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Update to M6 went OK but have now discovered Kalarm no longer works. A pop up message say "The Akonadi personal information management service is not running. This application cannot be used without it" There is start option button underneath the error message but clicking that just says The Akonadi personal information management service is not operational.
Running from a CLI gives a bit more info:

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kalarm
org.kde.pim.kidentitymanagement: IdentityManager: There was no default identity. Marking first one as default.
org.kde.pim.akonadicore: "QLocalSocket::connectToServer: Invalid name" "/home/me/.local/share/akonadi/akonadiserver-cmd.socket"
org.kde.akonadi.ETM: collection: QVector()
org.kde.akonadi.ETM: collection: QVector()
[me@localhost ~]$ /bin/mysqladmin: connect to server at 'localhost' failed
error: 'Can't connect to local MySQL server through socket '/tmp/akonadi-me.XLSDgq/mysql.socket' (111 "Connection refused")'
Check that mysqld is running and that the socket: '/tmp/akonadi-me.XLSDgq/mysql.socket' exists!

Well, I wasn't aware that Kalarm needed MySQL before the upgrade, however starting it doesn't fix the problem. The socket '/tmp/akonadi-me.XLSDgq/mysql.socket' does exist. Have also discovered that Korganizer also throws up the same error. Tried reinstalling Kalarm but no luck.
Any suggestions please?

Akonadi uses MySQL to store its data, but you don't need to start the system MySQL daemon, you only need to ensure that akonadi is running. Can you show the output as regular user of

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akonadictl status

This is what it looks like here:

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[doktor5000@Mageia5]─[17:53:03]─[~] akonadictl status
Akonadi Control: running                                                                                                                                                                                         
Akonadi Server: running
Akonadi Server Search Support: available (Remote Search)
Available Agent Types: akonadi_akonotes_resource, akonadi_archivemail_agent, akonadi_birthdays_resource, akonadi_contacts_resource, akonadi_davgroupware_resource, akonadi_followupreminder_agent, akonadi_googlecalendar_resource, akonadi_googlecontacts_resource, akonadi_ical_resource, akonadi_icaldir_resource, akonadi_imap_resource, akonadi_invitations_agent, akonadi_kalarm_dir_resource, akonadi_kalarm_resource, akonadi_knut_resource, akonadi_maildir_resource, akonadi_maildispatcher_agent, akonadi_mailfilter_agent, akonadi_mbox_resource, akonadi_migration_agent, akonadi_mixedmaildir_resource, akonadi_newmailnotifier_agent, akonadi_notes_agent, akonadi_notes_resource, akonadi_openxchange_resource, akonadi_pop3_resource, akonadi_sendlater_agent, akonadi_tomboynotes_resource, akonadi_vcard_resource, akonadi_vcarddir_resource

Hello,
akonadictl status is stopped. But trying to start it gives much the same error:

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akonadictl start
/bin/mysqladmin: connect to server at 'localhost' failed
error: 'Can't connect to local MySQL server through socket '/tmp/akonadi-me.XLSDgq/mysql.socket' (111 "Connection refused")'
Check that mysqld is running and that the socket: '/tmp/akonadi-me.XLSDgq/mysql.socket' exists!

Please show the content of ~/.config/akonadi/akonadiserverrc and the output/logfile as regular user of

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akonadiselftest

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cat akonadiserverrc
[Debug]
Tracer=null

[%General]
Driver=QMYSQL
ExternalPayload=false
SizeThreshold=4096

[QMYSQL]
Host=
Name=akonadi
Options="UNIX_SOCKET=/tmp/akonadi-me.XLSDgq/mysql.socket"
ServerPath=/usr/sbin/mysqld
StartServer=true

A few errors in the self test....

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Akonadi Server Self-Test Report
===============================

Test 1:  SUCCESS
--------

Database driver found.
Details: The QtSQL driver 'QMYSQL' is required by your current Akonadi server configuration and was found on your system.

File content of '/home/me/.config/akonadi/akonadiserverrc':
[Debug]
Tracer=null

[%General]
Driver=QMYSQL
ExternalPayload=false
SizeThreshold=4096

[QMYSQL]
Host=
Name=akonadi
Options="UNIX_SOCKET=/tmp/akonadi-me.XLSDgq/mysql.socket"
ServerPath=/usr/sbin/mysqld
StartServer=true


Test 2:  SUCCESS
--------

Akonadi is not running as root
Details: Akonadi is not running as a root/administrator user, which is the recommended setup for a secure system.

