AlphaFold
1. INCD Local Installation
The INCD team prepare a local installation of AlphaPhold using a container based on UDOCKER (instead of DOCKER) and includes the Genetic Database.
The local installation provide the AlphaFold version 2.1.1 over a container based on Ubuntu 18.04 distribution with cuda-11.0 and cudnn-8.
The main resource target of AlphaFold is the GPU but the application also execute only on the CPU although the performance is substantially worst, see the Run Exemples section bellow.
1.1 Environment
The environment is activate with command
$ module load udocker/alphaphold/2.1.1
this will activate automatically a virtual environment ready to start the AlphaFold container throught the python script run_udocker.py.
1.2 Data Base Location
The Genetic Database is installed bellow the filesystem directory
/users3/data/alphafoldon read-only mode, upgrades may be requested using the helpdesk@incd.pt address.
1.3 run_udocker.py Script
The run_udocker.py script was adapted from the run_docker.py script normally used by AlphaFold with the docker container technology.
The run_udocker.py accept the same options as the run_docker.py script with a few minor changes that we hope it will facilitate user interaction:
- option --data_dir: is optional and points to the local genetic database by default but the user can fill it with other location;