cbmckni / slurmflow

A collection of Docker containers for setting up a Slurm-based cluster, configured to run Nextflow workflows.

Docker SLURM Cluster

This repository is forked from Data Driven HPC that provides a set of containers that can be used to run a SLURM HPC cluster as a set of Docker containers. This version is configured with Nextflow to run sra2gev-slurm The project consists of three components:

1. docker-slurmctld provide a SLURM controller or "head node".

2. docker-slurmd provides a SLURM compute node.

3. docker-slurmbase is the base container from which both docker-slurmctld and docker-slurmd inherit.

This repository contains the container source files. The ready built container images are available via DockerHub: https://hub.docker.com/r/gromr1.

The Docker SLURM cluster is configured with the following software packages:

• Ubuntu 16.04 LTS
• SLURM 17.11.2
• GlusterFS 3.8
• Open MPI 1.10.2
• Nextflow

A user ddhpc is configured across all nodes for MPI job execution and a shared GlusterFS volume ddhpc is mounted on all nodes as /data/ddhpc. The head node runs an SSH server for accessing the cluster.

Launch a New SLURM cluster

Create a new directory with a docker-compose.yml file:

version: '2'

services:
  slurmflowctld:
    container_name: slurmflowctld
    environment:
      SLURM_CLUSTER_NAME: ddhpc
      SLURM_CONTROL_MACHINE: slurmflowctld
      SLURM_NODE_NAMES: slurmflowd
      INFLUXDB_HOST: influxdb
      INFLUXDB_DATABASE_NAME: docker_slurm
    tty: true
    hostname: slurmflowctld
    networks:
      default:
        aliases:
          - slurmflowctld
    image: cbmckni/slurmflowctld
    stdin_open: true
  slurmflowd:
    container_name: slurmflowd
    environment:
      SLURM_CONTROL_MACHINE: slurmflowctld
      SLURM_CLUSTER_NAME: ddhpc
      SLURM_NODE_NAMES: slurmflowd
      INFLUXDB_HOST: influxdb
      INFLUXDB_DATABASE_NAME: docker_slurm
    tty: true
    hostname: slurmflowd
    networks:
      default:
        aliases:
          - slurmflowd
    image: cbmckni/slurmflowd
    depends_on:
      - slurmflowctld
    stdin_open: true

After that you can create and run the configured containers with a command docker-compose up -d.

For a stopping them run docker-compose down.

Configuration variables:

• SLURM_CLUSTER_NAME: the name of the SLURM cluster.
• SLURM_CONTROL_MACHINE: the host name of the controller container. This should match hostname in the slurmctld section.
• SLURM_NODE_NAMES: the host name of the compute node container. This should match hostname in the slurmd section.
• INFLUXDB_HOST: the host name of the database host.
• INFLUXDB_DATABASE_NAME: the name of existing database in influxdb host. Database should exists a retention policy with name 'default'.