I discovered this morning that MariaDb had been removed from my server in the process of upgrading from FreeBSD 10.3 to 11.1. After getting the database engine reinstalled, and resolving the problems with my.cnf incompatibility, I finally got MariaDb working - except that now every user (other than root) is denied access to their database.

I tried resetting the password for a random user, but that didn't make any difference.

Where is there useful information about what's going wrong here? This is all the information that's in the server.err after restarting the database:

2018-03-10 11:45:00 34424848384 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2018-03-10 11:45:00 34424848384 [Note] InnoDB: Uses event mutexes
2018-03-10 11:45:00 34424848384 [Note] InnoDB: Compressed tables use zlib 1.2.11
2018-03-10 11:45:00 34424848384 [Note] InnoDB: Number of pools: 1
2018-03-10 11:45:00 34424848384 [Note] InnoDB: Using SSE2 crc32 instructions
2018-03-10 11:45:00 34424848384 [Note] InnoDB: Initializing buffer pool, total size = 2G, instances = 8, chunk size = 128M
2018-03-10 11:45:00 34424848384 [Note] InnoDB: Completed initialization of buffer pool
2018-03-10 11:45:00 34424848384 [Note] InnoDB: Highest supported file format is Barracuda.
2018-03-10 11:45:00 34424848384 [Note] InnoDB: 128 out of 128 rollback segments are active.
2018-03-10 11:45:00 34424848384 [Note] InnoDB: Creating shared tablespace for temporary tables
2018-03-10 11:45:00 34424848384 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
2018-03-10 11:45:00 34424848384 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
2018-03-10 11:45:00 34424848384 [Note] InnoDB: 5.7.21 started; log sequence number 25246709
2018-03-10 11:45:00 37094309376 [Note] InnoDB: Loading buffer pool(s) from /var/db/mysql/ib_buffer_pool
2018-03-10 11:45:00 34424848384 [Note] Plugin 'FEEDBACK' is disabled.
2018-03-10 11:45:00 37094309376 [Note] InnoDB: Buffer pool(s) load completed at 180310 11:45:00
2018-03-10 11:45:00 34424848384 [Note] Server socket created on IP: '::'.
2018-03-10 11:45:00 34424848384 [Note] Reading of all Master_info entries succeded
2018-03-10 11:45:00 34424848384 [Note] Added new Master_info '' to hash table
2018-03-10 11:45:00 34424848384 [Note] /usr/local/libexec/mysqld: ready for connections.
Version: '10.2.13-MariaDB-log'  socket: '/tmp/mysql.sock'  port: 3306  FreeBSD Ports
2018-03-10 11:45:12 37180893952 [Warning] Access denied for user '<username>'@'localhost' (using password: YES)
2018-03-10 11:45:17 37180893952 [Warning] Access denied for user '<username>'@'localhost' (using password: YES)
2018-03-10 11:46:27 37180893952 [Warning] Access denied for user '<username>'@'localhost' (using password: YES)

This was a working server before I started upgrading FreeBSD. I haven't done anything to change the permissions on any of the databases or files, in fact, the only things that I did change are the operating system and database engine - and I would have expected an "upgrade" to be transparent to the data!!


EDIT

I reviewed the output of mysql_upgrade and see there were a lot of errors related to the sys database. I don't know if these are related, or what I can or should do about them:

