Installation - umccr/aws_parallel_cluster GitHub Wiki

Installation

Prerequisites

You must have conda and jq before continuing.

Please ensure that you've configured your aws account, and installed the aws session manager plugin

  • MacOS users:

    • Must have brew installed
    • Must have coreutils installed (via brew)
      • This ensures greadlink is installed and is required in the install.sh script for MacOS users.

  • Windows users

    • Must be on Windows 10 with WSL2 installed (on Ubuntu).

  • Linux users

    • No additional prerequisites required. You've suffered for long enough.

Update conda

Ensure your base conda env is up to date before continuing

# Make sure conda is at the latest version
conda update --name base conda

Download/install via a release

Head to the releases page to download the latest release.

You can also run the following command assuming you are downloading the latest version

( \
  cd "$(mktemp -d)" && \
  wget "https://github.com/umccr/aws_parallel_cluster/releases/download/latest/release-latest.zip" && \
  unzip "release-latest" && \
  bash "release-latest/install.sh" \ 
)

Download/install from git source

Not recommended :construction: At the moment, we don't have a clear way for determining what ami should be 'latest'. If you want to access immediate changes to your env, please checkout our development page

You can also clone this github directory and checkout out the latest tag and run the installation script

git clone https://github.com/umccr/aws_parallel_cluster
git checkout latest
./install.sh

Setting up your ssm shortcut

This SSM shell function should be added to your .bashrc or equivalent:

ssm() {
    aws ssm start-session \
      --target "$1" \
      --document-name AWS-StartInteractiveCommand \
      --parameters command="sudo su - ec2-user"
}

So that logging into the instances becomes:

$ ssm i-XXXXXXXXXXXXX

This is only possible since AmazonSSMManagedInstanceCore is set by default as an additional policy in your parallel cluster config and the ssm service is started in the ami builder.