Mysql keep high cpu usage and I cannot tune it down

Question

I have an asp.net application which use Mysql as database server. In my application have some threading which will query mysql database. It always caused the Mysql database server CPU usage up to 99%. Then I try to edit the server parameters of Azure MySQL. I tuned as follows:

   innondb_buffer_pool_size : from 16106127360 bytes to 134217728 bytes.
   innodb_thread_concurrency: from 0 to 33
   wait_timeout: from 120 to 30
   interactive_timeout: from 28800 to 30

But it is not useful. When I run the application. The CPU usage of Azure MySQL still use 99%. The above tunning seems not useful. What tuning should I do to lower the CPU usage of Azure MySQL?

Here is the server variables

auto_increment_increment, 1
auto_increment_offset, 1
autocommit, ON
automatic_sp_privileges, ON
avoid_temporal_upgrade, OFF
back_log, 80
basedir, C:\Program Files\MySQL\MySQL Server 5.7\
big_tables, OFF
bind_address, *
binlog_cache_size, 32768
binlog_checksum, CRC32
binlog_direct_non_transactional_updates, OFF
binlog_error_action, ABORT_SERVER
binlog_format, ROW
binlog_group_commit_sync_delay, 0
binlog_group_commit_sync_no_delay_count, 0
binlog_gtid_simple_recovery, ON
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
binlog_transaction_dependency_history_size, 25000
binlog_transaction_dependency_tracking, COMMIT_ORDER
block_encryption_mode, aes-128-ecb
bulk_insert_buffer_size, 8388608
character_set_client, utf8
character_set_connection, utf8
character_set_database, utf8
character_set_filesystem, binary
character_set_results, utf8
character_set_server, utf8
character_set_system, utf8
character_sets_dir, C:\Program Files\MySQL\MySQL Server 5.7\share\charsets\
check_proxy_users, OFF
collation_connection, utf8_general_ci
collation_database, utf8_general_ci
collation_server, utf8_general_ci
completion_type, NO_CHAIN
concurrent_insert, AUTO
connect_timeout, 10
core_file, OFF
datadir, C:\ProgramData\MySQL\MySQL Server 5.7\Data\
date_format, %Y-%m-%d
datetime_format, %Y-%m-%d %H:%i:%s
default_authentication_plugin, mysql_native_password
default_password_lifetime, 0
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
disabled_storage_engines, 
disconnect_on_expired_password, ON
div_precision_increment, 4
end_markers_in_json, OFF
enforce_gtid_consistency, OFF
eq_range_index_dive_limit, 200
event_scheduler, OFF
expire_logs_days, 0
explicit_defaults_for_timestamp, OFF
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, ON
general_log_file, c:\MySQL_LOG\WIN-9BPM7TSIO9C.log
group_concat_max_len, 1024
gtid_executed, 
gtid_executed_compression_period, 1000
gtid_mode, OFF
gtid_owned, 
gtid_purged, 
have_compress, YES
have_crypt, NO
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_statement_timeout, YES
have_symlink, YES
host_cache_size, 329
hostname, WIN-9BPM7TSIO9C
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_hash_index_parts, 8
innodb_adaptive_max_sleep_delay, 150000
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_chunk_size, 134217728
innodb_buffer_pool_dump_at_shutdown, ON
innodb_buffer_pool_dump_now, OFF
innodb_buffer_pool_dump_pct, 25
innodb_buffer_pool_filename, ib_buffer_pool
innodb_buffer_pool_instances, 1
innodb_buffer_pool_load_abort, OFF
innodb_buffer_pool_load_at_startup, ON
innodb_buffer_pool_load_now, OFF
innodb_buffer_pool_size, 268435456
innodb_change_buffer_max_size, 25
innodb_change_buffering, all
innodb_checksum_algorithm, crc32
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_deadlock_detect, ON
innodb_default_row_format, dynamic
innodb_disable_sort_file_cache, OFF
innodb_doublewrite, ON
innodb_fast_shutdown, 1
innodb_file_format, Antelope
innodb_file_format_check, ON
innodb_file_format_max, Barracuda
innodb_file_per_table, ON
innodb_fill_factor, 100
innodb_flush_log_at_timeout, 1
innodb_flush_log_at_trx_commit, 1
innodb_flush_method, 
innodb_flush_neighbors, 1
innodb_flush_sync, ON
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, ON
innodb_lock_wait_timeout, 50
innodb_locks_unsafe_for_binlog, OFF
innodb_log_buffer_size, 8388608
innodb_log_checksums, ON
innodb_log_compressed_pages, ON
innodb_log_file_size, 50331648
innodb_log_files_in_group, 2
innodb_log_group_home_dir, .\
innodb_log_write_ahead_size, 8192
innodb_lru_scan_depth, 1024
innodb_max_dirty_pages_pct, 75.000000
innodb_max_dirty_pages_pct_lwm, 0.000000
innodb_max_purge_lag, 0
innodb_max_purge_lag_delay, 0
innodb_max_undo_log_size, 1073741824
