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/alphafold
on 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. The user may change the script behavour throught environment variables or command line options, we can see only the changes bellow:
Optional environment variables:
| Variable Name | Default Value | Comment |
|---|---|---|
| DOWNLOAD_DIR | none | Genetic database location |
| OUPTPUT_DIR | none | Output results directory |
Command line options:
| Command Option | Mandatory | Default Value | Comment |
|---|---|---|---|
| --data_dir | no | /users3/data/alphafold | Genetic database location, takes precedence over DOWNLOAD_DIR when both are selected |
| --output_dir | no | <working_dir>/output | Output results directory, takes precedence over OUTPUT_DIR when both are selected |
The option --data_dir is required on the standard AlphaFold run_docker.py script, we choose to select automatically the location of the genetic database but the user may change this path throught the environment variable DOWNLOAD_DIR or the command line option data_dir.
The AlphaFold standard output results directory location is /tmp/alphafold by default, please note that we change this location to the local working directory, the user can select a different path throught the environment variable OUTPUT_DIR or the command line option --output_dir.