Test 3:  SUCCESS
--------

MySQL server found.
Details: You have currently configured Akonadi to use the MySQL server '/usr/sbin/mysqld'.
Make sure you have the MySQL server installed, set the correct path and ensure you have the necessary read and execution rights on the server executable. The server executable is typically called 'mysqld'; its location varies depending on the distribution.

Test 4:  SUCCESS
--------

MySQL server is executable.
Details: MySQL server found: 2017-07-23 20:00:14 139899734370368 [Note] Using unique option prefix 'key_buffer' is error-prone and can break in the future. Please use the full name 'key_buffer_size' instead.
/usr/sbin/mysqld  Ver 10.1.24-MariaDB for Linux on x86_64 (Mageia MariaDB Server)


Test 5:  ERROR
--------

MySQL server log contains errors.
Details: The MySQL server error log file '<a href="/home/me/.local/share/akonadi/db_data/mysql.err">/home/me/.local/share/akonadi/db_data/mysql.err</a>' contains errors.

File content of '/home/me/.local/share/akonadi/db_data/mysql.err':
2017-07-16 20:28:43 7f4fb306c780 InnoDB: Warning: Using innodb_additional_mem_pool_size is DEPRECATED. This option may be removed in future releases, together with the option innodb_use_sys_malloc and with the InnoDB's internal memory allocator.
170716 20:28:43 [Note] InnoDB: innodb_empty_free_list_algorithm has been changed to legacy because of small buffer pool size. In order to use backoff, increase buffer pool at least up to 20MB.

170716 20:28:43 [Note] InnoDB: Using mutexes to ref count buffer pool pages
170716 20:28:43 [Note] InnoDB: The InnoDB memory heap is disabled
170716 20:28:43 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
170716 20:28:43 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier
170716 20:28:43 [Note] InnoDB: Compressed tables use zlib 1.2.8
170716 20:28:43 [Note] InnoDB: Using Linux native AIO
170716 20:28:43 [Note] InnoDB: Using CPU crc32 instructions
170716 20:28:43 [Note] InnoDB: Initializing buffer pool, size = 80.0M
170716 20:28:44 [Note] InnoDB: Completed initialization of buffer pool
170716 20:28:44 [Note] InnoDB: Highest supported file format is Barracuda.
170716 20:28:44 [Note] InnoDB: The log sequence numbers 2626179 and 2626179 in ibdata files do not match the log sequence number 3045217 in the ib_logfiles!
170716 20:28:46 [Note] InnoDB: Restoring possible half-written data pages from the doublewrite buffer...
InnoDB: Last MySQL binlog file position 0 14074, file name ./mysql-bin.000001
170716 20:28:51 [Note] InnoDB: 128 rollback segment(s) are active.
170716 20:28:51 [Note] InnoDB: Waiting for purge to start
170716 20:28:51 [Note] InnoDB:  Percona XtraDB (http://www.percona.com) 5.6.36-82.0 started; log sequence number 3045217
170716 20:28:52 [ERROR] Can't open and lock privilege tables: Table 'mysql.servers' doesn't exist
170716 20:28:52 [Warning] Can't open and lock time zone table: Table 'mysql.time_zone_leap_second' doesn't exist trying to live without them
170716 20:28:52 [ERROR] Native table 'performance_schema'.'cond_instances' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_waits_current' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_waits_history' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_waits_history_long' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_waits_summary_by_host_by_event_name' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_waits_summary_by_instance' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_waits_summary_by_thread_by_event_name' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_waits_summary_by_user_by_event_name' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_waits_summary_by_account_by_event_name' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_waits_summary_global_by_event_name' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'file_instances' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'file_summary_by_event_name' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'file_summary_by_instance' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'host_cache' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'mutex_instances' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'objects_summary_global_by_type' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'performance_timers' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'rwlock_instances' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'setup_actors' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'setup_consumers' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'setup_instruments' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'setup_objects' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'setup_timers' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'table_io_waits_summary_by_index_usage' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'table_io_waits_summary_by_table' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'table_lock_waits_summary_by_table' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'threads' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_stages_current' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_stages_history' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_stages_history_long' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_stages_summary_by_thread_by_event_name' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_stages_summary_by_account_by_event_name' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_stages_summary_by_user_by_event_name' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_stages_summary_by_host_by_event_name' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_stages_summary_global_by_event_name' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_statements_current' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_statements_history' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_statements_history_long' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_statements_summary_by_thread_by_event_name' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_statements_summary_by_account_by_event_name' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_statements_summary_by_user_by_event_name' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_statements_summary_by_host_by_event_name' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_statements_summary_global_by_event_name' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'events_statements_summary_by_digest' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'users' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'accounts' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'hosts' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'socket_instances' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'socket_summary_by_instance' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'socket_summary_by_event_name' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'session_connect_attrs' has the wrong structure
170716 20:28:52 [ERROR] Native table 'performance_schema'.'session_account_connect_attrs' has the wrong structure
170716 20:28:52 [Warning] Failed to load slave replication state from table mysql.gtid_slave_pos: 1146: Table 'mysql.gtid_slave_pos' doesn't exist
170716 20:28:52 [Note] Reading of all Master_info entries succeded
170716 20:28:52 [Note] Added new Master_info '' to hash table
170716 20:28:52 [Note] /usr/sbin/mysqld: ready for connections.
Version: '10.0.31-MariaDB'  socket: '/tmp/akonadi-me.XLSDgq/mysql.socket'  port: 0  Mageia MariaDB Server
2017-07-16 20:28:53 7f4fb2fbd700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.