Phase 3/7: Fixing views from mysql
sys.host_summary
Error    : Table 'performance_schema.memory_summary_by_host_by_event_name' doesn't exist
status   : Operation failed
sys.host_summary_by_file_io
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.host_summary_by_file_io_type
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.host_summary_by_stages
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.host_summary_by_statement_latency
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.host_summary_by_statement_type
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.innodb_buffer_stats_by_schema
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.innodb_buffer_stats_by_table
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.innodb_lock_waits
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.io_by_thread_by_latency
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.io_global_by_file_by_bytes
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.io_global_by_file_by_latency
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.io_global_by_wait_by_bytes
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.io_global_by_wait_by_latency
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.latest_file_io
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.memory_by_host_by_current_bytes
Error    : Table 'performance_schema.memory_summary_by_host_by_event_name' doesn't exist
Error    : View 'sys.memory_by_host_by_current_bytes' references invalid table(s) or column(s) or function(s) or definer/invoker of view lack rights to use them
Error    : Corrupt
sys.memory_by_thread_by_current_bytes
Error    : Table 'performance_schema.memory_summary_by_thread_by_event_name' doesn't exist
status   : Operation failed
sys.memory_by_user_by_current_bytes
Error    : Table 'performance_schema.memory_summary_by_user_by_event_name' doesn't exist
status   : Operation failed
sys.memory_global_by_current_bytes
Error    : Table 'performance_schema.memory_summary_global_by_event_name' doesn't exist
status   : Operation failed
sys.memory_global_total
Error    : Table 'performance_schema.memory_summary_global_by_event_name' doesn't exist
Error    : View 'sys.memory_global_total' references invalid table(s) or column(s) or function(s) or definer/invoker of view lack rights to use them
Error    : Corrupt
sys.metrics
Error    : Table 'performance_schema.global_status' doesn't exist
status   : Operation failed
sys.processlist
Error    : Table 'performance_schema.events_transactions_current' doesn't exist
status   : Operation failed
sys.ps_check_lost_instrumentation
Error    : Table 'performance_schema.global_status' doesn't exist
Error    : View 'sys.ps_check_lost_instrumentation' references invalid table(s) or column(s) or function(s) or definer/invoker of view lack rights to use them
Error    : Corrupt
sys.schema_index_statistics
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.schema_table_lock_waits
Error    : Table 'performance_schema.metadata_locks' doesn't exist
status   : Operation failed
sys.schema_table_statistics
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.schema_table_statistics_with_buffer
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.schema_tables_with_full_table_scans
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.session
Error    : Table 'performance_schema.events_transactions_current' doesn't exist
Error    : View 'sys.session' references invalid table(s) or column(s) or function(s) or definer/invoker of view lack rights to use them
Error    : Corrupt
sys.session_ssl_status
Error    : Table 'performance_schema.status_by_thread' doesn't exist
status   : Operation failed
sys.statement_analysis
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.statements_with_errors_or_warnings
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.statements_with_full_table_scans
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.statements_with_runtimes_in_95th_percentile
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.statements_with_sorting
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.statements_with_temp_tables
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.user_summary
