I set up mysql replication by adding references to binlogs, relay logs etc in my.cnf restarted mysql, it worked. I wanted to change it so I deleted all binlog related files including log-bin.index, removed binlog statements from my.cnf restarted server, works set master to '', purge master logs since now(), reset slave, stop slave, stop master. now, to set up replication again, I added binlog statements to the server. But then I hit this problem when restarting with: sudo mysqld (the only way to see mysql's startup errors) I get this error: /usr/sbin/mysqld: File '/etc/mysql/var/log-bin.index' not found (Errcode: 13) Because indeed, this file does not exist! (I deleted it, while trying to set up a new replication system) Hmm, if I change the config line to: log-bin-index = log-bin.index I get a different error: [ERROR] Can't generate a unique log-filename /etc/mysql/var/bin.(1-999) [ERROR] MSYQL_BIN_LOG::open failed to generate new file name. [ERROR] Aborting The first time I set up replication on this system, I didn't need to create this file. I did the same thing - added references to a previously non-existing file, and mysql created it. Same with relay logs, etc. I don't know why mysql insists on trying to read the old folder. Should I just reinstall the whole package again? That seems like overkill. my my.cnf: [client] port = 3306 socket = /var/run/mysqld/mysqld.sock [mysqld_safe] socket = /var/run/mysqld/mysqld.sock nice = 0 [mysqld] user = mysql socket = /var/run/mysqld/mysqld.sock port = 3306 basedir = /usr datadir = /var/lib/mysql tmpdir = /tmp skip-external-locking bind-address = IP key_buffer = 16M max_allowed_packet = 16M thread_stack = 192K thread_cache_size = 8 myisam-recover = BACKUP table_cache = 64 sort_buffer =64K net_buffer_length =2K query_cache_limit = 1M query_cache_size = 16M slow_query_log_file = /etc/mysql/var/mysql-slow.log long_query_time = 1 log-queries-not-using-indexes expire_logs_days = 10 max_binlog_size = 100M server-id = 3 log-bin = /etc/mysql/var/bin.log log-slave-updates log-bin-index = /etc/mysql/var/log-bin.index log-error = /etc/mysql/var/error.log relay-log = /etc/mysql/var/relay.log relay-log-info-file = /etc/mysql/var/relay-log.info relay-log-index = /etc/mysql/var/relay-log.index auto_increment_increment = 10 auto_increment_offset = 3 master-host = HOST master-user = USER master-password=PWD replicate-do-db = DBNAME collation_server=utf8_unicode_ci character_set_server=utf8 skip-character-set-client-handshake [mysqldump] quick quote-names max_allowed_packet = 16M [mysql] #no-auto-rehash [myisamchk] key_buffer_size = 16M sort_buffer_size = 8M [mysqlhotcopy] interactive-timeout !includedir /etc/mysql/conf.d/ Update: Changing all the /etc/mysql/var/xxx paths in binlog & relay log statements to local has somehow solved the problem. I thought it was apparmor causing it at first, but when I added /etc/mysql/* rw, to apparmor's config and restarted it, it still couldn't read the full path.