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Run the following commands:
# dpkg-reconfigure mysql-server-5.5 # perl /var/www/imscp/engine/setup/imscp-setup -dar sql
You must adapte the dpkg-reconfigure command according the SQL server/version you're using.
Since i-MSCP 1.3.x serie, i-MSCP uses its own SQL user. To update the i-MSCP SQL user password, simply run
# perl /var/www/imscp/engine/setup/imscp-setup -dar sql