Error    : Table 'performance_schema.memory_summary_by_user_by_event_name' doesn't exist
Error    : View 'sys.user_summary' references invalid table(s) or column(s) or function(s) or definer/invoker of view lack rights to use them
Error    : Corrupt
sys.user_summary_by_file_io
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.user_summary_by_file_io_type
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.user_summary_by_stages
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.user_summary_by_statement_latency
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.user_summary_by_statement_type
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.wait_classes_global_by_avg_latency
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.wait_classes_global_by_latency
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.waits_by_host_by_latency
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.waits_by_user_by_latency
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.waits_global_by_latency
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.x$host_summary
Error    : Table 'performance_schema.memory_summary_by_host_by_event_name' doesn't exist
Error    : View 'sys.x$host_summary' references invalid table(s) or column(s) or function(s) or definer/invoker of view lack rights to use them
Error    : Corrupt
sys.x$memory_by_host_by_current_bytes
Error    : Table 'performance_schema.memory_summary_by_host_by_event_name' doesn't exist
Error    : View 'sys.x$memory_by_host_by_current_bytes' references invalid table(s) or column(s) or function(s) or definer/invoker of view lack rights to use them
Error    : Corrupt
sys.x$memory_by_thread_by_current_bytes
Error    : Table 'performance_schema.memory_summary_by_thread_by_event_name' doesn't exist
Error    : View 'sys.x$memory_by_thread_by_current_bytes' references invalid table(s) or column(s) or function(s) or definer/invoker of view lack rights to use them
Error    : Corrupt
sys.x$memory_by_user_by_current_bytes
Error    : Table 'performance_schema.memory_summary_by_user_by_event_name' doesn't exist
Error    : View 'sys.x$memory_by_user_by_current_bytes' references invalid table(s) or column(s) or function(s) or definer/invoker of view lack rights to use them
Error    : Corrupt
sys.x$memory_global_by_current_bytes
Error    : Table 'performance_schema.memory_summary_global_by_event_name' doesn't exist
Error    : View 'sys.x$memory_global_by_current_bytes' references invalid table(s) or column(s) or function(s) or definer/invoker of view lack rights to use them
Error    : Corrupt
sys.x$memory_global_total
Error    : Table 'performance_schema.memory_summary_global_by_event_name' doesn't exist
Error    : View 'sys.x$memory_global_total' references invalid table(s) or column(s) or function(s) or definer/invoker of view lack rights to use them
Error    : Corrupt
sys.x$processlist
Error    : Table 'performance_schema.events_transactions_current' doesn't exist
Error    : View 'sys.x$processlist' references invalid table(s) or column(s) or function(s) or definer/invoker of view lack rights to use them
Error    : Corrupt
sys.x$ps_schema_table_statistics_io
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.x$schema_table_lock_waits
Error    : Table 'performance_schema.metadata_locks' doesn't exist
Error    : View 'sys.x$schema_table_lock_waits' references invalid table(s) or column(s) or function(s) or definer/invoker of view lack rights to use them
Error    : Corrupt
sys.x$schema_table_statistics
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.x$schema_table_statistics_with_buffer
Error    : Cannot load from mysql.proc. The table is probably corrupted
Error    : Corrupt
sys.x$session
Error    : Table 'performance_schema.events_transactions_current' doesn't exist
Error    : View 'sys.x$session' references invalid table(s) or column(s) or function(s) or definer/invoker of view lack rights to use them
Error    : Corrupt
sys.x$user_summary
Error    : Table 'performance_schema.memory_summary_by_user_by_event_name' doesn't exist
Error    : View 'sys.x$user_summary' references invalid table(s) or column(s) or function(s) or definer/invoker of view lack rights to use them
Error    : Corrupt

