ARCHER2¶

ARCHER2 is the UK research community supercomputing facility. The purpose of this note is to collect relevant information for accessing and working on this facility, specific to my needs and those of my group. There is a lot of general information available on the ARCHER2 website (links below).

** If just getting started, follow the Quickstart for Users documentation (see below) **

Useful links¶

Archer homepage : https://www.archer2.ac.uk/

Documentation homepage : https://docs.archer2.ac.uk/

Quickstart guides :

Getting an account, requesting access to projects, logging on, basic filesystem details: https://docs.archer2.ac.uk/quick-start/quickstart-users/
Compiling and running software : https://docs.archer2.ac.uk/quick-start/quickstart-developers/

User and Best Practice guide : https://docs.archer2.ac.uk/user-guide/

Organization¶

Adminisitrative details (e.g. accounts, projects, allocations) are handled via SAFE (safe.epcc.ed.ac.uk). Users need to sign up for an account on there, and through there, request access to a specific project (see project details below).

SAFE is also the place in which a project PI can approve users, check usage, and observe allocation.

Example .ssh/config entry

Host archer2
        Hostname login.archer2.ac.uk
        User graemem
        IdentityFile ~/.ssh/id_rsa_archer

Note that your ssh key has to have a password associated with it (in addition to your ARCHER2 (LDAP) password).

Directory structure¶

User directories are organized by projects, with space available in both /work/project_id/project_id/$USER and /home/project_id/project_id/$USER. The work directory has more storage space.

Within each project work directory there is a shared folder, which all user can read from and write to. If you wish to share something with users not in the project (e.g. ARCHER2 admin for debugging), you need to put it in /work/project_id/shared.

Project details¶

CO2 and climate change: high-latitude oceans¶

Project ID : e786
PI username/email : gam24@st-andrews.ac.uk

Analysis and running jobs¶

Details on partitions and slurm scheduler here.

Command for starting an interactive session on the data-viz partition (serial):

srun --nodes=1 --time=01:30:00 --account=e786 --partition=serial --qos=serial --pty /bin/bash

Software¶

Supporting documentation for using a wide array of Research Software on archer2 (including MITgcm, NEMO, and CESM2) is provided here.

Python, virtual environments, and package managers¶

General documentation on using python is included here.

For installing your own packages, you are recommended to use pip (documentation here) rather than conda, especially when hoping to use those packages on the compute nodes. You can do this in a virtual environment (recommended) using the venv software (follow the instructions at the link above).

Notes [Graeme] I have taken the approach of using pip to install modules that I hope to use on the compute nodes, e.g. for any large computation. This causes problems when certain software (e.g. OceanParcels) are configured quite specifically to be installed with conda. I have not yet worked around this.

I have also installed an instance of miniconda in my home directory, allowing me to install and use packages on the login nodes and data visualisation nodes (qos=serial).

Jupyter Lab¶

Jupyter lab can be run either from the login/data vis nodes, or from the compute nodes, following the procedure outlined here. The only addition made to this procedure is to select a port number (instead of the default 8888). Using the default can lead to errors if your local machine is already using that port.

The command to launch Jupyter Lab is:

jupyter lab --no-browser --ip=0.0.0.0 --port=8659

The ip flag is required; the port number can be whatever you want (within a certain range).

Additonal information¶

You should use the following phrase to acknowledge ARCHER2 for all research outputs that were generated using the ARCHER2 service:
This work used the ARCHER2 UK National Supercomputing Service (https://www.archer2.ac.uk).
You should also tag outputs with the keyword “ARCHER2” whenever possible.

Acknowledgments¶

From the ARCHER2 website:

ARCHER2