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, 300
innodb_optimize_fulltext_only, OFF
innodb_page_cleaners, 1
innodb_page_size, 16384
innodb_print_all_deadlocks, OFF
innodb_purge_batch_size, 300
innodb_purge_rseg_truncate_frequency, 128
innodb_purge_threads, 4
innodb_random_read_ahead, OFF
innodb_read_ahead_threshold, 56
innodb_read_io_threads, 8
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_include_delete_marked, OFF
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, ON
innodb_support_xa, ON
innodb_sync_array_size, 1
innodb_sync_spin_loops, 30
innodb_table_locks, ON
innodb_temp_data_file_path, ibtmp1:12M:autoextend
innodb_thread_concurrency, 0
innodb_thread_sleep_delay, 10000
innodb_tmpdir, 
innodb_undo_directory, .\
innodb_undo_log_truncate, OFF
innodb_undo_logs, 128
innodb_undo_tablespaces, 0
innodb_use_native_aio, ON
innodb_version, 5.7.22
innodb_write_io_threads, 8
interactive_timeout, 28800
internal_tmp_disk_storage_engine, InnoDB
join_buffer_size, 262144
keep_files_on_create, OFF
key_buffer_size, 10485760
key_cache_age_threshold, 300
key_cache_block_size, 1024
key_cache_division_limit, 100
keyring_operations, ON
large_files_support, ON
large_page_size, 0
large_pages, OFF
lc_messages, en_US
lc_messages_dir, C:\Program Files\MySQL\MySQL Server 5.7\share\
lc_time_names, en_US
license, GPL
local_infile, ON
lock_wait_timeout, 31536000
log_bin, OFF
log_bin_basename, 
log_bin_index, 
log_bin_trust_function_creators, OFF
log_bin_use_v1_row_events, OFF
log_builtin_as_identified_by_password, OFF
log_error, .\WIN-9BPM7TSIO9C.err
log_error_verbosity, 3
log_output, FILE
log_queries_not_using_indexes, OFF
log_slave_updates, OFF
log_slow_admin_statements, OFF
log_slow_slave_statements, OFF
log_statements_unsafe_for_binlog, ON
log_syslog, ON
log_syslog_tag, 
log_throttle_queries_not_using_indexes, 0
log_timestamps, UTC
log_warnings, 2
long_query_time, 1.000000
low_priority_updates, OFF
lower_case_file_system, ON
lower_case_table_names, 1
master_info_repository, FILE
master_verify_checksum, OFF
max_allowed_packet, 10485760
max_binlog_cache_size, 18446744073709547520
max_binlog_size, 1073741824
max_binlog_stmt_cache_size, 18446744073709547520
max_connect_errors, 100
max_connections, 201
max_delayed_threads, 20
max_digest_length, 1024
max_error_count, 64
max_execution_time, 0
max_heap_table_size, 16777216
max_insert_delayed_threads, 20
max_join_size, 18446744073709551615
max_length_for_sort_data, 1024
max_points_in_geometry, 65536
max_prepared_stmt_count, 16382
max_relay_log_size, 0
max_seeks_for_key, 4294967295
max_sort_length, 1024
max_sp_recursion_depth, 0
max_tmp_tables, 32
max_user_connections, 0
max_write_lock_count, 4294967295
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, 107374182400
myisam_mmap_size, 18446744073709551615
myisam_recover_options, OFF
myisam_repair_threads, 1
myisam_sort_buffer_size, 4294967296
myisam_stats_method, nulls_unequal
myisam_use_mmap, OFF
mysql_native_password_proxy_users, OFF
named_pipe, OFF
net_buffer_length, 16384
net_read_timeout, 999999
net_retry_count, 10
net_write_timeout, 999999
new, OFF
ngram_token_size, 2
offline_mode, OFF
old, OFF
old_alter_table, OFF
old_passwords, 0
open_files_limit, 6259
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,duplicateweedout=on,subquery_materialization_cost_based=on,use_index_extensions=on,condition_fanout_filter=on,derived_merge=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
parser_max_mem_size, 18446744073709551615
performance_schema, ON
performance_schema_accounts_size, -1
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_transactions_history_long_size, 10000
performance_schema_events_transactions_history_size, 10
performance_schema_events_waits_history_long_size, 10000
performance_schema_events_waits_history_size, 10
performance_schema_hosts_size, -1
performance_schema_max_cond_classes, 80
performance_schema_max_cond_instances, -1
performance_schema_max_digest_length, 1024
performance_schema_max_file_classes, 80
performance_schema_max_file_handles, 32768
performance_schema_max_file_instances, -1
performance_schema_max_index_stat, -1
performance_schema_max_memory_classes, 320
performance_schema_max_metadata_locks, -1
performance_schema_max_mutex_classes, 210
performance_schema_max_mutex_instances, -1
performance_schema_max_prepared_statements_instances, -1
performance_schema_max_program_instances, -1
performance_schema_max_rwlock_classes, 40
performance_schema_max_rwlock_instances, -1
performance_schema_max_socket_classes, 10
