I have MySQL 5.7.27 under Ubuntu 16.04.4, 64 bit, 4GB RAM and SSDs (it's a virtual machine). I am observing resident memory growth in mysqld until no more resources are available and the OS kills / restarts mysqld.
Some background - The system is used to collect information from remote locations, with 1 entity being collected from each location. Each entity might have many hundreds of data points. For each remote location, there are two databases, which supports two situations: each location is per customer (but one customer might have many - thousands - of such locations) and in some situations, it might be many thousands of entities being collected from each remote location. The two DBs correspond to raw data collected and "processed" summaries. In addition, there is one additional DB per customer recording admin and other data about each remote location. So, total DB count is C * ( 1 + 2L ) - C for customer, L for location. The first DB of 2L has 32 tables and a minimum size of 2MB (but I have at least one example which it 5.9GB - not in this current sample set) - it is "cleared" at the start of each collection event; the second has 12 tables and typical size in the current sample set is 1MB (although this accumulates for each collection event).
A remote collection is performed periodically, say once a week or once a month, per remote location. After each collection, a process is run to summarise data from the ALL of the 2L databases into the one unifying one.
In the system with the issue, there are C ( 1 + 2L ) equaling just over 5000. When the summarisation process is run, mysqld resident memory (viewed using top) grows from around 800MB to just under 3GB. The summarisation process completes and might then run again a short time afterwards. That process completes cleanly and correctly releases query results and closes DB connections. The application is PHP 7.2.24 CLI running locally (so, using sockets, not TCP).
I have tried "tuning":
open_files_limit = 11000
table_open_cache = 5200
innodb_lru_scan_depth = 128
innodb_flush_log_at_trx_commit = 2
innodb_buffer_pool_size = 1073741824
(see open_files_limit, table_open_cache, innodb_lru_scan_depth, innodb_flush_log_at_trx_commit, innodb_buffer_pool_size)
These either made no apparent change or worsened the rate of growth of memory usage. I also ran show engine performance_schema status; at three instances: when resident memory was at 2459MB, 2478MB and 2910MB. Between those three samples, I saw differences only in the following metrics:
2459MB 2478MB 2910MB
(digest_hash).count 4676 -> 4837 -> 4958
(filename_hash).count 121118 -> 121139 -> 121214
(table_share_hash).count 27229 -> 27247 -> 27276
mutex_instances.count 29696 -> 30720 -> 31744
mutex_instances.memory 3801088 -> 3932160 -> 4063232
performance_scheme.memory 426293432 -> 426424504 -> 4266886648
rwlock_instances.count 400384 -> 400384 -> 401408
rwlock_instances.memory 51249152 -> 51249152 -> 51380224
My expectation is that at the end of each summarisation run, either "temporary" buffer space in mysqld would be freed up, or would simply be reused at the next run of that process, given that it effectively is making the same sequence of queries (and very similar updates) across the same set of databases / tables. The fact that the memory footprint grows suggest to me that either there is a memory leak in mysqld, or that an intentional "buffer" related to some failure condition (connections, locks, mutexes?) is at least part of the cause of the memory growth. I suggest the latter, because I would look at what would persist in mysqld between subsequent runs of that summarisation process.
I have also tried running mysqltuner.pl (see http://mysqltuner.com), but this also causes the memory growth problem, which is undoubtedly related to the number of databases. However, if I might refer to https://dev.mysql.com/doc/refman/5.7/en/database-count-limit.html, whatever limit MySQL might or might not have to the number of databases and tables, the numbers here are not significant to mysqld itself, even if they might be to the underlying OS. I confess I was impressed that the server was apparently handling over 1000 SELECTS per second on a not very highly spec'd system.
So, What "monitoring" parameters should I be looking at to assist with tuning mysql, the OS or platform and what (mysql / OS) tuning parameters would be most helpful in this situation? I could just take the Jaws approach ("We're going to need a bigger boat"), but if the issue I'm experiencing is a memory leak, then just adding more RAM is only just postponing the inevitable.
------------ EDIT following answer by Rick James (2020/01/13) -
RAM - 4GB
SHOW VARIABLES; (less SSL related info) output:
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Innodb_truncated_status_writes 0
Innodb_available_undo_logs 128
Key_blocks_not_flushed 0
Key_blocks_unused 13396
Key_blocks_used 3
Key_read_requests 6
Key_reads 3
Key_write_requests 0
Key_writes 0
Locked_connects 0
Max_execution_time_exceeded 0
Max_execution_time_set 0
Max_execution_time_set_failed 0
Max_used_connections 14
Max_used_connections_time 10/01/20 15:50
Not_flushed_delayed_rows 0
Ongoing_anonymous_transaction_count 0
Open_files 0
Open_streams 0
Open_table_definitions 3464
Open_tables 5200
Opened_files 337104
Opened_table_definitions 140571
Opened_tables 76095
Performance_schema_accounts_lost 0
Performance_schema_cond_classes_lost 0
Performance_schema_cond_instances_lost 0
Performance_schema_digest_lost 0
Performance_schema_file_classes_lost 0
Performance_schema_file_handles_lost 0
Performance_schema_file_instances_lost 0
Performance_schema_hosts_lost 0
Performance_schema_index_stat_lost 0
Performance_schema_locker_lost 0
Performance_schema_memory_classes_lost 0
Performance_schema_metadata_lock_lost 0
Performance_schema_mutex_classes_lost 0
Performance_schema_mutex_instances_lost 0
Performance_schema_nested_statement_lost 0
Performance_schema_prepared_statements_lost 0
Performance_schema_program_lost 0
Performance_schema_rwlock_classes_lost 0
Performance_schema_rwlock_instances_lost 0
Performance_schema_session_connect_attrs_lost 0
Performance_schema_socket_classes_lost 0
Performance_schema_socket_instances_lost 0
Performance_schema_stage_classes_lost 0
Performance_schema_statement_classes_lost 0
Performance_schema_table_handles_lost 0
Performance_schema_table_instances_lost 0
Performance_schema_table_lock_stat_lost 0
Performance_schema_thread_classes_lost 0
Performance_schema_thread_instances_lost 0
Performance_schema_users_lost 0
Prepared_stmt_count 0
Qcache_free_blocks 1
Qcache_free_memory 16760152
Qcache_hits 0
Qcache_inserts 0
Qcache_lowmem_prunes 0
Qcache_not_cached 184049
Qcache_queries_in_cache 0
Qcache_total_blocks 1
Queries 687716
Questions 684326
Rsa_public_key <removed>
Select_full_join 2827
Select_full_range_join 319
Select_range 56255
Select_range_check 1525
Select_scan 156904
Slave_open_temp_tables 0
Slow_launch_threads 0
Slow_queries 0
Sort_merge_passes 0
Sort_range 61935
Sort_rows 116417
Sort_scan 99600
Table_locks_immediate 458
Table_locks_waited 0
Table_open_cache_hits 381570
Table_open_cache_misses 76095
Table_open_cache_overflows 70888
Tc_log_max_pages_used 0
Tc_log_page_size 0
Tc_log_page_waits 0
Threads_cached 7
Threads_connected 3
Threads_created 14
Threads_running 1
Uptime 424288
Uptime_since_flush_status 424288
CREATE TEMPORARY TABLE ..– Raymond Nijland