PostgreSQL Docker Image with RDKit Cartridge

This is a PostgreSQL Docker image with the RDKit cartridge installed.

This image inherits from the official postgres image, and therefore has all the same environment variables for configuration, and can be extended by adding entrypoint scripts to the /docker-entrypoint-initdb.d directory to be run on first launch.

Running

Start Postgres server running in the background:

docker run --platform linux/amd64 --name mypostgres -p 5432:5432 -e POSTGRES_PASSWORD=mypassword -d postgres16-rdkit2024_03_3

Or run with an application via Docker Compose:

services:

  db:
    image: postgres16-rdkit2024_03_3
    restart: always
    environment:
      POSTGRES_PASSWORD: mypassword
    volumes:
      - /path/to/pgdata:/var/lib/postgresql/data

This image exposes port 5432 (the postgres port), so standard container linking will make it automatically available to the linked containers.

Environment Variables

POSTGRES_PASSWORD: Superuser password for PostgreSQL.
POSTGRES_USER: Superuser username (default postgres).
POSTGRES_DB: Default database that is created when the image is first started.
PGDATA: Location for the database files (default /var/lib/postgresql/data).

See the official postgres image for more details.

Building

To build, run:

  docker run --network gpcrdb -d --platform linux/amd64 --name postgres16-rdkit2024_03_3 \
  -v postgres_data:/var/lib/postgresql/data \
  -e POSTGRES_USER=protwis \
  -e POSTGRES_PASSWORD=protwis \
  -p 5432:5432 \
  postgres16-rdkit2024_03_3

Performance optimization

Source: https://www.rdkit.org/docs/Cartridge.html#configuration

For building the database

To improve performance while storing RDKIT molecule objects and fingerprints into the database, and while building the indexes, a couple of PostgreSQL configuration settings in postgresql.conf can be changed:

synchronous_commit = off      # immediate fsync at commit
full_page_writes = off            # recover from partial page writes

synchronous_commit = off: speeds normal operation, but increases the change of losing commits to the database if a sudden postgresql server crash happens. Commits will be reported as executed even if there are not stored and flushed into a durable storage (e.g. a hard drive or SSD).

full_page_writes = off: speeds normal operation, but might lead to either unrecoverable data corruption, or silent data corruption, after a system failure.

For queries (structural searches)

And to improve search performance, we can allow postgresql to use more memory than the extremely conservative default settings:

shared_buffers = 2048MB           # min 128kB, PostgreSQL's "dedicated" RAM
                  # (change requires restart)
work_mem = 128MB              # min 64kB, maximum amount of RAM memory to be used by a query
                              # operation before it starts to use disk memory instead.

These settings increase the RAM requirements for PostgreSQL to run.