Test 6:  SUCCESS
--------

MySQL server default configuration found.
Details: The default configuration for the MySQL server was found and is readable at <a href="/etc/akonadi/mysql-global.conf">/etc/akonadi/mysql-global.conf</a>.

File content of '/etc/akonadi/mysql-global.conf':
#
# Global Akonadi MySQL server settings,
# These settings can be adjusted using $HOME/.config/akonadi/mysql-local.conf
#
# Based on advice by Kris Köhntopp <kris@mysql.com>
#
[mysqld]

# strict query parsing/interpretation
# TODO: make Akonadi work with those settings enabled
# sql_mode=strict_trans_tables,strict_all_tables,strict_error_for_division_by_zero,no_auto_create_user,no_auto_value_on_zero,no_engine_substitution,no_zero_date,no_zero_in_date,only_full_group_by,pipes_as_concat
# sql_mode=strict_trans_tables

# DEBUGGING:
# log all queries, useful for debugging but generates an enormous amount of data
# log=mysql.full
# log queries slower than n seconds, log file name relative to datadir (for debugging only)
# log_slow_queries=mysql.slow
# long_query_time=1
# log queries not using indices, debug only, disable for production use
# log_queries_not_using_indexes=1
#
# mesure database size and adjust innodb_buffer_pool_size
# SELECT sum(data_length) as bla, sum(index_length) as blub FROM information_schema.tables WHERE table_schema not in ("mysql", "information_schema");

# NOTES:
# Keep Innob_log_waits and keep Innodb_buffer_pool_wait_free small (see show global status like "inno%", show global variables)

#expire_logs_days=3

#sync_bin_log=0

# Use UTF-8 encoding for tables
character_set_server=utf8
collation_server=utf8_general_ci

# use InnoDB for transactions and better crash recovery
default_storage_engine=innodb

# memory pool InnoDB uses to store data dictionary information and other internal data structures (default:8M)
# Deprecated in MySQL >= 5.6.3, removed in 5.7 (works in MariaDB)
# innodb_additional_mem_pool_size=8M

# memory buffer InnoDB uses to cache data and indexes of its tables (default:128M)
# Larger values means less I/O
innodb_buffer_pool_size=80M

# Create a .ibd file for each table (default:0)
innodb_file_per_table=1

# Write out the log buffer to the log file at each commit (default:1)
innodb_flush_log_at_trx_commit=2

# Buffer size used to write to the log files on disk (default:1M for builtin, 8M for plugin)
# larger values means less I/O
innodb_log_buffer_size=1M

# Size of each log file in a log group (default:5M) larger means less I/O but more time for recovery.
innodb_log_file_size=64M