EDIT 2

N.B. In both of these edits, the "OK" tables are removed to cut the size of the text in the question.

I re-ran mysql_upgrade again because the search results I found for "mysql_upgrade Cannot load from mysql.proc. The table is probably corrupted" all seem to indicate such problems are fixed by running mysql_upgrade. (I had to run mysql_upgrade -p --force because without the --force parameter it just said "This installation of MySQL is already upgraded to 10.2.13-MariaDB")

Now I've got a different set of error messages that are equally opaque. (The sequence invalid table(s) ... to use them in each case below can be expanded to invalid table(s) or column(s) or function(s) or definer/invoker of view lack rights to use them - I had to do these replacements to fit the 30000 character question length limit.)

Phase 3/7: Fixing views
sys.host_summary
Error    : Table 'performance_schema.memory_summary_by_host_by_event_name' doesn't exist
Error    : View 'sys.host_summary' references invalid table(s) ... to use them
Error    : Corrupt
sys.host_summary_by_file_io
Error    : FUNCTION sys.format_time does not exist
Error    : View 'sys.host_summary_by_file_io' references invalid table(s) ... to use them
Error    : Corrupt
sys.host_summary_by_file_io_type
Error    : FUNCTION sys.format_time does not exist
Error    : View 'sys.host_summary_by_file_io_type' references invalid table(s) ... to use them
Error    : Corrupt
sys.host_summary_by_stages
Error    : FUNCTION sys.format_time does not exist
Error    : View 'sys.host_summary_by_stages' references invalid table(s) ... to use them
Error    : Corrupt
sys.host_summary_by_statement_latency
Error    : FUNCTION sys.format_time does not exist
Error    : View 'sys.host_summary_by_statement_latency' references invalid table(s) ... to use them
Error    : Corrupt
sys.host_summary_by_statement_type
Error    : FUNCTION sys.format_time does not exist
Error    : View 'sys.host_summary_by_statement_type' references invalid table(s) ... to use them
Error    : Corrupt
sys.innodb_buffer_stats_by_schema
Error    : FUNCTION sys.format_bytes does not exist
Error    : View 'sys.innodb_buffer_stats_by_schema' references invalid table(s) ... to use them
Error    : Corrupt
sys.innodb_buffer_stats_by_table
Error    : FUNCTION sys.format_bytes does not exist
Error    : View 'sys.innodb_buffer_stats_by_table' references invalid table(s) ... to use them
Error    : Corrupt
sys.innodb_lock_waits
Error    : FUNCTION sys.format_statement does not exist
Error    : View 'sys.innodb_lock_waits' references invalid table(s) ... to use them
Error    : Corrupt
sys.io_by_thread_by_latency
Error    : FUNCTION sys.format_time does not exist
Error    : View 'sys.io_by_thread_by_latency' references invalid table(s) ... to use them
Error    : Corrupt
sys.io_global_by_file_by_bytes
Error    : FUNCTION sys.format_path does not exist
Error    : View 'sys.io_global_by_file_by_bytes' references invalid table(s) ... to use them
Error    : Corrupt
sys.io_global_by_file_by_latency
Error    : FUNCTION sys.format_path does not exist
Error    : View 'sys.io_global_by_file_by_latency' references invalid table(s) ... to use them
Error    : Corrupt
sys.io_global_by_wait_by_bytes
Error    : FUNCTION sys.format_time does not exist
Error    : View 'sys.io_global_by_wait_by_bytes' references invalid table(s) ... to use them
Error    : Corrupt
sys.io_global_by_wait_by_latency
Error    : FUNCTION sys.format_time does not exist
Error    : View 'sys.io_global_by_wait_by_latency' references invalid table(s) ... to use them
Error    : Corrupt
sys.latest_file_io
Error    : FUNCTION sys.format_path does not exist
Error    : View 'sys.latest_file_io' references invalid table(s) ... to use them
Error    : Corrupt
sys.memory_by_host_by_current_bytes
Error    : Table 'performance_schema.memory_summary_by_host_by_event_name' doesn't exist
Error    : View 'sys.memory_by_host_by_current_bytes' references invalid table(s) ... to use them
Error    : Corrupt
sys.memory_by_thread_by_current_bytes
Error    : Table 'performance_schema.memory_summary_by_thread_by_event_name' doesn't exist
Error    : View 'sys.memory_by_thread_by_current_bytes' references invalid table(s) ... to use them
Error    : Corrupt
sys.memory_by_user_by_current_bytes
Error    : Table 'performance_schema.memory_summary_by_user_by_event_name' doesn't exist
Error    : View 'sys.memory_by_user_by_current_bytes' references invalid table(s) ... to use them
Error    : Corrupt
sys.memory_global_by_current_bytes
Error    : Table 'performance_schema.memory_summary_global_by_event_name' doesn't exist
Error    : View 'sys.memory_global_by_current_bytes' references invalid table(s) ... to use them
Error    : Corrupt
sys.memory_global_total
Error    : Table 'performance_schema.memory_summary_global_by_event_name' doesn't exist
