AlphaFold

Description

See Alphafold2 and Alphafold3.

AlphaFold in the FASRC Cannon cluster

Alphafold typically runs within a Docker container. However, Docker containers are not allowed in high performance computing (HPC) systems such as Cannon because Docker requires root/sudo privileges, which poses a security concern in HPC systems.

Instead, we use Singularity containers which was specifically designed for HPC systems.

Singularity images

The AlphaFold singularity images are stored in a cluster-wide location, meaning that individual users do not have to copy the singularity images to use them. Singularity images are located in:

/n/singularity_images/FAS/alphafold/

Each singularity image is tagged with the Alphafold version

[jharvard@holylogin03 ~]$ ls -l /n/singularity_images/FAS/alphafold/
total 17G
-rwxr-xr-x. 1 root root 4.8G May 25 2023 alphafold_2.3.1.sif
-rwxr-xr-x. 1 root root 2.9G May 25 2023 alphafold_2.3.2.sif
-rwxr-xr-x. 1 root root 4.9G Dec 16 11:47 alphafold_3.0.0.sif
-rwxr-xr-x. 1 root root 4.5G Nov 2 2022 alphafold_v2.2.4.sif
-rw-r--r--. 1 root root 817 Dec 5 13:35 readme.txt

• Version 3.0.0: Created by FASRC based on the published Dockerfile by Google Deepmind
• Version 2.3.2: Downloaded from Catguma DockerHub
• Version 2.3.1: Downloaded from TACC DockerHub
• Version 2.2.4: We build a Singularity container based on the Singularity definition file from https://github.com/prehensilecode/alphafold_singularity.

Databases

The Alphafold database is stored in a cluster-wide location, meaning that individual users do not have to download the AlphaFold database to run their simulations. The database is stored in SSD as recommended by the developers. Database locations:

Alphafold2

/n/holylfs04-ssd2/LABS/FAS/alphafold_database

Alphafold3

/n/holylfs04-ssd2/LABS/FAS/alphafold_databases/v3.0/

Model parameters

Alphafold3

To run Alphafold3, you must request the model parameters from Google. See Obtaining model parameters.

Google will provide a file file_name.bin.zst. Extract with unzstd file.bin.zst. Place file.bin in a lab share (do not put in netscratch) — this will be the location of you --model_dir.

Running Alphafold

You will find example scripts in the FARC User_Codes repo.

Resources

• Get Started with AlphaFold code examples on FASRC Github
• Alphafold3 Github
• Alphafold2 GitHub
• University of Virginia AlphaFold docs
• AlphaFold discussion about Singularity implementation
• Job Efficiency and Optimization Best Practices