performance_schema_max_socket_instances, -1
performance_schema_max_sql_text_length, 1024
performance_schema_max_stage_classes, 150
performance_schema_max_statement_classes, 193
performance_schema_max_statement_stack, 10
performance_schema_max_table_handles, -1
performance_schema_max_table_instances, -1
performance_schema_max_table_lock_stat, -1
performance_schema_max_thread_classes, 50
performance_schema_max_thread_instances, -1
performance_schema_session_connect_attrs_size, 512
performance_schema_setup_actors_size, -1
performance_schema_setup_objects_size, -1
performance_schema_users_size, -1
pid_file, C:\ProgramData\MySQL\MySQL Server 5.7\Data\WIN-9BPM7TSIO9C.pid
plugin_dir, C:\Program Files\MySQL\MySQL Server 5.7\lib\plugin\
port, 3306
preload_buffer_size, 32768
profiling, OFF
profiling_history_size, 15
protocol_version, 10
query_alloc_block_size, 8192
query_cache_limit, 1048576
query_cache_min_res_unit, 4096
query_cache_size, 1048576
query_cache_type, OFF
query_cache_wlock_invalidate, OFF
query_prealloc_size, 8192
range_alloc_block_size, 4096
range_optimizer_max_mem_size, 8388608
rbr_exec_mode, STRICT
read_buffer_size, 65536
read_only, OFF
read_rnd_buffer_size, 262144
relay_log, 
relay_log_basename, C:\ProgramData\MySQL\MySQL Server 5.7\Data\WIN-9BPM7TSIO9C-relay-bin
relay_log_index, C:\ProgramData\MySQL\MySQL Server 5.7\Data\WIN-9BPM7TSIO9C-relay-bin.index
relay_log_info_file, relay-log.info
relay_log_info_repository, FILE
relay_log_purge, ON
relay_log_recovery, OFF
relay_log_space_limit, 0
report_host, 
report_password, 
report_port, 3306
report_user, 
require_secure_transport, OFF
rpl_stop_slave_timeout, 31536000
secure_auth, ON
secure_file_priv, C:\ProgramData\MySQL\MySQL Server 5.7\Uploads\
server_id, 1
server_id_bits, 32
server_uuid, afda50c0-7b75-11e8-a524-000c294da226
session_track_gtids, OFF
session_track_schema, ON
session_track_state_change, OFF
session_track_system_variables, time_zone,autocommit,character_set_client,character_set_results,character_set_connection
session_track_transaction_info, OFF
sha256_password_proxy_users, OFF
shared_memory, OFF
shared_memory_base_name, MYSQL
show_compatibility_56, OFF
show_create_table_verbosity, OFF
show_old_temporals, OFF
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, C:\Windows\SERVIC~2\NETWOR~1\AppData\Local\Temp
slave_max_allowed_packet, 1073741824
slave_net_timeout, 60
slave_parallel_type, DATABASE
slave_parallel_workers, 0
slave_pending_jobs_size_max, 16777216
slave_preserve_commit_order, OFF
slave_rows_search_algorithms, TABLE_SCAN,INDEX_SCAN
slave_skip_errors, OFF
slave_sql_verify_checksum, ON
slave_transaction_retries, 10
slave_type_conversions, 
slow_launch_time, 2
slow_query_log, ON
slow_query_log_file, WIN-9BPM7TSIO9C-slow.log
socket, MySQL
sort_buffer_size, 262144
sql_auto_is_null, OFF
sql_big_selects, ON
sql_buffer_result, OFF
sql_log_off, OFF
sql_mode, STRICT_TRANS_TABLES,NO_AUTO_CREATE_USER,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, 
stored_program_cache, 256
super_read_only, OFF
sync_binlog, 1
sync_frm, ON
sync_master_info, 10000
sync_relay_log, 10000
sync_relay_log_info, 10000
system_time_zone, China Standard Time
table_definition_cache, 1400
table_open_cache, 2000
table_open_cache_instances, 16
thread_cache_size, 10
thread_handling, one-thread-per-connection
thread_stack, 262144
time_format, %H:%i:%s
time_zone, SYSTEM
tls_version, TLSv1,TLSv1.1
tmp_table_size, 2147483648
tmpdir, C:\Windows\SERVIC~2\NETWOR~1\AppData\Local\Temp
transaction_alloc_block_size, 8192
transaction_isolation, REPEATABLE-READ
transaction_prealloc_size, 4096
transaction_read_only, OFF
transaction_write_set_extraction, OFF
tx_isolation, REPEATABLE-READ
tx_read_only, OFF
unique_checks, ON
updatable_views_with_limit, YES
version, 5.7.22-log
version_comment, MySQL Community Server (GPL)
version_compile_machine, x86_64
version_compile_os, Win64
wait_timeout, 28800

Answer 1

What tuning should I do to lower the CPU usage of Azure MySQL?

Left to itself, MySQL will not consume large amounts of CPU.

It will do so, however, when it is asked to perform [lots of] CPU-intense queries.

You need to investigate the workload that your database is under and tune any poorly-performing queries.

I strongly suspect this is a case where you could spend huge amounts of time tweaking the server to gain 2-3 percentage points improvement, whereas changing the queries or the indexing or the table structures could realise 2-3 Orders of Magnitude improvement.