Error    : View 'sys.memory_global_total' references invalid table(s) ... to use them
Error    : Corrupt
sys.metrics
Error    : Table 'performance_schema.global_status' doesn't exist
Error    : View 'sys.metrics' references invalid table(s) ... to use them
Error    : Corrupt
sys.processlist
Error    : Table 'performance_schema.events_transactions_current' doesn't exist
Error    : View 'sys.processlist' references invalid table(s) ... to use them
Error    : Corrupt
sys.ps_check_lost_instrumentation
Error    : Table 'performance_schema.global_status' doesn't exist
Error    : View 'sys.ps_check_lost_instrumentation' references invalid table(s) ... to use them
Error    : Corrupt
sys.schema_index_statistics
Error    : FUNCTION sys.format_time does not exist
Error    : View 'sys.schema_index_statistics' references invalid table(s) ... to use them
Error    : Corrupt
sys.schema_table_lock_waits
Error    : Table 'performance_schema.metadata_locks' doesn't exist
Error    : View 'sys.schema_table_lock_waits' references invalid table(s) ... to use them
Error    : Corrupt
sys.schema_table_statistics
Error    : FUNCTION sys.extract_schema_from_file_name does not exist
Error    : View 'sys.schema_table_statistics' references invalid table(s) ... to use them
Error    : Corrupt
sys.schema_table_statistics_with_buffer
Error    : FUNCTION sys.extract_schema_from_file_name does not exist
Error    : View 'sys.schema_table_statistics_with_buffer' references invalid table(s) ... to use them
Error    : Corrupt
sys.schema_tables_with_full_table_scans
Error    : FUNCTION sys.format_time does not exist
Error    : View 'sys.schema_tables_with_full_table_scans' references invalid table(s) ... to use them
Error    : Corrupt
sys.session
Error    : Table 'performance_schema.events_transactions_current' doesn't exist
Error    : View 'sys.session' references invalid table(s) ... to use them
Error    : Corrupt
sys.session_ssl_status
Error    : Table 'performance_schema.status_by_thread' doesn't exist
Error    : View 'sys.session_ssl_status' references invalid table(s) ... to use them
Error    : Corrupt
sys.statement_analysis
Error    : FUNCTION sys.format_statement does not exist
Error    : View 'sys.statement_analysis' references invalid table(s) ... to use them
Error    : Corrupt
sys.statements_with_errors_or_warnings
Error    : FUNCTION sys.format_statement does not exist
Error    : View 'sys.statements_with_errors_or_warnings' references invalid table(s) ... to use them
Error    : Corrupt
sys.statements_with_full_table_scans
Error    : FUNCTION sys.format_statement does not exist
Error    : View 'sys.statements_with_full_table_scans' references invalid table(s) ... to use them
Error    : Corrupt
sys.statements_with_runtimes_in_95th_percentile
Error    : FUNCTION sys.format_statement does not exist
Error    : View 'sys.statements_with_runtimes_in_95th_percentile' references invalid table(s) ... to use them
Error    : Corrupt
sys.statements_with_sorting
Error    : FUNCTION sys.format_statement does not exist
Error    : View 'sys.statements_with_sorting' references invalid table(s) ... to use them
Error    : Corrupt
sys.statements_with_temp_tables
Error    : FUNCTION sys.format_statement does not exist
Error    : View 'sys.statements_with_temp_tables' references invalid table(s) ... to use them
Error    : Corrupt
sys.user_summary
Error    : Table 'performance_schema.memory_summary_by_user_by_event_name' doesn't exist
Error    : View 'sys.user_summary' references invalid table(s) ... to use them
Error    : Corrupt
sys.user_summary_by_file_io
Error    : FUNCTION sys.format_time does not exist
Error    : View 'sys.user_summary_by_file_io' references invalid table(s) ... to use them
Error    : Corrupt
sys.user_summary_by_file_io_type
Error    : FUNCTION sys.format_time does not exist
Error    : View 'sys.user_summary_by_file_io_type' references invalid table(s) ... to use them
Error    : Corrupt
sys.user_summary_by_stages
Error    : FUNCTION sys.format_time does not exist
Error    : View 'sys.user_summary_by_stages' references invalid table(s) ... to use them
Error    : Corrupt
sys.user_summary_by_statement_latency
Error    : FUNCTION sys.format_time does not exist
Error    : View 'sys.user_summary_by_statement_latency' references invalid table(s) ... to use them
Error    : Corrupt
sys.user_summary_by_statement_type
Error    : FUNCTION sys.format_time does not exist
Error    : View 'sys.user_summary_by_statement_type' references invalid table(s) ... to use them
Error    : Corrupt
sys.wait_classes_global_by_avg_latency
Error    : FUNCTION sys.format_time does not exist
Error    : View 'sys.wait_classes_global_by_avg_latency' references invalid table(s) ... to use them
Error    : Corrupt
sys.wait_classes_global_by_latency
