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AlphaFold

Description

AlphaFold is an AI system developed by DeepMind that predicts a protein’s 3D structure from its amino acid sequence.

License

Free to use and open source under Apache License 2.0.

Available

Version on CSC's Servers

  • Puhti: 2.0.1, 2.3.0, 2.3.2-1

Usage

To initialize in Puhti use:

module load alphafold

The following instructions are for versions starting from 2.3.2-1. For older versions see the help message printed out by module load command.

Loading the AlphaFold module will print out commands you can use to check the available command line options, e.g:

python3 $ALPHAFOLD_DIR/run_singularity.py --helpshort

There are example batch job scripts available:

$ALPHAFOLD_DIR/alphafold_cpu.slurm
$ALPHAFOLD_DIR/alphafold_gpu.slurm

Which version to use

AlphaFold analysis consists of three stages: - Multiple sequence alignment (CPU only) - Structure prediction (GPU enabled) - Optional: Chain relaxation (GPU enabled)

Building the multiple sequen alignments takes a considerable amount of time, and in case of short and simple sequences using GPU will only speed up the overall time a litle. In these cases you will probably get better throughput using the CPU version, as there are more CPU resources available.

In case of longer and more complex strutures GPU will speed up the process considerably.

It may be difficult to know beforehand, so do some testing. If the run is taking more than 3-4 hours on CPU, you should try using GPU.

Database

AlphaFold needs a set of sequence databases to run. The total size of of these databases is almost 3 TiB.

CSC maintains a copy of these databases compatible with the latest version of AlphaFold. Databases are mounted on all compute nodes in path /mnt/datasets/alphafold. The path to databases is set with variable $ALPHAFOLD_DATADIR. See example batch job scripts for usage.

export ALPHAFOLD_DATADIR=/mnt/datasets/alphafold

Due to the size of these databases CSC is only able to maintain one copy. If you need a different version, you will need to download your own copy.

You can follow the download instructions on the AlphaFold home page.

apptainer exec --bind /scratch $SING_IMAGE /scripts/download_all_data.sh <DOWNLOAD_DIR>

AlphaFold is very disk I/O heavy, so for use the databases should be copied to $LOCAL_SCRATCH. Even if copying takes some time (depends on file system load on Puhti, but typically ~1 h) the net gain on run time is considerable.

When copying databases from /scratch to $LOCAL_SCRATCH, you should avoid overloading the file system on /scratch, so aggressive multi-threaded copying approaches should be avoided.

Use for example:

cd $LOCAL_SCRATCH
cp -r /scratch/project_12345/alphafold_db .
export ALPHAFOLD_DATADIR=$LOCAL_SCRATCH/alphafold_db

More Information

Last update: October 12, 2023