Docker SciDB

Scripts for building a Docker image of the array database SciDB

Files:

• .pam_environment - User's environmental variable file.
• Dockerfile - Docker file for building a Docker Image.
• LICENSE - License file.
• README.md - This file.
• conf - SHIM configuration file.
• config.ini - SciDB's configuration file.
• containerSetup.sh - Commands for setting up SciDB inside a container. It also creates some test data.
• iquery.conf - IQUERY configuration file.
• setup.sh - Host script for removing existing containers and images from host machine. Then, it creates a Docker image called "scidb_img".
• startScidb.sh - Simple script for starting SciDB.
• stopScidb.sh - Simple script for stopping SciDB.

Prerequisites:

• Docker

Instructions:

1. Clone the project and CD to the docker_scidb folder: git clone https://github.com/albhasan/docker_scidb.git
2. Modify the scripts to fit your needs:
   • Dockerfile sets up the passwords for root, postgres and scidb users.
   • config.ini sets up the user and password for scidb user on postgres.
3. Enable setup.sh for execution (chmod +x setup.sh) and run it (./setup.sh): This creates a new image from the Dockerfile. WARNING: This will delete all the stopped containers and unused images.
4. Start a container. For example, these examples create a container called "scidb1" from the "scidb_img" image:
   • Keep all the data in the container: docker run -d -P --name="scidb1" -p 49901:49901 -p 49903:49903 -p 49904:49904 --expose=49902 --expose=49910 scidb_img
   • Keep SciDB's data on a host's folder: docker run -d -P --name="scidb1" -p 49901:49901 -p 49903:49903 -p 49904:49904 --expose=49902 --expose=49910 -v /var/bliss/scidb/test/data:/home/scidb/data scidb_img
   • Keep SciDB's data and catalog (postgres) data on host's folders: docker run -d -P --name="scidb1" -p 49901:49901 -p 49903:49903 -p 49904:49904 --expose=49902 --expose=49910 -v /var/bliss/scidb/test/data:/home/scidb/data -v /var/bliss/scidb/test/catalog:/home/scidb/catalog scidb_img
5. Log into the container: ssh -p 49901 root@localhost
6. Execute the commands in /home/root/containerSetup.sh. NOTE: You need to copy & paste the commands to a terminal

NOTES:

containerSetup.sh despite the extension, this file is not meant to be ran as a bash script.

containerSetup.sh includes instructions on moving postgres files to a different folder. Mounting a volume on that folder enable storage of catalog data in the host.

When using volumes, match user's ID of a container-user "scidb" to a host-user with the proper writing rights.

Changing SciDB setup requires the addition of a new configuration to config.ini and later a modification on startScidb.sh. For example, changing single instance default configuration for one with 7 instances would require changing the lines on startScidb.sh:

• scidb.py initall scidb_docker
• scidb.py startall scidb_docker
• scidb.py status scidb_docker

For these:

• scidb.py initall scidb_docker_bigdata
• scidb.py startall scidb_docker_bigdata
• scidb.py status scidb_docker_bigdata