Error    : FUNCTION sys.format_time does not exist
Error    : View 'sys.wait_classes_global_by_latency' references invalid table(s) ... to use them
Error    : Corrupt
sys.waits_by_host_by_latency
Error    : FUNCTION sys.format_time does not exist
Error    : View 'sys.waits_by_host_by_latency' references invalid table(s) ... to use them
Error    : Corrupt
sys.waits_by_user_by_latency
Error    : FUNCTION sys.format_time does not exist
Error    : View 'sys.waits_by_user_by_latency' references invalid table(s) ... to use them
Error    : Corrupt
sys.waits_global_by_latency
Error    : FUNCTION sys.format_time does not exist
Error    : View 'sys.waits_global_by_latency' references invalid table(s) ... to use them
Error    : Corrupt
sys.x$host_summary
Error    : Table 'performance_schema.memory_summary_by_host_by_event_name' doesn't exist
Error    : View 'sys.x$host_summary' references invalid table(s) ... to use them
Error    : Corrupt
sys.x$memory_by_host_by_current_bytes
Error    : Table 'performance_schema.memory_summary_by_host_by_event_name' doesn't exist
Error    : View 'sys.x$memory_by_host_by_current_bytes' references invalid table(s) ... to use them
Error    : Corrupt
sys.x$memory_by_thread_by_current_bytes
Error    : Table 'performance_schema.memory_summary_by_thread_by_event_name' doesn't exist
Error    : View 'sys.x$memory_by_thread_by_current_bytes' references invalid table(s) ... to use them
Error    : Corrupt
sys.x$memory_by_user_by_current_bytes
Error    : Table 'performance_schema.memory_summary_by_user_by_event_name' doesn't exist
Error    : View 'sys.x$memory_by_user_by_current_bytes' references invalid table(s) ... to use them
Error    : Corrupt
sys.x$memory_global_by_current_bytes
Error    : Table 'performance_schema.memory_summary_global_by_event_name' doesn't exist
Error    : View 'sys.x$memory_global_by_current_bytes' references invalid table(s) ... to use them
Error    : Corrupt
sys.x$memory_global_total
Error    : Table 'performance_schema.memory_summary_global_by_event_name' doesn't exist
Error    : View 'sys.x$memory_global_total' references invalid table(s) ... to use them
Error    : Corrupt
sys.x$processlist
Error    : Table 'performance_schema.events_transactions_current' doesn't exist
Error    : View 'sys.x$processlist' references invalid table(s) ... to use them
Error    : Corrupt
sys.x$ps_schema_table_statistics_io
Error    : FUNCTION sys.extract_schema_from_file_name does not exist
Error    : View 'sys.x$ps_schema_table_statistics_io' references invalid table(s) ... to use them
Error    : Corrupt
sys.x$schema_table_lock_waits
Error    : Table 'performance_schema.metadata_locks' doesn't exist
Error    : View 'sys.x$schema_table_lock_waits' references invalid table(s) ... to use them
Error    : Corrupt
sys.x$schema_table_statistics
Error    : FUNCTION sys.extract_schema_from_file_name does not exist
Error    : View 'sys.x$schema_table_statistics' references invalid table(s) ... to use them
Error    : Corrupt
sys.x$schema_table_statistics_with_buffer
Error    : FUNCTION sys.extract_schema_from_file_name does not exist
Error    : View 'sys.x$schema_table_statistics_with_buffer' references invalid table(s) ... to use them
Error    : Corrupt
sys.x$session
Error    : Table 'performance_schema.events_transactions_current' doesn't exist
Error    : View 'sys.x$session' references invalid table(s) ... to use them
Error    : Corrupt
sys.x$user_summary
Error    : Table 'performance_schema.memory_summary_by_user_by_event_name' doesn't exist
Error    : View 'sys.x$user_summary' references invalid table(s) ... to use them
Error    : Corrupt

I tried running mysqlcheck -r sys -p -v and it tells me

Enter password:
Processing databases
sys
sys.sys_config
Error    : Table '    sys.sys_config' doesn't exist in engine
status   : Operation failed

Is this the root of my problem? If so, how do I fix it?

  • Did you run mysql_upgrade? – Michael Hampton Mar 10 at 18:21
  • yes, I did run mysql_upgrade - and taking another look at the results, I see there were a lot of errors in Phase 3/7: Fixing views from mysql related to tables in the sys database with error messages like Cannot load from mysql.proc. The table is probably corrupted - I will add the error messages to my question. – FKEinternet Mar 10 at 19:05
  • Another good idea would be to revert to the previous version first and verify whether that would work for you. On FreeBSD pkg should write the package names added/removed to /var/log/messages. – kworr Mar 11 at 15:38
  • I came to the same conclusion, reverted the database server and restored the data from my backup. At least now my system is working again, and I can investigate the problem with less stress. – FKEinternet Mar 11 at 22:51

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