# # error log file name, relative to datadir (default:hostname.err)
log_error=mysql.err

# print warnings and connection errors (default:1)
log_warnings=2

# Convert table named to lowercase
lower_case_table_names=1

# Maximum size of one packet or any generated/intermediate string. (default:1M)
max_allowed_packet=32M

# Maximum simultaneous connections allowed (default:100)
max_connections=256

# The two options below make no sense with prepared statements and/or transactions
# (make sense when having the same query multiple times)

# Memory allocated for caching query results (default:0 (disabled))
query_cache_size=0

# Do not cache results (default:1)
query_cache_type=0

# Do not use the privileges mechanisms
skip_grant_tables

# Do not listen for TCP/IP connections at all
skip_networking

# The number of open tables for all threads. (default:64)
table_open_cache=200

# How many threads the server should cache for reuse (default:0)
thread_cache_size=3

# wait 365d before dropping the DB connection (default:8h)
wait_timeout=31536000

# We use InnoDB, so don't let MyISAM eat up memory
key_buffer_size=16K

[client]
default-character-set=utf8


Test 7:  SKIP
--------

MySQL server custom configuration not available.
Details: The custom configuration for the MySQL server was not found but is optional.

Test 8:  SUCCESS
--------

MySQL server configuration is usable.
Details: The MySQL server configuration was found at <a href="/home/me/.local/share/akonadi/mysql.conf">/home/me/.local/share/akonadi/mysql.conf</a> and is readable.

File content of '/home/me/.local/share/akonadi/mysql.conf':
#
# Global Akonadi MySQL server settings,
# These settings can be adjusted using $HOME/.config/akonadi/mysql-local.conf
#
# Based on advice by Kris Köhntopp <kris@mysql.com>
#
[mysqld]

# strict query parsing/interpretation
# TODO: make Akonadi work with those settings enabled
# sql_mode=strict_trans_tables,strict_all_tables,strict_error_for_division_by_zero,no_auto_create_user,no_auto_value_on_zero,no_engine_substitution,no_zero_date,no_zero_in_date,only_full_group_by,pipes_as_concat
# sql_mode=strict_trans_tables

# DEBUGGING:
# log all queries, useful for debugging but generates an enormous amount of data
# log=mysql.full
# log queries slower than n seconds, log file name relative to datadir (for debugging only)
# log_slow_queries=mysql.slow
# long_query_time=1
# log queries not using indices, debug only, disable for production use
# log_queries_not_using_indexes=1
#
# mesure database size and adjust innodb_buffer_pool_size
# SELECT sum(data_length) as bla, sum(index_length) as blub FROM information_schema.tables WHERE table_schema not in ("mysql", "information_schema");

# NOTES:
# Keep Innob_log_waits and keep Innodb_buffer_pool_wait_free small (see show global status like "inno%", show global variables)

#expire_logs_days=3

#sync_bin_log=0

# Use UTF-8 encoding for tables
character_set_server=utf8
collation_server=utf8_general_ci

# use InnoDB for transactions and better crash recovery
default_storage_engine=innodb

# memory pool InnoDB uses to store data dictionary information and other internal data structures (default:8M)
# Deprecated in MySQL >= 5.6.3, removed in 5.7 (works in MariaDB)
# innodb_additional_mem_pool_size=8M

# memory buffer InnoDB uses to cache data and indexes of its tables (default:128M)
# Larger values means less I/O
innodb_buffer_pool_size=80M

# Create a .ibd file for each table (default:0)
innodb_file_per_table=1

# Write out the log buffer to the log file at each commit (default:1)
innodb_flush_log_at_trx_commit=2

# Buffer size used to write to the log files on disk (default:1M for builtin, 8M for plugin)
# larger values means less I/O
innodb_log_buffer_size=1M

# Size of each log file in a log group (default:5M) larger means less I/O but more time for recovery.
innodb_log_file_size=64M

# # error log file name, relative to datadir (default:hostname.err)
log_error=mysql.err

# print warnings and connection errors (default:1)
log_warnings=2

# Convert table named to lowercase
lower_case_table_names=1

# Maximum size of one packet or any generated/intermediate string. (default:1M)
max_allowed_packet=32M

# Maximum simultaneous connections allowed (default:100)
max_connections=256

# The two options below make no sense with prepared statements and/or transactions
# (make sense when having the same query multiple times)

