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Setup

MYSQL setup

We recommend using a Docker container to run your first MySQL server. This is the easiest way to get started.

Option 1: Use a Docker container

Please make sure you have docker installed and configured. You can follow the instructions at the Docker official documentation. To test your installation, execute

docker run hello-world

Once Docker is installed and configured, we will run a mySQL server using the official Docker image. We require to two ingredients to setup the MySQL server:

  • A port number to communicate with the server. MySQL server uses port 3306 by default.
  • A password for the root user.

Execute the following command to pull the image and run the MySQL server in a Docker container:

docker run -d --name=myfirst-sqlserver -p 3306:3306 --env="MYSQL_ROOT_PASSWORD=mypassword" mysql

Here we named the container as myfirst-sqlserver. It is running on host localhost and port 3306. A user with name root already exists with the password that you set in the environment variable MYSQL_ROOT_PASSWORD.

Port conflict issues

If you run into a port conflict issue (because the port is already in use, for example), then you can map the port number to a different one. Something like port XXXX in -p XXXX:3306 in the above Docker command. {: .callout}

Never use weak passwords in production!

Probably obvious, but this is a friendly reminder. Use strong passwords when you are working with real data in databases that are accessible from outside your computer. {: .callout}

To test that if everything is up and running, execute the following command:

docker exec -it myfirst-sqlserver bash -c "mysql -uroot -pmypassword"

you should see the mysql prompt as mysql>. If yes, then everything is working.

You can type exit; in the mysql command prompt to exit.

Option 2: Setup a MySQL server via Apptainer

If you are working on institutional computers, then you might not have the permission to install or run Docker. In that case, you can use Apptainer, which allows you to run containers in shared resources without installing Docker. Chances are that you already have Apptainer available in institutional computers, check by executing the following command:

apptainer --version

We will use the same image as in Option 1. Appteiner images are readonly if overlayfs is not available, so we'll be mounting the socket and database directories. This allows also for some persistency. Depending on the system settings unprivileged Apptainer may not be allowed to bind to ports, so we'll use a socket file to connect to the server. First move to a local directory: the image is not small and disk access will be faster, e.g. mkdir /scratch/<username>/mysql-apptainer; cd /scratch/<username>/mysql-apptainer. Then execute the following commands to run the MySQL server in an Apptainer instance (replace mypassword with your password):

echo "SET PASSWORD FOR 'root'@'localhost' = 'mypassword';" > .mysqlrootpw
mkdir -p ./mysql/var/lib/mysql/ ./mysql/run/mysqld
apptainer pull --name mysql.sif docker://mysql
apptainer instance start --bind ${PWD} --bind ${PWD}/mysql/var/lib/mysql/:/var/lib/mysql --bind ${PWD}/mysql/run/mysqld:/run/mysqld  ./mysql.sif mysql
apptainer instance list    # just to make sure the instance started
apptainer exec instance://mysql mysqld --init-file=${PWD}/.mysqlrootpw &

If you don't run the last command in background the terminal will be used by the server console and you'll have to use another terminal for other commands.

To test that if everything is up and running, execute the following command:

apptainer exec instance://mysql mysql -S /var/run/mysqld/mysql.sock -u root -pmypassword

Remember to use it also throughout the tutorial instead of the docker command.

You may want to use a different password and a safer way to run mysql id to avoid to put the password in the command line, e.g. save in mysqlclient.ini the following:

[client]
password="mypassword"

And then run with (--defaults-extra-file must be the first option):

apptainer exec instance://mysql mysql --defaults-extra-file=myconf -S /var/run/mysqld/mysql.sock -u root

If you are interested on learning more about Apptainer, take a look at the HSF Training on Apptainer

Option 3: Use a MySQL server on a remote machine

If you have access to a remote machine with a MySQL server (provided by your university or your laboratory), then you can use that.

Option 4: Use a MySQL/MariaDB server installed on your computer

If you want to install MySQL server on your computer, then you can follow the instructions at the official documentation.

Or you can use MariaDB, which is an open source fork of MySQL. You can follow the instructions at the official documentation. At the time of writing this document, both basic MySQL and MariaDB commands are compatible with each other.

Opensearch setup

docker run -d -p 9200:9200 -p 9600:9600 -e "discovery.type=single-node" -e "OPENSEARCH_INITIAL_ADMIN_PASSWORD=<custom-admin-password>" opensearchproject/opensearch:latest

Replace: <custom-admin-password> to a secure password of your choice.

Choosing a safe password

If you run with -it instead of -d and the password is not secure you will see the following message and the container will exit immediately.

Password <your-admin-password> failed validation:

< reason for failure >

Please re-try with a minimum 8 character password and must contain at least one uppercase letter, one lowercase letter, one digit, and one special character that is strong. Password strength can be tested here: https://lowe.github.io/tryzxcvbn

{: .output}

{: .callout}

To test that if everything is up and running, execute the following command:

curl https://localhost:9200 -ku 'admin:<custom-admin-password>'