Having a hard time tracking this down. I tested on Jaunty (amd64), it does not have the problem. But on Hardy, after upgrading from mysql 5.0 to mariadb 5.1, the mysql_upgrade does not complete, and mysqld_safe hangs when stopping the server. Upon next restart, mysql_upgrade completes successfully, and everything seems ok. I have appended logs below, note how the mysqlcheck and mysql_upgrade seems to abort early, without any visible error messages. Here is the log from /etc/mysql/debian-start from the first, unsuccessful start: Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5418]: Upgrading MySQL tables if necessary. Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: /usr/bin/mysql_upgrade: the '--basedir' option is always ignored Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: Looking for 'mysql' as: /usr/bin/mysql Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: Looking for 'mysqlcheck' as: /usr/bin/mysqlcheck Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: Running 'mysqlcheck' with connection arguments: '--port=3306' '--socket=/var/run/mysqld/mysqld.sock' '--host=localhost' '--socket=/var/run/mysqld/mysqld.sock' '--socket=/var/run/mysqld/mysqld.sock' Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: Running 'mysqlcheck' with connection arguments: '--port=3306' '--socket=/var/run/mysqld/mysqld.sock' '--host=localhost' '--socket=/var/run/mysqld/mysqld.sock' '--socket=/var/run/mysqld/mysqld.sock' Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: mysql.columns_priv OK Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: mysql.db OK Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: mysql.event OK Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: mysql.func OK Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: mysql.general_log Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: Error : You can't use locks with log tables. Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: status : OK Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: mysql.help_category Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: error : Table upgrade required. Please do "REPAIR TABLE `help_category`" or dump/reload to fix it! Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: mysql.help_keyword Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: error : Table upgrade required. Please do "REPAIR TABLE `help_keyword`" or dump/reload to fix it! Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: mysql.help_relation OK Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: mysql.help_topic Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: error : Table upgrade required. Please do "REPAIR TABLE `help_topic`" or dump/reload to fix it! Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: mysql.host OK Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: mysql.ndb_binlog_index OK Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: mysql.plugin OK Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: mysql.proc Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: error : Table upgrade required. Please do "REPAIR TABLE `proc`" or dump/reload to fix it! Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: mysql.procs_priv OK Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: mysql.servers OK Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: mysql.slow_log Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: Error : You can't use locks with log tables. Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: status : OK Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: mysql.tables_priv OK Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: mysql.time_zone OK Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: mysql.time_zone_leap_second OK Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: mysql.time_zone_name Dec 15 10:54:17 vm-hardy-amd64 /etc/mysql/debian-start[5425]: error : Table upgrade required. Please do "REPAIR TABLE `time_zone_name`" or dump/reload to fix it! And here is the output after server stop and restart, this time successful: Dec 15 10:24:53 vm-jaunty-amd64 /etc/mysql/debian-start[4442]: Upgrading MySQL tables if necessary. Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: Looking for 'mysql' as: /usr/bin/mysql Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: Looking for 'mysqlcheck' as: /usr/bin/mysqlcheck Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: Running 'mysqlcheck'... Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: Running 'mysqlcheck'... Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.columns_priv OK Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.db OK Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.event OK Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.func OK Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.general_log Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: Error : You can't use locks with log tables. Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: status : OK Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.help_category Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: error : Table upgrade required. Please do "REPAIR TABLE `help_category`" to fix it! Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.help_keyword Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: error : Table upgrade required. Please do "REPAIR TABLE `help_keyword`" to fix it! Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.help_relation OK Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.help_topic Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: error : Table upgrade required. Please do "REPAIR TABLE `help_topic`" to fix it! Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.host OK Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.ndb_binlog_index OK Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.plugin OK Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.proc Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: error : Table upgrade required. Please do "REPAIR TABLE `proc`" to fix it! Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.procs_priv OK Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.servers OK Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.slow_log Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: Error : You can't use locks with log tables. Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: status : OK Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.tables_priv OK Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.time_zone OK Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.time_zone_leap_second OK Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.time_zone_name Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: error : Table upgrade required. Please do "REPAIR TABLE `time_zone_name`" to fix it! Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.time_zone_transition OK Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.time_zone_transition_type OK Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.user OK Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mytest.t OK Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: Repairing tables Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.help_category OK Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.help_keyword OK Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.help_topic OK Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.proc OK Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: mysql.time_zone_name OK Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: Running 'mysql_fix_privilege_tables'... Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4448]: OK Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4472]: Checking for insecure root accounts. Dec 15 10:24:54 vm-jaunty-amd64 /etc/mysql/debian-start[4476]: Triggering myisam-recover for all MyISAM tables