# Memory allocated for caching query results (default:0 (disabled))
query_cache_size=0

# Do not cache results (default:1)
query_cache_type=0

# Do not use the privileges mechanisms
skip_grant_tables

# Do not listen for TCP/IP connections at all
skip_networking

# The number of open tables for all threads. (default:64)
table_open_cache=200

# How many threads the server should cache for reuse (default:0)
thread_cache_size=3

# wait 365d before dropping the DB connection (default:8h)
wait_timeout=31536000

# We use InnoDB, so don't let MyISAM eat up memory
key_buffer_size=16K

[client]
default-character-set=utf8


Test 9:  SUCCESS
--------

akonadictl found and usable
Details: The program '/bin/akonadictl' to control the Akonadi server was found and could be executed successfully.
Result:
akonadictl 5.4.3


Test 10:  ERROR
--------

Akonadi control process not registered at D-Bus.
Details: The Akonadi control process is not registered at D-Bus which typically means it was not started or encountered a fatal error during startup.

Test 11:  ERROR
--------

Akonadi server process not registered at D-Bus.
Details: The Akonadi server process is not registered at D-Bus which typically means it was not started or encountered a fatal error during startup.

Test 12:  SKIP
--------

Protocol version check not possible.
Details: Without a connection to the server it is not possible to check if the protocol version meets the requirements.

Test 13:  ERROR
--------

No resource agents found.
Details: No resource agents have been found, Akonadi is not usable without at least one. This usually means that no resource agents are installed or that there is a setup problem. The following paths have been searched: '/usr/share/akonadi/agents'. The XDG_DATA_DIRS environment variable is set to '/var/lib/plasma5-profiles/common/share:/usr/local/share:/usr/share'; make sure this includes all paths where Akonadi agents are installed.

Directory listing of '/usr/share/akonadi/agents':
akonadiindexingagent.desktop
akonotesresource.desktop
birthdaysresource.desktop
contactsresource.desktop
davgroupwareresource.desktop
googlecalendarresource.desktop
googlecontactsresource.desktop
icaldirresource.desktop
icalresource.desktop
imapresource.desktop
invitationsagent.desktop
kalarmdirresource.desktop
kalarmresource.desktop
knutresource.desktop
maildirresource.desktop
maildispatcheragent.desktop
mboxresource.desktop
migrationagent.desktop
mixedmaildirresource.desktop
newmailnotifieragent.desktop
notesresource.desktop
openxchangeresource.desktop
pop3resource.desktop
tomboynotesresource.desktop
vcarddirresource.desktop
vcardresource.desktop

Environment variable XDG_DATA_DIRS is set to '/var/lib/plasma5-profiles/common/share:/usr/local/share:/usr/share'

Test 14:  SUCCESS
--------

No current Akonadi server error log found.
Details: The Akonadi server did not report any errors during its current startup.

Test 15:  ERROR
--------

Previous Akonadi server error log found.
Details: The Akonadi server reported errors during its previous startup. The log can be found in <a href="/home/me/.local/share/akonadi/akonadiserver.error.old">/home/me/.local/share/akonadi/akonadiserver.error.old</a>.

File content of '/home/me/.local/share/akonadi/akonadiserver.error.old':
Failed to connect to database!Database error: "Can't connect to local MySQL server through socket '/tmp/akonadi-me.XLSDgq/mysql.socket' (111 \"Connection refused\") QMYSQL: Unable to connect"Failed to remove runtime connection config file

Test 16:  SUCCESS
--------

No current Akonadi control error log found.
Details: The Akonadi control process did not report any errors during its current startup.


Update
Looks like a permissions problem?? As creating a new user and running Kalarm /Korganizer works OK.

Well, seems the internal mysql database that akonadi used and/or the akonadi configuration was not migrated properly, you would need to recreate those from scratch, that's probably the cleanest way.

So try stopping akonadi via akonadictl stop and then move away/rename ~/.local/share/akonadi

You could also try via akonadictl fsck but I'm not sure if that will fix problems in the underlying database schema

Good Morning doktor5000,
Akonadi was already stopped so simply renaming the ~/.local/share/akonadi directory and then running akonadictl start as you suggested fixed the problem. It threw up some errors but then recreated what it needed.
Thanks for your help, much appreciated.