buffer_length   16384
net_read_timeout    30
net_retry_count 10
net_write_timeout   60
new OFF
old OFF
old_alter_table OFF
old_passwords   0
open_files_limit    5000
optimizer_prune_level   1
optimizer_search_depth  62
optimizer_switch    index_merge=on,index_merge_union=on,index_merge_sort_union=on,index_merge_intersection=on,engine_condition_pushdown=on,index_condition_pushdown=on,mrr=on,mrr_cost_based=on,block_nested_loop=on,batched_key_access=off,materialization=on,semijoin=on,loosescan=on,firstmatch=on,subquery_materialization_cost_based=on,use_index_extensions=on
optimizer_trace enabled=off,one_line=off
optimizer_trace_features    greedy_search=on,range_optimizer=on,dynamic_range=on,repeated_subselect=on
optimizer_trace_limit   1
optimizer_trace_max_mem_size    16384
optimizer_trace_offset  -1
performance_schema  ON
performance_schema_accounts_size    100
performance_schema_digests_size 10000
performance_schema_events_stages_history_long_size  10000
performance_schema_events_stages_history_size   10
performance_schema_events_statements_history_long_size  10000
performance_schema_events_statements_history_size   10
performance_schema_events_waits_history_long_size   10000
performance_schema_events_waits_history_size    10
performance_schema_hosts_size   100
performance_schema_max_cond_classes 80
performance_schema_max_cond_instances   5900
performance_schema_max_file_classes 50
performance_schema_max_file_handles 32768
performance_schema_max_file_instances   7693
performance_schema_max_mutex_classes    200
performance_schema_max_mutex_instances  19500
performance_schema_max_rwlock_classes   40
performance_schema_max_rwlock_instances 10300
performance_schema_max_socket_classes   10
performance_schema_max_socket_instances 1520
performance_schema_max_stage_classes    150
performance_schema_max_statement_classes    168
performance_schema_max_table_handles    4000
performance_schema_max_table_instances  12500
performance_schema_max_thread_classes   50
performance_schema_max_thread_instances 1600
performance_schema_session_connect_attrs_size   512
performance_schema_setup_actors_size    100
performance_schema_setup_objects_size   100
performance_schema_users_size   100
pid_file    /var/run/mysqld/mysqld.pid
plugin_dir  /usr/lib64/mysql/plugin/
port    3306
preload_buffer_size 32768
profiling   OFF
profiling_history_size  15
protocol_version    10
proxy_user  
pseudo_slave_mode   OFF
pseudo_thread_id    2018
query_alloc_block_size  8192
query_cache_limit   1048576
query_cache_min_res_unit    4096
query_cache_size    1048576000
query_cache_type    ON
query_cache_wlock_invalidate    OFF
query_prealloc_size 8192
rand_seed1  0
rand_seed2  0
range_alloc_block_size  4096
read_buffer_size    131072
read_only   OFF
read_rnd_buffer_size    262144
relay_log   
relay_log_basename  
relay_log_index 
relay_log_info_file relay-log.info
relay_log_info_repository   TABLE
relay_log_purge ON
relay_log_recovery  OFF
relay_log_space_limit   0
report_host 10.129.156.251
report_password 
report_port 3306
report_user 
rpl_stop_slave_timeout  31536000
secure_auth ON
secure_file_priv    
server_id   1
server_id_bits  32
server_uuid 96bcdb70-44c5-11e5-8df9-0401654ee301
skip_external_locking   ON
skip_name_resolve   OFF
skip_networking OFF
skip_show_database  OFF
slave_allow_batching    OFF
slave_checkpoint_group  512
slave_checkpoint_period 300
slave_compressed_protocol   OFF
slave_exec_mode STRICT
slave_load_tmpdir   /tmp
slave_max_allowed_packet    1073741824
slave_net_timeout   3600
slave_parallel_workers  0
slave_pending_jobs_size_max 16777216
slave_rows_search_algorithms    TABLE_SCAN,INDEX_SCAN
slave_skip_errors   ALL
slave_sql_verify_checksum   ON
slave_transaction_retries   10
slave_type_conversions  
slow_launch_time    2
slow_query_log  OFF
slow_query_log_file /var/lib/mysql/xxxx-slow.log
socket  /var/lib/mysql/mysql.sock
sort_buffer_size    262144
sql_auto_is_null    OFF
sql_big_selects ON
sql_buffer_result   OFF
sql_log_bin ON
sql_log_off OFF
sql_mode    STRICT_TRANS_TABLES,NO_ENGINE_SUBSTITUTION
sql_notes   ON
sql_quote_show_create   ON
sql_safe_updates    OFF
sql_select_limit    18446744073709551615
sql_slave_skip_counter  0
sql_warnings    OFF
ssl_ca  
ssl_capath  
ssl_cert    
ssl_cipher  
ssl_crl 
ssl_crlpath 
ssl_key 
storage_engine  InnoDB
stored_program_cache    256
sync_binlog 0
sync_frm    ON
sync_master_info    1
sync_relay_log  10000
sync_relay_log_info 10000
system_time_zone    EST
table_definition_cache  1400
table_open_cache    2000
table_open_cache_instances  1
thread_cache_size   15
thread_concurrency  10
thread_handling one-thread-per-connection
thread_stack    262144
time_format %H:%i:%s
time_zone   SYSTEM
timed_mutexes   OFF
timestamp   1457343545.452900
tmp_table_size  16777216
tmpdir  /tmp
transaction_alloc_block_size    8192
transaction_allow_batching  OFF
transaction_prealloc_size   4096
tx_isolation    REPEATABLE-READ
tx_read_only    OFF
unique_checks   ON
updatable_views_with_limit  YES
version 5.6.19-log
version_comment MySQL Community Server (GPL)
version_compile_machine x86_64
version_compile_os  Linux
wait_timeout    28800
warning_count   0

If there is any more relevant info you need, please let me know and I will update the question accordingly. I unfortunately have no clue anymore what I am looking for.