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Running temporary PostgreSQL database in SD Desktop

  1. Request access to the tools-for-sd-connect or upload your own PostgreSQL singularity container to SD Connect. Start a SD Desktop Virtual Machine that has data volume that is big enough for your data. Login to your SD Desktop, open Data Gateway connection to SD Connect and open a terminal session.

  2. In the terminal session, create directory /media/volume/psql and move there

    mkdir/media/volume/psql
cd /media/volume/psql

  3. Import Apptainer container containing PostreSQL

    cp $HOME/Projects/SD\ connect/*/tools-for-sd-desktop/apptainer/postgres_14.2-alpine3.15.sif ./

  4. Create PostgreSQL environment file (pg.env) to be used.

    module load nano
nano pg.env

  5. Add following settings to the file

    export TZ=Europe/Helsinki
export POSTGRES_USER=pguser
export POSTGRES_PASSWORD=pg123
export POSTGRES_DB=mydb
export POSTGRES_INITDB_ARGS="--encoding=UTF-8"

    Then save and exit nano.

  6. Create directories for PostgreSQL server

    mkdir pgdata
mkdir pgrun

  7. Start a screen session in your terminal session and launch database server using the container:

    screen
apptainer run -B pgdata:/var/lib/postgresql/data -B pgrun:/var/run/postgresql -e -C --env-file pg.env postgres_14.2-alpine3.15.sif

    Then leave the screen session by pressing:

    Ctrl-a-d

    The server should now continue running in the screen session.

  8. Open a shell session into your PostgreSQL container. Remember to mount the directory where you have your data (e.g. /shared-directory)

    apptainer shell -B /shared-directory:/shared-directory postgres_14.2-alpine3.15.sif

    Inside container, move to your data directory and star working with your database:

    cd  /shared-directory
psql -h localhost -p 5432 -d mydb -U pguser

    For example

    psql -h localhost -p 5432 -d mydb -U pguser f psql_dump_file.sql
Last update: October 27, 2023