AlphaFold Usage on HPCC
3 minute read
View source codeAlphaFold3
Loading the module
You can load AlphaFold3 using the following commands:
You can also run AlphaFold3 with a gpu. If you wish to use a GPU, log into an A100 gpu node and then use the following commands:
Using AlphaFold databases
A handful of databases are available at $ALPHAFOLD_DB
(available after loading the alphafold/3
module).
An example command is as follows:
More information on using Alphafold3 can be found in the Alphafold3 GitHub repo, including input documentation and output documentation.
Processing Large Datasets
Sometimes the dataset cannot fit within the memory of a single GPU. In this case you’ll need to use Unified Memory (“Combined” GPU and System memory). This does come with a drop in performance, but might be the only way to get large datasets processed.
To use Unified Memory, you can add these additional flags to the alphafold command:
For example:
AlphaFold2
Description of AlphaFold2
Loading the module
You can load AlphaFold2 using the following commands:
You can also run AlphaFold2 with a gpu. If you wish to use a GPU, log into a P100 gpu node and then use the following commands:
Using Alphafold Databases
When running the alphafold command, you will be asked for certain databases. These databases can be found under the path $DATABASE_DIR/alphafold/$$ALPHAFOLD_DB
environment variable that is automatically set after loading the alphafold module.
Here is an example of how to write your alphafold command using the monomer preset:
and an example using the multimer preset:
Remember to fill in your fasta path and output dir if you wish to use these templates.
Additionally, these are not the only two methods of running AlphaFold, and different modes might require different sets of arguments to be passed to alphafold.py
. For more details regarding what parameters are available, as well as more examples, please refer to the Alphafold Github Repo.