AlphaFold

Description

See AlphaFold.

AlphaFold in the FASRC Cannon cluster

AlphaFold 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 13G
-rwxr-xr-x. 1 root root 4.8G May 25 18:06 alphafold_2.3.1.sif
-rwxr-xr-x. 1 root root 2.9G May 25 18:10 alphafold_2.3.2.sif
-rwxr-xr-x. 1 root root 4.5G Nov  2  2022 alphafold_v2.2.4.sif
-rw-r--r--. 1 root root  733 May 25 18:13 readme.txt

• 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.

AlphaFold database

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 location:/holylfs04-ssd2/LABS/FAS/alphafold_database

Submitting a slurm batch job that runs AlphaFold

Log in to Cannon (see login instructions). Go to the directory where your code is located. Then submit a slurm batch job ( man sbatch ).


Examples

You will find example scripts in the FARC User_Codes repo.

Resources

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