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Confluence not starting after mysql upgrade

Johan Johansson

I have Confluence 7.3.1 with mysql version 5.7.27 on Linux 64 bit.

After the upgrade of mysql (from v 5.5) Confluence is no longer starting.

The error message I get is

ERROR [Catalina-utility-1] [confluence.setup.dbcheck.MySQLChecker] checkIsolationLevel MySQL isolation level could not be read. Isolation level must be 'READ-COMMITTED'. See http://confluence.atlassian.com/x/GAtmDg

When logging in to the mysql both the global and the session isolation level is READ-COMMITTED. So I dont get this error message.

I have tried to add the parameter to the connection string to, but to no avail.

The upgrade was made on error but unfortunately we didnt use it for a long time so we no longer have a backup of the one before the upgrade..

EDIT:

Anyway, after fiddling for ages with mysql, I have been able to get forward, but still I get startup errors. Does anyone have an idea what this means:

2020-03-10 13:47:01,387 ERROR [perm-delta-cache-receiver] [gatekeeper.evaluator.cache.GroupMembersCache] error Loading group members from database failed: could not extract ResultSet
2020-03-10 13:47:01,403 ERROR [perm-delta-cache-receiver] [gatekeeper.evaluator.cache.CacheUpdateReceiver] error Failed to initialize evaluator cache
Failed to initialize evaluator cache^C
informa_jojo@jiratest2:~$
informa_jojo@jiratest2:~$ ERROR [perm-delta-cache-receiver] [engine.jdbc.spi.SqlExceptionHelper]2020-03-10 13:47:01,386 ERROR [perm-delta-cache-receiver] [engine.jdbc.spi.SqlExceptionHelper] logExceptions Unknown column 'hibernatem0_.child_user_id' in 'where clause'
-bash: ERROR: command not found
informa_jojo@jiratest2:~$ 2020-03-10 13:47:01,387 ERROR [perm-delta-cache-receiver] [gatekeeper.evaluator.cache.GroupMembersCache] error Loading group members from database failed: could not extract ResultSet
-bash: 2020-03-10: command not found
informa_jojo@jiratest2:~$ 2020-03-10 13:47:01,403 ERROR [perm-delta-cache-receiver] [gatekeeper.evaluator.cache.CacheUpdateReceiver] error Failed to initialize evaluator cache
-bash: 2020-03-10: command not found

thanks

any ideas please?

Many thanks

Accepted answers

Johan Johansson

Anyway, I was finally able to get it up and running.

It turned out I had imported the database dump with foregin key checks active, so some data had not been imported. So recreating the database with that turned off did the trick.

All comments

Nicolas Werle

Hi @Johan Johansson ,

can you please provide your my.cnf file (usually to find under /etc/my.cnf) so that we can investigate further?
Many thanks in advance.
Best,
Nicolas

Johan Johansson

#
# The MySQL database server configuration file.
#
# You can copy this to one of:
# - "/etc/mysql/my.cnf" to set global options,
# - "~/.my.cnf" to set user-specific options.
#
# One can use all long options that the program supports.
# Run program with --help to get a list of available options and with
# --print-defaults to see which it would actually understand and use.
#
# For explanations see
# http://dev.mysql.com/doc/mysql/en/server-system-variables.html

# This will be passed to all mysql clients
# It has been reported that passwords should be enclosed with ticks/quotes
# escpecially if they contain "#" chars...
# Remember to edit /etc/mysql/debian.cnf when changing the socket location.
[client]
port = 3306
socket = /var/run/mysqld/mysqld.sock

# Here is entries for some specific programs
# The following values assume you have at least 32M ram

# This was formally known as [safe_mysqld]. Both versions are currently parsed.
[mysqld_safe]
socket = /var/run/mysqld/mysqld.sock
nice = 0

[mysqld]
#
# * Basic Settings
#
user = mysql
pid-file = /var/run/mysqld/mysqld.pid
socket = /var/run/mysqld/mysqld.sock
port = 3306
basedir = /usr
datadir = /var/lib/mysql
tmpdir = /tmp
lc-messages-dir = /usr/share/mysql
skip-external-locking
character-set-server=utf8
collation-server=utf8_bin
transaction-isolation=READ-COMMITTED
#
# Instead of skip-networking the default is now to listen only on
# localhost which is more compatible and is not less secure.
bind-address = 127.0.0.1
#
# * Fine Tuning
#
key_buffer = 16M
max_allowed_packet = 256M
thread_stack = 192K
thread_cache_size = 8
# This replaces the startup script and checks MyISAM tables if needed
# the first time they are touched
myisam-recover = BACKUP
#max_connections = 100
#table_cache = 64
#thread_concurrency = 10
#
# * Query Cache Configuration
#
query_cache_limit = 1M
query_cache_size = 16M
#
#
# * Logging and Replication
#
# Both location gets rotated by the cronjob.
# Be aware that this log type is a performance killer.
# As of 5.1 you can enable the log at runtime!
#general_log_file = /var/log/mysql/mysql.log
#general_log = 1
#
# Error log - should be very few entries.
#
log_error = /var/log/mysql/error.log
#
# Here you can see queries with especially long duration
#slow_query_log_file = /var/log/mysql/mysql-slow.log
#slow_query_log = 1
#long_query_time = 2
#log_queries_not_using_indexes
#
# The following can be used as easy to replay backup logs or for replication.
# note: if you are setting up a replication slave, see README.Debian about
# other settings you may need to change.
#server-id = 1
#log_bin = /var/log/mysql/mysql-bin.log
expire_logs_days = 10
max_binlog_size = 100M
#binlog_do_db = include_database_name
#binlog_ignore_db = include_database_name
#
# * InnoDB
#
# InnoDB is enabled by default with a 10MB datafile in /var/lib/mysql/.
# Read the manual for more InnoDB related options. There are many!
#
# * Security Features
#
# Read the manual, too, if you want chroot!
# chroot = /var/lib/mysql/
#
# For generating SSL certificates I recommend the OpenSSL GUI "tinyca".
#
# ssl-ca=/etc/mysql/cacert.pem
# ssl-cert=/etc/mysql/server-cert.pem
# ssl-key=/etc/mysql/server-key.pem
innodb_log_file_size=256M

[mysqldump]
quick
quote-names
max_allowed_packet = 16M

[mysql]
#no-auto-rehash # faster start of mysql but no tab completition

[isamchk]
key_buffer = 16M

#
# * IMPORTANT: Additional settings that can override those from this file!
# The files must end with '.cnf', otherwise they'll be ignored.
#
!includedir /etc/mysql/conf.d/

Johan Johansson

Anyway, I was finally able to get it up and running.

It turned out I had imported the database dump with foregin key checks active, so some data had not been imported. So recreating the database with that turned off did the trick.

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