MySQL hangs due to large delete

[Akshay Viswanathan]

Hello!
We are currently using MySQL 5.5 running on Ubuntu 12.04.
We have quite a big table and we are doing several large deletes on this table in one batch (We use the executeBatch() method from our JDBC connector). Surprisingly, this causes MySQL to hang completely and not perform any reads or writes for 10-20s.
Its not just the db that is blocking as we have 2 dbs on the same MySQL instance and they both are hanging.

The table itself is an InnoDB table and these are the relevant variables:

| ignore_builtin_innodb | OFF |
| 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 | 47689236480 |
| 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 | 0 |
| 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 | 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 | 1073741824 |
| 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 | 16384 |
| 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 | 4 |
| 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 | 5.6.17 |
| innodb_write_io_threads | 4 |


| binlog_cache_size | 32768 |
| binlog_stmt_cache_size | 32768 |
| have_query_cache | YES |
| host_cache_size | 654 |
| key_cache_age_threshold | 300 |
| key_cache_block_size | 1024 |
| key_cache_division_limit | 100 |
| max_binlog_cache_size | 18446744073709547520 |
| max_binlog_stmt_cache_size | 18446744073709547520 |
| metadata_locks_cache_size | 1024 |
| query_cache_limit | 67108864 |
| query_cache_min_res_unit | 4096 |
| query_cache_size | 0 |
| query_cache_type | OFF |
| query_cache_wlock_invalidate | OFF |
| stored_program_cache | 256 |
| table_definition_cache | 16384 |
| table_open_cache | 16384 |
| table_open_cache_instances | 1 |
| thread_cache_size | 18


Any help with this would be appreciated!