MySQL frequent communication link error

[Sai Zhang]

Hi,
I am using MySQL in my streaming program, which is that we will have a storm cluster to generate multi threads to concurrently read/write MySQL database.To make it more efficient, I am using a connection pool - C3P0.

But I frequently meet the following problems after my application ran about 10 or 20 minutes, sometime less than 10 minutes:

-Communications link failure during rollback()
-Communications link failure during commit()
-The last packet successfully received from the server was 1,714 milliseconds ago. The last packet sent successfully to the server was 1,714 milliseconds ago.
-NewPooledConnection [WARN] [c3p0] A PooledConnection that has already signalled a Connection error is still in use!
-Could not retrieve transation read-only status server
-Caused by: java.net.SocketException: Broken pipe

My MySQL is using innodb engine, and the configuration is:

connect_timeout 28800
delayed_insert_timeout 300
innodb_flush_log_at_timeout 1
innodb_lock_wait_timeout 300
innodb_rollback_on_timeout OFF
interactive_timeout 28800
lock_wait_timeout 31536000
net_read_timeout 300
net_write_timeout 600
rpl_stop_slave_timeout 31536000
slave_net_timeout 3600
wait_timeout 28800


For more configuration, in the end is the complete list.

I also tried to tune TCP/IP of my OS: (Red Hat Enterprise Linux Server release 6.6)
echo 2048 > /proc/sys/net/core/somaxconn
echo 10240 > /proc/sys/net/ipv4/tcp_max_syn_backlog

vim /etc/sysctl.conf

net.core.rmem_max = 16777216
net.core.wmem_max = 16777216
net.ipv4.tcp_rmem = 4096 87380 16777216
net.ipv4.tcp_wmem = 4096 65536 16777216
net.ipv4.tcp_fin_timeout = 30
net.ipv4.tcp_tw_recycle = 1
net.ipv4.tcp_timestamps = 0
net.ipv4.tcp_window_scaling = 0
net.ipv4.tcp_sack = 0
net.core.netdev_max_backlog = 30000
net.ipv4.tcp_no_metrics_save = 1
net.core.somaxconn = 262144
net.ipv4.tcp_syncookies = 0
net.ipv4.tcp_max_orphans = 262144
net.ipv4.tcp_max_syn_backlog = 262144
net.ipv4.tcp_synack_retries = 2
net.ipv4.tcp_syn_retries = 2


I have searched the web for about one week, but didn't solve this problem. Please kindly help.

Result of show variables:

auto_increment_increment 1
auto_increment_offset 1
autocommit ON
automatic_sp_privileges ON
avoid_temporal_upgrade OFF
back_log 600
basedir /usr
big_tables OFF
bind_address *
binlog_cache_size 32768
binlog_checksum CRC32
binlog_direct_non_transactional_updates OFF
binlog_error_action IGNORE_ERROR
binlog_format STATEMENT
binlog_gtid_simple_recovery OFF
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
binlogging_impossible_mode IGNORE_ERROR
block_encryption_mode aes-128-ecb
bulk_insert_buffer_size 8388608
character_set_client latin1
character_set_connection latin1
character_set_database latin1
character_set_filesystem binary
character_set_results
character_set_server latin1
character_set_system utf8
character_sets_dir /usr/share/mysql/charsets/
collation_connection latin1_swedish_ci
collation_database latin1_swedish_ci
collation_server latin1_swedish_ci
completion_type NO_CHAIN
concurrent_insert AUTO
connect_timeout 28800
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 OFF
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/c9t07982.log
group_concat_max_len 1024
gtid_executed
gtid_mode OFF
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 YES
host_cache_size 679
hostname c9t07982.itcs.hp.com
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 8589934592
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 ON
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
innodb_flush_neighbors 1
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 2000
innodb_io_capacity_max 4000
innodb_large_prefix OFF
innodb_lock_wait_timeout 300
innodb_locks_unsafe_for_binlog OFF
innodb_log_buffer_size 8388608
innodb_log_compressed_pages ON
innodb_log_file_size 134217728
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 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_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 0
innodb_undo_directory .
innodb_undo_logs 128
innodb_undo_tablespaces 0
innodb_use_native_aio ON
innodb_use_sys_malloc ON
innodb_version 5.6.26
innodb_write_io_threads 8
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 OFF
log_bin_basename
log_bin_index
log_bin_trust_function_creators OFF
log_bin_use_v1_row_events OFF
log_error /var/lib/mysql/c9t07982.itcs.hp.com.err
log_output FILE
log_queries_not_using_indexes OFF
log_slave_updates OFF
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 FILE
master_verify_checksum OFF
max_allowed_packet 33554432
max_binlog_cache_size 18446744073709547520
max_binlog_size 1073741824
max_binlog_stmt_cache_size 18446744073709547520
max_connect_errors 100
max_connections 1536
max_delayed_threads 20
max_digest_length 1024
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 1024
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 300
net_retry_count 10
net_write_timeout 600
new OFF
old OFF
old_alter_table OFF
old_passwords 0
open_files_limit 10240
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 9044
performance_schema_max_digest_length 1024
performance_schema_max_file_classes 50
performance_schema_max_file_handles 32768
performance_schema_max_file_instances 15754
performance_schema_max_mutex_classes 200
performance_schema_max_mutex_instances 24216
performance_schema_max_rwlock_classes 40
performance_schema_max_rwlock_instances 11872
performance_schema_max_socket_classes 10
performance_schema_max_socket_instances 3092
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 3172
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/lib/mysql/c9t07982.itcs.hp.com.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 100349
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
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 FILE
relay_log_purge ON
relay_log_recovery OFF
relay_log_space_limit 0
report_host
report_password
report_port 3306
report_user
rpl_stop_slave_timeout 31536000
secure_auth ON
secure_file_priv
server_id 0
server_id_bits 32
server_uuid c50b0d64-3538-11e5-a893-0050568b3ea6
show_old_temporals OFF
simplified_binlog_gtid_recovery OFF
skip_external_locking ON
skip_name_resolve ON
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 OFF
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/c9t07982-slow.log
socket /var/lib/mysql/mysql.sock
sort_buffer_size 2097152
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 100000
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 10000
sync_relay_log 10000
sync_relay_log_info 10000
system_time_zone UCT
table_definition_cache 1400
table_open_cache 2000
table_open_cache_instances 1
thread_cache_size 23
thread_concurrency 10
thread_handling one-thread-per-connection
thread_stack 262144
time_format %H:%i:%s
time_zone SYSTEM
timed_mutexes OFF
timestamp 1440033995.654965
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 5.6.26
version_comment MySQL Community Server (GPL)
version_compile_machine x86_64
version_compile_os Linux
wait_timeout 28800
warning_count 0