apptainer_cmd.md

Use Apptainer on SuperPod/M3

Author: Junhao Shen email: [email protected]

• OS:MacOS/Linux
• reference: https://apptainer.org/docs/user/latest/quick_start.html
  https://ponyland.science.ru.nl/ponyland/development_tips/mysql_with_apptainer/

Mysql use case

1. Connect to SuperPod/M3

...

2. Create a file that contains an initial MySQL command that sets the root password:

echo "SET PASSWORD FOR 'root'@'localhost' = '<root_password>';" > .mysqlrootpw

Repalce root_password with your password

3. Create a new container instance by pulling the MySQL-Docker image:

apptainer pull --name mysql.simg docker://mysql

run pwd to get the current directory, and replace ${PWD} with the output of pwd or PWD= the output of pwd

4. Start the MySQL container instance:

apptainer instance start --bind ${PWD} --bind ${PWD}/mysql/var/lib/mysql/:/var/lib/mysql --bind ${PWD}/mysql/run/mysqld:/run/mysqld ./mysql.simg mysql

--bind makes sure that some directories in the current directory are also available in the container.

5. Initialize the MySQL database:

apptainer exec instance://mysql mysqld --initialize --init-file=${PWD}/.mysqlrootpw

6. Run the daemon:

apptainer exec instance://mysql mysqld --init-file=${PWD}/.mysqlrootpw

check if the container is running on port 3306: lsof -i:3306

7. Connect to the MySQL container instance:

apptainer shell instance://mysql mysql -S mysql/run/mysqld/mysqld.sock -u root -p

Enter the password you set in step 2.

Once you have complete above steps you only need to start your instance and run the daemon to start the mysql server by following step 4, 6, 7.